diff --git a/DESCRIPTION b/DESCRIPTION
index baef314e0..9adc9410b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -18,17 +18,20 @@ Imports:
EnvStats,
FAdist,
fitdistrplus,
+ flexsurv,
FrF2,
ggplot2,
ggrepel,
goftest,
ggpp,
+ ggh4x,
irr,
jaspBase,
jaspDescriptives,
jaspGraphs,
lubridate,
psych,
+ qc,
qcc,
rsm,
Rspc,
@@ -36,11 +39,11 @@ Imports:
tibble,
vipor,
weibullness,
- utils,
- flexsurv
+ utils
Remotes:
jasp-stats/jaspBase,
jasp-stats/jaspDescriptives,
- jasp-stats/jaspGraphs
+ jasp-stats/jaspGraphs,
+ FBartos/qc
Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.2
+RoxygenNote: 7.3.3
diff --git a/NAMESPACE b/NAMESPACE
index 96de90472..52c01626f 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,6 +1,7 @@
# Generated by roxygen2: do not edit by hand
export(attributesCharts)
+export(bayesianProcessCapabilityStudies)
export(doeAnalysis)
export(doeFactorial)
export(doeResponseSurfaceMethodology)
@@ -13,10 +14,11 @@ export(msaTestRetest)
export(msaType1Gauge)
export(probabilityOfDetection)
export(processCapabilityStudies)
-export(timeWeightedCharts)
export(rareEventCharts)
+export(timeWeightedCharts)
export(variablesChartsIndividuals)
export(variablesChartsSubgroups)
+importFrom(jaspBase,"%setOrRetrieve%")
importFrom(jaspBase,.extractErrorMessage)
importFrom(jaspBase,.hasErrors)
importFrom(jaspBase,.readDataSetToEnd)
@@ -26,3 +28,5 @@ importFrom(jaspBase,createJaspPlot)
importFrom(jaspBase,createJaspState)
importFrom(jaspBase,createJaspTable)
importFrom(jaspBase,isTryError)
+importFrom(jaspBase,jaspDeps)
+importFrom(rlang,.data)
diff --git a/R/bayesianProcessCapabilityStudies.R b/R/bayesianProcessCapabilityStudies.R
new file mode 100644
index 000000000..f344e8161
--- /dev/null
+++ b/R/bayesianProcessCapabilityStudies.R
@@ -0,0 +1,1001 @@
+#
+# Copyright (C) 2013-2025 University of Amsterdam
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see .
+#
+
+#'@importFrom jaspBase jaspDeps %setOrRetrieve%
+#'@importFrom rlang .data
+
+
+#'@export
+bayesianProcessCapabilityStudies <- function(jaspResults, dataset, options) {
+
+ fit <- .bpcsCapabilityTable(jaspResults, dataset, options, position = 1)
+ priorFit <- .bpcsSamplePosteriorOrPrior(jaspResults, dataset, options, prior = TRUE)
+
+ .bpcsCapabilityPlot(jaspResults, options, fit, priorFit, position = 2)
+ .bpcsCapabilityPlot(jaspResults, options, fit, priorFit, position = 3, base = "priorDistributionPlot")
+
+ .bpcsIntervalTable(jaspResults, options, fit, position = 4)
+
+ .bpcsSequentialPointEstimatePlot( jaspResults, dataset, options, fit, position = 5)
+ .bpcsSequentialIntervalEstimatePlot(jaspResults, dataset, options, fit, position = 6)
+
+ .bpcsPlotPredictive(jaspResults, dataset, options, fit, position = 7, base = "posteriorPredictiveDistributionPlot")
+ .bpcsPlotPredictive(jaspResults, dataset, options, priorFit, position = 8, base = "priorPredictiveDistributionPlot")
+
+}
+
+.bpcsIsReady <- function(options) {
+ # hasData <- if (options[["dataFormat"]] == "longFormat") {
+ # length(options[["measurementLongFormat"]]) > 0L && options[["measurementLongFormat"]] != ""
+ # } else {
+ # length(options[["measurementsWideFormat"]]) > 0L
+ # }
+ hasData <- length(options[["measurementLongFormat"]]) > 0L && options[["measurementLongFormat"]] != ""
+ hasData &&
+ options[["lowerSpecificationLimit"]] &&
+ options[["upperSpecificationLimit"]] &&
+ options[["target"]]
+}
+
+.bpcsStateDeps <- function() {
+ c(
+ # data
+ # "dataFormat", "measurementLongFormat", "measurementsWideFormat",
+ # "subgroupSizeType", "manualSubgroupSizeValue", "subgroup", "groupingVariableMethod",
+ # "stagesLongFormat", "stagesWideFormat",
+ "measurementLongFormat",
+ # specification
+ "target", "lowerSpecificationLimit", "upperSpecificationLimit",
+ "targetValue", "lowerSpecificationLimitValue", "upperSpecificationLimitValue",
+ # likelihood
+ "capabilityStudyType",
+ # prior
+ "priorSettings", "normalModelComponentsList", "tModelComponentsList",
+ # MCMC settings
+ "noIterations", "noWarmup", "noChains"
+ )
+}
+
+.bpcsDefaultDeps <- function() {
+ c(
+ .bpcsStateDeps(),
+ "axisLabels",
+ # metrics
+ "Cp", "Cpu", "Cpl", "Cpk", "Cpc", "Cpm"
+ )
+}
+
+.bpcsPlotLayoutDeps <- function(base, hasPrior = TRUE, hasEstimate = TRUE, hasCi = TRUE, hasType = FALSE, hasAxes = TRUE) {
+ c(
+ base,
+ if (hasEstimate) .bpcsPlotLayoutEstimateDeps(base),
+ if (hasCi) .bpcsPlotLayoutCiDeps(base),
+ if (hasType) .bpcsPlotLayoutTypeDeps(base),
+ if (hasAxes) .bpcsPlotLayoutAxesDeps(base),
+ if (hasPrior) .bpcsPlotLayoutPriorDeps(base)
+ )
+}
+
+.bpcsPlotLayoutEstimateDeps <- function(base) { paste0(base, c("IndividualPointEstimate", "IndividualPointEstimateType")) }
+.bpcsPlotLayoutCiDeps <- function(base) { paste0(base, c("IndividualCi", "IndividualCiType", "IndividualCiMass", "IndividualCiLower", "IndividualCiUpper", "IndividualCiBf")) }
+.bpcsPlotLayoutTypeDeps <- function(base) { paste0(base, c("TypeLower", "TypeUpper")) }
+.bpcsPlotLayoutAxesDeps <- function(base) { paste0(base, c("PanelLayout", "Axes", "custom_x_min", "custom_x_max", "custom_y_min", "custom_y_max")) }
+.bpcsPlotLayoutPriorDeps <- function(base) { paste0(base, "PriorDistribution") }
+
+.bpcsProcessCriteriaDeps <- function() {
+ c(paste0("interval", 1:4), paste0("intervalLabel", 1:5))
+}
+
+.bpcsPriorComponentByName <- function(options, name) {
+ components <- options$normalModelComponentsList
+ for (comp in components) {
+ if (comp$name == name)
+ return(comp)
+ }
+ return(NULL)
+}
+
+.bpcsPriorFromComponent <- function(optionsPrior, paramName) {
+ if (is.null(optionsPrior))
+ return(NULL)
+
+ if (optionsPrior$type == "jeffreys")
+ return(paste0("Jeffreys_", paramName))
+
+ arguments <- list()
+
+ arguments[["distribution"]] <- switch(
+ optionsPrior[["type"]],
+ "gammaAB" = "gamma",
+ "gammaK0" = "gamma",
+ optionsPrior[["type"]]
+ )
+
+ arguments[["parameters"]] <- switch(
+ optionsPrior[["type"]],
+ "normal" = list("mean" = optionsPrior[["mu"]], "sd" = optionsPrior[["sigma"]]),
+ "t" = list("location" = optionsPrior[["mu"]], "scale" = optionsPrior[["sigma"]], "df" = optionsPrior[["nu"]]),
+ "cauchy" = list("location" = optionsPrior[["mu"]], "scale" = optionsPrior[["theta"]]),
+ "gammaAB" = list("shape" = optionsPrior[["alpha"]], "rate" = optionsPrior[["beta"]]),
+ "gammaK0" = list("shape" = optionsPrior[["k"]], "rate" = 1/optionsPrior[["theta"]]),
+ "invgamma" = list("shape" = optionsPrior[["alpha"]], "scale" = optionsPrior[["beta"]]),
+ "lognormal" = list("meanlog" = optionsPrior[["mu"]], "sdlog" = optionsPrior[["sigma"]]),
+ "beta" = list("alpha" = optionsPrior[["alpha"]], "beta" = optionsPrior[["beta"]]),
+ "uniform" = list("a" = optionsPrior[["a"]], "b" = optionsPrior[["b"]]),
+ "exponential" = list("rate" = optionsPrior[["lambda"]]),
+ "spike" = list("location" = optionsPrior[["x0"]])
+ )
+
+ if(!arguments[["distribution"]] %in% c("spike", "uniform")) {
+ arguments[["truncation"]] <- list(
+ lower = optionsPrior[["truncationLower"]],
+ upper = optionsPrior[["truncationUpper"]]
+ )
+ }
+
+ return(do.call(BayesTools::prior, arguments))
+}
+
+.bpcsMuPriorFromOptions <- function(options) {
+ if (options$priorSettings == "default") {
+ return("Jeffreys_mu")
+ } else {
+ comp <- .bpcsPriorComponentByName(options, "mean")
+ return(.bpcsPriorFromComponent(comp, "mu"))
+ }
+}
+
+.bpcsSigmaPriorFromOptions <- function(options) {
+ if (options$priorSettings == "default") {
+ return("Jeffreys_sigma")
+ } else {
+ comp <- .bpcsPriorComponentByName(options, "sigma")
+ return(.bpcsPriorFromComponent(comp, "sigma"))
+ }
+}
+.bpcsTPriorFromOptions <- function(options) {
+
+ switch(options[["capabilityStudyType"]],
+ "normalCapabilityAnalysis" = NULL,
+ "tCapabilityAnalysis" = .bpcsPriorFromComponent(.bpcsPriorComponentByName(options, "df"), "df"),
+
+ stop("Unknown capability study type: ", options[["capabilityStudyType"]])
+ )
+}
+
+.bpcsPriorHelper <- function(options) {
+ if (options$priorSettings == "default") {
+ if (options[["capabilityStudyType"]] == "normalCapabilityAnalysis") {
+ return("DCSI")
+ }
+ return("Jeffreys")
+ }
+
+ mu_prior <- .bpcsMuPriorFromOptions(options)
+ sigma_prior <- .bpcsSigmaPriorFromOptions(options)
+ nu_prior <- .bpcsTPriorFromOptions(options)
+
+ args <- list(mu = mu_prior, sigma = sigma_prior)
+ if (!is.null(nu_prior)) {
+ args$nu <- nu_prior
+ }
+
+ do.call(qc::prior_independent, args)
+}
+
+# Tables ----
+.bpcsCapabilityTable <- function(jaspResults, dataset, options, position) {
+
+ # Check if we already have the results cached
+ if (!is.null(jaspResults[["bpcsCapabilityTable"]]))
+ return(.bpcsSamplePosteriorOrPrior(jaspResults, dataset, options)) # will return object from state (if it exists)
+
+ table <- .bpcsCapabilityTableMeta(jaspResults, options, position = position)
+ if (!.bpcsIsReady(options)) {
+
+ if (options[["measurementLongFormat"]] != "" || length(options[["measurementsWideFormat"]]) > 0)
+ table$addFootnote(gettext(
+ "Please specify the Lower Specification Limit, Upper Specification Limit, and Target Value to compute the capability measures."
+ ))
+
+ return(NULL)
+ }
+
+ resultsObject <- .bpcsSamplePosteriorOrPrior(jaspResults, dataset, options)
+
+ .bpcsCapabilityTableFill(table, resultsObject, options)
+ return(resultsObject)
+
+}
+
+.bpcsSamplePosteriorOrPrior <- function(jaspResults, dataset, options, prior = FALSE) {
+
+ base <- if (prior) "bpcsPriors" else "bpcs"
+ if (prior && !.bpcsCanSampleFromPriors(options))
+ return(NULL)
+
+ if (!is.null(jaspResults[[paste0(base, "ResultsObject")]]))
+ return(jaspResults[[paste0(base, "ResultsObject")]]$object)
+
+ x <- if (ncol(dataset) > 0L) dataset[[1L]] else NULL
+
+ rawfit <- jaspResults[[paste0(base, "State")]] %setOrRetrieve% (
+ qc::bpc(
+ x, chains = 1, warmup = 1000, iter = 5000, silent = TRUE, seed = 1,
+ target = options[["targetValue"]],
+ LSL = options[["lowerSpecificationLimitValue"]],
+ USL = options[["upperSpecificationLimitValue"]],
+ prior = .bpcsPriorHelper(options),
+ sample_priors = prior
+ ) |>
+ createJaspState(jaspDeps(.bpcsStateDeps()))
+ )
+
+ summaryObject <- jaspResults[[paste0(base, "SummaryState")]] %setOrRetrieve% (
+ summary(
+ rawfit, ci.level = options[["credibleIntervalWidth"]]
+ ) |>
+ createJaspState(jaspDeps(
+ options = c(.bpcsStateDeps(), "credibleIntervalWidth")
+ ))
+ )
+
+ resultsObject <- list(
+ rawfit = rawfit,
+ summaryObject = summaryObject
+ )
+
+ jaspResults[[paste0(base, "ResultsObject")]] <- createJaspState(resultsObject)
+
+ return(resultsObject)
+}
+
+.bpcsCanSampleFromPriors <- function(options) {
+ if (options$priorSettings != "default") {
+ return(TRUE)
+ }
+ options[["capabilityStudyType"]] == "normalCapabilityAnalysis"
+}
+
+.bpcsCapabilityTableMeta <- function(jaspResults, options, position) {
+
+ table <- createJaspTable(title = gettext("Capability Table"), position = position)
+ table$addColumnInfo(name = "metric", title = gettext("Measure"), type = "string")
+ table$addColumnInfo(name = "mean", title = gettext("Mean"), type = "number")
+ table$addColumnInfo(name = "median", title = gettext("Median"), type = "number")
+ table$addColumnInfo(name = "sd", title = gettext("Std"), type = "number")
+
+ overtitle <- gettextf("%s%% Credible Interval", 100 * options[["credibleIntervalWidth"]])
+ table$addColumnInfo(name = "lower", title = gettext("Lower"), type = "number", overtitle = overtitle)
+ table$addColumnInfo(name = "upper", title = gettext("Upper"), type = "number", overtitle = overtitle)
+
+ table$dependOn(c(.bpcsDefaultDeps(), "credibleIntervalWidth"))
+
+ jaspResults[["bpcsCapabilityTable"]] <- table
+ return(table)
+
+}
+
+.bpcsGetSelectedMetrics <- function(options) {
+ allMetrics <- c("Cp", "CpU", "CpL", "Cpk", "Cpc", "Cpm")
+ selectedMetrics <- allMetrics[c(options[["Cp"]], options[["Cpu"]], options[["Cpl"]],
+ options[["Cpk"]], options[["Cpc"]], options[["Cpm"]])]
+ return(selectedMetrics)
+}
+
+getCustomAxisLimits <- function(options, base) {
+ keys <- c(paste0(base, "custom_x_", c("min", "max")), paste0(base, "custom_y_", c("min", "max")))
+ values <- lapply(keys, function(k) options[[k]])
+ names(values) <- c("xmin", "xmax", "ymin", "ymax")
+ values
+}
+# end utils
+
+.bpcsCapabilityTableFill <- function(table, resultsObject, options) {
+
+ df <- as.data.frame(resultsObject[["summaryObject"]][["summary"]])
+
+ # Filter metrics based on user selection
+ selectedMetrics <- .bpcsGetSelectedMetrics(options)
+
+ if (length(selectedMetrics) > 0) {
+ df <- df[df$metric %in% selectedMetrics, , drop = FALSE]
+ }
+
+ table$setData(df)
+
+}
+
+.bpcsIntervalTable <- function(jaspResults, options, fit, position) {
+
+ if (!options[["intervalTable"]])
+ return()
+
+ table <- .bpcsIntervalTableMeta(jaspResults, options, position)
+ if (!.bpcsIsReady(options) || is.null(fit))
+ return()
+
+ selectedMetrics <- .bpcsGetSelectedMetrics(options)
+ tryCatch({
+
+ # qc does c(-Inf, interval_probability, Inf)
+ interval_probability <- unlist(options[paste0("interval", 1:4)], use.names = FALSE)
+ interval_summary <- summary(fit[["rawfit"]], interval_probability = interval_probability)[["interval_summary"]]
+ colnames(interval_summary) <- c("metric", paste0("interval", 1:5))
+ interval_summary <- subset(interval_summary, metric %in% selectedMetrics)
+ table$setData(interval_summary)
+
+ }, error = function(e) {
+
+ table$setError(gettextf("Unexpected error in interval table: %s", e$message))
+
+ })
+
+ return()
+}
+
+.bpcsIntervalTableMeta <- function(jaspResults, options, position) {
+
+ table <- createJaspTable(title = gettext("Interval Table"), position = position)
+
+ table$addColumnInfo(name = "metric", title = gettext("Capability\nMeasure"), type = "string")
+
+ intervalBounds <- c(-Inf, unlist(options[paste0("interval", 1:4)], use.names = FALSE), Inf)
+ intervalNames <- unlist(options[paste0("intervalLabel", 1:5)], use.names = FALSE)
+ n <- length(intervalBounds)
+
+ # custom format helper. we don't use e.g., %.3f directly because that adds trailing zeros (2.000 instead of 2)
+ fmt <- \(x) formatC(x, digits = 3, format = "f", drop0trailing = TRUE)
+ for (i in 1:(n - 1)) {
+ j <- i + 1
+ lhs <- if (i == 1) "(" else "["
+ rhs <- if (i == n - 1) ")" else "]"
+ title <- sprintf("%s %s%s, %s%s", intervalNames[i], lhs, fmt(intervalBounds[i]), fmt(intervalBounds[j]), rhs)
+ table$addColumnInfo(name = paste0("interval", i), title = title, type = "number")
+ }
+ table$dependOn(c("intervalTable", .bpcsDefaultDeps(), .bpcsProcessCriteriaDeps()))
+
+ jaspResults[["bpcsIntervalTable"]] <- table
+ return(table)
+}
+
+
+# Plots ----
+.bpcsCapabilityPlot <- function(jaspResults, options, fit, priorFit, position, base = "posteriorDistributionPlot") {
+
+ if (!options[[base]] || !is.null(jaspResults[[base]]))
+ return()
+
+ singlePanel <- options[[paste0(base, "PanelLayout")]] != "multiplePanels"
+
+ isPost <- base == "posteriorDistributionPlot"
+ summaryObject <- if (isPost) fit$summaryObject else priorFit$summaryObject
+ # only if the user asked for it
+ priorSummaryObject <- if (isPost && options[[paste0(base, "PriorDistribution")]]) priorFit$summaryObject else NULL
+
+ jaspPlt <- createJaspPlot(
+ title = if (isPost) gettext("Posterior Distribution") else gettext("Prior Distribution"),
+ width = 400 * (if (singlePanel) 1 else 3),
+ height = 400 * (if (singlePanel) 1 else 2),
+ position = position,
+ dependencies = jaspDeps(
+ options = c(
+ .bpcsDefaultDeps(),
+ # .bpcsPosteriorPlotDeps(options),
+ .bpcsPlotLayoutDeps(base, hasType = FALSE)
+ )
+ )
+ )
+ jaspResults[[base]] <- jaspPlt
+
+ if (!.bpcsIsReady(options) || (isPost && is.null(fit)) || (!isPost && is.null(priorFit)))
+ return()
+
+ if (!isPost && !.bpcsCanSampleFromPriors(options)) {
+ jaspPlt$width <- 400
+ jaspPlt$height <- 400
+ jaspPlt$setError(gettext("Prior distribution cannot be shown for improper priors."))
+ return()
+ }
+
+ tryCatch({
+
+ # Get selected metrics
+ selectedMetrics <- .bpcsGetSelectedMetrics(options)
+
+ if (length(selectedMetrics) == 0) {
+ NULL
+ } else {
+
+ jaspPlt$plotObject <- qc::plot_density(
+ summaryObject,
+ what = selectedMetrics,
+ point_estimate = if (options[[paste0(base, "IndividualPointEstimate")]]) options[[paste0(base, "IndividualPointEstimateType")]] else "none",
+ ci = if (options[[paste0(base, "IndividualCi")]]) options[[paste0(base, "IndividualCiType")]] else "none",
+ ci_level = options[[paste0(base, "IndividualCiMass")]],
+ ci_custom_left = options[[paste0(base, "IndividualCiLower")]],
+ ci_custom_right = options[[paste0(base, "IndividualCiUpper")]],
+ bf_support = options[[paste0(base, "IndividualCiBf")]],
+ single_panel = singlePanel,
+ axes = options[[paste0(base, "Axes")]],
+ axes_custom = getCustomAxisLimits(options, base),
+ priorSummaryObject = priorSummaryObject
+ ) +
+ jaspGraphs::geom_rangeframe() +
+ jaspGraphs::themeJaspRaw()
+
+
+ }
+ }, error = function(e) {
+ jaspPlt$width <- 400
+ jaspPlt$height <- 400
+ jaspPlt$setError(
+ if (isPost) gettextf("Unexpected error in posterior distribution plot: %s", e$message)
+ else gettextf("Unexpected error in prior distribution plot: %s", e$message)
+ )
+ })
+
+}
+
+# .bpcsPosteriorPlotDeps <- function(options) {
+# c(
+# "posteriorDistributionPlot",
+# "posteriorDistributionPlotIndividualPointEstimate",
+# "posteriorDistributionPlotIndividualPointEstimateType",
+# "posteriorDistributionPlotPriorDistribution",
+# "posteriorDistributionPlotIndividualCi",
+# "posteriorDistributionPlotIndividualCiType",
+# # these match which options are conditionally enabled in the qml file.
+# switch(options[["posteriorDistributionPlotIndividualCiType"]],
+# "central" = "posteriorDistributionPlotIndividualCiMass",
+# "HPD" = "posteriorDistributionPlotIndividualCiMass",
+# "custom" = c("posteriorDistributionPlotIndividualCiLower", "posteriorDistributionPlotIndividualCiUpper"),
+# "support" = "posteriorDistributionPlotIndividualCiBf"
+# )
+# )
+# }
+
+.bpcsSequentialPointEstimatePlot <- function(jaspResults, dataset, options, fit, position) {
+
+ base <- "sequentialAnalysisPointEstimatePlot"
+ # "sequentialAnalysisPointIntervalPlot"
+ if (!options[[base]] || !is.null(jaspResults[[base]]))
+ return()
+
+ w <- 400
+ plt <- createJaspPlot(title = gettext("Sequential Analysis Point Estimate"), width = 3*w, height = 2*w,
+ position = position,
+ dependencies = jaspDeps(c(
+ .bpcsDefaultDeps(),
+ .bpcsPlotLayoutDeps(base, hasPrior = FALSE),
+ "sequentialAnalysisPlotAdditionalInfo"
+ )))
+ jaspResults[[base]] <- plt
+
+ if (!.bpcsIsReady(options) || jaspResults$getError()) return()
+
+ sequentialPlotData <- .bpcsGetSequentialAnalysis(jaspResults, dataset, options, fit)
+
+ if (!is.null(sequentialPlotData$error)) {
+ plt$setError(sequentialPlotData$error)
+ } else {
+ tryCatch({
+ plt$plotObject <- .bpcsMakeSequentialPlot(sequentialPlotData$data, options, base)
+ }, error = function(e) {
+ plt$setError(gettextf("Unexpected error in sequential analysis point estimate plot: %s", e$message))
+ }
+ )
+ }
+}
+
+.bpcsSequentialIntervalEstimatePlot <- function(jaspResults, dataset, options, fit, position) {
+
+ # base <- "sequentialAnalysisPointEstimatePlot"
+ base <- "sequentialAnalysisPointIntervalPlot"
+ if (!options[[base]] || !is.null(jaspResults[[base]]))
+ return()
+
+ w <- 400
+ plt <- createJaspPlot(title = gettext("Sequential Analysis Interval Estimate"), width = 3*w, height = 2*w,
+ position = position,
+ dependencies = jaspDeps(c(
+ .bpcsDefaultDeps(),
+ .bpcsPlotLayoutDeps(base, hasPrior = FALSE)
+ )))
+ jaspResults[[base]] <- plt
+
+ if (!.bpcsIsReady(options) || jaspResults$getError()) return()
+
+ sequentialPlotData <- .bpcsGetSequentialAnalysis(jaspResults, dataset, options, fit)
+
+ if (!is.null(sequentialPlotData$error)) {
+ plt$setError(sequentialPlotData$error)
+ } else {
+ tryCatch({
+ plt$plotObject <- .bpcsMakeSequentialPlot(sequentialPlotData$data, options, base, custom = TRUE)
+ }, error = function(e) {
+ plt$setError(gettextf("Unexpected error in sequential analysis interval estimate plot: %s", e$message))
+ }
+ )
+ }
+}
+
+.bpcsGetSequentialAnalysis <- function(jaspResults, dataset, options, fit) {
+
+ if (!.bpcsIsReady(options) || jaspResults$getError()) return()
+
+ base1 <- "sequentialAnalysisPointEstimatePlot"
+ base2 <- "sequentialAnalysisPointIntervalPlot"
+
+ baseData <- "SequentialAnalysisData"
+ tryCatch({
+ sequentialPlotData <- jaspResults[[baseData]] %setOrRetrieve% (
+ .bpcsComputeSequentialAnalysis(dataset, options, fit) |>
+ createJaspState(dependencies = jaspDeps(
+ options = c(.bpcsStateDeps(),
+ paste0(base2, c("TypeLower", "TypeUpper")))
+ ))
+ )
+
+ return(list(data = sequentialPlotData, error = NULL))
+
+ }, error = function(e) {
+
+ return(list(data = NULL, error = e$message))
+
+ })
+
+}
+
+.bpcsComputeSequentialAnalysis <- function(dataset, options, fit) {
+
+ n <- nrow(dataset)
+ if (!is.finite(n) || n < 3L) {
+ stop("Sequential analysis requires at least 3 observations.", call. = FALSE)
+ }
+ nfrom <- 3L
+ nto <- n
+ nby <- 1L
+ nseq <- seq(nfrom, nto, by = nby)
+ estimates <- array(NA, c(6, 5, length(nseq)))
+
+ hasCustom <- options$sequentialAnalysisPointIntervalPlot
+ customBounds <- c(options$sequentialAnalysisPointIntervalPlotTypeLower,
+ options$sequentialAnalysisPointIntervalPlotTypeUpper)
+
+ keys <- c("mean", "median", "lower", "upper", "custom")
+ dimnames(estimates) <- list(list(), keys, list())
+
+ x <- dataset[[1L]]
+
+ jaspBase::startProgressbar(length(nseq), label = gettext("Running sequential analysis"))
+
+ prior <- .bpcsPriorHelper(options)
+ n_failed <- 0L
+ for (i in seq_along(nseq)) {
+
+ x_i <- x[1:nseq[i]]
+ fit_i <- tryCatch(
+ qc::bpc(
+ x_i, chains = 1, warmup = 1000, iter = 5000, silent = TRUE, seed = 1,
+ target = options[["targetValue"]],
+ LSL = options[["lowerSpecificationLimitValue"]],
+ USL = options[["upperSpecificationLimitValue"]],
+ prior = prior
+ ),
+ error = function(e) NULL
+ )
+
+ if (is.null(fit_i)) {
+ n_failed <- n_failed + 1L
+ jaspBase::progressbarTick()
+ next
+ }
+
+ sum_fit_i <- summary(fit_i, interval_probability = customBounds)
+ sum_i <- sum_fit_i$summary
+ custom_i <- sum_fit_i$interval_summary[, 3, drop = FALSE]
+ colnames(custom_i) <- "custom"
+ sum_i <- cbind(sum_i, custom_i)
+
+ if (is.null(rownames(estimates)))
+ rownames(estimates) <- sum_i$metric
+
+ estimates[, , i] <- as.matrix(sum_i[keys])
+ jaspBase::progressbarTick()
+ }
+
+ if (n_failed > 0L && n_failed / length(nseq) > 0.1) {
+ stop(
+ sprintf(
+ "%d of %d sequential fits failed (%.0f%%). Cannot render plot.",
+ n_failed, length(nseq), 100 * n_failed / length(nseq)
+ ),
+ call. = FALSE
+ )
+ }
+
+ attr(estimates, "nseq") <- nseq
+
+ # we could use this one, but only if the CI width is exactly equal to the one requested here.
+ # that would be nice to add at some point so the values in the table are identical to those in the plot
+ # sum_n <- summary(fit)$summary
+ # estimates[, , n] <- as.matrix(sum_n[keys])
+
+ return(estimates)
+}
+
+.bpcsMakeSequentialPlot <- function(estimates, options, base, custom = FALSE) {
+
+ # this function should move to qc, and these are the arguments that should be passed to the arguments of that function
+ single_panel <- options[[paste0(base, "PanelLayout")]] != "multiplePanels"
+ axes <- options[[paste0(base, "Axes")]]
+ axes_custom <- getCustomAxisLimits(options, base)
+
+ pointEstimateOption <- paste0(base, "IndividualPointEstimateType")
+ pointEstimateName <- if (options[[pointEstimateOption]] == "mean") "mean" else "median"
+ add_additional_info <- options[["sequentialAnalysisPlotAdditionalInfo"]]
+
+ selectedMetrics <- .bpcsGetSelectedMetrics(options)
+ if (length(selectedMetrics) == 0L)
+ return(NULL)
+
+ ciOption <- paste0(base, "IndividualCi")
+ has_ci <- options[[ciOption]]
+
+ if (custom) {
+ has_ci <- FALSE
+ pointEstimateName <- "custom"
+ add_additional_info <- FALSE
+ y_limits <- c(0, 1)
+ y_title <- gettextf("P(%1$.3f \u2264 x \u2264 %2$.3f)",
+ options$sequentialAnalysisPointIntervalPlotTypeLower,
+ options$sequentialAnalysisPointIntervalPlotTypeUpper)
+ } else {
+
+ y_title <- if (has_ci) {
+ gettextf("Estimate with 95%% credible interval")
+ } else {
+ gettext("Estimate")
+ }
+ }
+
+ # this is somewhat ugly, but we convert the 3d array to a tibble for plotting
+ # we don't create the tibble immediately in the previous function, because
+ # it takes up more space in the state (which means larger jasp files)
+
+ categoryNames <- c(gettext("Incapable"), gettext("Capable"), gettext("Satisfactory"), gettext("Excellent"), gettext("Super"))
+ gridLines <- c(1, 4/3, 3/2, 2)
+ # the extrema are missing here, these should be determined based on any leftover space.
+ defaultCategoryPositions <- (gridLines[-1] + gridLines[-length(gridLines)]) / 2
+
+ nseq <- attr(estimates, "nseq")
+
+ tb <- tibble::tibble(
+ metric = factor(rep(rownames(estimates), times = length(nseq))),
+ n = rep(nseq, each = nrow(estimates)),
+ mean = as.vector(estimates[, pointEstimateName, ]),
+ lower = as.vector(estimates[, "lower", ]),
+ upper = as.vector(estimates[, "upper", ]),
+ )
+ tb <- tb[tb$metric %in% selectedMetrics, , drop = FALSE]
+ if (length(selectedMetrics) == 1L)
+ single_panel <- TRUE
+
+ # get y scales per facet
+ if (single_panel) {
+
+ observedRange <- range(tb$lower, tb$upper, na.rm = TRUE)
+ if (!all(is.finite(observedRange))) {
+ observedRange <- c(0, 1)
+ }
+ dist <- observedRange[2L] - observedRange[1L]
+
+ observedRange[1L] <- min(observedRange[1L], gridLines[1L] - 0.1 * dist)
+ observedRange[2L] <- max(observedRange[2L], gridLines[length(gridLines)] + 0.1 * dist)
+
+ leftBreaks <- jaspGraphs::getPrettyAxisBreaks(observedRange)
+ leftLimits <- range(leftBreaks)
+
+ rightAxis <- ggplot2::waiver()
+ if (add_additional_info) {
+ rightBreaksShown <- c(
+ (leftLimits[1L] + gridLines[1L]) / 2,
+ defaultCategoryPositions,
+ (leftLimits[2L] + gridLines[length(gridLines)]) / 2
+ )
+ rightBreaks <- numeric(2L*length(rightBreaksShown) + 1L)
+ rightBreaks[1L] <- leftLimits[1L]
+ rightBreaks[seq(2, length(rightBreaks), 2)] <- rightBreaksShown
+ rightBreaks[seq(3, length(rightBreaks) - 2, 2)] <- gridLines
+ rightBreaks[length(rightBreaks)] <- leftLimits[2L]
+
+ rightLabels <- character(length(rightBreaks))
+ rightLabels[seq(2, length(rightLabels), 2)] <- categoryNames
+ rightAxis <- ggplot2::sec_axis(identity, breaks = rightBreaks, labels = rightLabels)
+ }
+
+ y_breaks_per_scale <- ggplot2::scale_y_continuous(breaks = leftBreaks, limits = range(leftBreaks),
+ minor_breaks = gridLines,
+ sec.axis = rightAxis)
+
+ } else {
+ y_breaks_per_scale <- tapply(tb, tb$metric, \(x) {
+
+ # x <- tb[tb$metric == tb$metric[1L], , drop = FALSE]
+ observedRange <- range(x$lower, x$upper, na.rm = TRUE)
+ if (!all(is.finite(observedRange))) {
+ observedRange <- c(0, 1)
+ }
+ dist <- observedRange[2L] - observedRange[1L]
+
+ observedRange[1L] <- min(observedRange[1L], gridLines[1L] - 0.1 * dist)
+ observedRange[2L] <- max(observedRange[2L], gridLines[length(gridLines)] + 0.1 * dist)
+
+ if (custom) {
+ observedRange[1L] <- max(observedRange[1L], y_limits[1L])
+ observedRange[2L] <- min(observedRange[2L], y_limits[2L])
+ }
+
+ leftBreaks <- jaspGraphs::getPrettyAxisBreaks(observedRange)
+ leftLimits <- range(leftBreaks)
+
+ rightAxis <- ggplot2::waiver()
+ if (add_additional_info) {
+ rightBreaksShown <- c(
+ (leftLimits[1L] + gridLines[1L]) / 2,
+ defaultCategoryPositions,
+ (leftLimits[2L] + gridLines[length(gridLines)]) / 2
+ )
+ rightBreaks <- numeric(2L*length(rightBreaksShown) + 1L)
+ rightBreaks[1L] <- leftLimits[1L]
+ rightBreaks[seq(2, length(rightBreaks), 2)] <- rightBreaksShown
+ rightBreaks[seq(3, length(rightBreaks) - 2, 2)] <- gridLines
+ rightBreaks[length(rightBreaks)] <- leftLimits[2L]
+
+ rightLabels <- character(length(rightBreaks))
+ rightLabels[seq(2, length(rightLabels), 2)] <- categoryNames
+ rightAxis <- ggplot2::sec_axis(identity, breaks = rightBreaks, labels = rightLabels)
+ }
+
+ ggplot2::scale_y_continuous(breaks = leftBreaks, limits = range(leftBreaks),
+ minor_breaks = gridLines,
+ sec.axis = rightAxis)
+ }, simplify = FALSE)
+ }
+
+ ribbon <- NULL
+ if (has_ci)
+ ribbon <- ggplot2::geom_ribbon(ggplot2::aes(ymin = .data$lower, ymax = .data$upper), alpha = 0.3)
+
+ extraTheme <- gridLinesLayer <- NULL
+ sides <- "bl"
+ if (add_additional_info) {
+ # there are 11 ticks, the outermost we hide (NA) because one of their bounds is infinite
+ # the inner ticks alternate between black and NA, so there is a tick at the grid lines
+ # but no tick at the criteria text (which is secretly an axis tick label).
+ rightTickColors <- c(NA, rep(c(NA, "black"), length.out = 9), NA)
+ extraTheme <- ggplot2::theme(axis.ticks.y.right = ggplot2::element_line(colour = rightTickColors))
+ sides <- "blr"
+ # I tried using minor.breaks for this, but these are not drawn properly with facet_grid and facetted_pos_scales
+ gridLinesLayer <- ggplot2::geom_hline(
+ data = data.frame(yintercept = gridLines),
+ ggplot2::aes(yintercept = .data$yintercept),
+ # show.legend = FALSE,
+ linewidth = .5, color = "lightgray", linetype = "dashed"
+ )
+
+ }
+
+ scale_x <- scale_facet <- facet <- NULL
+ noMetrics <- nrow(estimates)
+ if (noMetrics == 1L || single_panel) {
+ xBreaks <- jaspGraphs::getPrettyAxisBreaks(tb$n)
+ xLimits <- range(tb$n)
+ scale_x <- ggplot2::scale_x_continuous(breaks = xBreaks, limits = xLimits)
+ scale_facet <- y_breaks_per_scale
+ } else {
+ scales <- switch(axes,
+ "automatic" = "free_y",
+ "fixed" = "fixed",
+ "free" = "free_y",
+ "custom" = "fixed",
+ stop("Unknown axes option.")
+ )
+ if (axes == "custom") {
+ if (!is.null(axes_custom[["xmin"]]) && !is.null(axes_custom[["xmax"]])) {
+ xbreaks <- jaspGraphs::getPrettyAxisBreaks(c(axes_custom[["xmin"]], axes_custom[["xmax"]]))
+ scale_x <- ggplot2::scale_x_continuous(limits = sort(c(axes_custom[["xmin"]], axes_custom[["xmax"]])))
+ }
+ if (!is.null(axes_custom[["ymin"]]) && !is.null(axes_custom[["ymax"]])) {
+ ybreaks <- jaspGraphs::getPrettyAxisBreaks(c(axes_custom[["ymin"]], axes_custom[["ymax"]]))
+ leftLimits <- sort(c(axes_custom[["ymin"]], axes_custom[["ymax"]]))
+ rightAxis <- ggplot2::waiver()
+ if (add_additional_info) {
+ rightBreaksShown <- c(
+ (leftLimits[1L] + gridLines[1L]) / 2,
+ defaultCategoryPositions,
+ (leftLimits[2L] + gridLines[length(gridLines)]) / 2
+ )
+ rightBreaks <- numeric(2L*length(rightBreaksShown) + 1L)
+ rightBreaks[1L] <- leftLimits[1L]
+ rightBreaks[seq(2, length(rightBreaks), 2)] <- rightBreaksShown
+ rightBreaks[seq(3, length(rightBreaks) - 2, 2)] <- gridLines
+ rightBreaks[length(rightBreaks)] <- leftLimits[2L]
+
+ rightLabels <- character(length(rightBreaks))
+ rightLabels[seq(2, length(rightLabels), 2)] <- categoryNames
+ rightAxis <- ggplot2::sec_axis(identity, breaks = rightBreaks, labels = rightLabels)
+ }
+ scale_facet <- ggplot2::scale_y_continuous(breaks = ybreaks, limits = leftLimits,
+ minor_breaks = gridLines, sec.axis = rightAxis)
+ }
+ } else if (axes == "automatic" || axes == "free") {
+ scale_facet <- ggh4x::facetted_pos_scales(y = y_breaks_per_scale)
+ }
+ facet <- ggplot2::facet_wrap(~metric, scales = scales)
+ }
+
+ ggplot2::ggplot(tb, ggplot2::aes(x = .data$n, y = .data$mean, group = .data$metric,
+ color = .data$metric, fill = .data$metric)) +
+ gridLinesLayer +
+ ribbon +
+ ggplot2::geom_line(linewidth = 1) +
+ facet + scale_facet + scale_x +
+ ggplot2::labs(
+ x = gettext("Number of observations"),
+ y = y_title,
+ color = gettext("Metric"),
+ fill = gettext("Metric")
+ ) +
+ jaspGraphs::geom_rangeframe(sides = sides) +
+ jaspGraphs::themeJaspRaw(legend.position = if (single_panel) "right" else "none") +
+ extraTheme
+
+}
+
+# Additional plot functions ----
+.bpcsPlotPredictive <- function(jaspResults, dataset, options, fit, position, base = c("posteriorPredictiveDistributionPlot", "priorPredictiveDistributionPlot")) {
+
+ base <- match.arg(base)
+ isPrior <- base == "priorPredictiveDistributionPlot"
+
+ if (!options[[base]] || !is.null(jaspResults[[base]]))
+ return()
+
+ plot <- createJaspPlot(
+ title = if (isPrior) gettext("Prior predictive distribution") else gettext("Posterior Predictive Distribution"),
+ width = 400,
+ height = 400,
+ position = position,
+ dependencies = c(
+ .bpcsDefaultDeps(),
+ base,
+ paste0(base, "IndividualPointEstimate"),
+ paste0(base, "IndividualPointEstimateType"),
+ paste0(base, "IndividualCi"),
+ paste0(base, "IndividualCiType"),
+ paste0(base, "IndividualCiMass"),
+ paste0(base, "IndividualCiLower"),
+ paste0(base, "IndividualCiUpper")
+ ))
+
+ jaspResults[[base]] <- plot
+
+ if (!.bpcsIsReady(options) || is.null(fit) || jaspResults$getError()) return()
+
+ tryCatch({
+ rawfit <- fit$rawfit
+ if (identical(rawfit$method, "integration")) {
+ if (inherits(rawfit$prior_resolved, "PriorConjugate")) {
+ # based on Murphy, K. P. (2007). Conjugate Bayesian analysis of the Gaussian distribution. def, 1(2σ2), 16.
+ # TODO: since we have access to the distribution we could avoid sampling and plot the density directly
+ prior <- rawfit$prior_resolved
+ state <- rawfit$integration_result$cached_state
+ post <- qc:::.nig_posterior(prior, state$n, state$x_bar, state$sse)
+ df <- 2 * post$alpha_n
+ scale <- sqrt(post$beta_n * (1 + 1 / post$k_n) / post$alpha_n)
+ predictiveSamples <- post$mu_n + scale * stats::rt(5000, df)
+ } else {
+ rawfit <- qc::bpc(
+ x = if (ncol(dataset) > 0L) dataset[[1L]] else NULL,
+ method = "mcmc",
+ distribution = rawfit$distribution %||% "normal",
+ prior = rawfit$prior,
+ LSL = options[["lowerSpecificationLimitValue"]],
+ USL = options[["upperSpecificationLimitValue"]],
+ target = options[["targetValue"]],
+ chains = 1, warmup = 1000, iter = 5000, silent = TRUE, seed = 1,
+ sample_priors = isPrior
+ )
+ raw_samples <- qc:::extract_samples(rawfit, bootstrap = FALSE)
+ samples <- qc:::samples_to_mu_and_sigma(raw_samples)
+ predictiveSamples <- qc:::samples_to_posterior_predictives(samples)
+ }
+ } else {
+ raw_samples <- qc:::extract_samples(rawfit, bootstrap = FALSE)
+ samples <- qc:::samples_to_mu_and_sigma(raw_samples)
+ predictiveSamples <- qc:::samples_to_posterior_predictives(samples)
+ }
+
+ plt <- jaspGraphs::jaspHistogram(
+ predictiveSamples,
+ xName = if (isPrior) gettext("Prior predictive") else gettext("Posterior predictive"),
+ density = TRUE
+ )
+
+ # Calculate density for positioning elements above histogram
+ dens <- stats::density(predictiveSamples)
+ maxDensity <- max(dens$y)
+
+ # Add point estimate if requested
+ if (options[[paste0(base, "IndividualPointEstimate")]]) {
+ pointEstimateType <- options[[paste0(base, "IndividualPointEstimateType")]]
+ pointEstimate <- switch(pointEstimateType,
+ "mean" = mean(predictiveSamples),
+ "median" = stats::median(predictiveSamples),
+ "mode" = dens$x[which.max(dens$y)]
+ )
+ plt <- plt + ggplot2::geom_point(
+ data = data.frame(x = pointEstimate, y = 0),
+ ggplot2::aes(x = .data$x, y = .data$y),
+ size = 3,
+ inherit.aes = FALSE
+ )
+ }
+
+ # Add CI if requested
+ if (options[[paste0(base, "IndividualCi")]]) {
+ ciType <- options[[paste0(base, "IndividualCiType")]]
+
+ ciInterval <- if (ciType == "custom") {
+ c(options[[paste0(base, "IndividualCiLower")]],
+ options[[paste0(base, "IndividualCiUpper")]])
+ } else {
+ ciMass <- options[[paste0(base, "IndividualCiMass")]] / 100
+ if (ciType == "central") {
+ stats::quantile(predictiveSamples, probs = c((1 - ciMass) / 2, (1 + ciMass) / 2))
+ } else if (ciType == "HPD") {
+ # For HPD, we need HDInterval package or implement it
+ if (requireNamespace("HDInterval", quietly = TRUE)) {
+ HDInterval::hdi(predictiveSamples, credMass = ciMass)
+ } else {
+ # Fallback to central interval
+ stats::quantile(predictiveSamples, probs = c((1 - ciMass) / 2, (1 + ciMass) / 2))
+ }
+ }
+ }
+
+ # Position errorbar above the histogram
+ yPosition <- maxDensity * 1.1
+ plt <- plt + ggplot2::geom_errorbarh(
+ data = data.frame(x = mean(ciInterval), xmin = ciInterval[1], xmax = ciInterval[2], y = yPosition),
+ ggplot2::aes(x = .data$x, xmin = .data$xmin, xmax = .data$xmax, y = .data$y),
+ height = maxDensity * 0.05,
+ linewidth = 0.75,
+ inherit.aes = FALSE
+ )
+ }
+
+ plot$plotObject <- plt
+ }, error = function(e) {
+ plot$setError(
+ if (isPrior) gettextf("Unexpected error in prior predictive distribution plot: %s", e$message)
+ else gettextf("Unexpected error in posterior predictive distribution plot: %s", e$message)
+ )
+ })
+}
diff --git a/example.csv b/example.csv
new file mode 100644
index 000000000..c44d9b0a8
--- /dev/null
+++ b/example.csv
@@ -0,0 +1,51 @@
+"x"
+-0.410208141645563
+1.28869313968671
+0.0817165750903773
+-0.0686356396501049
+-0.0589226209836481
+0.555475416432164
+-0.294680841233279
+0.422743712149071
+0.428073502390818
+1.76937764118663
+0.464949886950047
+-1.02211993709862
+-0.227070527653629
+0.111891767810994
+0.112577948928265
+-0.190865217539092
+-0.35316235325419
+-0.298407824715572
+0.238127738565468
+0.760187723885965
+1.08752327910633
+-0.780714189131605
+-0.236024109255296
+-0.18879779045873
+-0.524187380397202
+-0.401928776043767
+-0.0598257599490922
+-0.0385345622509108
+-0.164056314050029
+-0.508110824869724
+-1.01827413755015
+0.927040891732172
+-0.43052682984179
+0.649646238402503
+0.489082281331912
+-0.227586109270053
+-0.604552534585311
+0.479358861347001
+-0.208346274791059
+-0.336026180481188
+0.176234681992498
+0.155297268400196
+0.236724975748945
+0.426712263096906
+0.0718331012938521
+-0.20341360336477
+0.810567498058392
+-0.105134751449411
+2.11547527131408
+0.799016074792607
diff --git a/inst/Description.qml b/inst/Description.qml
index 5fe0968a8..1e9d8c2a9 100644
--- a/inst/Description.qml
+++ b/inst/Description.qml
@@ -126,4 +126,11 @@ Description
func: "doeAnalysis"
requiresData: true
}
+
+ Analysis
+ {
+ title: qsTr("Bayesian Process Capability Study")
+ func: "bayesianProcessCapabilityStudies"
+ preloadData: true
+ }
}
diff --git a/inst/qml/bayesianProcessCapabilityStudies.qml b/inst/qml/bayesianProcessCapabilityStudies.qml
new file mode 100644
index 000000000..f0ffdc7ea
--- /dev/null
+++ b/inst/qml/bayesianProcessCapabilityStudies.qml
@@ -0,0 +1,463 @@
+// Copyright (C) 2013-2018 University of Amsterdam
+// This program is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Affero General Public License as
+// published by the Free Software Foundation, either version 3 of the
+// License, or (at your option) any later version.
+// This program is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+// GNU Affero General Public License for more details.
+// You should have received a copy of the GNU Affero General Public
+// License along with this program. If not, see
+// .
+//
+
+import QtQuick
+import QtQuick.Layouts
+import JASP.Controls
+
+import "./common" as Common
+
+Form
+{
+ function sortIntervalValues() {
+
+ var values = [
+ interval1.displayValue,
+ interval2.displayValue,
+ interval3.displayValue,
+ interval4.displayValue
+ ]
+ values.sort(function(a, b) { return a - b })
+ interval1.value = values[0]
+ interval2.value = values[1]
+ interval3.value = values[2]
+ interval4.value = values[3]
+ interval1b.value = values[0]
+ interval2b.value = values[1]
+ interval3b.value = values[2]
+ interval4b.value = values[3]
+ }
+ function sortIntervalValuesb() {
+
+ var values = [
+ interval1b.displayValue,
+ interval2b.displayValue,
+ interval3b.displayValue,
+ interval4b.displayValue
+ ]
+ values.sort(function(a, b) { return a - b })
+ interval1.value = values[0]
+ interval2.value = values[1]
+ interval3.value = values[2]
+ interval4.value = values[3]
+ interval1b.value = values[0]
+ interval2b.value = values[1]
+ interval3b.value = values[2]
+ interval4b.value = values[3]
+ }
+ columns: 2
+
+ VariablesForm
+ {
+ id: variablesFormLongFormat
+
+ AvailableVariablesList
+ {
+ name: "variablesFormLongFormat"
+ }
+
+ AssignedVariablesList
+ {
+ name: "measurementLongFormat"
+ title: qsTr("Measurement")
+ id: measurementLongFormat
+ allowedColumns: ["scale"]
+ singleVariable: true
+ }
+
+ }
+
+
+ // Section
+ // {
+ // title: qsTr("Process capability options")
+
+ Group
+ {
+ title: qsTr("Type of data distribution")
+
+
+ RadioButtonGroup
+ {
+ name: "capabilityStudyType"
+ id: capabilityStudyType
+
+ RadioButton
+ {
+ name: "normalCapabilityAnalysis"
+ id : normalCapabilityAnalysis
+ label: qsTr("Normal distribution")
+ checked: true
+ }
+
+ RadioButton
+ {
+ name: "tCapabilityAnalysis"
+ id : tCapabilityAnalysis
+ label: qsTr("Student's t-distribution")
+ // checked: true
+ }
+
+ }
+ }
+
+ Group
+ {
+ columns: 2
+ title: qsTr("Metrics")
+ info: qsTr("Select the process capability metrics to report.")
+ CheckBox { name: "Cp"; label: qsTr("Cp"); checked: true }
+ CheckBox { name: "Cpu"; label: qsTr("Cpu"); checked: true }
+ CheckBox { name: "Cpl"; label: qsTr("Cpl"); checked: true }
+ CheckBox { name: "Cpk"; label: qsTr("Cpk"); checked: true }
+ CheckBox { name: "Cpc"; label: qsTr("Cpc"); checked: true }
+ CheckBox { name: "Cpm"; label: qsTr("Cpm"); checked: true }
+ }
+
+ Group
+ {
+ title: qsTr("Capability Study")
+
+ CheckBox
+ {
+ name: "lowerSpecificationLimit"
+ label: qsTr("Lower specification limit")
+ id: lowerSpecificationLimit
+ childrenOnSameRow: true
+
+ DoubleField
+ {
+ name: "lowerSpecificationLimitValue"
+ id: lowerSpecificationLimitValue
+ negativeValues: true
+ defaultValue: -1
+ decimals: 9
+ }
+
+ }
+
+ CheckBox
+ {
+ name: "target"
+ label: qsTr("Target value")
+ id: target
+ childrenOnSameRow: true
+
+ DoubleField
+ {
+ name: "targetValue"
+ id: targetValue
+ negativeValues: true
+ defaultValue: 0
+ decimals: 9
+ }
+ }
+
+ CheckBox
+ {
+ name: "upperSpecificationLimit"
+ label: qsTr("Upper specification limit")
+ id: upperSpecificationLimit
+ childrenOnSameRow: true
+
+ DoubleField
+ {
+ name: "upperSpecificationLimitValue"
+ id: upperSpecificationLimitValue
+ negativeValues: true
+ defaultValue: 1
+ decimals: 9
+ }
+
+ }
+
+ }
+
+ Group
+ {
+
+ title: qsTr("Process Criteria")
+ GridLayout
+ {
+ // title: qsTr("Process Criteria")
+ columns: 5
+ columnSpacing: 2
+ rowSpacing: jaspTheme.rowGridSpacing / 3
+ id: intervalRow
+ property int dbWidth: 50
+ property int txtWidth: 100
+
+ // Row 0: Headers
+ Label {text: qsTr("Left bound")}
+ Item{}
+ Label {text: qsTr("Classification")}
+ Item{}
+ Label {text: qsTr("Right bound")}
+
+ // Row 1: Incapable
+ Item{}
+ Item{}
+ TextField { name: "intervalLabel1"; defaultValue: qsTr("Incapable"); fieldWidth: intervalRow.txtWidth}
+ Label { text: "<"; }
+ DoubleField { name: "interval1"; id: interval1; fieldWidth: intervalRow.dbWidth; defaultValue: 1.00; onEditingFinished: sortIntervalValues() }
+
+ // Row 2: Capable
+ DoubleField { name: "interval1b";id: interval1b; fieldWidth: intervalRow.dbWidth; editable: true; value: interval1.value; onEditingFinished: {sortIntervalValuesb()} }
+ Label { text: "<"; }
+ TextField { name: "intervalLabel2"; defaultValue: qsTr("Capable"); fieldWidth: intervalRow.txtWidth}
+ Label { text: "≤"; }
+ DoubleField { name: "interval2"; id: interval2; fieldWidth: intervalRow.dbWidth; defaultValue: 1.33; onEditingFinished: sortIntervalValues() }
+
+ // Row 3: Satisfactory
+ DoubleField { name: "interval2b"; id: interval2b; fieldWidth: intervalRow.dbWidth; editable: true; value: interval2.value; onEditingFinished: {sortIntervalValuesb()} }
+ Label { text: "<"; }
+ TextField { name: "intervalLabel3"; defaultValue: qsTr("Satisfactory"); fieldWidth: intervalRow.txtWidth}
+ Label { text: "≤"; }
+ DoubleField { name: "interval3"; id: interval3; fieldWidth: intervalRow.dbWidth; defaultValue: 1.50; onEditingFinished: sortIntervalValues() }
+
+ // Row 4: Excellent
+ DoubleField { name: "interval3b"; id: interval3b; fieldWidth: intervalRow.dbWidth; editable: true; value: interval3.value; onEditingFinished: {sortIntervalValuesb()} }
+ Label { text: "<"; }
+ TextField { name: "intervalLabel4"; defaultValue: qsTr("Excellent"); fieldWidth: intervalRow.txtWidth}
+ Label { text: "≤"; }
+ DoubleField { name: "interval4"; id: interval4; fieldWidth: intervalRow.dbWidth; defaultValue: 2.00; onEditingFinished: sortIntervalValues() }
+
+ // Row 5: Super
+ DoubleField { name: "interval4b"; id: interval4b; fieldWidth: intervalRow.dbWidth; editable: true; value: interval4.value; onEditingFinished: {sortIntervalValuesb()} }
+ Label { text: ">"; }
+ TextField { name: "intervalLabel5"; defaultValue: qsTr("Super"); fieldWidth: intervalRow.txtWidth}
+ Item{}
+ Item{}
+ }
+ }
+
+ // }
+
+ // Section
+ // {
+ // title: qsTr("Prior distributions")
+
+ // }
+
+ Section
+ {
+ title: qsTr("Tables")
+ CheckBox
+ {
+ name: "intervalTable"
+ label: qsTr("Interval table")
+ info: qsTr("Show the posterior probabilities of the interval specified with the input on the right. Note that the input is automatically sorted and that the first and last fields are always negative and positive infinity.")
+ }
+ CIField
+ {
+ name: "credibleIntervalWidth"
+ label: qsTr("Credible interval")
+ info: qsTr("Width of the credible interval used for the posterior distribution in the Capability table.")
+ }
+ }
+
+ Section
+ {
+
+ title: qsTr("Prior and Posterior Inference")
+
+ Common.PlotLayout {}
+
+ Common.PlotLayout
+ {
+ baseName: "priorDistributionPlot"
+ baseLabel: qsTr("Prior distribution")
+ hasPrior: false
+ }
+
+ }
+
+ Section
+ {
+ title: qsTr("Sequential Analysis")
+
+ Common.PlotLayout
+ {
+ id: sequentialAnalysisPointEstimatePlot
+ baseName: "sequentialAnalysisPointEstimatePlot"
+ baseLabel: qsTr("Point estimate plot")
+ hasPrior: false
+ }
+
+ Common.PlotLayout
+ {
+ id: sequentialAnalysisIntervalEstimatePlot
+ baseName: "sequentialAnalysisPointIntervalPlot"
+ baseLabel: qsTr("Interval estimate plot")
+ hasPrior: false
+ hasEstimate: false
+ hasCi: false
+ hasType: true
+ }
+
+ Group
+ {
+ CheckBox
+ {
+ enabled: sequentialAnalysisPointEstimatePlot.checked || sequentialAnalysisIntervalEstimatePlot.checked
+ id: sequentialAnalysisAdditionalInfo
+ name: "sequentialAnalysisPlotAdditionalInfo"
+ label: qsTr("Show process criteria")
+ checked: true
+ info: qsTr("Add a secondary right axis with condition bounds for the process")
+ }
+
+ CheckBox
+ {
+ // TODO:
+ enabled: sequentialAnalysisPointEstimatePlot.checked || sequentialAnalysisIntervalEstimatePlot.checked
+ name: "sequentialAnalysisUpdatingTable"
+ label: qsTr("Posterior updating table")
+ checked: false
+ info: qsTr("Show the data from the sequential analysis in a table. Will show both the information for the point estimate and interval estimate plots, if both are selected.")
+ }
+ }
+ }
+
+ Section
+ {
+
+ title: qsTr("Prior and Posterior Predictive Plots")
+
+ Common.PlotLayout
+ {
+ baseName: "posteriorPredictiveDistributionPlot"
+ baseLabel: qsTr("Posterior predictive distribution")
+ hasPrior: false
+ hasAxes: false
+ hasPanels: false
+ }
+
+ Common.PlotLayout
+ {
+ baseName: "priorPredictiveDistributionPlot"
+ baseLabel: qsTr("Prior predictive distribution")
+ hasPrior: false
+ hasAxes: false
+ hasPanels: false
+ }
+
+ }
+
+
+ Section
+ {
+ title: qsTr("Prior distributions")
+
+ // TODO: this dropdown should just show the same GUI as the custom one
+ // but disable e.g., the DropDown itself and instead show the prior
+ // also disable all truncation for non-custom ones
+ // NOTE: the above is done, but default values cannot be set yet.
+
+ DropDown
+ {
+ id: priorSettings
+ name: "priorSettings"
+ label: qsTr("Prior distributions")
+ values:
+ [
+ {label: qsTr("Default"), value: "default"},
+ {label: qsTr("Informed conjugate"), value: "conjugate"},
+ // {label: qsTr("Informed conjugate"), value: "weaklyInformativeConjugate"},
+ {label: qsTr("Informed uniform"), value: "weaklyInformativeUniform"},
+ {label: qsTr("Custom informative"), value: "customInformative"},
+ ]
+ }
+
+ Common.PriorsNew
+ {
+
+ // visible: priorSettings.currentValue === "customInformative"
+ priorType: capabilityStudyType.value === "normalCapabilityAnalysis" ? "normalModel" : "tModel"
+
+ hasTruncation: priorSettings.currentValue === "customInformative"
+ hasParameters: priorSettings.currentValue !== "default"
+ visible: priorSettings.currentValue !== "default"
+
+ dropDownValuesMap: {
+ switch (priorSettings.currentValue) {
+ case "default":
+ return {
+ "mean": [{ label: qsTr("Jeffreys"), value: "jeffreys"}],
+ "sigma": [{ label: qsTr("Jeffreys"), value: "jeffreys"}],
+ "df": [{ label: qsTr("Gamma(α,β)"), value: "gammaAB" }]
+ }
+ case "conjugate":
+ return {
+ "mean": [{ label: qsTr("Normal(μ,σ)"), value: "normal"}],
+ "sigma": [{ label: qsTr("Gamma(α,β)"), value: "gammaAB" }],
+ "df": [{ label: qsTr("Gamma(α,β)"), value: "gammaAB" }]
+ };
+ // case "weaklyInformativeConjugate":
+ // return {
+ // "mean": [{ label: qsTr("Normal(μ,σ)"), value: "normal"}],
+ // "sigma": [{ label: qsTr("Gamma(α,β)"), value: "gammaAB" }],
+ // "df": [{ label: qsTr("Gamma(α,β)"), value: "gammaAB" }]
+ // }
+ case "weaklyInformativeUniform":
+ return {
+ "mean": [{ label: qsTr("Uniform(a,b)"), value: "uniform"}],
+ "sigma": [{ label: qsTr("Uniform(a,b)"), value: "uniform"}],
+ "df": [{ label: qsTr("Gamma(α,β)"), value: "gammaAB" }]
+ }
+ case "customInformative":
+ return undefined;
+ }
+ }
+ }
+ }
+
+ Section
+ {
+ title: qsTr("Advanced options")
+
+ Group
+ {
+ title: qsTr("MCMC Settings")
+ info: qsTr("Adjust the Markov Chain Monte Carlo (MCMC) settings for estimating the posterior distribution.")
+ IntegerField
+ {
+ name: "noIterations"
+ label: qsTr("No. iterations")
+ defaultValue: 5000
+ min: 100
+ max: 100000000
+ info: qsTr("Number of MCMC iterations used for estimating the posterior distribution.")
+ }
+ IntegerField
+ {
+ name: "noWarmup"
+ label: qsTr("No. warmup samples")
+ defaultValue: 1000
+ min: 0
+ max: 100000000
+ info: qsTr("Number of initial MCMC samples to discard.")
+ }
+ IntegerField
+ {
+ name: "noChains"
+ label: qsTr("No. chains")
+ defaultValue: 1
+ min: 1
+ max: 128
+ info: qsTr("Number of MCMC chains to run.")
+ }
+ }
+ }
+}
diff --git a/inst/qml/common/PlotLayout.qml b/inst/qml/common/PlotLayout.qml
new file mode 100644
index 000000000..abc3957c8
--- /dev/null
+++ b/inst/qml/common/PlotLayout.qml
@@ -0,0 +1,266 @@
+//
+// Copyright (C) 2013-2018 University of Amsterdam
+//
+// This program is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Affero General Public License as
+// published by the Free Software Foundation, either version 3 of the
+// License, or (at your option) any later version.
+//
+// This program is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+// GNU Affero General Public License for more details.
+//
+// You should have received a copy of the GNU Affero General Public
+// License along with this program. If not, see
+// .
+//
+import QtQuick
+import QtQuick.Layouts
+import JASP
+import JASP.Controls
+
+
+Group
+{
+ id: root
+ property string baseName: "posteriorDistributionPlot"
+ property string baseLabel: qsTr("Posterior distribution")
+ property bool hasPrior: true
+ property bool hasEstimate: true
+ property bool hasCi: true
+ property bool hasType: false
+ property bool hasAxes: true
+ property bool hasPanels: true
+
+ readonly property alias checked: mainCheckBox.checked
+
+ CheckBox
+ {
+ id: mainCheckBox
+ name: baseName
+ label: baseLabel
+
+ // Group so the options are shown in a 2-column layout
+ Group
+ {
+
+ columns: 2
+ columnSpacing: 10 * jaspTheme.columnGroupSpacing
+
+ // Group so point estimate and CI options are shown in a single column
+ Group
+ {
+ enabled: hasEstimate || hasCi
+ visible: hasEstimate || hasCi
+
+ CheckBox
+ {
+ enabled: hasEstimate
+ visible: hasEstimate
+ label: qsTr("Point estimate")
+ name: baseName + "IndividualPointEstimate"
+ childrenOnSameRow: true
+
+ DropDown
+ {
+ name: baseName + "IndividualPointEstimateType"
+ label: ""
+ values: [
+ {label: qsTr("mean"), value: "mean"},
+ {label: qsTr("median"), value: "median"},
+ {label: qsTr("mode"), value: "mode"}
+ ]
+ }
+ }
+
+ // Group so CI checkbox and options are shown in a single column (with subgroup so CI options are indented)
+ Group
+ {
+ enabled: hasCi
+ visible: hasCi
+
+ columns: 1
+ CheckBox
+ {
+ name: baseName + "IndividualCi"
+ label: qsTr("CI")
+ id: posteriorPlotIndividualCI
+ childrenOnSameRow: true
+
+ DropDown
+ {
+ name: baseName + "IndividualCiType"
+ label: ""
+ id: posteriorPlotIndividualType
+ values: [
+ {label: qsTr("central"), value: "central"},
+ {label: qsTr("HPD"), value: "HPD"},
+ {label: qsTr("custom"), value: "custom"}//,
+ // {label: qsTr("support"), value: "support"}
+ ]
+ }
+ }
+
+ Group
+ {
+ columns: 2
+ indent: true
+ enabled: posteriorPlotIndividualCI.checked
+
+ CIField
+ {
+ visible: posteriorPlotIndividualType.currentValue === "central" || posteriorPlotIndividualType.currentValue === "HPD"
+ name: baseName + "IndividualCiMass"
+ label: qsTr("Mass")
+ fieldWidth: 50
+ defaultValue: 95
+ min: 1
+ max: 100
+ inclusive: JASP.MinMax
+ }
+
+ DoubleField
+ {
+ visible: posteriorPlotIndividualType.currentValue === "custom"
+ name: baseName + "IndividualCiLower"
+ label: qsTr("Lower")
+ id: plotsPosteriorLower
+ fieldWidth: 50
+ defaultValue: 0
+ negativeValues: true
+ inclusive: JASP.MinMax
+ }
+
+ DoubleField
+ {
+ visible: posteriorPlotIndividualType.currentValue === "custom"
+ name: baseName + "IndividualCiUpper"
+ label: qsTr("Upper")
+ id: plotsPosteriorUpper
+ fieldWidth: 50
+ defaultValue: 1
+ negativeValues: true
+ inclusive: JASP.MinMax
+ }
+
+ FormulaField
+ {
+ visible: posteriorPlotIndividualType.currentValue === "support"
+ name: baseName + "IndividualCiBf"
+ label: qsTr("BF")
+ fieldWidth: 50
+ defaultValue: "1"
+ min: 0
+ inclusive: JASP.None
+ }
+ }
+ }
+ }
+
+ Group
+ {
+ enabled: hasType
+ visible: hasType
+
+ title: qsTr("Type")
+
+ columns: 2
+ FormulaField
+ {
+ name: baseName + "TypeLower"
+ label: qsTr("Lower")
+ id: typeLower
+ fieldWidth: 50
+ defaultValue: 0.0
+ max: typeUpper.value
+ }
+
+ FormulaField
+ {
+ name: baseName + "TypeUpper"
+ label: qsTr("Upper")
+ id: typeUpper
+ fieldWidth: 50
+ defaultValue: 1.0
+ min: typeLower.value
+
+ }
+ }
+
+ RadioButtonGroup
+ {
+ enabled: hasPanels
+ visible: hasPanels
+ name: baseName + "PanelLayout"
+ title: qsTr("Layout")
+ id: posteriorDistributionPlotPanelLayout
+
+ RadioButton { value: "multiplePanels"; label: qsTr("One plot per metric"); checked: true }
+ RadioButton { value: "singlePanel"; label: qsTr("All metrics in one plot") }
+
+ }
+
+ RadioButtonGroup
+ {
+ enabled: hasAxes
+ visible: hasAxes
+ name: baseName + "Axes"
+ title: qsTr("Axes")
+ id: posteriorDistributionPlotAxes
+
+ RadioButton { value: "free"; label: qsTr("Automatic"); checked: true }
+ RadioButton { value: "fixed"; label: qsTr("Identical across panels"); enabled: posteriorDistributionPlotPanelLayout.value === "multiplePanels" }
+ RadioButton { value: "custom"; label: qsTr("Custom axes"); }
+ }
+
+ Group
+ {
+
+ title: qsTr("Custom axes")
+ enabled: hasAxes && posteriorDistributionPlotAxes.value === "custom"
+ visible: hasAxes && posteriorDistributionPlotAxes.value === "custom"
+
+ GridLayout
+ {
+ columns: 5
+ columnSpacing: 2
+ rowSpacing: jaspTheme.rowGridSpacing / 3
+ id: customAxesLayout
+ property int dbWidth: 50
+ property int txtWidth: 100
+
+ // Row 0: Headers
+ Label {text: qsTr("Axis")}
+ Item{}
+ Label {text: qsTr("Min")}
+ Item{}
+ Label {text: qsTr("Max")}
+
+ // Row 1: x axis
+ Label { text: qsTr("x axis"); }
+ Item{}
+ DoubleField { name: baseName + "custom_x_min"; id: custom_x_min; fieldWidth: customAxesLayout.dbWidth; defaultValue: 0.00; negativeValues: true; max: custom_x_max.value}
+ Item{}
+ DoubleField { name: baseName + "custom_x_max"; id: custom_x_max; fieldWidth: customAxesLayout.dbWidth; defaultValue: 1.00; negativeValues: true; min: custom_x_min.value}
+
+ // Row 2: y axis
+ Label { text: qsTr("y axis"); }
+ Item{}
+ DoubleField { name: baseName + "custom_y_min"; id: custom_y_min; fieldWidth: customAxesLayout.dbWidth; defaultValue: 0.00; negativeValues: false; max: custom_y_max.value}
+ Item{}
+ DoubleField { name: baseName + "custom_y_max"; id: custom_y_max; fieldWidth: customAxesLayout.dbWidth; defaultValue: 1.00; negativeValues: false; min: custom_y_min.value}
+ }
+ }
+
+ CheckBox
+ {
+ enabled: hasPrior
+ visible: hasPrior
+ name: baseName + "PriorDistribution"
+ label: qsTr("Show prior distribution")
+ checked: false
+ }
+ }
+ }
+}
\ No newline at end of file
diff --git a/inst/qml/common/Priors.qml b/inst/qml/common/Priors.qml
new file mode 100644
index 000000000..49bf75ba1
--- /dev/null
+++ b/inst/qml/common/Priors.qml
@@ -0,0 +1,211 @@
+//
+// Copyright (C) 2013-2018 University of Amsterdam
+//
+// This program is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Affero General Public License as
+// published by the Free Software Foundation, either version 3 of the
+// License, or (at your option) any later version.
+//
+// This program is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+// GNU Affero General Public License for more details.
+//
+// You should have received a copy of the GNU Affero General Public
+// License along with this program. If not, see
+// .
+//
+import QtQuick
+import QtQuick.Layouts
+import JASP.Controls
+
+Group
+{
+ columns: 2
+
+ property string baseName: "populationMeanPrior"
+ property string baseLabel: qsTr("Population mean")
+
+ property bool fullRealLLine: true
+ property bool hasJeffreys: true
+
+// TODO: should be dropdown, see RBMAP
+ RadioButtonGroup
+ {
+ id: priorChoice
+ title: baseLabel
+ name: baseName
+
+ RadioButton
+ {
+ visible: hasJeffreys
+ enabled: hasJeffreys
+ label: qsTr("Jeffreys")
+ name: baseName + "jeffreys"
+ checked: hasJeffreys
+ }
+
+ RadioButton
+ {
+ id: uniformInformative
+ label: qsTr("Uniform")
+ name: baseName + "uniform"
+ checked: !hasJeffreys
+ childrenOnSameRow: true
+
+ DoubleField
+ {
+ id: uniformLower
+ label: qsTr("Lower:")
+ name: baseName + "uniformLower"
+ visible: uniformInformative.checked
+ defaultValue: fullRealLLine ? -3 : 0
+ negativeValues: fullRealLLine ? true : false
+ max: uniformUpper.value
+ }
+
+ DoubleField
+ {
+ id: uniformUpper
+ label: qsTr("Upper:");
+ name: baseName + "uniformUpper"
+ visible: uniformInformative.checked
+ defaultValue: 3
+ fieldWidth: 50
+ negativeValues: fullRealLLine ? true : false
+ min: uniformLower.value
+ }
+ }
+
+ RadioButton
+ {
+ id: cauchyInformative
+ label: fullRealLLine ? qsTr("Cauchy") : qsTr("Truncated Cauchy")
+ name: baseName + "cauchy"
+ childrenOnSameRow: true
+
+ DoubleField
+ {
+ label: qsTr("location:")
+ name: baseName + "cauchyLocation"
+ visible: cauchyInformative.checked
+ defaultValue: 0
+ negativeValues: true
+ }
+
+ DoubleField
+ {
+ label: qsTr("scale:");
+ name: baseName + "cauchyScale"
+ visible: cauchyInformative.checked
+ defaultValue: 0.707
+ fieldWidth: 50
+ }
+ }
+
+ RadioButton
+ {
+ id: normalInformative
+ label: fullRealLLine ? qsTr("Normal") : qsTr("Truncated Normal")
+ name: baseName + "normal"
+ childrenOnSameRow: true
+
+ DoubleField
+ {
+ label: qsTr("mean:")
+ name: baseName + "normalMean"
+ visible: normalInformative.checked
+ defaultValue: 0
+ negativeValues: true
+ }
+
+ DoubleField
+ {
+ label: qsTr("std:")
+ name: baseName + "normalSd"
+ visible: normalInformative.checked
+ defaultValue: 0.707
+ fieldWidth: 50
+ }
+
+
+ }
+
+ RadioButton
+ {
+ id: tInformative
+ label: fullRealLLine ? qsTr("t") : qsTr("Truncated t")
+ name: baseName + "t"
+ childrenOnSameRow: true
+
+ DoubleField
+ {
+ label: qsTr("location:")
+ name: baseName + "tLocation"
+ visible: tInformative.checked
+ defaultValue: 0
+ negativeValues: true
+ }
+
+ DoubleField
+ {
+ label: qsTr("scale:")
+ name: baseName + "tScale"
+ visible: tInformative.checked
+ defaultValue: 0.707
+ fieldWidth: 50
+ }
+
+ IntegerField
+ {
+ label: qsTr("df:");
+ name: baseName + "tDf";
+ visible: tInformative.checked;
+ min: 1
+ defaultValue: 1
+ }
+ }
+ }
+
+ Group
+ {
+ title: qsTr("Truncation")
+ enabled: priorChoice.value !== baseName + "jeffreys"
+ visible: priorChoice.value !== baseName + "jeffreys"
+
+ CheckBox
+ {
+ name: baseName + "truncationLowerBound"
+ childrenOnSameRow: true
+
+ FormulaField
+ {
+ id: lowerTT
+ name: baseName + "truncationLowerBoundValue"
+ label: qsTr("Lower bound:")
+ fieldWidth: 50
+ defaultValue: fullRealLLine ? -Infinity : 0
+ max: upperTT.value
+ min: fullRealLLine ? -Infinity : 0
+ }
+ }
+
+ CheckBox
+ {
+ name: baseName + "truncationUpperBound"
+ childrenOnSameRow: true
+
+ FormulaField
+ {
+ id: upperTT
+ name: baseName + "truncationUpperBoundValue"
+ label: qsTr("Upper bound:")
+ fieldWidth: 50
+ defaultValue: Infinity
+ min: Math.max(fullRealLLine ? -Infinity : 0, lowerTT.value)
+
+ }
+ }
+ }
+
+}
diff --git a/inst/qml/common/PriorsNew.qml b/inst/qml/common/PriorsNew.qml
new file mode 100644
index 000000000..1693e7364
--- /dev/null
+++ b/inst/qml/common/PriorsNew.qml
@@ -0,0 +1,352 @@
+//
+// Copyright (C) 2013-2018 University of Amsterdam
+//
+// This program is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Affero General Public License as
+// published by the Free Software Foundation, either version 3 of the
+// License, or (at your option) any later version.
+//
+// This program is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+// GNU Affero General Public License for more details.
+//
+// You should have received a copy of the GNU Affero General Public
+// License along with this program. If not, see
+// .
+//
+import QtQuick
+import QtQuick.Layouts
+import JASP.Controls
+import JASP
+
+ColumnLayout
+{
+ spacing: 0
+ property string priorType: "normalModel"
+ property bool hasTruncation: false
+ property bool hasParameters: true
+
+ Component.onCompleted: {
+ console.log("Component completed, priorType: " + priorType);
+ console.log("Current component values: " + JSON.stringify(currentComponentValues));
+ }
+
+ onPriorTypeChanged: {
+ // this is not shown?
+ console.log("Prior type changed to: " + priorType);
+ }
+
+ // TODO: these should not be fixed, no?
+ // property var meanValues: { "name": "mean", "type": "normal", "mu": "0", "sigma": "1" }
+ // property var sigmaValues: { "name": "sigma", "type": "invgamma", "alpha": "1", "beta": "0.15", "truncationLower": 0 }
+ // property var dfValues: { "name": "t", "type": "invgamma", "alpha": "1", "beta": "0.15", "truncationLower": 0, "hasJeffreys": false }
+
+ property var nameMap: {
+ "mean": "Mean",
+ "sigma": "Sigma",
+ "df": "df"
+ }
+ property var defaultDistributionMap: {
+ "mean": "normal",
+ "sigma": "invgamma",
+ "df": "invgamma"
+ }
+ property var truncationLowerMap: {
+ "mean": -Infinity,
+ "sigma": 0,
+ "df": 0
+ }
+ property var allPriors : [
+ { label: qsTr("Normal(μ,σ)"), value: "normal"},
+ { label: qsTr("Student-t(μ,σ,v)"), value: "t"},
+ { label: qsTr("Cauchy(x₀,θ)"), value: "cauchy"},
+ { label: qsTr("Jeffreys"), value: "jeffreys"},
+ { label: qsTr("Gamma(α,β)"), value: "gammaAB"},
+ { label: qsTr("Gamma(k,θ)"), value: "gammaK0"},
+ { label: qsTr("Inverse-Gamma(α,β)"), value: "invgamma"},
+ { label: qsTr("Log-Normal(μ,σ)"), value: "lognormal"},
+ { label: qsTr("Beta(α,β)"), value: "beta"},
+ { label: qsTr("Uniform(a,b)"), value: "uniform"}
+ ]
+ property var priorTruncationMap: {
+ "normal" : [-Infinity, Infinity],
+ "t" : [-Infinity, Infinity],
+ "cauchy" : [-Infinity, Infinity],
+ "jeffreys": [-Infinity, Infinity],
+ "gammaAB": [0, Infinity],
+ "gammaK0": [0, Infinity],
+ "invgamma": [0, Infinity],
+ "lognormal": [0, Infinity],
+ "beta": [0, 1 ],
+ "uniform": [-Infinity, Infinity]
+ }
+ property var defaultDropDownValuesMap: {
+ "mean": allPriors,
+ "sigma": allPriors,
+ "df": allPriors.filter(p => p.value !== "jeffreys")
+ }
+ property var dropDownValuesMap: undefined
+ property var activeDropDownValuesMap: dropDownValuesMap !== undefined ? dropDownValuesMap : defaultDropDownValuesMap
+ property var hasJeffreysMap: {
+ "mean": true,
+ "sigma": true,
+ "df": false
+ }
+
+ onDropDownValuesMapChanged: console.log("dropDownValuesMap changed: " + dropDownValuesMap)
+ // property var defaultParametersMap: {
+ // "mean": { "mu": "0", "sigma": "1" },
+ // "sigma": { "alpha": "1", "beta": "0.15", "truncationLower": 0 },
+ // "t": { "alpha": "1", "beta": "0.15", "truncationLower": 0, "hasJeffreys": false }
+ // }
+
+ property var currentComponentValues: {
+ switch (priorType) {
+ case "normalModel":
+ return [ "mean", "sigma" ];
+ case "tModel":
+ return [ "mean", "sigma", "df" ];
+ }
+ // switch (priorType) {
+ // case "normalModel":
+ // return [ meanValues, sigmaValues ];
+ // case "tModel":
+ // return [ meanValues, sigmaValues, dfValues ];
+ // }
+ }
+
+
+ // TODO: this could also be a gridLayout, no?
+ property double width1: 70 * preferencesModel.uiScale;
+ property double width2: 140 * preferencesModel.uiScale;
+ property double width3: 155 * preferencesModel.uiScale;
+ property double width4: 130 * preferencesModel.uiScale;
+
+ RowLayout
+ {
+ Label { text: qsTr("Parameter"); Layout.preferredWidth: width1; Layout.leftMargin: 5 * preferencesModel.uiScale}
+ Label { text: qsTr("Distribution"); Layout.preferredWidth: width2; Layout.leftMargin: 5 * preferencesModel.uiScale}
+ Label { text: qsTr("Parameters"); Layout.preferredWidth: width3 ; visible: hasParameters }
+ Label { text: qsTr("Truncation"); Layout.preferredWidth: width4 ; visible: hasTruncation }
+ }
+
+
+ ComponentsList
+ {
+ name: priorType + "ComponentsList"
+ optionKey: "name"
+
+ addItemManually: false
+
+ // defaultValues: currentComponentValues
+ values: currentComponentValues
+
+ rowComponent: RowLayout
+ {
+ Row
+ {
+ spacing: 4 * preferencesModel.uiScale
+ Layout.preferredWidth: width1
+ Label { text: nameMap[rowValue] }
+ }
+
+ Row
+ {
+ spacing: 4 * preferencesModel.uiScale
+ Layout.preferredWidth: width2
+
+ DropDown
+ {
+ visible: activeDropDownValuesMap[rowValue].length > 1
+ id: typeItem
+ name: "type"
+ useExternalBorder: true
+ value: defaultDistributionMap[rowValue]
+ values: activeDropDownValuesMap[rowValue]
+ }
+
+ Label
+ {
+ visible: activeDropDownValuesMap[rowValue].length === 1
+ text: activeDropDownValuesMap[rowValue][0].label
+ }
+ }
+
+ Row
+ {
+ spacing: 4 * preferencesModel.uiScale
+ Layout.preferredWidth: width3
+ visible: hasParameters
+
+ FormulaField
+ {
+ label: "μ"
+ name: "mu"
+ visible: typeItem.currentValue === "normal" ||
+ typeItem.currentValue === "lognormal" ||
+ typeItem.currentValue === "t"
+ value: "0"
+ inclusive: JASP.None
+ fieldWidth: 40 * preferencesModel.uiScale
+ useExternalBorder: false
+ showBorder: true
+
+ }
+ FormulaField
+ {
+ label: "x₀"
+ name: "x0"
+ visible: typeItem.currentValue === "cauchy" ||
+ typeItem.currentValue === "spike"
+ value: "0"
+ inclusive: JASP.None
+ fieldWidth: 40 * preferencesModel.uiScale
+ useExternalBorder: false
+ showBorder: true
+ }
+ FormulaField
+ {
+ label: "σ"
+ name: "sigma"
+ id: sigma
+ visible: typeItem.currentValue === "normal" ||
+ typeItem.currentValue === "lognormal" ||
+ typeItem.currentValue === "t"
+ value: "1"
+ min: 0
+ inclusive: JASP.None
+ fieldWidth: 40 * preferencesModel.uiScale
+ useExternalBorder: false
+ showBorder: true
+ }
+ FormulaField
+ {
+ label: "k "
+ name: "k"
+ visible: typeItem.currentValue === "gammaK0"
+ value: "1"
+ min: 0
+ inclusive: JASP.None
+ fieldWidth: 40 * preferencesModel.uiScale
+ useExternalBorder: false
+ }
+ FormulaField
+ {
+ label: "θ"
+ name: "theta"
+ visible: typeItem.currentValue === "cauchy" ||
+ typeItem.currentValue === "gammaK0"
+ value: "1"
+ min: 0
+ inclusive: JASP.None
+ fieldWidth: 40 * preferencesModel.uiScale
+ useExternalBorder: false
+ showBorder: true
+ }
+ FormulaField
+ {
+ label: "ν"
+ name: "nu"
+ visible: typeItem.currentValue === "t"
+ value: "2"
+ min: 1
+ inclusive: JASP.MinOnly
+ fieldWidth: 40 * preferencesModel.uiScale
+ useExternalBorder: false
+ showBorder: true
+ }
+ FormulaField
+ {
+ label: "α "
+ name: "alpha"
+ visible: typeItem.currentValue === "gammaAB" ||
+ typeItem.currentValue === "invgamma" ||
+ typeItem.currentValue === "beta"
+ value: "1"
+ min: 0
+ inclusive: JASP.None
+ fieldWidth: 40 * preferencesModel.uiScale
+ useExternalBorder: false
+ showBorder: true
+ }
+ FormulaField
+ {
+ label: "β"
+ name: "beta"
+ visible: typeItem.currentValue === "gammaAB" ||
+ typeItem.currentValue === "invgamma" ||
+ typeItem.currentValue === "beta"
+ value: "0.15"
+ min: 0
+ inclusive: JASP.None
+ fieldWidth: 40 * preferencesModel.uiScale
+ useExternalBorder: false
+ showBorder: true
+ }
+ FormulaField
+ {
+ label: "a "
+ name: "a"
+ id: a
+ visible: typeItem.currentValue === "uniform"
+ value: "0"
+ max: b.value
+ inclusive: JASP.None
+ fieldWidth: 40 * preferencesModel.uiScale
+ useExternalBorder: false
+ showBorder: true
+ }
+ FormulaField
+ {
+ label: "b"
+ name: "b"
+ id: b
+ visible: typeItem.currentValue === "uniform"
+ value: "1"
+ min: a.value
+ inclusive: JASP.None
+ fieldWidth: 40 * preferencesModel.uiScale
+ useExternalBorder: false
+ showBorder: true
+ }
+ }
+
+ Row
+ {
+ spacing: 4 * preferencesModel.uiScale
+ Layout.preferredWidth: width4
+
+ FormulaField
+ {
+ id: truncationLower
+ label: qsTr("lower")
+ name: "truncationLower"
+ visible: hasTruncation && typeItem.currentValue !== "spike" && typeItem.currentValue !== "uniform" && typeItem.currentValue !== "jeffreys"
+ value: Math.max((priorTruncationMap[typeItem.currentValue] || [-Infinity, Infinity])[0], truncationLowerMap[rowValue])
+ min: Math.max((priorTruncationMap[typeItem.currentValue] || [-Infinity, Infinity])[0], truncationLowerMap[rowValue])
+ max: truncationUpper.value
+ inclusive: JASP.MinOnly
+ fieldWidth: 40 * preferencesModel.uiScale
+ useExternalBorder: false
+ showBorder: true
+ }
+ FormulaField
+ {
+ id: truncationUpper
+ label: qsTr("upper")
+ name: "truncationUpper"
+ visible: hasTruncation && typeItem.currentValue !== "spike" && typeItem.currentValue !== "uniform" && typeItem.currentValue !== "jeffreys"
+ value: (priorTruncationMap[typeItem.currentValue] || [-Infinity, Infinity])[1]
+ max: (priorTruncationMap[typeItem.currentValue] || [-Infinity, Infinity])[1]
+ min: truncationLower ? truncationLower.value : 0
+ inclusive: JASP.MaxOnly
+ fieldWidth: 40 * preferencesModel.uiScale
+ useExternalBorder: false
+ showBorder: true
+ }
+ }
+ }
+ }
+
+}
diff --git a/jaspQualityControl.Rproj b/jaspQualityControl.Rproj
index 27aef215c..3afa55d15 100644
--- a/jaspQualityControl.Rproj
+++ b/jaspQualityControl.Rproj
@@ -18,4 +18,6 @@ StripTrailingWhitespace: Yes
BuildType: Package
PackageUseDevtools: Yes
+PackageCleanBeforeInstall: No
PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace
diff --git a/man/dot-PRESS.Rd b/man/dot-PRESS.Rd
new file mode 100644
index 000000000..4d5e76922
--- /dev/null
+++ b/man/dot-PRESS.Rd
@@ -0,0 +1,13 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/doeAnalysis.R
+\name{.PRESS}
+\alias{.PRESS}
+\title{calculate the predictive residuals
+calculate the PRESS}
+\usage{
+.PRESS(linear.model)
+}
+\description{
+calculate the predictive residuals
+calculate the PRESS
+}
diff --git a/man/dot-pred_r_squared.Rd b/man/dot-pred_r_squared.Rd
new file mode 100644
index 000000000..4446c563f
--- /dev/null
+++ b/man/dot-pred_r_squared.Rd
@@ -0,0 +1,13 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/doeAnalysis.R
+\name{.pred_r_squared}
+\alias{.pred_r_squared}
+\title{Use anova() to get the sum of squares for the linear model
+Calculate the total sum of squares}
+\usage{
+.pred_r_squared(linear.model)
+}
+\description{
+Use anova() to get the sum of squares for the linear model
+Calculate the total sum of squares
+}
diff --git a/renv.lock b/renv.lock
index d3a023ef4..52c9365c4 100644
--- a/renv.lock
+++ b/renv.lock
@@ -2,21 +2,19 @@
"R": {
"Version": "4.5.2",
"Repositories": [
- {
- "Name": "RSPM",
- "URL": "https://packagemanager.posit.co/cran/2026-04-22"
- },
- {
- "Name": "RPSM2",
- "URL": "https://packagemanager.posit.co/cran/2026-03-18"
- },
{
"Name": "CRAN",
- "URL": "https://cran.rstudio.com"
+ "URL": "https://cloud.r-project.org"
}
]
},
"Packages": {
+ "BH": {
+ "Package": "BH",
+ "Version": "1.90.0-1",
+ "Source": "Repository",
+ "Requirements": []
+ },
"BayesFactor": {
"Package": "BayesFactor",
"Version": "0.9.12-4.8",
@@ -68,7 +66,179 @@
"NeedsCompilation": "yes",
"Author": "Richard D. Morey [aut, cre, cph], Jeffrey N. Rouder [aut], Tahira Jamil [ctb, cph], Simon Urbanek [ctb, cph], Karl Forner [ctb, cph], Alexander Ly [ctb, cph]",
"Maintainer": "Richard D. Morey ",
- "Repository": "RSPM"
+ "Repository": "CRAN"
+ },
+ "BayesTools": {
+ "Package": "BayesTools",
+ "Version": "0.2.23",
+ "Source": "Repository",
+ "Title": "Tools for Bayesian Analyses",
+ "Description": "Provides tools for conducting Bayesian analyses and Bayesian model averaging (Kass and Raftery, 1995, , Hoeting et al., 1999, ). The package contains functions for creating a wide range of prior distribution objects, mixing posterior samples from 'JAGS' and 'Stan' models, plotting posterior distributions, and etc... The tools for working with prior distribution span from visualization, generating 'JAGS' and 'bridgesampling' syntax to basic functions such as rng, quantile, and distribution functions.",
+ "Maintainer": "František Bartoš ",
+ "Authors@R": "c( person(\"František\", \"Bartoš\", role = c(\"aut\", \"cre\"), email = \"f.bartos96@gmail.com\", comment = c(ORCID = \"0000-0002-0018-5573\")) )",
+ "URL": "https://fbartos.github.io/BayesTools/",
+ "BugReports": "https://github.com/FBartos/BayesTools/issues",
+ "License": "GPL-3",
+ "Encoding": "UTF-8",
+ "LazyData": "true",
+ "RoxygenNote": "7.3.2",
+ "SystemRequirements": "JAGS >= 4.3.0 (https://mcmc-jags.sourceforge.io/)",
+ "Depends": [
+ "stats"
+ ],
+ "Imports": [
+ "graphics",
+ "extraDistr",
+ "mvtnorm",
+ "coda",
+ "bridgesampling",
+ "parallel",
+ "ggplot2",
+ "Rdpack",
+ "rlang"
+ ],
+ "Suggests": [
+ "scales",
+ "testthat",
+ "vdiffr",
+ "covr",
+ "knitr",
+ "rstan",
+ "rjags",
+ "runjags",
+ "BayesFactor",
+ "RoBMA",
+ "rmarkdown"
+ ],
+ "RdMacros": "Rdpack",
+ "VignetteBuilder": "knitr",
+ "NeedsCompilation": "no",
+ "Author": "František Bartoš [aut, cre] (ORCID: )",
+ "Repository": "https://packagemanager.posit.co/cran/latest"
+ },
+ "BayesTools": {
+ "Package": "BayesTools",
+ "Version": "0.2.23",
+ "Source": "Repository",
+ "Title": "Tools for Bayesian Analyses",
+ "Description": "Provides tools for conducting Bayesian analyses and Bayesian model averaging (Kass and Raftery, 1995, , Hoeting et al., 1999, ). The package contains functions for creating a wide range of prior distribution objects, mixing posterior samples from 'JAGS' and 'Stan' models, plotting posterior distributions, and etc... The tools for working with prior distribution span from visualization, generating 'JAGS' and 'bridgesampling' syntax to basic functions such as rng, quantile, and distribution functions.",
+ "Maintainer": "František Bartoš ",
+ "Authors@R": "c( person(\"František\", \"Bartoš\", role = c(\"aut\", \"cre\"), email = \"f.bartos96@gmail.com\", comment = c(ORCID = \"0000-0002-0018-5573\")) )",
+ "URL": "https://fbartos.github.io/BayesTools/",
+ "BugReports": "https://github.com/FBartos/BayesTools/issues",
+ "License": "GPL-3",
+ "Encoding": "UTF-8",
+ "LazyData": "true",
+ "RoxygenNote": "7.3.2",
+ "SystemRequirements": "JAGS >= 4.3.0 (https://mcmc-jags.sourceforge.io/)",
+ "Depends": [
+ "stats"
+ ],
+ "Imports": [
+ "graphics",
+ "extraDistr",
+ "mvtnorm",
+ "coda",
+ "bridgesampling",
+ "parallel",
+ "ggplot2",
+ "Rdpack",
+ "rlang"
+ ],
+ "Suggests": [
+ "scales",
+ "testthat",
+ "vdiffr",
+ "covr",
+ "knitr",
+ "rstan",
+ "rjags",
+ "runjags",
+ "BayesFactor",
+ "RoBMA",
+ "rmarkdown"
+ ],
+ "RdMacros": "Rdpack",
+ "VignetteBuilder": "knitr",
+ "NeedsCompilation": "no",
+ "Author": "František Bartoš [aut, cre] (ORCID: )",
+ "Repository": "https://packagemanager.posit.co/cran/latest"
+ },
+ "Brobdingnag": {
+ "Package": "Brobdingnag",
+ "Version": "1.2-9",
+ "Source": "Repository",
+ "Type": "Package",
+ "Title": "Very Large Numbers in R",
+ "Authors@R": "person(given=c(\"Robin\", \"K. S.\"), family=\"Hankin\", role = c(\"aut\",\"cre\"), email=\"hankin.robin@gmail.com\", comment = c(ORCID = \"0000-0001-5982-0415\"))",
+ "Maintainer": "Robin K. S. Hankin ",
+ "Depends": [
+ "R (>= 2.13.0)",
+ "methods",
+ "Matrix (>= 1.5-0)"
+ ],
+ "Description": "Very large numbers in R. Real numbers are held using their natural logarithms, plus a logical flag indicating sign. Functionality for complex numbers is also provided. The package includes a vignette that gives a step-by-step introduction to using S4 methods.",
+ "Suggests": [
+ "cubature",
+ "testthat"
+ ],
+ "License": "GPL",
+ "Repository": "CRAN",
+ "URL": "https://github.com/RobinHankin/Brobdingnag",
+ "NeedsCompilation": "no",
+ "Author": "Robin K. S. Hankin [aut, cre] ()"
+ },
+ "Brobdingnag": {
+ "Package": "Brobdingnag",
+ "Version": "1.2-9",
+ "Source": "Repository",
+ "Type": "Package",
+ "Title": "Very Large Numbers in R",
+ "Authors@R": "person(given=c(\"Robin\", \"K. S.\"), family=\"Hankin\", role = c(\"aut\",\"cre\"), email=\"hankin.robin@gmail.com\", comment = c(ORCID = \"0000-0001-5982-0415\"))",
+ "Maintainer": "Robin K. S. Hankin ",
+ "Depends": [
+ "R (>= 2.13.0)",
+ "methods",
+ "Matrix (>= 1.5-0)"
+ ],
+ "Description": "Very large numbers in R. Real numbers are held using their natural logarithms, plus a logical flag indicating sign. Functionality for complex numbers is also provided. The package includes a vignette that gives a step-by-step introduction to using S4 methods.",
+ "Suggests": [
+ "cubature",
+ "testthat"
+ ],
+ "License": "GPL",
+ "Repository": "CRAN",
+ "URL": "https://github.com/RobinHankin/Brobdingnag",
+ "NeedsCompilation": "no",
+ "Author": "Robin K. S. Hankin [aut, cre] ()"
+ },
+ "Cairo": {
+ "Package": "Cairo",
+ "Version": "1.7-0",
+ "Source": "Repository",
+ "Title": "R Graphics Device using Cairo Graphics Library for Creating High-Quality Bitmap (PNG, JPEG, TIFF), Vector (PDF, SVG, PostScript) and Display (X11 and Win32) Output",
+ "Author": "Simon Urbanek [aut, cre, cph] (https://urbanek.org, ORCID: ), Jeffrey Horner [aut]",
+ "Maintainer": "Simon Urbanek ",
+ "Authors@R": "c(person(\"Simon\", \"Urbanek\", role=c(\"aut\",\"cre\",\"cph\"), email=\"Simon.Urbanek@r-project.org\", comment=c(\"https://urbanek.org\", ORCID=\"0000-0003-2297-1732\")), person(\"Jeffrey\", \"Horner\", role=\"aut\", email=\"jeff.horner@vanderbilt.edu\"))",
+ "Depends": [
+ "R (>= 2.7.0)"
+ ],
+ "Imports": [
+ "grDevices",
+ "graphics"
+ ],
+ "Suggests": [
+ "png"
+ ],
+ "Enhances": [
+ "FastRWeb"
+ ],
+ "Description": "R graphics device using cairographics library that can be used to create high-quality vector (PDF, PostScript and SVG) and bitmap output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11 and Win32). Since it uses the same back-end for all output, copying across formats is WYSIWYG. Files are created without the dependence on X11 or other external programs. This device supports alpha channel (semi-transparent drawing) and resulting images can contain transparent and semi-transparent regions. It is ideal for use in server environments (file output) and as a replacement for other devices that don't have Cairo's capabilities such as alpha support or anti-aliasing. Backends are modular such that any subset of backends is supported.",
+ "License": "GPL-2 | GPL-3",
+ "SystemRequirements": "cairo (>= 1.2 http://www.cairographics.org/)",
+ "URL": "http://www.rforge.net/Cairo/",
+ "NeedsCompilation": "yes",
+ "Repository": "CRAN"
},
"Cairo": {
"Package": "Cairo",
@@ -148,7 +318,7 @@
"NeedsCompilation": "no",
"Author": "R Special Interest Group on Databases (R-SIG-DB) [aut], Hadley Wickham [aut], Kirill Müller [aut, cre] (ORCID: ), R Consortium [fnd]",
"Maintainer": "Kirill Müller ",
- "Repository": "RSPM"
+ "Repository": "CRAN"
},
"Deriv": {
"Package": "Deriv",
@@ -320,109 +490,55 @@
},
"GPArotation": {
"Package": "GPArotation",
- "Version": "2026.4-1",
+ "Version": "2026.6-1",
"Source": "Repository",
- "Title": "Gradient Projection Factor Rotation",
- "Authors@R": "c( person(\"Coen\", \"Bernaards\", email = \"cab.gparotation@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Paul\", \"Gilbert\", role = \"aut\"), person(\"Robert\", \"Jennrich\", role = \"aut\") )",
- "Depends": [
- "R (>= 3.5.0)"
- ],
- "Description": "Gradient projection algorithms for orthogonal and oblique rotation of factor loadings matrices in factor analysis. Implements a comprehensive set of rotation criteria including quartimax, quartimin, oblimin, geomin, simplimax, the Crawford-Ferguson family, and target rotation, among others. Supports multiple random starts. For details see Bernaards and Jennrich (2005) .",
- "License": "GPL (>= 2)",
- "URL": "https://cran.r-project.org/package=GPArotation",
- "Imports": [
- "stats"
- ],
- "LazyData": "yes",
- "NeedsCompilation": "no",
- "Author": "Coen Bernaards [aut, cre], Paul Gilbert [aut], Robert Jennrich [aut]",
- "Maintainer": "Coen Bernaards ",
- "Repository": "RSPM",
- "Encoding": "UTF-8"
+ "Requirements": [
+ "graphics",
+ "grDevices",
+ "R",
+ "stats",
+ "utils"
+ ]
+ },
+ "HDInterval": {
+ "Package": "HDInterval",
+ "Version": "0.2.4",
+ "Source": "Repository",
+ "Requirements": []
},
"Hmisc": {
"Package": "Hmisc",
- "Version": "5.2-5",
+ "Version": "5.2-6",
"Source": "Repository",
- "Date": "2026-01-08",
- "Title": "Harrell Miscellaneous",
- "Authors@R": "c(person(given = \"Frank E\", family = \"Harrell Jr\", role = c(\"aut\", \"cre\"), email = \"fh@fharrell.com\", comment = c(ORCID = \"0000-0002-8271-5493\")), person(given = \"Cole\", family = \"Beck\", role = c(\"ctb\"), email = \"cole.beck@vumc.org\" ), person(given = \"Charles\", family = \"Dupont\", role = \"ctb\") )",
- "Depends": [
- "R (>= 4.2.0)"
- ],
- "Imports": [
- "methods",
- "ggplot2",
+ "Requirements": [
+ "base64enc",
"cluster",
- "rpart",
- "nnet",
+ "colorspace",
+ "data.table",
"foreign",
- "gtable",
+ "Formula",
+ "ggplot2",
"grid",
"gridExtra",
- "data.table",
- "htmlTable (>= 1.11.0)",
- "viridisLite",
+ "gtable",
+ "htmlTable",
"htmltools",
- "base64enc",
- "colorspace",
- "rmarkdown",
"knitr",
- "Formula"
- ],
- "Suggests": [
- "survival",
- "qreport",
- "acepack",
- "chron",
- "rms",
- "mice",
- "rstudioapi",
- "tables",
- "plotly (>= 4.5.6)",
- "rlang",
- "VGAM",
- "leaps",
- "pcaPP",
- "digest",
- "parallel",
- "polspline",
- "abind",
- "kableExtra",
- "rio",
- "lattice",
- "latticeExtra",
- "gt",
- "sparkline",
- "jsonlite",
- "htmlwidgets",
- "qs",
- "getPass",
- "keyring",
- "safer",
- "htm2txt",
- "boot"
- ],
- "Description": "Contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, simulation, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX and html code, recoding variables, caching, simplified parallel computing, encrypting and decrypting data using a safe workflow, general moving window statistical estimation, and assistance in interpreting principal component analysis.",
- "License": "GPL (>= 2)",
- "LazyLoad": "Yes",
- "URL": "https://hbiostat.org/R/Hmisc/",
- "Encoding": "UTF-8",
- "RoxygenNote": "7.3.3",
- "NeedsCompilation": "yes",
- "Author": "Frank E Harrell Jr [aut, cre] (ORCID: ), Cole Beck [ctb], Charles Dupont [ctb]",
- "Maintainer": "Frank E Harrell Jr ",
- "Repository": "CRAN"
+ "methods",
+ "nnet",
+ "R",
+ "rmarkdown",
+ "rpart",
+ "viridisLite"
+ ]
},
"MASS": {
"Package": "MASS",
"Version": "7.3-65",
"Source": "Repository",
- "Priority": "recommended",
- "Date": "2025-02-19",
- "Revision": "$Rev: 3681 $",
- "Depends": [
- "R (>= 4.4.0)",
+ "Requirements": [
+ "methods",
+ "R",
"grDevices",
"graphics",
"stats",
@@ -493,7 +609,7 @@
"NeedsCompilation": "yes",
"Author": "Douglas Bates [aut] (ORCID: ), Martin Maechler [aut, cre] (ORCID: ), Mikael Jagan [aut] (ORCID: ), Timothy A. Davis [ctb] (ORCID: , SuiteSparse libraries, collaborators listed in dir(system.file(\"doc\", \"SuiteSparse\", package=\"Matrix\"), pattern=\"License\", full.names=TRUE, recursive=TRUE)), George Karypis [ctb] (ORCID: , METIS library, Copyright: Regents of the University of Minnesota), Jason Riedy [ctb] (ORCID: , GNU Octave's condest() and onenormest(), Copyright: Regents of the University of California), Jens Oehlschlägel [ctb] (initial nearPD()), R Core Team [ctb] (ROR: , base R's matrix implementation)",
"Maintainer": "Martin Maechler ",
- "Repository": "RSPM"
+ "Repository": "https://packagemanager.posit.co/cran/latest"
},
"MatrixModels": {
"Package": "MatrixModels",
@@ -525,6 +641,58 @@
"Maintainer": "Martin Maechler ",
"Repository": "CRAN"
},
+ "QuickJSR": {
+ "Package": "QuickJSR",
+ "Version": "1.9.0",
+ "Source": "Repository",
+ "Title": "Interface for the 'QuickJS-NG' Lightweight 'JavaScript' Engine",
+ "Authors@R": "c( person(c(\"Andrew\", \"R.\"), \"Johnson\", , \"andrew.johnson@arjohnsonau.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-7000-8065\")), person(\"QuickJS\", \"Authors\", role = c(\"cph\"), comment = \"QuickJS sources and headers\"), person(\"QuickJS-NG\", \"Authors\", role = c(\"cph\"), comment = \"QuickJS-NG sources and headers\") )",
+ "Description": "An 'R' interface to the 'QuickJS' portable 'JavaScript' engine. The engine and all 'R' to 'JavaScript' interoperability is bundled within the package, requiring no dependencies beyond a 'C' compiler.",
+ "License": "MIT + file LICENSE",
+ "URL": "https://github.com/andrjohns/QuickJSR, https://github.com/quickjs-ng/quickjs",
+ "BugReports": "https://github.com/andrjohns/QuickJSR/issues",
+ "Suggests": [
+ "knitr",
+ "rmarkdown",
+ "tinytest"
+ ],
+ "Encoding": "UTF-8",
+ "Language": "en-AU",
+ "NeedsCompilation": "yes",
+ "RoxygenNote": "7.3.3",
+ "SystemRequirements": "GNU make",
+ "VignetteBuilder": "knitr",
+ "Config/build/compilation-database": "true",
+ "Author": "Andrew R. Johnson [aut, cre] (ORCID: ), QuickJS Authors [cph] (QuickJS sources and headers), QuickJS-NG Authors [cph] (QuickJS-NG sources and headers)",
+ "Maintainer": "Andrew R. Johnson ",
+ "Repository": "CRAN"
+ },
+ "QuickJSR": {
+ "Package": "QuickJSR",
+ "Version": "1.9.0",
+ "Source": "Repository",
+ "Title": "Interface for the 'QuickJS-NG' Lightweight 'JavaScript' Engine",
+ "Authors@R": "c( person(c(\"Andrew\", \"R.\"), \"Johnson\", , \"andrew.johnson@arjohnsonau.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-7000-8065\")), person(\"QuickJS\", \"Authors\", role = c(\"cph\"), comment = \"QuickJS sources and headers\"), person(\"QuickJS-NG\", \"Authors\", role = c(\"cph\"), comment = \"QuickJS-NG sources and headers\") )",
+ "Description": "An 'R' interface to the 'QuickJS' portable 'JavaScript' engine. The engine and all 'R' to 'JavaScript' interoperability is bundled within the package, requiring no dependencies beyond a 'C' compiler.",
+ "License": "MIT + file LICENSE",
+ "URL": "https://github.com/andrjohns/QuickJSR, https://github.com/quickjs-ng/quickjs",
+ "BugReports": "https://github.com/andrjohns/QuickJSR/issues",
+ "Suggests": [
+ "knitr",
+ "rmarkdown",
+ "tinytest"
+ ],
+ "Encoding": "UTF-8",
+ "Language": "en-AU",
+ "NeedsCompilation": "yes",
+ "RoxygenNote": "7.3.3",
+ "SystemRequirements": "GNU make",
+ "VignetteBuilder": "knitr",
+ "Config/build/compilation-database": "true",
+ "Author": "Andrew R. Johnson [aut, cre] (ORCID: ), QuickJS Authors [cph] (QuickJS sources and headers), QuickJS-NG Authors [cph] (QuickJS-NG sources and headers)",
+ "Maintainer": "Andrew R. Johnson ",
+ "Repository": "CRAN"
+ },
"R6": {
"Package": "R6",
"Version": "2.6.1",
@@ -636,6 +804,7 @@
],
"Imports": [
"methods",
+ "R",
"utils"
],
"Suggests": [
@@ -654,15 +823,15 @@
"NeedsCompilation": "yes",
"Author": "Dirk Eddelbuettel [aut, cre] (ORCID: ), Romain Francois [aut] (ORCID: ), JJ Allaire [aut] (ORCID: ), Kevin Ushey [aut] (ORCID: ), Qiang Kou [aut] (ORCID: ), Nathan Russell [aut], Iñaki Ucar [aut] (ORCID: ), Doug Bates [aut] (ORCID: ), John Chambers [aut]",
"Maintainer": "Dirk Eddelbuettel ",
- "Repository": "CRAN"
+ "Repository": "https://packagemanager.posit.co/cran/latest"
},
"RcppArmadillo": {
"Package": "RcppArmadillo",
- "Version": "15.2.6-1",
+ "Version": "15.4.0-1",
"Source": "Repository",
"Type": "Package",
"Title": "'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library",
- "Date": "2026-04-20",
+ "Date": "2026-05-29",
"Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Romain\", \"Francois\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Doug\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Binxiang\", \"Ni\", role = \"aut\"), person(\"Conrad\", \"Sanderson\", role = \"aut\", comment = c(ORCID = \"0000-0002-0049-4501\")))",
"Description": "'Armadillo' is a templated C++ linear algebra library aiming towards a good balance between speed and ease of use. It provides high-level syntax and functionality deliberately similar to Matlab. It is useful for algorithm development directly in C++, or quick conversion of research code into production environments. It provides efficient classes for vectors, matrices and cubes where dense and sparse matrices are supported. Integer, floating point and complex numbers are supported. A sophisticated expression evaluator (based on template meta-programming) automatically combines several operations to increase speed and efficiency. Dynamic evaluation automatically chooses optimal code paths based on detected matrix structures. Matrix decompositions are provided through integration with LAPACK, or one of its high performance drop-in replacements (such as 'MKL' or 'OpenBLAS'). It can automatically use 'OpenMP' multi-threading (parallelisation) to speed up computationally expensive operations. . The 'RcppArmadillo' package includes the header files from the 'Armadillo' library; users do not need to install 'Armadillo' itself in order to use 'RcppArmadillo'. Starting from release 15.0.0, the minimum compilation standard is C++14. . Since release 7.800.0, 'Armadillo' is licensed under Apache License 2; previous releases were under licensed as MPL 2.0 from version 3.800.0 onwards and LGPL-3 prior to that; 'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.",
"License": "GPL (>= 2)",
@@ -694,7 +863,7 @@
"NeedsCompilation": "yes",
"Author": "Dirk Eddelbuettel [aut, cre] (ORCID: ), Romain Francois [aut] (ORCID: ), Doug Bates [aut] (ORCID: ), Binxiang Ni [aut], Conrad Sanderson [aut] (ORCID: )",
"Maintainer": "Dirk Eddelbuettel ",
- "Repository": "RSPM"
+ "Repository": "CRAN"
},
"RcppEigen": {
"Package": "RcppEigen",
@@ -733,40 +902,98 @@
"Maintainer": "Dirk Eddelbuettel ",
"Repository": "CRAN"
},
- "Rdpack": {
- "Package": "Rdpack",
- "Version": "2.6.6",
+ "RcppParallel": {
+ "Package": "RcppParallel",
+ "Version": "5.1.11-1",
"Source": "Repository",
"Type": "Package",
- "Title": "Update and Manipulate Rd Documentation Objects",
- "Authors@R": "c( person(given = c(\"Georgi\", \"N.\"), family = \"Boshnakov\", role = c(\"aut\", \"cre\"), email = \"georgi.boshnakov@manchester.ac.uk\", comment = c(ORCID = \"0000-0003-2839-346X\")), person(given = \"Duncan\", family = \"Murdoch\", role = \"ctb\", email = \"murdoch.duncan@gmail.com\") )",
- "Description": "Functions for manipulation of R documentation objects, including functions reprompt() and ereprompt() for updating 'Rd' documentation for functions, methods and classes; 'Rd' macros for citations and import of references from 'bibtex' files for use in 'Rd' files and 'roxygen2' comments; 'Rd' macros for evaluating and inserting snippets of 'R' code and the results of its evaluation or creating graphics on the fly; and many functions for manipulation of references and Rd files.",
- "URL": "https://geobosh.github.io/Rdpack/ (doc), https://CRAN.R-project.org/package=Rdpack",
- "BugReports": "https://github.com/GeoBosh/Rdpack/issues",
+ "Title": "Parallel Programming Tools for 'Rcpp'",
+ "Authors@R": "c( person(\"JJ\", \"Allaire\", role = c(\"aut\"), email = \"jj@rstudio.com\"), person(\"Romain\", \"Francois\", role = c(\"aut\", \"cph\")), person(\"Kevin\", \"Ushey\", role = c(\"aut\", \"cre\"), email = \"kevin@rstudio.com\"), person(\"Gregory\", \"Vandenbrouck\", role = \"aut\"), person(\"Marcus\", \"Geelnard\", role = c(\"aut\", \"cph\"), comment = \"TinyThread library, https://tinythreadpp.bitsnbites.eu/\"), person(\"Hamada S.\", \"Badr\", email = \"badr@jhu.edu\", role = c(\"ctb\"), comment = c(ORCID = \"0000-0002-9808-2344\")), person(family = \"Posit, PBC\", role = \"cph\"), person(family = \"Intel\", role = c(\"aut\", \"cph\"), comment = \"Intel TBB library, https://www.threadingbuildingblocks.org/\"), person(family = \"Microsoft\", role = \"cph\") )",
+ "Description": "High level functions for parallel programming with 'Rcpp'. For example, the 'parallelFor()' function can be used to convert the work of a standard serial \"for\" loop into a parallel one and the 'parallelReduce()' function can be used for accumulating aggregate or other values.",
"Depends": [
- "R (>= 2.15.0)",
- "methods"
- ],
- "Imports": [
- "tools",
- "utils",
- "rbibutils (> 2.4)"
+ "R (>= 3.0.2)"
],
"Suggests": [
- "grDevices",
- "testthat",
- "rstudioapi",
- "rprojroot",
- "gbRd"
+ "Rcpp",
+ "RUnit",
+ "knitr",
+ "rmarkdown"
],
- "License": "GPL (>= 2)",
+ "SystemRequirements": "GNU make, Intel TBB, Windows: cmd.exe and cscript.exe, Solaris: g++ is required",
+ "License": "GPL (>= 3)",
+ "URL": "https://rcppcore.github.io/RcppParallel/, https://github.com/RcppCore/RcppParallel",
+ "BugReports": "https://github.com/RcppCore/RcppParallel/issues",
+ "Biarch": "TRUE",
+ "RoxygenNote": "7.1.1",
+ "Encoding": "UTF-8",
+ "NeedsCompilation": "yes",
+ "Author": "JJ Allaire [aut], Romain Francois [aut, cph], Kevin Ushey [aut, cre], Gregory Vandenbrouck [aut], Marcus Geelnard [aut, cph] (TinyThread library, https://tinythreadpp.bitsnbites.eu/), Hamada S. Badr [ctb] (ORCID: ), Posit, PBC [cph], Intel [aut, cph] (Intel TBB library, https://www.threadingbuildingblocks.org/), Microsoft [cph]",
+ "Maintainer": "Kevin Ushey ",
+ "Repository": "CRAN"
+ },
+ "RcppParallel": {
+ "Package": "RcppParallel",
+ "Version": "5.1.11-1",
+ "Source": "Repository",
+ "Type": "Package",
+ "Title": "Parallel Programming Tools for 'Rcpp'",
+ "Authors@R": "c( person(\"JJ\", \"Allaire\", role = c(\"aut\"), email = \"jj@rstudio.com\"), person(\"Romain\", \"Francois\", role = c(\"aut\", \"cph\")), person(\"Kevin\", \"Ushey\", role = c(\"aut\", \"cre\"), email = \"kevin@rstudio.com\"), person(\"Gregory\", \"Vandenbrouck\", role = \"aut\"), person(\"Marcus\", \"Geelnard\", role = c(\"aut\", \"cph\"), comment = \"TinyThread library, https://tinythreadpp.bitsnbites.eu/\"), person(\"Hamada S.\", \"Badr\", email = \"badr@jhu.edu\", role = c(\"ctb\"), comment = c(ORCID = \"0000-0002-9808-2344\")), person(family = \"Posit, PBC\", role = \"cph\"), person(family = \"Intel\", role = c(\"aut\", \"cph\"), comment = \"Intel TBB library, https://www.threadingbuildingblocks.org/\"), person(family = \"Microsoft\", role = \"cph\") )",
+ "Description": "High level functions for parallel programming with 'Rcpp'. For example, the 'parallelFor()' function can be used to convert the work of a standard serial \"for\" loop into a parallel one and the 'parallelReduce()' function can be used for accumulating aggregate or other values.",
+ "Depends": [
+ "R (>= 3.0.2)"
+ ],
+ "Suggests": [
+ "Rcpp",
+ "RUnit",
+ "knitr",
+ "rmarkdown"
+ ],
+ "SystemRequirements": "GNU make, Intel TBB, Windows: cmd.exe and cscript.exe, Solaris: g++ is required",
+ "License": "GPL (>= 3)",
+ "URL": "https://rcppcore.github.io/RcppParallel/, https://github.com/RcppCore/RcppParallel",
+ "BugReports": "https://github.com/RcppCore/RcppParallel/issues",
+ "Biarch": "TRUE",
+ "RoxygenNote": "7.1.1",
+ "Encoding": "UTF-8",
+ "NeedsCompilation": "yes",
+ "Author": "JJ Allaire [aut], Romain Francois [aut, cph], Kevin Ushey [aut, cre], Gregory Vandenbrouck [aut], Marcus Geelnard [aut, cph] (TinyThread library, https://tinythreadpp.bitsnbites.eu/), Hamada S. Badr [ctb] (ORCID: ), Posit, PBC [cph], Intel [aut, cph] (Intel TBB library, https://www.threadingbuildingblocks.org/), Microsoft [cph]",
+ "Maintainer": "Kevin Ushey ",
+ "Repository": "CRAN"
+ },
+ "Rdpack": {
+ "Package": "Rdpack",
+ "Version": "2.6.6",
+ "Source": "Repository",
+ "Type": "Package",
+ "Title": "Update and Manipulate Rd Documentation Objects",
+ "Authors@R": "c( person(given = c(\"Georgi\", \"N.\"), family = \"Boshnakov\", role = c(\"aut\", \"cre\"), email = \"georgi.boshnakov@manchester.ac.uk\", comment = c(ORCID = \"0000-0003-2839-346X\")), person(given = \"Duncan\", family = \"Murdoch\", role = \"ctb\", email = \"murdoch.duncan@gmail.com\") )",
+ "Description": "Functions for manipulation of R documentation objects, including functions reprompt() and ereprompt() for updating 'Rd' documentation for functions, methods and classes; 'Rd' macros for citations and import of references from 'bibtex' files for use in 'Rd' files and 'roxygen2' comments; 'Rd' macros for evaluating and inserting snippets of 'R' code and the results of its evaluation or creating graphics on the fly; and many functions for manipulation of references and Rd files.",
+ "URL": "https://geobosh.github.io/Rdpack/ (doc), https://CRAN.R-project.org/package=Rdpack",
+ "BugReports": "https://github.com/GeoBosh/Rdpack/issues",
+ "Depends": [
+ "R (>= 2.15.0)",
+ "methods"
+ ],
+ "Imports": [
+ "tools",
+ "utils",
+ "rbibutils (> 2.4)"
+ ],
+ "Suggests": [
+ "grDevices",
+ "testthat",
+ "rstudioapi",
+ "rprojroot",
+ "gbRd"
+ ],
+ "License": "GPL (>= 2)",
"LazyLoad": "yes",
"Encoding": "UTF-8",
"RoxygenNote": "7.1.1",
"NeedsCompilation": "no",
"Author": "Georgi N. Boshnakov [aut, cre] (ORCID: ), Duncan Murdoch [ctb]",
"Maintainer": "Georgi N. Boshnakov ",
- "Repository": "RSPM"
+ "Repository": "https://packagemanager.posit.co/cran/latest"
},
"Rspc": {
"Package": "Rspc",
@@ -830,7 +1057,46 @@
"NeedsCompilation": "yes",
"Author": "Object-Oriented Programming Working Group [cph], Davis Vaughan [aut], Jim Hester [aut] (ORCID: ), Tomasz Kalinowski [aut], Will Landau [aut], Michael Lawrence [aut], Martin Maechler [aut] (ORCID: ), Luke Tierney [aut], Hadley Wickham [aut, cre] (ORCID: )",
"Maintainer": "Hadley Wickham ",
- "Repository": "CRAN"
+ "Repository": "https://packagemanager.posit.co/cran/latest"
+ },
+ "S7": {
+ "Package": "S7",
+ "Version": "0.2.2",
+ "Source": "Repository",
+ "Title": "An Object Oriented System Meant to Become a Successor to S3 and S4",
+ "Authors@R": "c( person(\"Object-Oriented Programming Working Group\", role = \"cph\"), person(\"Davis\", \"Vaughan\", role = \"aut\"), person(\"Jim\", \"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Tomasz\", \"Kalinowski\", role = \"aut\"), person(\"Will\", \"Landau\", role = \"aut\"), person(\"Michael\", \"Lawrence\", role = \"aut\"), person(\"Martin\", \"Maechler\", role = \"aut\", comment = c(ORCID = \"0000-0002-8685-9910\")), person(\"Luke\", \"Tierney\", role = \"aut\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4757-117X\")) )",
+ "Description": "A new object oriented programming system designed to be a successor to S3 and S4. It includes formal class, generic, and method specification, and a limited form of multiple dispatch. It has been designed and implemented collaboratively by the R Consortium Object-Oriented Programming Working Group, which includes representatives from R-Core, 'Bioconductor', 'Posit'/'tidyverse', and the wider R community.",
+ "License": "MIT + file LICENSE",
+ "URL": "https://rconsortium.github.io/S7/, https://github.com/RConsortium/S7",
+ "BugReports": "https://github.com/RConsortium/S7/issues",
+ "Depends": [
+ "R (>= 3.5.0)"
+ ],
+ "Imports": [
+ "utils"
+ ],
+ "Suggests": [
+ "bench",
+ "callr",
+ "covr",
+ "knitr",
+ "methods",
+ "rmarkdown",
+ "testthat (>= 3.2.0)",
+ "tibble"
+ ],
+ "VignetteBuilder": "knitr",
+ "Config/build/compilation-database": "true",
+ "Config/Needs/website": "sloop",
+ "Config/testthat/edition": "3",
+ "Config/testthat/parallel": "TRUE",
+ "Config/testthat/start-first": "external-generic",
+ "Encoding": "UTF-8",
+ "RoxygenNote": "7.3.3",
+ "NeedsCompilation": "yes",
+ "Author": "Object-Oriented Programming Working Group [cph], Davis Vaughan [aut], Jim Hester [aut] (ORCID: ), Tomasz Kalinowski [aut], Will Landau [aut], Michael Lawrence [aut], Martin Maechler [aut] (ORCID: ), Luke Tierney [aut], Hadley Wickham [aut, cre] (ORCID: )",
+ "Maintainer": "Hadley Wickham ",
+ "Repository": "https://packagemanager.posit.co/cran/latest"
},
"SparseM": {
"Package": "SparseM",
@@ -859,43 +1125,92 @@
"Author": "Roger Koenker [cre, aut], Pin Tian Ng [ctb] (Contributions to Sparse QR code), Yousef Saad [ctb] (author of sparskit2), Ben Shaby [ctb] (author of chol2csr), Martin Maechler [ctb] (chol() tweaks; S4, )",
"Repository": "CRAN"
},
- "TH.data": {
- "Package": "TH.data",
- "Version": "1.1-5",
+ "StanHeaders": {
+ "Package": "StanHeaders",
+ "Version": "2.32.10",
"Source": "Repository",
- "Title": "TH's Data Archive",
- "Date": "2025-11-17",
- "Authors@R": "c(person(\"Torsten\", \"Hothorn\", role = c(\"aut\", \"cre\"), email = \"Torsten.Hothorn@R-project.org\"))",
- "Description": "Contains data sets used in other packages Torsten Hothorn maintains.",
+ "Title": "C++ Header Files for Stan",
+ "Authors@R": "c(person(\"Ben\",family=\"Goodrich\", email=\"benjamin.goodrich@columbia.edu\", role=c('cre','aut')), person(\"Joshua\", \"Pritikin\", role = \"ctb\"), person(\"Andrew\", \"Gelman\", role = \"aut\"), person(\"Bob\", \"Carpenter\", role = \"aut\"), person(\"Matt\", \"Hoffman\", role = \"aut\"), person(\"Daniel\", \"Lee\", role = \"aut\"), person(\"Michael\", \"Betancourt\", role = \"aut\"), person(\"Marcus\", \"Brubaker\", role = \"aut\"), person(\"Jiqiang\", \"Guo\", role = \"aut\"), person(\"Peter\", \"Li\", role = \"aut\"), person(\"Allen\", \"Riddell\", role = \"aut\"), person(\"Marco\", \"Inacio\", role = \"aut\"), person(\"Mitzi\", \"Morris\", role = \"aut\"), person(\"Jeffrey\", \"Arnold\", role = \"aut\"), person(\"Rob\", \"Goedman\", role = \"aut\"), person(\"Brian\", \"Lau\", role = \"aut\"), person(\"Rob\", \"Trangucci\", role = \"aut\"), person(\"Jonah\", \"Gabry\", role = \"aut\"), person(\"Alp\", \"Kucukelbir\", role = \"aut\"), person(\"Robert\", \"Grant\", role = \"aut\"), person(\"Dustin\", \"Tran\", role = \"aut\"), person(\"Michael\", \"Malecki\", role = \"aut\"), person(\"Yuanjun\", \"Gao\", role = \"aut\"), person(\"Hamada S.\", \"Badr\", role = c(\"aut\"), email = \"badr@jhu.edu\", comment = c(ORCID = \"0000-0002-9808-2344\")), person(\"Trustees of\", \"Columbia University\", role = \"cph\"), person(\"Lawrence Livermore\", \"National Security\", role = \"cph\", comment = \"CVODES\"), person(\"The Regents of the\", \"University of California\", role = \"cph\", comment = \"CVODES\"), person(\"Southern Methodist\", \"University\", role = \"cph\", comment = \"CVODES\"))",
+ "URL": "https://mc-stan.org/",
+ "Description": "The C++ header files of the Stan project are provided by this package, but it contains little R code or documentation. The main reference is the vignette. There is a shared object containing part of the 'CVODES' library, but its functionality is not accessible from R. 'StanHeaders' is primarily useful for developers who want to utilize the 'LinkingTo' directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full or approximate Bayesian statistical inference via Markov Chain Monte Carlo or 'variational' methods and implements (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, 'templated' statistical and linear algebra functions that can handle the automatically 'differentiable' scalar types (and doubles, 'ints', etc.), and a parser for the Stan language. The 'rstan' package provides user-facing R functions to parse, compile, test, estimate, and analyze Stan models.",
+ "Imports": [
+ "RcppParallel (>= 5.1.4)"
+ ],
+ "Suggests": [
+ "Rcpp",
+ "BH (>= 1.75.0-0)",
+ "knitr (>= 1.36)",
+ "rmarkdown",
+ "Matrix",
+ "methods",
+ "rstan",
+ "withr"
+ ],
+ "LinkingTo": [
+ "RcppEigen (>= 0.3.4.0.0)",
+ "RcppParallel (>= 5.1.4)"
+ ],
+ "VignetteBuilder": "knitr",
+ "SystemRequirements": "GNU make, pandoc",
"Depends": [
- "R (>= 3.5.0)",
- "survival",
- "MASS"
+ "R (>= 3.4.0)"
+ ],
+ "License": "BSD_3_clause + file LICENSE",
+ "Encoding": "UTF-8",
+ "RoxygenNote": "7.1.2",
+ "NeedsCompilation": "yes",
+ "Author": "Ben Goodrich [cre, aut], Joshua Pritikin [ctb], Andrew Gelman [aut], Bob Carpenter [aut], Matt Hoffman [aut], Daniel Lee [aut], Michael Betancourt [aut], Marcus Brubaker [aut], Jiqiang Guo [aut], Peter Li [aut], Allen Riddell [aut], Marco Inacio [aut], Mitzi Morris [aut], Jeffrey Arnold [aut], Rob Goedman [aut], Brian Lau [aut], Rob Trangucci [aut], Jonah Gabry [aut], Alp Kucukelbir [aut], Robert Grant [aut], Dustin Tran [aut], Michael Malecki [aut], Yuanjun Gao [aut], Hamada S. Badr [aut] (), Trustees of Columbia University [cph], Lawrence Livermore National Security [cph] (CVODES), The Regents of the University of California [cph] (CVODES), Southern Methodist University [cph] (CVODES)",
+ "Maintainer": "Ben Goodrich ",
+ "Repository": "CRAN"
+ },
+ "StanHeaders": {
+ "Package": "StanHeaders",
+ "Version": "2.32.10",
+ "Source": "Repository",
+ "Title": "C++ Header Files for Stan",
+ "Authors@R": "c(person(\"Ben\",family=\"Goodrich\", email=\"benjamin.goodrich@columbia.edu\", role=c('cre','aut')), person(\"Joshua\", \"Pritikin\", role = \"ctb\"), person(\"Andrew\", \"Gelman\", role = \"aut\"), person(\"Bob\", \"Carpenter\", role = \"aut\"), person(\"Matt\", \"Hoffman\", role = \"aut\"), person(\"Daniel\", \"Lee\", role = \"aut\"), person(\"Michael\", \"Betancourt\", role = \"aut\"), person(\"Marcus\", \"Brubaker\", role = \"aut\"), person(\"Jiqiang\", \"Guo\", role = \"aut\"), person(\"Peter\", \"Li\", role = \"aut\"), person(\"Allen\", \"Riddell\", role = \"aut\"), person(\"Marco\", \"Inacio\", role = \"aut\"), person(\"Mitzi\", \"Morris\", role = \"aut\"), person(\"Jeffrey\", \"Arnold\", role = \"aut\"), person(\"Rob\", \"Goedman\", role = \"aut\"), person(\"Brian\", \"Lau\", role = \"aut\"), person(\"Rob\", \"Trangucci\", role = \"aut\"), person(\"Jonah\", \"Gabry\", role = \"aut\"), person(\"Alp\", \"Kucukelbir\", role = \"aut\"), person(\"Robert\", \"Grant\", role = \"aut\"), person(\"Dustin\", \"Tran\", role = \"aut\"), person(\"Michael\", \"Malecki\", role = \"aut\"), person(\"Yuanjun\", \"Gao\", role = \"aut\"), person(\"Hamada S.\", \"Badr\", role = c(\"aut\"), email = \"badr@jhu.edu\", comment = c(ORCID = \"0000-0002-9808-2344\")), person(\"Trustees of\", \"Columbia University\", role = \"cph\"), person(\"Lawrence Livermore\", \"National Security\", role = \"cph\", comment = \"CVODES\"), person(\"The Regents of the\", \"University of California\", role = \"cph\", comment = \"CVODES\"), person(\"Southern Methodist\", \"University\", role = \"cph\", comment = \"CVODES\"))",
+ "URL": "https://mc-stan.org/",
+ "Description": "The C++ header files of the Stan project are provided by this package, but it contains little R code or documentation. The main reference is the vignette. There is a shared object containing part of the 'CVODES' library, but its functionality is not accessible from R. 'StanHeaders' is primarily useful for developers who want to utilize the 'LinkingTo' directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full or approximate Bayesian statistical inference via Markov Chain Monte Carlo or 'variational' methods and implements (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, 'templated' statistical and linear algebra functions that can handle the automatically 'differentiable' scalar types (and doubles, 'ints', etc.), and a parser for the Stan language. The 'rstan' package provides user-facing R functions to parse, compile, test, estimate, and analyze Stan models.",
+ "Imports": [
+ "RcppParallel (>= 5.1.4)"
],
"Suggests": [
- "trtf",
- "tram",
- "rms",
- "coin",
- "ATR",
- "multcomp",
- "gridExtra",
- "vcd",
- "colorspace",
- "lattice",
- "knitr",
- "dplyr",
- "openxlsx",
- "plyr"
+ "Rcpp",
+ "BH (>= 1.75.0-0)",
+ "knitr (>= 1.36)",
+ "rmarkdown",
+ "Matrix",
+ "methods",
+ "rstan",
+ "withr"
+ ],
+ "LinkingTo": [
+ "RcppEigen (>= 0.3.4.0.0)",
+ "RcppParallel (>= 5.1.4)"
],
- "LazyData": "yes",
"VignetteBuilder": "knitr",
- "License": "GPL-3",
- "NeedsCompilation": "no",
- "Author": "Torsten Hothorn [aut, cre]",
- "Maintainer": "Torsten Hothorn ",
+ "SystemRequirements": "GNU make, pandoc",
+ "Depends": [
+ "R (>= 3.4.0)"
+ ],
+ "License": "BSD_3_clause + file LICENSE",
+ "Encoding": "UTF-8",
+ "RoxygenNote": "7.1.2",
+ "NeedsCompilation": "yes",
+ "Author": "Ben Goodrich [cre, aut], Joshua Pritikin [ctb], Andrew Gelman [aut], Bob Carpenter [aut], Matt Hoffman [aut], Daniel Lee [aut], Michael Betancourt [aut], Marcus Brubaker [aut], Jiqiang Guo [aut], Peter Li [aut], Allen Riddell [aut], Marco Inacio [aut], Mitzi Morris [aut], Jeffrey Arnold [aut], Rob Goedman [aut], Brian Lau [aut], Rob Trangucci [aut], Jonah Gabry [aut], Alp Kucukelbir [aut], Robert Grant [aut], Dustin Tran [aut], Michael Malecki [aut], Yuanjun Gao [aut], Hamada S. Badr [aut] (), Trustees of Columbia University [cph], Lawrence Livermore National Security [cph] (CVODES), The Regents of the University of California [cph] (CVODES), Southern Methodist University [cph] (CVODES)",
+ "Maintainer": "Ben Goodrich ",
"Repository": "CRAN"
},
+ "TH.data": {
+ "Package": "TH.data",
+ "Version": "1.1-5",
+ "Source": "Repository",
+ "Requirements": [
+ "MASS",
+ "R",
+ "survival"
+ ]
+ },
"abind": {
"Package": "abind",
"Version": "1.4-8",
@@ -983,23 +1298,9 @@
"Package": "assertthat",
"Version": "0.2.1",
"Source": "Repository",
- "Title": "Easy Pre and Post Assertions",
- "Authors@R": "person(\"Hadley\", \"Wickham\", , \"hadley@rstudio.com\", c(\"aut\", \"cre\"))",
- "Description": "An extension to stopifnot() that makes it easy to declare the pre and post conditions that you code should satisfy, while also producing friendly error messages so that your users know what's gone wrong.",
- "License": "GPL-3",
- "Imports": [
+ "Requirements": [
"tools"
- ],
- "Suggests": [
- "testthat",
- "covr"
- ],
- "RoxygenNote": "6.0.1",
- "Collate": "'assert-that.r' 'on-failure.r' 'assertions-file.r' 'assertions-scalar.R' 'assertions.r' 'base.r' 'base-comparison.r' 'base-is.r' 'base-logical.r' 'base-misc.r' 'utils.r' 'validate-that.R'",
- "NeedsCompilation": "no",
- "Author": "Hadley Wickham [aut, cre]",
- "Maintainer": "Hadley Wickham ",
- "Repository": "CRAN"
+ ]
},
"backports": {
"Package": "backports",
@@ -1021,7 +1322,7 @@
"Encoding": "UTF-8",
"RoxygenNote": "7.3.3",
"Author": "Michel Lang [cre, aut] (ORCID: ), Duncan Murdoch [aut], R Core Team [aut]",
- "Repository": "RSPM"
+ "Repository": "https://packagemanager.posit.co/cran/latest"
},
"base64enc": {
"Package": "base64enc",
@@ -1048,65 +1349,50 @@
"Package": "bbmle",
"Version": "1.0.25.1",
"Source": "Repository",
- "Title": "Tools for General Maximum Likelihood Estimation",
- "Description": "Methods and functions for fitting maximum likelihood models in R. This package modifies and extends the 'mle' classes in the 'stats4' package.",
- "Authors@R": "c(person(\"Ben\",\"Bolker\",email=\"bolker@mcmaster.ca\",role=c(\"aut\",\"cre\"), comment=c(ORCID=\"0000-0002-2127-0443\")), person(\"R Development Core Team\",role=c(\"aut\")), person(\"Iago Giné-Vázquez\", role=c(\"ctb\")) )",
- "Depends": [
- "R (>= 3.0.0)",
- "stats4"
- ],
- "Imports": [
- "stats",
- "numDeriv",
+ "Requirements": [
+ "bdsmatrix",
"lattice",
"MASS",
- "methods",
- "bdsmatrix",
"Matrix",
- "mvtnorm"
- ],
- "Suggests": [
- "emdbook",
- "rms",
- "ggplot2",
- "RUnit",
- "MuMIn",
- "AICcmodavg",
- "Hmisc",
- "optimx (>= 2013.8.6)",
- "knitr",
- "testthat"
- ],
- "VignetteBuilder": "knitr",
- "BuildVignettes": "yes",
- "License": "GPL",
- "URL": "https://github.com/bbolker/bbmle",
- "Collate": "'mle2-class.R' 'mle2-methods.R' 'mle.R' 'confint.R' 'predict.R' 'profile.R' 'update.R' 'dists.R' 'IC.R' 'slice.R' 'impsamp.R' 'TMB.R'",
- "RoxygenNote": "7.1.0",
- "Encoding": "UTF-8",
- "NeedsCompilation": "no",
- "Author": "Ben Bolker [aut, cre] (), R Development Core Team [aut], Iago Giné-Vázquez [ctb]",
- "Maintainer": "Ben Bolker ",
- "Repository": "CRAN"
+ "methods",
+ "mvtnorm",
+ "numDeriv",
+ "R",
+ "stats",
+ "stats4"
+ ]
},
"bdsmatrix": {
"Package": "bdsmatrix",
"Version": "1.3-7",
"Source": "Repository",
- "Title": "Routines for Block Diagonal Symmetric Matrices",
- "Maintainer": "Terry Therneau ",
- "Date": "2024-03-01",
- "Depends": [
+ "Requirements": [
"methods",
- "R (>= 2.0.0)"
+ "R"
+ ]
+ },
+ "beeswarm": {
+ "Package": "beeswarm",
+ "Version": "0.4.0",
+ "Source": "Repository",
+ "Title": "The Bee Swarm Plot, an Alternative to Stripchart",
+ "Description": "The bee swarm plot is a one-dimensional scatter plot like \"stripchart\", but with closely-packed, non-overlapping points.",
+ "Date": "2021-05-07",
+ "Authors@R": "c( person(\"Aron\", \"Eklund\", , \"aroneklund@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-0861-1001\")), person(\"James\", \"Trimble\", role = \"aut\", comment = c(ORCID = \"0000-0001-7282-8745\")) )",
+ "Imports": [
+ "stats",
+ "graphics",
+ "grDevices",
+ "utils"
],
- "LazyLoad": "Yes",
- "Author": "Terry Therneau",
- "Description": "This is a special case of sparse matrices, used by coxme.",
- "License": "LGPL-2",
- "Collate": "bdsmatrix.R gchol.R gchol.bdsmatrix.R as.matrix.bdsmatrix.R bdsBlock.R bdsI.R bdsmatrix.ibd.R bdsmatrix.reconcile.R diag.bdsmatrix.R listbdsmatrix.R multiply.bdsmatrix.R solve.bdsmatrix.R solve.gchol.R solve.gchol.bdsmatrix.R backsolve.R",
"NeedsCompilation": "yes",
- "Repository": "CRAN"
+ "License": "Artistic-2.0",
+ "URL": "https://github.com/aroneklund/beeswarm",
+ "BugReports": "https://github.com/aroneklund/beeswarm/issues",
+ "Author": "Aron Eklund [aut, cre] (), James Trimble [aut] ()",
+ "Maintainer": "Aron Eklund ",
+ "Repository": "https://packagemanager.posit.co/cran/latest",
+ "Encoding": "UTF-8"
},
"beeswarm": {
"Package": "beeswarm",
@@ -1128,7 +1414,8 @@
"BugReports": "https://github.com/aroneklund/beeswarm/issues",
"Author": "Aron Eklund [aut, cre] (), James Trimble [aut] ()",
"Maintainer": "Aron Eklund ",
- "Repository": "CRAN"
+ "Repository": "https://packagemanager.posit.co/cran/latest",
+ "Encoding": "UTF-8"
},
"bit": {
"Package": "bit",
@@ -1235,15 +1522,8 @@
"Package": "boot",
"Version": "1.3-32",
"Source": "Repository",
- "Priority": "recommended",
- "Date": "2025-08-29",
- "Authors@R": "c(person(\"Angelo\", \"Canty\", role = \"aut\", email = \"cantya@mcmaster.ca\", comment = \"author of original code for S\"), person(\"Brian\", \"Ripley\", role = c(\"aut\", \"trl\"), email = \"Brian.Ripley@R-project.org\", comment = \"conversion to R, maintainer 1999--2022, author of parallel support\"), person(\"Alessandra R.\", \"Brazzale\", role = c(\"ctb\", \"cre\"), email = \"brazzale@stat.unipd.it\", comment = \"minor bug fixes\"))",
- "Maintainer": "Alessandra R. Brazzale ",
- "Note": "Maintainers are not available to give advice on using a package they did not author.",
- "Description": "Functions and datasets for bootstrapping from the book \"Bootstrap Methods and Their Application\" by A. C. Davison and D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.",
- "Title": "Bootstrap Functions",
- "Depends": [
- "R (>= 3.0.0)",
+ "Requirements": [
+ "R",
"graphics",
"stats"
],
@@ -1258,27 +1538,129 @@
"Author": "Angelo Canty [aut] (author of original code for S), Brian Ripley [aut, trl] (conversion to R, maintainer 1999--2022, author of parallel support), Alessandra R. Brazzale [ctb, cre] (minor bug fixes)",
"Repository": "CRAN"
},
- "brio": {
- "Package": "brio",
- "Version": "1.1.5",
+ "bridgesampling": {
+ "Package": "bridgesampling",
+ "Version": "1.2-1",
"Source": "Repository",
- "Title": "Basic R Input Output",
- "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
- "Description": "Functions to handle basic input output, these functions always read and write UTF-8 (8-bit Unicode Transformation Format) files and provide more explicit control over line endings.",
- "License": "MIT + file LICENSE",
- "URL": "https://brio.r-lib.org, https://github.com/r-lib/brio",
- "BugReports": "https://github.com/r-lib/brio/issues",
+ "Type": "Package",
+ "Title": "Bridge Sampling for Marginal Likelihoods and Bayes Factors",
+ "Authors@R": "c(person(given=\"Quentin F.\", family=\"Gronau\", role=c(\"aut\", \"cre\"), email=\"Quentin.F.Gronau@gmail.com\", comment=c(ORCID=\"0000-0001-5510-6943\")), person(given=\"Henrik\", family=\"Singmann\", role=\"aut\", comment=c(ORCID=\"0000-0002-4842-3657\")), person(given=\"Jonathan J.\", family=\"Forster\", role=\"ctb\"), person(given=\"Eric-Jan\", family=\"Wagenmakers\", role=\"ths\"), person(family=\"The JASP Team\", role=\"ctb\"), person(\"Jiqiang\", \"Guo\", role = \"ctb\"), person(\"Jonah\", \"Gabry\", role = \"ctb\"), person(\"Ben\", \"Goodrich\", role = c(\"ctb\")), person(\"Kees\", \"Mulder\", role = c(\"ctb\")), person(\"Perry\", \"de Valpine\", role = c(\"ctb\")), person(given=\"Aki\", family=\"Vehtari\", role = c(\"ctb\")), person(given=\"Giorgio\", family=\"Micaletto\", role = c(\"ctb\")) )",
"Depends": [
- "R (>= 3.6)"
+ "R (>= 3.0.0)"
],
- "Suggests": [
- "covr",
- "testthat (>= 3.0.0)"
+ "Imports": [
+ "mvtnorm",
+ "Matrix",
+ "Brobdingnag",
+ "stringr",
+ "coda",
+ "parallel",
+ "scales",
+ "utils",
+ "methods"
],
- "Config/Needs/website": "tidyverse/tidytemplate",
- "Config/testthat/edition": "3",
- "Encoding": "UTF-8",
- "RoxygenNote": "7.2.3",
+ "Suggests": [
+ "testthat",
+ "Rcpp",
+ "RcppEigen",
+ "R2jags",
+ "rjags",
+ "runjags",
+ "knitr",
+ "rmarkdown",
+ "R.rsp",
+ "BayesFactor",
+ "rstan",
+ "rstanarm",
+ "nimble",
+ "MCMCpack",
+ "cmdstanr (>= 0.6.0)"
+ ],
+ "Description": "Provides functions for estimating marginal likelihoods, Bayes factors, posterior model probabilities, and normalizing constants in general, via different versions of bridge sampling (Meng & Wong, 1996, ). Gronau, Singmann, & Wagenmakers (2020) .",
+ "Additional_repositories": "https://stan-dev.r-universe.dev/",
+ "License": "GPL (>= 2)",
+ "LazyData": "true",
+ "RoxygenNote": "7.3.3",
+ "Encoding": "UTF-8",
+ "VignetteBuilder": "knitr, R.rsp",
+ "URL": "https://github.com/quentingronau/bridgesampling",
+ "NeedsCompilation": "no",
+ "Author": "Quentin F. Gronau [aut, cre] (ORCID: ), Henrik Singmann [aut] (ORCID: ), Jonathan J. Forster [ctb], Eric-Jan Wagenmakers [ths], The JASP Team [ctb], Jiqiang Guo [ctb], Jonah Gabry [ctb], Ben Goodrich [ctb], Kees Mulder [ctb], Perry de Valpine [ctb], Aki Vehtari [ctb], Giorgio Micaletto [ctb]",
+ "Maintainer": "Quentin F. Gronau ",
+ "Repository": "CRAN"
+ },
+ "bridgesampling": {
+ "Package": "bridgesampling",
+ "Version": "1.2-1",
+ "Source": "Repository",
+ "Type": "Package",
+ "Title": "Bridge Sampling for Marginal Likelihoods and Bayes Factors",
+ "Authors@R": "c(person(given=\"Quentin F.\", family=\"Gronau\", role=c(\"aut\", \"cre\"), email=\"Quentin.F.Gronau@gmail.com\", comment=c(ORCID=\"0000-0001-5510-6943\")), person(given=\"Henrik\", family=\"Singmann\", role=\"aut\", comment=c(ORCID=\"0000-0002-4842-3657\")), person(given=\"Jonathan J.\", family=\"Forster\", role=\"ctb\"), person(given=\"Eric-Jan\", family=\"Wagenmakers\", role=\"ths\"), person(family=\"The JASP Team\", role=\"ctb\"), person(\"Jiqiang\", \"Guo\", role = \"ctb\"), person(\"Jonah\", \"Gabry\", role = \"ctb\"), person(\"Ben\", \"Goodrich\", role = c(\"ctb\")), person(\"Kees\", \"Mulder\", role = c(\"ctb\")), person(\"Perry\", \"de Valpine\", role = c(\"ctb\")), person(given=\"Aki\", family=\"Vehtari\", role = c(\"ctb\")), person(given=\"Giorgio\", family=\"Micaletto\", role = c(\"ctb\")) )",
+ "Depends": [
+ "R (>= 3.0.0)"
+ ],
+ "Imports": [
+ "mvtnorm",
+ "Matrix",
+ "Brobdingnag",
+ "stringr",
+ "coda",
+ "parallel",
+ "scales",
+ "utils",
+ "methods"
+ ],
+ "Suggests": [
+ "testthat",
+ "Rcpp",
+ "RcppEigen",
+ "R2jags",
+ "rjags",
+ "runjags",
+ "knitr",
+ "rmarkdown",
+ "R.rsp",
+ "BayesFactor",
+ "rstan",
+ "rstanarm",
+ "nimble",
+ "MCMCpack",
+ "cmdstanr (>= 0.6.0)"
+ ],
+ "Description": "Provides functions for estimating marginal likelihoods, Bayes factors, posterior model probabilities, and normalizing constants in general, via different versions of bridge sampling (Meng & Wong, 1996, ). Gronau, Singmann, & Wagenmakers (2020) .",
+ "Additional_repositories": "https://stan-dev.r-universe.dev/",
+ "License": "GPL (>= 2)",
+ "LazyData": "true",
+ "RoxygenNote": "7.3.3",
+ "Encoding": "UTF-8",
+ "VignetteBuilder": "knitr, R.rsp",
+ "URL": "https://github.com/quentingronau/bridgesampling",
+ "NeedsCompilation": "no",
+ "Author": "Quentin F. Gronau [aut, cre] (ORCID: ), Henrik Singmann [aut] (ORCID: ), Jonathan J. Forster [ctb], Eric-Jan Wagenmakers [ths], The JASP Team [ctb], Jiqiang Guo [ctb], Jonah Gabry [ctb], Ben Goodrich [ctb], Kees Mulder [ctb], Perry de Valpine [ctb], Aki Vehtari [ctb], Giorgio Micaletto [ctb]",
+ "Maintainer": "Quentin F. Gronau ",
+ "Repository": "CRAN"
+ },
+ "brio": {
+ "Package": "brio",
+ "Version": "1.1.5",
+ "Source": "Repository",
+ "Title": "Basic R Input Output",
+ "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
+ "Description": "Functions to handle basic input output, these functions always read and write UTF-8 (8-bit Unicode Transformation Format) files and provide more explicit control over line endings.",
+ "License": "MIT + file LICENSE",
+ "URL": "https://brio.r-lib.org, https://github.com/r-lib/brio",
+ "BugReports": "https://github.com/r-lib/brio/issues",
+ "Depends": [
+ "R (>= 3.6)"
+ ],
+ "Suggests": [
+ "covr",
+ "testthat (>= 3.0.0)"
+ ],
+ "Config/Needs/website": "tidyverse/tidytemplate",
+ "Config/testthat/edition": "3",
+ "Encoding": "UTF-8",
+ "RoxygenNote": "7.2.3",
"NeedsCompilation": "yes",
"Author": "Jim Hester [aut] (), Gábor Csárdi [aut, cre], Posit Software, PBC [cph, fnd]",
"Maintainer": "Gábor Csárdi ",
@@ -1466,6 +1848,93 @@
"NeedsCompilation": "no",
"Author": "Carson Sievert [aut, cre] (ORCID: ), Joe Cheng [aut], Garrick Aden-Buie [aut] (ORCID: ), Posit Software, PBC [cph, fnd], Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Javi Aguilar [ctb, cph] (Bootstrap colorpicker library), Thomas Park [ctb, cph] (Bootswatch library), PayPal [ctb, cph] (Bootstrap accessibility plugin)",
"Maintainer": "Carson Sievert ",
+ "Repository": "https://packagemanager.posit.co/cran/latest"
+ },
+ "bslib": {
+ "Package": "bslib",
+ "Version": "0.11.0",
+ "Source": "Repository",
+ "Title": "Custom 'Bootstrap' 'Sass' Themes for 'shiny' and 'rmarkdown'",
+ "Authors@R": "c( person(\"Carson\", \"Sievert\", , \"carson@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Garrick\", \"Aden-Buie\", , \"garrick@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0002-7111-0077\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(, \"Bootstrap contributors\", role = \"ctb\", comment = \"Bootstrap library\"), person(, \"Twitter, Inc\", role = \"cph\", comment = \"Bootstrap library\"), person(\"Javi\", \"Aguilar\", role = c(\"ctb\", \"cph\"), comment = \"Bootstrap colorpicker library\"), person(\"Thomas\", \"Park\", role = c(\"ctb\", \"cph\"), comment = \"Bootswatch library\"), person(, \"PayPal\", role = c(\"ctb\", \"cph\"), comment = \"Bootstrap accessibility plugin\") )",
+ "Description": "Simplifies custom 'CSS' styling of both 'shiny' and 'rmarkdown' via 'Bootstrap' 'Sass'. Supports 'Bootstrap' 3, 4 and 5 as well as their various 'Bootswatch' themes. An interactive widget is also provided for previewing themes in real time.",
+ "License": "MIT + file LICENSE",
+ "URL": "https://rstudio.github.io/bslib/, https://github.com/rstudio/bslib",
+ "BugReports": "https://github.com/rstudio/bslib/issues",
+ "Depends": [
+ "R (>= 2.10)"
+ ],
+ "Imports": [
+ "base64enc",
+ "cachem",
+ "fastmap (>= 1.1.1)",
+ "grDevices",
+ "htmltools (>= 0.5.8)",
+ "jquerylib (>= 0.1.3)",
+ "jsonlite",
+ "lifecycle",
+ "memoise (>= 2.0.1)",
+ "mime",
+ "rlang",
+ "sass (>= 0.4.9)"
+ ],
+ "Suggests": [
+ "brand.yml",
+ "bsicons",
+ "curl",
+ "fontawesome",
+ "future",
+ "ggplot2",
+ "knitr",
+ "lattice",
+ "magrittr",
+ "rappdirs",
+ "rmarkdown (>= 2.7)",
+ "shiny (>= 1.11.1.9000)",
+ "testthat",
+ "thematic",
+ "tools",
+ "utils",
+ "withr",
+ "yaml"
+ ],
+ "Config/Needs/deploy": "BH, chiflights22, colourpicker, commonmark, cpp11, cpsievert/chiflights22, cpsievert/histoslider, dplyr, DT, ggplot2, ggridges, gt, hexbin, histoslider, htmlwidgets, lattice, leaflet, lubridate, markdown, modelr, plotly, reactable, reshape2, rprojroot, rsconnect, rstudio/shiny, scales, styler, tibble",
+ "Config/Needs/routine": "chromote, desc, renv",
+ "Config/Needs/website": "brio, crosstalk, dplyr, DT, ggplot2, glue, htmlwidgets, leaflet, lorem, palmerpenguins, plotly, purrr, rprojroot, rstudio/htmltools, scales, stringr, tidyr, webshot2",
+ "Config/roxygen2/version": "8.0.0",
+ "Config/testthat/edition": "3",
+ "Config/testthat/parallel": "true",
+ "Config/testthat/start-first": "zzzz-bs-sass, fonts, zzz-precompile, theme-*, rmd-*",
+ "Encoding": "UTF-8",
+ "Collate": "'accordion.R' 'breakpoints.R' 'bs-current-theme.R' 'bs-dependencies.R' 'bs-global.R' 'bs-remove.R' 'bs-theme-layers.R' 'bs-theme-preset-bootswatch.R' 'bs-theme-preset-brand.R' 'bs-theme-preset-builtin.R' 'bs-theme-preset.R' 'utils.R' 'bs-theme-preview.R' 'bs-theme-update.R' 'bs-theme.R' 'bslib-package.R' 'buttons.R' 'card.R' 'deprecated.R' 'files.R' 'fill.R' 'imports.R' 'input-code-editor.R' 'input-dark-mode.R' 'input-submit.R' 'input-switch.R' 'layout.R' 'nav-items.R' 'nav-update.R' 'navbar_options.R' 'navs-legacy.R' 'navs.R' 'onLoad.R' 'page.R' 'popover.R' 'precompiled.R' 'print.R' 'shiny-devmode.R' 'sidebar.R' 'staticimports.R' 'toast.R' 'toolbar.R' 'tooltip.R' 'utils-deps.R' 'utils-shiny.R' 'utils-tags.R' 'value-box.R' 'version-default.R' 'versions.R'",
+ "NeedsCompilation": "no",
+ "Author": "Carson Sievert [aut, cre] (ORCID: ), Joe Cheng [aut], Garrick Aden-Buie [aut] (ORCID: ), Posit Software, PBC [cph, fnd], Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Javi Aguilar [ctb, cph] (Bootstrap colorpicker library), Thomas Park [ctb, cph] (Bootswatch library), PayPal [ctb, cph] (Bootstrap accessibility plugin)",
+ "Maintainer": "Carson Sievert ",
+ "Repository": "https://packagemanager.posit.co/cran/latest"
+ },
+ "cachem": {
+ "Package": "cachem",
+ "Version": "1.1.0",
+ "Source": "Repository",
+ "Title": "Cache R Objects with Automatic Pruning",
+ "Description": "Key-value stores with automatic pruning. Caches can limit either their total size or the age of the oldest object (or both), automatically pruning objects to maintain the constraints.",
+ "Authors@R": "c( person(\"Winston\", \"Chang\", , \"winston@posit.co\", c(\"aut\", \"cre\")), person(family = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")))",
+ "License": "MIT + file LICENSE",
+ "Encoding": "UTF-8",
+ "ByteCompile": "true",
+ "URL": "https://cachem.r-lib.org/, https://github.com/r-lib/cachem",
+ "Imports": [
+ "rlang",
+ "fastmap (>= 1.2.0)"
+ ],
+ "Suggests": [
+ "testthat"
+ ],
+ "RoxygenNote": "7.2.3",
+ "Config/Needs/routine": "lobstr",
+ "Config/Needs/website": "pkgdown",
+ "NeedsCompilation": "yes",
+ "Author": "Winston Chang [aut, cre], Posit Software, PBC [cph, fnd]",
+ "Maintainer": "Winston Chang ",
"Repository": "CRAN"
},
"cachem": {
@@ -1496,19 +1965,12 @@
},
"callr": {
"Package": "callr",
- "Version": "3.7.6",
+ "Version": "3.8.0",
"Source": "Repository",
- "Title": "Call R from R",
- "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\", \"cph\"), comment = c(ORCID = \"0000-0001-7098-9676\")), person(\"Winston\", \"Chang\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(\"Ascent Digital Services\", role = c(\"cph\", \"fnd\")) )",
- "Description": "It is sometimes useful to perform a computation in a separate R process, without affecting the current R process at all. This packages does exactly that.",
- "License": "MIT + file LICENSE",
- "URL": "https://callr.r-lib.org, https://github.com/r-lib/callr",
- "BugReports": "https://github.com/r-lib/callr/issues",
- "Depends": [
- "R (>= 3.4)"
- ],
- "Imports": [
- "processx (>= 3.6.1)",
+ "Requirements": [
+ "otel",
+ "processx",
+ "R",
"R6",
"utils"
],
@@ -1588,7 +2050,8 @@
"NeedsCompilation": "no",
"Author": "John Fox [aut], Sanford Weisberg [aut], Brad Price [aut, cre], Daniel Adler [ctb], Douglas Bates [ctb], Gabriel Baud-Bovy [ctb], Ben Bolker [ctb], Steve Ellison [ctb], David Firth [ctb], Michael Friendly [ctb], Gregor Gorjanc [ctb], Spencer Graves [ctb], Richard Heiberger [ctb], Pavel Krivitsky [ctb], Rafael Laboissiere [ctb], Martin Maechler [ctb], Georges Monette [ctb], Duncan Murdoch [ctb], Henric Nilsson [ctb], Derek Ogle [ctb], Iain Proctor [ctb], Brian Ripley [ctb], Tom Short [ctb], William Venables [ctb], Steve Walker [ctb], David Winsemius [ctb], Achim Zeileis [ctb], R-Core [ctb]",
"Maintainer": "Brad Price ",
- "Repository": "CRAN"
+ "Repository": "https://packagemanager.posit.co/cran/latest",
+ "Encoding": "UTF-8"
},
"carData": {
"Package": "carData",
@@ -1611,6 +2074,50 @@
"NeedsCompilation": "no",
"Author": "John Fox [aut], Sanford Weisberg [aut], Brad Price [aut, cre]",
"Maintainer": "Brad Price ",
+ "Repository": "https://packagemanager.posit.co/cran/latest",
+ "Encoding": "UTF-8"
+ },
+ "checkmate": {
+ "Package": "checkmate",
+ "Version": "2.3.4",
+ "Source": "Repository",
+ "Type": "Package",
+ "Title": "Fast and Versatile Argument Checks",
+ "Description": "Tests and assertions to perform frequent argument checks. A substantial part of the package was written in C to minimize any worries about execution time overhead.",
+ "Authors@R": "c( person(\"Michel\", \"Lang\", NULL, \"michellang@gmail.com\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0001-9754-0393\")), person(\"Bernd\", \"Bischl\", NULL, \"bernd_bischl@gmx.net\", role = \"ctb\"), person(\"Dénes\", \"Tóth\", NULL, \"toth.denes@kogentum.hu\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4262-3217\")) )",
+ "URL": "https://mllg.github.io/checkmate/, https://github.com/mllg/checkmate",
+ "URLNote": "https://github.com/mllg/checkmate",
+ "BugReports": "https://github.com/mllg/checkmate/issues",
+ "NeedsCompilation": "yes",
+ "ByteCompile": "yes",
+ "Encoding": "UTF-8",
+ "Depends": [
+ "R (>= 3.0.0)"
+ ],
+ "Imports": [
+ "backports (>= 1.1.0)",
+ "utils"
+ ],
+ "Suggests": [
+ "R6",
+ "fastmatch",
+ "data.table (>= 1.9.8)",
+ "devtools",
+ "ggplot2",
+ "knitr",
+ "magrittr",
+ "microbenchmark",
+ "rmarkdown",
+ "testthat (>= 3.0.4)",
+ "tinytest (>= 1.1.0)",
+ "tibble"
+ ],
+ "License": "BSD_3_clause + file LICENSE",
+ "VignetteBuilder": "knitr",
+ "RoxygenNote": "7.3.3",
+ "Collate": "'AssertCollection.R' 'allMissing.R' 'anyInfinite.R' 'anyMissing.R' 'anyNaN.R' 'asInteger.R' 'assert.R' 'helper.R' 'makeExpectation.R' 'makeTest.R' 'makeAssertion.R' 'checkAccess.R' 'checkArray.R' 'checkAtomic.R' 'checkAtomicVector.R' 'checkCharacter.R' 'checkChoice.R' 'checkClass.R' 'checkComplex.R' 'checkCount.R' 'checkDataFrame.R' 'checkDataTable.R' 'checkDate.R' 'checkDirectoryExists.R' 'checkDisjunct.R' 'checkDouble.R' 'checkEnvironment.R' 'checkFALSE.R' 'checkFactor.R' 'checkFileExists.R' 'checkFlag.R' 'checkFormula.R' 'checkFunction.R' 'checkInt.R' 'checkInteger.R' 'checkIntegerish.R' 'checkList.R' 'checkLogical.R' 'checkMatrix.R' 'checkMultiClass.R' 'checkNamed.R' 'checkNames.R' 'checkNull.R' 'checkNumber.R' 'checkNumeric.R' 'checkOS.R' 'checkPOSIXct.R' 'checkPathForOutput.R' 'checkPermutation.R' 'checkR6.R' 'checkRaw.R' 'checkScalar.R' 'checkScalarNA.R' 'checkSetEqual.R' 'checkString.R' 'checkSubset.R' 'checkTRUE.R' 'checkTibble.R' 'checkVector.R' 'coalesce.R' 'isIntegerish.R' 'matchArg.R' 'qassert.R' 'qassertr.R' 'vname.R' 'wfwl.R' 'zzz.R'",
+ "Author": "Michel Lang [cre, aut] (ORCID: ), Bernd Bischl [ctb], Dénes Tóth [ctb] (ORCID: )",
+ "Maintainer": "Michel Lang ",
"Repository": "CRAN"
},
"checkmate": {
@@ -1654,7 +2161,7 @@
"Collate": "'AssertCollection.R' 'allMissing.R' 'anyInfinite.R' 'anyMissing.R' 'anyNaN.R' 'asInteger.R' 'assert.R' 'helper.R' 'makeExpectation.R' 'makeTest.R' 'makeAssertion.R' 'checkAccess.R' 'checkArray.R' 'checkAtomic.R' 'checkAtomicVector.R' 'checkCharacter.R' 'checkChoice.R' 'checkClass.R' 'checkComplex.R' 'checkCount.R' 'checkDataFrame.R' 'checkDataTable.R' 'checkDate.R' 'checkDirectoryExists.R' 'checkDisjunct.R' 'checkDouble.R' 'checkEnvironment.R' 'checkFALSE.R' 'checkFactor.R' 'checkFileExists.R' 'checkFlag.R' 'checkFormula.R' 'checkFunction.R' 'checkInt.R' 'checkInteger.R' 'checkIntegerish.R' 'checkList.R' 'checkLogical.R' 'checkMatrix.R' 'checkMultiClass.R' 'checkNamed.R' 'checkNames.R' 'checkNull.R' 'checkNumber.R' 'checkNumeric.R' 'checkOS.R' 'checkPOSIXct.R' 'checkPathForOutput.R' 'checkPermutation.R' 'checkR6.R' 'checkRaw.R' 'checkScalar.R' 'checkScalarNA.R' 'checkSetEqual.R' 'checkString.R' 'checkSubset.R' 'checkTRUE.R' 'checkTibble.R' 'checkVector.R' 'coalesce.R' 'isIntegerish.R' 'matchArg.R' 'qassert.R' 'qassertr.R' 'vname.R' 'wfwl.R' 'zzz.R'",
"Author": "Michel Lang [cre, aut] (ORCID: ), Bernd Bischl [ctb], Dénes Tóth [ctb] (ORCID: )",
"Maintainer": "Michel Lang ",
- "Repository": "RSPM"
+ "Repository": "CRAN"
},
"cli": {
"Package": "cli",
@@ -1702,7 +2209,49 @@
"NeedsCompilation": "yes",
"Author": "Gábor Csárdi [aut, cre], Hadley Wickham [ctb], Kirill Müller [ctb], Salim Brüggemann [ctb] (ORCID: ), Posit Software, PBC [cph, fnd] (ROR: )",
"Maintainer": "Gábor Csárdi ",
- "Repository": "RSPM"
+ "Repository": "https://p3m.dev/cran/latest"
+ },
+ "cluster": {
+ "Package": "cluster",
+ "Version": "2.1.8.1",
+ "Source": "Repository",
+ "VersionNote": "Last CRAN: 2.1.8 on 2024-12-10; 2.1.7 on 2024-12-06; 2.1.6 on 2023-11-30; 2.1.5 on 2023-11-27",
+ "Date": "2025-03-11",
+ "Priority": "recommended",
+ "Title": "\"Finding Groups in Data\": Cluster Analysis Extended Rousseeuw et al.",
+ "Description": "Methods for Cluster analysis. Much extended the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".",
+ "Maintainer": "Martin Maechler ",
+ "Authors@R": "c(person(\"Martin\",\"Maechler\", role = c(\"aut\",\"cre\"), email=\"maechler@stat.math.ethz.ch\", comment = c(ORCID = \"0000-0002-8685-9910\")) ,person(\"Peter\", \"Rousseeuw\", role=\"aut\", email=\"peter.rousseeuw@kuleuven.be\", comment = c(\"Fortran original\", ORCID = \"0000-0002-3807-5353\")) ,person(\"Anja\", \"Struyf\", role=\"aut\", comment= \"S original\") ,person(\"Mia\", \"Hubert\", role=\"aut\", email= \"Mia.Hubert@uia.ua.ac.be\", comment = c(\"S original\", ORCID = \"0000-0001-6398-4850\")) ,person(\"Kurt\", \"Hornik\", role=c(\"trl\", \"ctb\"), email=\"Kurt.Hornik@R-project.org\", comment=c(\"port to R; maintenance(1999-2000)\", ORCID=\"0000-0003-4198-9911\")) ,person(\"Matthias\", \"Studer\", role=\"ctb\") ,person(\"Pierre\", \"Roudier\", role=\"ctb\") ,person(\"Juan\", \"Gonzalez\", role=\"ctb\") ,person(\"Kamil\", \"Kozlowski\", role=\"ctb\") ,person(\"Erich\", \"Schubert\", role=\"ctb\", comment = c(\"fastpam options for pam()\", ORCID = \"0000-0001-9143-4880\")) ,person(\"Keefe\", \"Murphy\", role=\"ctb\", comment = \"volume.ellipsoid({d >= 3})\") #not yet ,person(\"Fischer-Rasmussen\", \"Kasper\", role = \"ctb\", comment = \"Gower distance for CLARA\") )",
+ "Depends": [
+ "R (>= 3.5.0)"
+ ],
+ "Imports": [
+ "graphics",
+ "grDevices",
+ "stats",
+ "utils"
+ ],
+ "Suggests": [
+ "MASS",
+ "Matrix"
+ ],
+ "SuggestsNote": "MASS: two examples using cov.rob() and mvrnorm(); Matrix tools for testing",
+ "Enhances": [
+ "mvoutlier",
+ "fpc",
+ "ellipse",
+ "sfsmisc"
+ ],
+ "EnhancesNote": "xref-ed in man/*.Rd",
+ "LazyLoad": "yes",
+ "LazyData": "yes",
+ "ByteCompile": "yes",
+ "BuildResaveData": "no",
+ "License": "GPL (>= 2)",
+ "URL": "https://svn.r-project.org/R-packages/trunk/cluster/",
+ "NeedsCompilation": "yes",
+ "Author": "Martin Maechler [aut, cre] (), Peter Rousseeuw [aut] (Fortran original, ), Anja Struyf [aut] (S original), Mia Hubert [aut] (S original, ), Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000), ), Matthias Studer [ctb], Pierre Roudier [ctb], Juan Gonzalez [ctb], Kamil Kozlowski [ctb], Erich Schubert [ctb] (fastpam options for pam(), ), Keefe Murphy [ctb] (volume.ellipsoid({d >= 3}))",
+ "Repository": "CRAN"
},
"cluster": {
"Package": "cluster",
@@ -1974,9 +2523,37 @@
"Author": "Taiyun Wei [cre, aut], Viliam Simko [aut], Michael Levy [ctb], Yihui Xie [ctb], Yan Jin [ctb], Jeff Zemla [ctb], Moritz Freidank [ctb], Jun Cai [ctb], Tomas Protivinsky [ctb]",
"Repository": "CRAN"
},
- "cowplot": {
- "Package": "cowplot",
- "Version": "1.2.0",
+ "corrplot": {
+ "Package": "corrplot",
+ "Version": "0.95",
+ "Source": "Repository",
+ "Type": "Package",
+ "Title": "Visualization of a Correlation Matrix",
+ "Date": "2024-10-14",
+ "Authors@R": "c( person('Taiyun', 'Wei', email = 'weitaiyun@gmail.com', role = c('cre', 'aut')), person('Viliam', 'Simko', email = 'viliam.simko@gmail.com', role = 'aut'), person('Michael', 'Levy', email = 'michael.levy@healthcatalyst.com', role = 'ctb'), person('Yihui', 'Xie', email = 'xie@yihui.name', role = 'ctb'), person('Yan', 'Jin', email = 'jyfeather@gmail.com', role = 'ctb'), person('Jeff', 'Zemla', email = 'zemla@wisc.edu', role = 'ctb'), person('Moritz', 'Freidank', email = 'freidankm@googlemail.com', role = 'ctb'), person('Jun', 'Cai', email = 'cai-j12@mails.tsinghua.edu.cn', role = 'ctb'), person('Tomas', 'Protivinsky', email = 'tomas.protivinsky@gmail.com', role = 'ctb') )",
+ "Maintainer": "Taiyun Wei ",
+ "Suggests": [
+ "seriation",
+ "knitr",
+ "RColorBrewer",
+ "rmarkdown",
+ "magrittr",
+ "prettydoc",
+ "testthat"
+ ],
+ "Description": "Provides a visual exploratory tool on correlation matrix that supports automatic variable reordering to help detect hidden patterns among variables.",
+ "License": "MIT + file LICENSE",
+ "URL": "https://github.com/taiyun/corrplot",
+ "BugReports": "https://github.com/taiyun/corrplot/issues",
+ "VignetteBuilder": "knitr",
+ "RoxygenNote": "7.2.1",
+ "NeedsCompilation": "no",
+ "Author": "Taiyun Wei [cre, aut], Viliam Simko [aut], Michael Levy [ctb], Yihui Xie [ctb], Yan Jin [ctb], Jeff Zemla [ctb], Moritz Freidank [ctb], Jun Cai [ctb], Tomas Protivinsky [ctb]",
+ "Repository": "CRAN"
+ },
+ "cowplot": {
+ "Package": "cowplot",
+ "Version": "1.2.0",
"Source": "Repository",
"Title": "Streamlined Plot Theme and Plot Annotations for 'ggplot2'",
"Authors@R": "person( given = \"Claus O.\", family = \"Wilke\", role = c(\"aut\", \"cre\"), email = \"wilke@austin.utexas.edu\", comment = c(ORCID = \"0000-0002-7470-9261\") )",
@@ -2069,7 +2646,7 @@
"NeedsCompilation": "no",
"Author": "Davis Vaughan [aut, cre] (ORCID: ), Jim Hester [aut] (ORCID: ), Romain François [aut] (ORCID: ), Benjamin Kietzman [ctb], Posit Software, PBC [cph, fnd]",
"Maintainer": "Davis Vaughan ",
- "Repository": "CRAN"
+ "Repository": "https://packagemanager.posit.co/cran/latest"
},
"crayon": {
"Package": "crayon",
@@ -2133,6 +2710,104 @@
"Maintainer": "Carson Sievert ",
"Repository": "CRAN"
},
+ "crosstalk": {
+ "Package": "crosstalk",
+ "Version": "1.2.2",
+ "Source": "Repository",
+ "Type": "Package",
+ "Title": "Inter-Widget Interactivity for HTML Widgets",
+ "Authors@R": "c( person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Carson\", \"Sievert\", , \"carson@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(, \"jQuery Foundation\", role = \"cph\", comment = \"jQuery library and jQuery UI library\"), person(, \"jQuery contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt\"), person(\"Mark\", \"Otto\", role = \"ctb\", comment = \"Bootstrap library\"), person(\"Jacob\", \"Thornton\", role = \"ctb\", comment = \"Bootstrap library\"), person(, \"Bootstrap contributors\", role = \"ctb\", comment = \"Bootstrap library\"), person(, \"Twitter, Inc\", role = \"cph\", comment = \"Bootstrap library\"), person(\"Brian\", \"Reavis\", role = c(\"ctb\", \"cph\"), comment = \"selectize.js library\"), person(\"Kristopher Michael\", \"Kowal\", role = c(\"ctb\", \"cph\"), comment = \"es5-shim library\"), person(, \"es5-shim contributors\", role = c(\"ctb\", \"cph\"), comment = \"es5-shim library\"), person(\"Denis\", \"Ineshin\", role = c(\"ctb\", \"cph\"), comment = \"ion.rangeSlider library\"), person(\"Sami\", \"Samhuri\", role = c(\"ctb\", \"cph\"), comment = \"Javascript strftime library\") )",
+ "Description": "Provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e. static .html files). Currently supports linked brushing and filtering.",
+ "License": "MIT + file LICENSE",
+ "URL": "https://rstudio.github.io/crosstalk/, https://github.com/rstudio/crosstalk",
+ "BugReports": "https://github.com/rstudio/crosstalk/issues",
+ "Imports": [
+ "htmltools (>= 0.3.6)",
+ "jsonlite",
+ "lazyeval",
+ "R6"
+ ],
+ "Suggests": [
+ "bslib",
+ "ggplot2",
+ "sass",
+ "shiny",
+ "testthat (>= 2.1.0)"
+ ],
+ "Config/Needs/website": "jcheng5/d3scatter, DT, leaflet, rmarkdown",
+ "Encoding": "UTF-8",
+ "RoxygenNote": "7.3.2",
+ "NeedsCompilation": "no",
+ "Author": "Joe Cheng [aut], Carson Sievert [aut, cre] (ORCID: ), Posit Software, PBC [cph, fnd], jQuery Foundation [cph] (jQuery library and jQuery UI library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Brian Reavis [ctb, cph] (selectize.js library), Kristopher Michael Kowal [ctb, cph] (es5-shim library), es5-shim contributors [ctb, cph] (es5-shim library), Denis Ineshin [ctb, cph] (ion.rangeSlider library), Sami Samhuri [ctb, cph] (Javascript strftime library)",
+ "Maintainer": "Carson Sievert ",
+ "Repository": "CRAN"
+ },
+ "cubature": {
+ "Package": "cubature",
+ "Version": "2.1.4-1",
+ "Source": "Repository",
+ "Type": "Package",
+ "Title": "Adaptive Multivariate Integration over Hypercubes",
+ "VignetteBuilder": "knitr",
+ "SystemRequirements": "GNU make and USE_C17",
+ "URL": "https://bnaras.github.io/cubature/",
+ "BugReports": "https://github.com/bnaras/cubature/issues",
+ "Authors@R": "c(person(\"Balasubramanian\", \"Narasimhan\", role=c(\"aut\", \"cre\"), email = \"naras@stat.stanford.edu\"), person(\"Manuel\", \"Koller\", role=c(\"ctb\"), email = \"koller.manuel@gmail.com\"), person(\"Dirk\", \"Eddelbuettel\", role=c(\"ctb\"), email = \"edd@debian.org\"),\t\t person(c(\"Steven\", \"G.\"), \"Johnson\", role=c(\"aut\")), person(\"Thomas\", \"Hahn\", role=c(\"aut\")), person(\"Annie\", \"Bouvier\", role=c(\"aut\")), person(\"Kiên\", \"Kiêu\", role=c(\"aut\"), email = \"Kien.Kieu@jouy.inra.fr\"), person(\"Simen\", \"Gaure\", role=c(\"ctb\"), email = \"simen.gaure@frisch.uio.no\"))",
+ "Description": "R wrappers around the cubature C library of Steven G. Johnson for adaptive multivariate integration over hypercubes and the Cuba C library of Thomas Hahn for deterministic and Monte Carlo integration. Scalar and vector interfaces for cubature and Cuba routines are provided; the vector interfaces are highly recommended as demonstrated in the package vignette.",
+ "License": "GPL-3",
+ "Encoding": "UTF-8",
+ "LinkingTo": [
+ "Rcpp"
+ ],
+ "Imports": [
+ "Rcpp"
+ ],
+ "NeedsCompilation": "yes",
+ "RoxygenNote": "7.3.3",
+ "Suggests": [
+ "testthat",
+ "knitr",
+ "mvtnorm",
+ "bench",
+ "rmarkdown"
+ ],
+ "Author": "Balasubramanian Narasimhan [aut, cre], Manuel Koller [ctb], Dirk Eddelbuettel [ctb], Steven G. Johnson [aut], Thomas Hahn [aut], Annie Bouvier [aut], Kiên Kiêu [aut], Simen Gaure [ctb]",
+ "Maintainer": "Balasubramanian Narasimhan ",
+ "Repository": "https://packagemanager.posit.co/cran/latest"
+ },
+ "cubature": {
+ "Package": "cubature",
+ "Version": "2.1.4-1",
+ "Source": "Repository",
+ "Type": "Package",
+ "Title": "Adaptive Multivariate Integration over Hypercubes",
+ "VignetteBuilder": "knitr",
+ "SystemRequirements": "GNU make and USE_C17",
+ "URL": "https://bnaras.github.io/cubature/",
+ "BugReports": "https://github.com/bnaras/cubature/issues",
+ "Authors@R": "c(person(\"Balasubramanian\", \"Narasimhan\", role=c(\"aut\", \"cre\"), email = \"naras@stat.stanford.edu\"), person(\"Manuel\", \"Koller\", role=c(\"ctb\"), email = \"koller.manuel@gmail.com\"), person(\"Dirk\", \"Eddelbuettel\", role=c(\"ctb\"), email = \"edd@debian.org\"),\t\t person(c(\"Steven\", \"G.\"), \"Johnson\", role=c(\"aut\")), person(\"Thomas\", \"Hahn\", role=c(\"aut\")), person(\"Annie\", \"Bouvier\", role=c(\"aut\")), person(\"Kiên\", \"Kiêu\", role=c(\"aut\"), email = \"Kien.Kieu@jouy.inra.fr\"), person(\"Simen\", \"Gaure\", role=c(\"ctb\"), email = \"simen.gaure@frisch.uio.no\"))",
+ "Description": "R wrappers around the cubature C library of Steven G. Johnson for adaptive multivariate integration over hypercubes and the Cuba C library of Thomas Hahn for deterministic and Monte Carlo integration. Scalar and vector interfaces for cubature and Cuba routines are provided; the vector interfaces are highly recommended as demonstrated in the package vignette.",
+ "License": "GPL-3",
+ "Encoding": "UTF-8",
+ "LinkingTo": [
+ "Rcpp"
+ ],
+ "Imports": [
+ "Rcpp"
+ ],
+ "NeedsCompilation": "yes",
+ "RoxygenNote": "7.3.3",
+ "Suggests": [
+ "testthat",
+ "knitr",
+ "mvtnorm",
+ "bench",
+ "rmarkdown"
+ ],
+ "Author": "Balasubramanian Narasimhan [aut, cre], Manuel Koller [ctb], Dirk Eddelbuettel [ctb], Steven G. Johnson [aut], Thomas Hahn [aut], Annie Bouvier [aut], Kiên Kiêu [aut], Simen Gaure [ctb]",
+ "Maintainer": "Balasubramanian Narasimhan ",
+ "Repository": "https://packagemanager.posit.co/cran/latest"
+ },
"curl": {
"Package": "curl",
"Version": "7.1.0",
@@ -2228,7 +2903,41 @@
"NeedsCompilation": "yes",
"Author": "Tyson Barrett [aut, cre] (ORCID: ), Matt Dowle [aut], Arun Srinivasan [aut], Jan Gorecki [aut], Michael Chirico [aut] (ORCID: ), Toby Hocking [aut] (ORCID: ), Benjamin Schwendinger [aut] (ORCID: ), Ivan Krylov [aut] (ORCID: ), Pasha Stetsenko [ctb], Tom Short [ctb], Steve Lianoglou [ctb], Eduard Antonyan [ctb], Markus Bonsch [ctb], Hugh Parsonage [ctb], Scott Ritchie [ctb], Kun Ren [ctb], Xianying Tan [ctb], Rick Saporta [ctb], Otto Seiskari [ctb], Xianghui Dong [ctb], Michel Lang [ctb], Watal Iwasaki [ctb], Seth Wenchel [ctb], Karl Broman [ctb], Tobias Schmidt [ctb], David Arenburg [ctb], Ethan Smith [ctb], Francois Cocquemas [ctb], Matthieu Gomez [ctb], Philippe Chataignon [ctb], Nello Blaser [ctb], Dmitry Selivanov [ctb], Andrey Riabushenko [ctb], Cheng Lee [ctb], Declan Groves [ctb], Daniel Possenriede [ctb], Felipe Parages [ctb], Denes Toth [ctb], Mus Yaramaz-David [ctb], Ayappan Perumal [ctb], James Sams [ctb], Martin Morgan [ctb], Michael Quinn [ctb], @javrucebo [ctb] (GitHub user), Marc Halperin [ctb], Roy Storey [ctb], Manish Saraswat [ctb], Morgan Jacob [ctb], Michael Schubmehl [ctb], Davis Vaughan [ctb], Leonardo Silvestri [ctb], Jim Hester [ctb], Anthony Damico [ctb], Sebastian Freundt [ctb], David Simons [ctb], Elliott Sales de Andrade [ctb], Cole Miller [ctb], Jens Peder Meldgaard [ctb], Vaclav Tlapak [ctb], Kevin Ushey [ctb], Dirk Eddelbuettel [ctb], Tony Fischetti [ctb], Ofek Shilon [ctb], Vadim Khotilovich [ctb], Hadley Wickham [ctb], Bennet Becker [ctb], Kyle Haynes [ctb], Boniface Christian Kamgang [ctb], Olivier Delmarcell [ctb], Josh O'Brien [ctb], Dereck de Mezquita [ctb], Michael Czekanski [ctb], Dmitry Shemetov [ctb], Nitish Jha [ctb], Joshua Wu [ctb], Iago Giné-Vázquez [ctb], Anirban Chetia [ctb], Doris Amoakohene [ctb], Angel Feliz [ctb], Michael Young [ctb], Mark Seeto [ctb], Philippe Grosjean [ctb], Vincent Runge [ctb], Christian Wia [ctb], Elise Maigné [ctb], Vincent Rocher [ctb], Vijay Lulla [ctb], Aljaž Sluga [ctb], Bill Evans [ctb], Reino Bruner [ctb], @badasahog [ctb] (GitHub user), Vinit Thakur [ctb], Mukul Kumar [ctb], Ildikó Czeller [ctb], Manmita Das [ctb], Tarun Thammisetty [ctb]",
"Maintainer": "Tyson Barrett ",
- "Repository": "CRAN"
+ "Repository": "https://packagemanager.posit.co/cran/latest"
+ },
+ "data.table": {
+ "Package": "data.table",
+ "Version": "1.18.4",
+ "Source": "Repository",
+ "Title": "Extension of `data.frame`",
+ "Depends": [
+ "R (>= 3.4.0)"
+ ],
+ "Imports": [
+ "methods"
+ ],
+ "Suggests": [
+ "bit64 (>= 4.0.0)",
+ "bit (>= 4.0.4)",
+ "R.utils (>= 2.13.0)",
+ "xts",
+ "zoo (>= 1.8-1)",
+ "yaml",
+ "knitr",
+ "markdown"
+ ],
+ "Description": "Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.",
+ "License": "MPL-2.0 | file LICENSE",
+ "URL": "https://r-datatable.com, https://Rdatatable.gitlab.io/data.table, https://github.com/Rdatatable/data.table",
+ "BugReports": "https://github.com/Rdatatable/data.table/issues",
+ "VignetteBuilder": "knitr",
+ "Encoding": "UTF-8",
+ "ByteCompile": "TRUE",
+ "Authors@R": "c( person(\"Tyson\",\"Barrett\", role=c(\"aut\",\"cre\"), email=\"t.barrett88@gmail.com\", comment = c(ORCID=\"0000-0002-2137-1391\")), person(\"Matt\",\"Dowle\", role=\"aut\", email=\"mattjdowle@gmail.com\"), person(\"Arun\",\"Srinivasan\", role=\"aut\", email=\"asrini@pm.me\"), person(\"Jan\",\"Gorecki\", role=\"aut\", email=\"j.gorecki@wit.edu.pl\"), person(\"Michael\",\"Chirico\", role=\"aut\", email=\"michaelchirico4@gmail.com\", comment = c(ORCID=\"0000-0003-0787-087X\")), person(\"Toby\",\"Hocking\", role=\"aut\", email=\"toby.hocking@r-project.org\", comment = c(ORCID=\"0000-0002-3146-0865\")), person(\"Benjamin\",\"Schwendinger\",role=\"aut\", comment = c(ORCID=\"0000-0003-3315-8114\")), person(\"Ivan\", \"Krylov\", role=\"aut\", email=\"ikrylov@disroot.org\", comment = c(ORCID=\"0000-0002-0172-3812\")), person(\"Pasha\",\"Stetsenko\", role=\"ctb\"), person(\"Tom\",\"Short\", role=\"ctb\"), person(\"Steve\",\"Lianoglou\", role=\"ctb\"), person(\"Eduard\",\"Antonyan\", role=\"ctb\"), person(\"Markus\",\"Bonsch\", role=\"ctb\"), person(\"Hugh\",\"Parsonage\", role=\"ctb\"), person(\"Scott\",\"Ritchie\", role=\"ctb\"), person(\"Kun\",\"Ren\", role=\"ctb\"), person(\"Xianying\",\"Tan\", role=\"ctb\"), person(\"Rick\",\"Saporta\", role=\"ctb\"), person(\"Otto\",\"Seiskari\", role=\"ctb\"), person(\"Xianghui\",\"Dong\", role=\"ctb\"), person(\"Michel\",\"Lang\", role=\"ctb\"), person(\"Watal\",\"Iwasaki\", role=\"ctb\"), person(\"Seth\",\"Wenchel\", role=\"ctb\"), person(\"Karl\",\"Broman\", role=\"ctb\"), person(\"Tobias\",\"Schmidt\", role=\"ctb\"), person(\"David\",\"Arenburg\", role=\"ctb\"), person(\"Ethan\",\"Smith\", role=\"ctb\"), person(\"Francois\",\"Cocquemas\", role=\"ctb\"), person(\"Matthieu\",\"Gomez\", role=\"ctb\"), person(\"Philippe\",\"Chataignon\", role=\"ctb\"), person(\"Nello\",\"Blaser\", role=\"ctb\"), person(\"Dmitry\",\"Selivanov\", role=\"ctb\"), person(\"Andrey\",\"Riabushenko\", role=\"ctb\"), person(\"Cheng\",\"Lee\", role=\"ctb\"), person(\"Declan\",\"Groves\", role=\"ctb\"), person(\"Daniel\",\"Possenriede\", role=\"ctb\"), person(\"Felipe\",\"Parages\", role=\"ctb\"), person(\"Denes\",\"Toth\", role=\"ctb\"), person(\"Mus\",\"Yaramaz-David\", role=\"ctb\"), person(\"Ayappan\",\"Perumal\", role=\"ctb\"), person(\"James\",\"Sams\", role=\"ctb\"), person(\"Martin\",\"Morgan\", role=\"ctb\"), person(\"Michael\",\"Quinn\", role=\"ctb\"), person(given=\"@javrucebo\", role=\"ctb\", comment=\"GitHub user\"), person(\"Marc\",\"Halperin\", role=\"ctb\"), person(\"Roy\",\"Storey\", role=\"ctb\"), person(\"Manish\",\"Saraswat\", role=\"ctb\"), person(\"Morgan\",\"Jacob\", role=\"ctb\"), person(\"Michael\",\"Schubmehl\", role=\"ctb\"), person(\"Davis\",\"Vaughan\", role=\"ctb\"), person(\"Leonardo\",\"Silvestri\", role=\"ctb\"), person(\"Jim\",\"Hester\", role=\"ctb\"), person(\"Anthony\",\"Damico\", role=\"ctb\"), person(\"Sebastian\",\"Freundt\", role=\"ctb\"), person(\"David\",\"Simons\", role=\"ctb\"), person(\"Elliott\",\"Sales de Andrade\", role=\"ctb\"), person(\"Cole\",\"Miller\", role=\"ctb\"), person(\"Jens Peder\",\"Meldgaard\", role=\"ctb\"), person(\"Vaclav\",\"Tlapak\", role=\"ctb\"), person(\"Kevin\",\"Ushey\", role=\"ctb\"), person(\"Dirk\",\"Eddelbuettel\", role=\"ctb\"), person(\"Tony\",\"Fischetti\", role=\"ctb\"), person(\"Ofek\",\"Shilon\", role=\"ctb\"), person(\"Vadim\",\"Khotilovich\", role=\"ctb\"), person(\"Hadley\",\"Wickham\", role=\"ctb\"), person(\"Bennet\",\"Becker\", role=\"ctb\"), person(\"Kyle\",\"Haynes\", role=\"ctb\"), person(\"Boniface Christian\",\"Kamgang\", role=\"ctb\"), person(\"Olivier\",\"Delmarcell\", role=\"ctb\"), person(\"Josh\",\"O'Brien\", role=\"ctb\"), person(\"Dereck\",\"de Mezquita\", role=\"ctb\"), person(\"Michael\",\"Czekanski\", role=\"ctb\"), person(\"Dmitry\", \"Shemetov\", role=\"ctb\"), person(\"Nitish\", \"Jha\", role=\"ctb\"), person(\"Joshua\", \"Wu\", role=\"ctb\"), person(\"Iago\", \"Giné-Vázquez\", role=\"ctb\"), person(\"Anirban\", \"Chetia\", role=\"ctb\"), person(\"Doris\", \"Amoakohene\", role=\"ctb\"), person(\"Angel\", \"Feliz\", role=\"ctb\"), person(\"Michael\",\"Young\", role=\"ctb\"), person(\"Mark\", \"Seeto\", role=\"ctb\"), person(\"Philippe\", \"Grosjean\", role=\"ctb\"), person(\"Vincent\", \"Runge\", role=\"ctb\"), person(\"Christian\", \"Wia\", role=\"ctb\"), person(\"Elise\", \"Maigné\", role=\"ctb\"), person(\"Vincent\", \"Rocher\", role=\"ctb\"), person(\"Vijay\", \"Lulla\", role=\"ctb\"), person(\"Aljaž\", \"Sluga\", role=\"ctb\"), person(\"Bill\", \"Evans\", role=\"ctb\"), person(\"Reino\", \"Bruner\", role=\"ctb\"), person(given=\"@badasahog\", role=\"ctb\", comment=\"GitHub user\"), person(\"Vinit\", \"Thakur\", role=\"ctb\"), person(\"Mukul\", \"Kumar\", role=\"ctb\"), person(\"Ildikó\", \"Czeller\", role=\"ctb\"), person(\"Manmita\", \"Das\", role=\"ctb\"), person(\"Tarun\", \"Thammisetty\", role=\"ctb\") )",
+ "NeedsCompilation": "yes",
+ "Author": "Tyson Barrett [aut, cre] (ORCID: ), Matt Dowle [aut], Arun Srinivasan [aut], Jan Gorecki [aut], Michael Chirico [aut] (ORCID: ), Toby Hocking [aut] (ORCID: ), Benjamin Schwendinger [aut] (ORCID: ), Ivan Krylov [aut] (ORCID: ), Pasha Stetsenko [ctb], Tom Short [ctb], Steve Lianoglou [ctb], Eduard Antonyan [ctb], Markus Bonsch [ctb], Hugh Parsonage [ctb], Scott Ritchie [ctb], Kun Ren [ctb], Xianying Tan [ctb], Rick Saporta [ctb], Otto Seiskari [ctb], Xianghui Dong [ctb], Michel Lang [ctb], Watal Iwasaki [ctb], Seth Wenchel [ctb], Karl Broman [ctb], Tobias Schmidt [ctb], David Arenburg [ctb], Ethan Smith [ctb], Francois Cocquemas [ctb], Matthieu Gomez [ctb], Philippe Chataignon [ctb], Nello Blaser [ctb], Dmitry Selivanov [ctb], Andrey Riabushenko [ctb], Cheng Lee [ctb], Declan Groves [ctb], Daniel Possenriede [ctb], Felipe Parages [ctb], Denes Toth [ctb], Mus Yaramaz-David [ctb], Ayappan Perumal [ctb], James Sams [ctb], Martin Morgan [ctb], Michael Quinn [ctb], @javrucebo [ctb] (GitHub user), Marc Halperin [ctb], Roy Storey [ctb], Manish Saraswat [ctb], Morgan Jacob [ctb], Michael Schubmehl [ctb], Davis Vaughan [ctb], Leonardo Silvestri [ctb], Jim Hester [ctb], Anthony Damico [ctb], Sebastian Freundt [ctb], David Simons [ctb], Elliott Sales de Andrade [ctb], Cole Miller [ctb], Jens Peder Meldgaard [ctb], Vaclav Tlapak [ctb], Kevin Ushey [ctb], Dirk Eddelbuettel [ctb], Tony Fischetti [ctb], Ofek Shilon [ctb], Vadim Khotilovich [ctb], Hadley Wickham [ctb], Bennet Becker [ctb], Kyle Haynes [ctb], Boniface Christian Kamgang [ctb], Olivier Delmarcell [ctb], Josh O'Brien [ctb], Dereck de Mezquita [ctb], Michael Czekanski [ctb], Dmitry Shemetov [ctb], Nitish Jha [ctb], Joshua Wu [ctb], Iago Giné-Vázquez [ctb], Anirban Chetia [ctb], Doris Amoakohene [ctb], Angel Feliz [ctb], Michael Young [ctb], Mark Seeto [ctb], Philippe Grosjean [ctb], Vincent Runge [ctb], Christian Wia [ctb], Elise Maigné [ctb], Vincent Rocher [ctb], Vijay Lulla [ctb], Aljaž Sluga [ctb], Bill Evans [ctb], Reino Bruner [ctb], @badasahog [ctb] (GitHub user), Vinit Thakur [ctb], Mukul Kumar [ctb], Ildikó Czeller [ctb], Manmita Das [ctb], Tarun Thammisetty [ctb]",
+ "Maintainer": "Tyson Barrett ",
+ "Repository": "https://packagemanager.posit.co/cran/latest"
},
"deSolve": {
"Package": "deSolve",
@@ -2257,7 +2966,8 @@
"URL": "https://github.com/tpetzoldt/deSolve/",
"LazyData": "yes",
"NeedsCompilation": "yes",
- "Repository": "CRAN"
+ "Repository": "RSPM",
+ "Encoding": "UTF-8"
},
"desc": {
"Package": "desc",
@@ -2382,6 +3092,92 @@
"Maintainer": "Dirk Eddelbuettel ",
"Repository": "CRAN"
},
+ "distributional": {
+ "Package": "distributional",
+ "Version": "0.6.0",
+ "Source": "Repository",
+ "Title": "Vectorised Probability Distributions",
+ "Authors@R": "c(person(given = \"Mitchell\", family = \"O'Hara-Wild\", role = c(\"aut\", \"cre\"), email = \"mail@mitchelloharawild.com\", comment = c(ORCID = \"0000-0001-6729-7695\")), person(given = \"Matthew\", family = \"Kay\", role = c(\"aut\"), comment = c(ORCID = \"0000-0001-9446-0419\")), person(given = \"Alex\", family = \"Hayes\", role = c(\"aut\"), comment = c(ORCID = \"0000-0002-4985-5160\")), person(given = \"Rob\", family = \"Hyndman\", role = c(\"aut\"), comment = c(ORCID = \"0000-0002-2140-5352\")), person(given = \"Earo\", family = \"Wang\", role = c(\"ctb\"), comment = c(ORCID = \"0000-0001-6448-5260\")), person(given = \"Vencislav\", family = \"Popov\", role = c(\"ctb\"), comment = c(ORCID = \"0000-0002-8073-4199\")))",
+ "Description": "Vectorised distribution objects with tools for manipulating, visualising, and using probability distributions. Designed to allow model prediction outputs to return distributions rather than their parameters, allowing users to directly interact with predictive distributions in a data-oriented workflow. In addition to providing generic replacements for p/d/q/r functions, other useful statistics can be computed including means, variances, intervals, and highest density regions.",
+ "License": "GPL-3",
+ "Depends": [
+ "R (>= 4.0.0)"
+ ],
+ "Imports": [
+ "vctrs (>= 0.3.0)",
+ "rlang (>= 0.4.5)",
+ "generics",
+ "stats",
+ "numDeriv",
+ "utils",
+ "lifecycle",
+ "pillar"
+ ],
+ "Suggests": [
+ "testthat (>= 2.1.0)",
+ "covr",
+ "mvtnorm",
+ "actuar (>= 2.0.0)",
+ "evd",
+ "ggdist",
+ "ggplot2",
+ "gk",
+ "pkgdown"
+ ],
+ "RdMacros": "lifecycle",
+ "URL": "https://pkg.mitchelloharawild.com/distributional/, https://github.com/mitchelloharawild/distributional",
+ "BugReports": "https://github.com/mitchelloharawild/distributional/issues",
+ "Encoding": "UTF-8",
+ "Language": "en-GB",
+ "RoxygenNote": "7.3.3",
+ "NeedsCompilation": "no",
+ "Author": "Mitchell O'Hara-Wild [aut, cre] (ORCID: ), Matthew Kay [aut] (ORCID: ), Alex Hayes [aut] (ORCID: ), Rob Hyndman [aut] (ORCID: ), Earo Wang [ctb] (ORCID: ), Vencislav Popov [ctb] (ORCID: )",
+ "Maintainer": "Mitchell O'Hara-Wild ",
+ "Repository": "https://packagemanager.posit.co/cran/latest"
+ },
+ "distributional": {
+ "Package": "distributional",
+ "Version": "0.6.0",
+ "Source": "Repository",
+ "Title": "Vectorised Probability Distributions",
+ "Authors@R": "c(person(given = \"Mitchell\", family = \"O'Hara-Wild\", role = c(\"aut\", \"cre\"), email = \"mail@mitchelloharawild.com\", comment = c(ORCID = \"0000-0001-6729-7695\")), person(given = \"Matthew\", family = \"Kay\", role = c(\"aut\"), comment = c(ORCID = \"0000-0001-9446-0419\")), person(given = \"Alex\", family = \"Hayes\", role = c(\"aut\"), comment = c(ORCID = \"0000-0002-4985-5160\")), person(given = \"Rob\", family = \"Hyndman\", role = c(\"aut\"), comment = c(ORCID = \"0000-0002-2140-5352\")), person(given = \"Earo\", family = \"Wang\", role = c(\"ctb\"), comment = c(ORCID = \"0000-0001-6448-5260\")), person(given = \"Vencislav\", family = \"Popov\", role = c(\"ctb\"), comment = c(ORCID = \"0000-0002-8073-4199\")))",
+ "Description": "Vectorised distribution objects with tools for manipulating, visualising, and using probability distributions. Designed to allow model prediction outputs to return distributions rather than their parameters, allowing users to directly interact with predictive distributions in a data-oriented workflow. In addition to providing generic replacements for p/d/q/r functions, other useful statistics can be computed including means, variances, intervals, and highest density regions.",
+ "License": "GPL-3",
+ "Depends": [
+ "R (>= 4.0.0)"
+ ],
+ "Imports": [
+ "vctrs (>= 0.3.0)",
+ "rlang (>= 0.4.5)",
+ "generics",
+ "stats",
+ "numDeriv",
+ "utils",
+ "lifecycle",
+ "pillar"
+ ],
+ "Suggests": [
+ "testthat (>= 2.1.0)",
+ "covr",
+ "mvtnorm",
+ "actuar (>= 2.0.0)",
+ "evd",
+ "ggdist",
+ "ggplot2",
+ "gk",
+ "pkgdown"
+ ],
+ "RdMacros": "lifecycle",
+ "URL": "https://pkg.mitchelloharawild.com/distributional/, https://github.com/mitchelloharawild/distributional",
+ "BugReports": "https://github.com/mitchelloharawild/distributional/issues",
+ "Encoding": "UTF-8",
+ "Language": "en-GB",
+ "RoxygenNote": "7.3.3",
+ "NeedsCompilation": "no",
+ "Author": "Mitchell O'Hara-Wild [aut, cre] (ORCID: ), Matthew Kay [aut] (ORCID: ), Alex Hayes [aut] (ORCID: ), Rob Hyndman [aut] (ORCID: ), Earo Wang [ctb] (ORCID: ), Vencislav Popov [ctb] (ORCID: )",
+ "Maintainer": "Mitchell O'Hara-Wild ",
+ "Repository": "https://packagemanager.posit.co/cran/latest"
+ },
"doBy": {
"Package": "doBy",
"Version": "4.7.1",
@@ -2410,7 +3206,8 @@
"MASS",
"Matrix",
"modelr",
- "microbenchmark",
+ "purrr",
+ "R",
"rlang",
"purrr",
"tibble",
@@ -2490,7 +3287,7 @@
"NeedsCompilation": "yes",
"Author": "Hadley Wickham [aut, cre] (ORCID: ), Romain François [aut] (ORCID: ), Lionel Henry [aut], Kirill Müller [aut] (ORCID: ), Davis Vaughan [aut] (ORCID: ), Posit Software, PBC [cph, fnd]",
"Maintainer": "Hadley Wickham ",
- "Repository": "RSPM"
+ "Repository": "https://p3m.dev/cran/latest"
},
"elliptic": {
"Package": "elliptic",
@@ -2583,57 +3380,153 @@
"Maintainer": "Hadley Wickham ",
"Repository": "CRAN"
},
- "farver": {
- "Package": "farver",
- "Version": "2.1.2",
+ "evaluate": {
+ "Package": "evaluate",
+ "Version": "1.0.5",
"Source": "Repository",
"Type": "Package",
- "Title": "High Performance Colour Space Manipulation",
- "Authors@R": "c( person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Berendea\", \"Nicolae\", role = \"aut\", comment = \"Author of the ColorSpace C++ library\"), person(\"Romain\", \"François\", , \"romain@purrple.cat\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )",
- "Description": "The encoding of colour can be handled in many different ways, using different colour spaces. As different colour spaces have different uses, efficient conversion between these representations are important. The 'farver' package provides a set of functions that gives access to very fast colour space conversion and comparisons implemented in C++, and offers speed improvements over the 'convertColor' function in the 'grDevices' package.",
+ "Title": "Parsing and Evaluation Tools that Provide More Details than the Default",
+ "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Yihui\", \"Xie\", role = \"aut\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Michael\", \"Lawrence\", role = \"ctb\"), person(\"Thomas\", \"Kluyver\", role = \"ctb\"), person(\"Jeroen\", \"Ooms\", role = \"ctb\"), person(\"Barret\", \"Schloerke\", role = \"ctb\"), person(\"Adam\", \"Ryczkowski\", role = \"ctb\"), person(\"Hiroaki\", \"Yutani\", role = \"ctb\"), person(\"Michel\", \"Lang\", role = \"ctb\"), person(\"Karolis\", \"Koncevičius\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
+ "Description": "Parsing and evaluation tools that make it easy to recreate the command line behaviour of R.",
"License": "MIT + file LICENSE",
- "URL": "https://farver.data-imaginist.com, https://github.com/thomasp85/farver",
- "BugReports": "https://github.com/thomasp85/farver/issues",
+ "URL": "https://evaluate.r-lib.org/, https://github.com/r-lib/evaluate",
+ "BugReports": "https://github.com/r-lib/evaluate/issues",
+ "Depends": [
+ "R (>= 3.6.0)"
+ ],
"Suggests": [
+ "callr",
"covr",
- "testthat (>= 3.0.0)"
+ "ggplot2 (>= 3.3.6)",
+ "lattice",
+ "methods",
+ "pkgload",
+ "ragg (>= 1.4.0)",
+ "rlang (>= 1.1.5)",
+ "knitr",
+ "testthat (>= 3.0.0)",
+ "withr"
],
+ "Config/Needs/website": "tidyverse/tidytemplate",
"Config/testthat/edition": "3",
"Encoding": "UTF-8",
- "RoxygenNote": "7.3.1",
- "NeedsCompilation": "yes",
- "Author": "Thomas Lin Pedersen [cre, aut] (), Berendea Nicolae [aut] (Author of the ColorSpace C++ library), Romain François [aut] (), Posit, PBC [cph, fnd]",
- "Maintainer": "Thomas Lin Pedersen ",
+ "RoxygenNote": "7.3.2",
+ "NeedsCompilation": "no",
+ "Author": "Hadley Wickham [aut, cre], Yihui Xie [aut] (ORCID: ), Michael Lawrence [ctb], Thomas Kluyver [ctb], Jeroen Ooms [ctb], Barret Schloerke [ctb], Adam Ryczkowski [ctb], Hiroaki Yutani [ctb], Michel Lang [ctb], Karolis Koncevičius [ctb], Posit Software, PBC [cph, fnd]",
+ "Maintainer": "Hadley Wickham ",
"Repository": "CRAN"
},
- "fastGHQuad": {
- "Package": "fastGHQuad",
- "Version": "1.0.1",
+ "extraDistr": {
+ "Package": "extraDistr",
+ "Version": "1.10.0.2",
"Source": "Repository",
"Type": "Package",
- "Title": "Fast 'Rcpp' Implementation of Gauss-Hermite Quadrature",
- "Date": "2022-05-03",
- "Author": "Alexander W Blocker",
- "Maintainer": "Alexander W Blocker ",
- "Description": "Fast, numerically-stable Gauss-Hermite quadrature rules and utility functions for adaptive GH quadrature. See Liu, Q. and Pierce, D. A. (1994) for a reference on these methods.",
- "License": "MIT + file LICENSE",
- "LazyLoad": "yes",
- "URL": "https://github.com/awblocker/fastGHQuad",
+ "Title": "Additional Univariate and Multivariate Distributions",
+ "Date": "2026-01-19",
+ "Authors@R": "c(person(given = \"Tymoteusz\", family = \"Wolodzko\", role = \"aut\", email = \"twolodzko+extradistr@gmail.com\"), person(given = \"Sigbert\", family = \"Klinke\", role = \"cre\", email = \"sigbert@wiwi.hu-berlin.de\"))",
+ "Description": "Density, distribution function, quantile function and random generation for a number of univariate and multivariate distributions. This package implements the following distributions: Bernoulli, beta-binomial, beta-negative binomial, beta prime, Bhattacharjee, Birnbaum-Saunders, bivariate normal, bivariate Poisson, categorical, Dirichlet, Dirichlet-multinomial, discrete gamma, discrete Laplace, discrete normal, discrete uniform, discrete Weibull, Frechet, gamma-Poisson, generalized extreme value, Gompertz, generalized Pareto, Gumbel, half-Cauchy, half-normal, half-t, Huber density, inverse chi-squared, inverse-gamma, Kumaraswamy, Laplace, location-scale t, logarithmic, Lomax, multivariate hypergeometric, multinomial, negative hypergeometric, non-standard beta, normal mixture, Poisson mixture, Pareto, power, reparametrized beta, Rayleigh, shifted Gompertz, Skellam, slash, triangular, truncated binomial, truncated normal, truncated Poisson, Tukey lambda, Wald, zero-inflated binomial, zero-inflated negative binomial, zero-inflated Poisson.",
+ "License": "GPL-2",
+ "URL": "https://github.com/sigbertklinke/extraDistr",
+ "Encoding": "UTF-8",
"Depends": [
- "Rcpp (>= 0.11.0)"
+ "R (>= 3.1.0)"
],
"LinkingTo": [
+ "Rcpp",
+ "RcppArmadillo"
+ ],
+ "Imports": [
"Rcpp"
],
+ "Suggests": [
+ "testthat",
+ "LaplacesDemon",
+ "VGAM",
+ "evd",
+ "skellam",
+ "triangle",
+ "actuar"
+ ],
+ "RoxygenNote": "7.3.3",
"NeedsCompilation": "yes",
- "Repository": "CRAN"
+ "Author": "Tymoteusz Wolodzko [aut], Sigbert Klinke [cre]",
+ "Maintainer": "Sigbert Klinke ",
+ "Repository": "https://packagemanager.posit.co/cran/latest"
},
- "fastmap": {
- "Package": "fastmap",
- "Version": "1.2.0",
+ "extraDistr": {
+ "Package": "extraDistr",
+ "Version": "1.10.0.2",
"Source": "Repository",
- "Title": "Fast Data Structures",
- "Authors@R": "c( person(\"Winston\", \"Chang\", email = \"winston@posit.co\", role = c(\"aut\", \"cre\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(given = \"Tessil\", role = \"cph\", comment = \"hopscotch_map library\") )",
+ "Type": "Package",
+ "Title": "Additional Univariate and Multivariate Distributions",
+ "Date": "2026-01-19",
+ "Authors@R": "c(person(given = \"Tymoteusz\", family = \"Wolodzko\", role = \"aut\", email = \"twolodzko+extradistr@gmail.com\"), person(given = \"Sigbert\", family = \"Klinke\", role = \"cre\", email = \"sigbert@wiwi.hu-berlin.de\"))",
+ "Description": "Density, distribution function, quantile function and random generation for a number of univariate and multivariate distributions. This package implements the following distributions: Bernoulli, beta-binomial, beta-negative binomial, beta prime, Bhattacharjee, Birnbaum-Saunders, bivariate normal, bivariate Poisson, categorical, Dirichlet, Dirichlet-multinomial, discrete gamma, discrete Laplace, discrete normal, discrete uniform, discrete Weibull, Frechet, gamma-Poisson, generalized extreme value, Gompertz, generalized Pareto, Gumbel, half-Cauchy, half-normal, half-t, Huber density, inverse chi-squared, inverse-gamma, Kumaraswamy, Laplace, location-scale t, logarithmic, Lomax, multivariate hypergeometric, multinomial, negative hypergeometric, non-standard beta, normal mixture, Poisson mixture, Pareto, power, reparametrized beta, Rayleigh, shifted Gompertz, Skellam, slash, triangular, truncated binomial, truncated normal, truncated Poisson, Tukey lambda, Wald, zero-inflated binomial, zero-inflated negative binomial, zero-inflated Poisson.",
+ "License": "GPL-2",
+ "URL": "https://github.com/sigbertklinke/extraDistr",
+ "Encoding": "UTF-8",
+ "Depends": [
+ "R (>= 3.1.0)"
+ ],
+ "LinkingTo": [
+ "Rcpp",
+ "RcppArmadillo"
+ ],
+ "Imports": [
+ "Rcpp"
+ ],
+ "Suggests": [
+ "testthat",
+ "LaplacesDemon",
+ "VGAM",
+ "evd",
+ "skellam",
+ "triangle",
+ "actuar"
+ ],
+ "RoxygenNote": "7.3.3",
+ "NeedsCompilation": "yes",
+ "Author": "Tymoteusz Wolodzko [aut], Sigbert Klinke [cre]",
+ "Maintainer": "Sigbert Klinke ",
+ "Repository": "https://packagemanager.posit.co/cran/latest"
+ },
+ "farver": {
+ "Package": "farver",
+ "Version": "2.1.2",
+ "Source": "Repository",
+ "Type": "Package",
+ "Title": "High Performance Colour Space Manipulation",
+ "Authors@R": "c( person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Berendea\", \"Nicolae\", role = \"aut\", comment = \"Author of the ColorSpace C++ library\"), person(\"Romain\", \"François\", , \"romain@purrple.cat\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )",
+ "Description": "The encoding of colour can be handled in many different ways, using different colour spaces. As different colour spaces have different uses, efficient conversion between these representations are important. The 'farver' package provides a set of functions that gives access to very fast colour space conversion and comparisons implemented in C++, and offers speed improvements over the 'convertColor' function in the 'grDevices' package.",
+ "License": "MIT + file LICENSE",
+ "URL": "https://farver.data-imaginist.com, https://github.com/thomasp85/farver",
+ "BugReports": "https://github.com/thomasp85/farver/issues",
+ "Suggests": [
+ "covr",
+ "testthat (>= 3.0.0)"
+ ],
+ "Config/testthat/edition": "3",
+ "Encoding": "UTF-8",
+ "RoxygenNote": "7.3.1",
+ "NeedsCompilation": "yes",
+ "Author": "Thomas Lin Pedersen [cre, aut] (), Berendea Nicolae [aut] (Author of the ColorSpace C++ library), Romain François [aut] (), Posit, PBC [cph, fnd]",
+ "Maintainer": "Thomas Lin Pedersen ",
+ "Repository": "CRAN"
+ },
+ "fastGHQuad": {
+ "Package": "fastGHQuad",
+ "Version": "1.0.1",
+ "Source": "Repository",
+ "Requirements": [
+ "Rcpp"
+ ]
+ },
+ "fastmap": {
+ "Package": "fastmap",
+ "Version": "1.2.0",
+ "Source": "Repository",
+ "Title": "Fast Data Structures",
+ "Authors@R": "c( person(\"Winston\", \"Chang\", email = \"winston@posit.co\", role = c(\"aut\", \"cre\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(given = \"Tessil\", role = \"cph\", comment = \"hopscotch_map library\") )",
"Description": "Fast implementation of data structures, including a key-value store, stack, and queue. Environments are commonly used as key-value stores in R, but every time a new key is used, it is added to R's global symbol table, causing a small amount of memory leakage. This can be problematic in cases where many different keys are used. Fastmap avoids this memory leak issue by implementing the map using data structures in C++.",
"License": "MIT + file LICENSE",
"Encoding": "UTF-8",
@@ -2740,74 +3633,36 @@
"RemoteType": "github",
"RemoteUsername": "dustinfife",
"RemoteRepo": "flexplot",
- "RemoteRef": "master",
- "RemoteSha": "cae36ba45502ce1794ad35cfeaf0155275db3056",
- "RemoteHost": "api.github.com"
+ "RemoteSha": "cae36ba45502ce1794ad35cfeaf0155275db3056"
},
"flexsurv": {
"Package": "flexsurv",
"Version": "2.3.2",
"Source": "Repository",
- "Type": "Package",
- "Title": "Flexible Parametric Survival and Multi-State Models",
- "Date": "2024-08-16",
- "Authors@R": "c(person(\"Christopher\", \"Jackson\", email=\"chris.jackson@mrc-bsu.cam.ac.uk\", role=c(\"aut\", \"cre\")), person(\"Paul\", \"Metcalfe\", role=c(\"ctb\")), person(\"Jordan\", \"Amdahl\", role=c(\"ctb\")), person(\"Matthew T.\", \"Warkentin\", role = c(\"ctb\")), person(\"Michael\", \"Sweeting\", role = c(\"ctb\")), person(\"Kevin\", \"Kunzmann\", role = c(\"ctb\")) )",
- "Description": "Flexible parametric models for time-to-event data, including the Royston-Parmar spline model, generalized gamma and generalized F distributions. Any user-defined parametric distribution can be fitted, given at least an R function defining the probability density or hazard. There are also tools for fitting and predicting from fully parametric multi-state models, based on either cause-specific hazards or mixture models.",
- "License": "GPL (>= 2)",
- "Depends": [
- "survival",
- "R (>= 2.15.0)"
- ],
- "Imports": [
+ "Requirements": [
"assertthat",
"deSolve",
+ "dplyr",
"generics",
+ "ggplot2",
"magrittr",
- "mstate (>= 0.2.10)",
"Matrix",
+ "mstate",
"muhaz",
"mvtnorm",
"numDeriv",
+ "purrr",
"quadprog",
- "Rcpp (>= 0.11.5)",
+ "R",
+ "Rcpp",
"rlang",
"rstpm2",
- "purrr",
"statmod",
+ "survival",
"tibble",
"tidyr",
- "dplyr",
- "tidyselect",
- "ggplot2"
- ],
- "Encoding": "UTF-8",
- "Suggests": [
- "splines2",
- "flexsurvcure",
- "survminer",
- "lubridate",
- "rmarkdown",
- "colorspace",
- "eha",
- "knitr",
- "msm",
- "testthat",
- "TH.data",
- "broom",
- "covr"
- ],
- "URL": "https://github.com/chjackson/flexsurv, http://chjackson.github.io/flexsurv/",
- "BugReports": "https://github.com/chjackson/flexsurv/issues",
- "VignetteBuilder": "knitr",
- "LazyData": "yes",
- "LinkingTo": [
- "Rcpp"
- ],
- "RoxygenNote": "7.3.1",
- "NeedsCompilation": "yes",
- "Author": "Christopher Jackson [aut, cre], Paul Metcalfe [ctb], Jordan Amdahl [ctb], Matthew T. Warkentin [ctb], Michael Sweeting [ctb], Kevin Kunzmann [ctb]",
- "Maintainer": "Christopher Jackson ",
- "Repository": "CRAN"
+ "tidyselect"
+ ]
},
"fontBitstreamVera": {
"Package": "fontBitstreamVera",
@@ -2884,6 +3739,41 @@
"Maintainer": "Richard Iannone ",
"Repository": "CRAN"
},
+ "fontawesome": {
+ "Package": "fontawesome",
+ "Version": "0.5.3",
+ "Source": "Repository",
+ "Type": "Package",
+ "Title": "Easily Work with 'Font Awesome' Icons",
+ "Description": "Easily and flexibly insert 'Font Awesome' icons into 'R Markdown' documents and 'Shiny' apps. These icons can be inserted into HTML content through inline 'SVG' tags or 'i' tags. There is also a utility function for exporting 'Font Awesome' icons as 'PNG' images for those situations where raster graphics are needed.",
+ "Authors@R": "c( person(\"Richard\", \"Iannone\", , \"rich@posit.co\", c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-3925-190X\")), person(\"Christophe\", \"Dervieux\", , \"cderv@posit.co\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4474-2498\")), person(\"Winston\", \"Chang\", , \"winston@posit.co\", role = \"ctb\"), person(\"Dave\", \"Gandy\", role = c(\"ctb\", \"cph\"), comment = \"Font-Awesome font\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
+ "License": "MIT + file LICENSE",
+ "URL": "https://github.com/rstudio/fontawesome, https://rstudio.github.io/fontawesome/",
+ "BugReports": "https://github.com/rstudio/fontawesome/issues",
+ "Encoding": "UTF-8",
+ "ByteCompile": "true",
+ "RoxygenNote": "7.3.2",
+ "Depends": [
+ "R (>= 3.3.0)"
+ ],
+ "Imports": [
+ "rlang (>= 1.0.6)",
+ "htmltools (>= 0.5.1.1)"
+ ],
+ "Suggests": [
+ "covr",
+ "dplyr (>= 1.0.8)",
+ "gt (>= 0.9.0)",
+ "knitr (>= 1.31)",
+ "testthat (>= 3.0.0)",
+ "rsvg"
+ ],
+ "Config/testthat/edition": "3",
+ "NeedsCompilation": "no",
+ "Author": "Richard Iannone [aut, cre] (), Christophe Dervieux [ctb] (), Winston Chang [ctb], Dave Gandy [ctb, cph] (Font-Awesome font), Posit Software, PBC [cph, fnd]",
+ "Maintainer": "Richard Iannone ",
+ "Repository": "CRAN"
+ },
"fontquiver": {
"Package": "fontquiver",
"Version": "0.2.1",
@@ -3040,6 +3930,36 @@
"Maintainer": "R Core Team ",
"Repository": "CRAN"
},
+ "foreign": {
+ "Package": "foreign",
+ "Version": "0.8-90",
+ "Source": "Repository",
+ "Priority": "recommended",
+ "Date": "2025-03-31",
+ "Title": "Read Data Stored by 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', 'dBase', ...",
+ "Depends": [
+ "R (>= 4.0.0)"
+ ],
+ "Imports": [
+ "methods",
+ "utils",
+ "stats"
+ ],
+ "Authors@R": "c( person(\"R Core Team\", email = \"R-core@R-project.org\", role = c(\"aut\", \"cph\", \"cre\"), comment = c(ROR = \"02zz1nj61\")), person(\"Roger\", \"Bivand\", role = c(\"ctb\", \"cph\")), person(c(\"Vincent\", \"J.\"), \"Carey\", role = c(\"ctb\", \"cph\")), person(\"Saikat\", \"DebRoy\", role = c(\"ctb\", \"cph\")), person(\"Stephen\", \"Eglen\", role = c(\"ctb\", \"cph\")), person(\"Rajarshi\", \"Guha\", role = c(\"ctb\", \"cph\")), person(\"Swetlana\", \"Herbrandt\", role = \"ctb\"), person(\"Nicholas\", \"Lewin-Koh\", role = c(\"ctb\", \"cph\")), person(\"Mark\", \"Myatt\", role = c(\"ctb\", \"cph\")), person(\"Michael\", \"Nelson\", role = \"ctb\"), person(\"Ben\", \"Pfaff\", role = \"ctb\"), person(\"Brian\", \"Quistorff\", role = \"ctb\"), person(\"Frank\", \"Warmerdam\", role = c(\"ctb\", \"cph\")), person(\"Stephen\", \"Weigand\", role = c(\"ctb\", \"cph\")), person(\"Free Software Foundation, Inc.\", role = \"cph\"))",
+ "Contact": "see 'MailingList'",
+ "Copyright": "see file COPYRIGHTS",
+ "Description": "Reading and writing data stored by some versions of 'Epi Info', 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', and for reading and writing some 'dBase' files.",
+ "ByteCompile": "yes",
+ "Biarch": "yes",
+ "License": "GPL (>= 2)",
+ "BugReports": "https://bugs.r-project.org",
+ "MailingList": "R-help@r-project.org",
+ "URL": "https://svn.r-project.org/R-packages/trunk/foreign/",
+ "NeedsCompilation": "yes",
+ "Author": "R Core Team [aut, cph, cre] (02zz1nj61), Roger Bivand [ctb, cph], Vincent J. Carey [ctb, cph], Saikat DebRoy [ctb, cph], Stephen Eglen [ctb, cph], Rajarshi Guha [ctb, cph], Swetlana Herbrandt [ctb], Nicholas Lewin-Koh [ctb, cph], Mark Myatt [ctb, cph], Michael Nelson [ctb], Ben Pfaff [ctb], Brian Quistorff [ctb], Frank Warmerdam [ctb, cph], Stephen Weigand [ctb, cph], Free Software Foundation, Inc. [cph]",
+ "Maintainer": "R Core Team ",
+ "Repository": "CRAN"
+ },
"fracdiff": {
"Package": "fracdiff",
"Version": "1.5-4",
@@ -3106,7 +4026,49 @@
"NeedsCompilation": "yes",
"Author": "Jim Hester [aut], Hadley Wickham [aut], Gábor Csárdi [aut], Jeroen Ooms [cre], libuv project contributors [cph] (libuv library), Joyent, Inc. and other Node contributors [cph] (libuv library), Posit Software, PBC [cph, fnd] (ROR: )",
"Maintainer": "Jeroen Ooms ",
- "Repository": "RSPM"
+ "Repository": "https://packagemanager.posit.co/cran/latest"
+ },
+ "fs": {
+ "Package": "fs",
+ "Version": "2.1.0",
+ "Source": "Repository",
+ "Title": "Cross-Platform File System Operations Based on 'libuv'",
+ "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Hadley\", \"Wickham\", role = \"aut\"), person(\"Gábor\", \"Csárdi\", role = \"aut\"), person(\"Jeroen\", \"Ooms\", , \"jeroenooms@gmail.com\", role = \"cre\"), person(\"libuv project contributors\", role = \"cph\", comment = \"libuv library\"), person(\"Joyent, Inc. and other Node contributors\", role = \"cph\", comment = \"libuv library\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )",
+ "Description": "A cross-platform interface to file system operations, built on top of the 'libuv' C library.",
+ "License": "MIT + file LICENSE",
+ "URL": "https://fs.r-lib.org, https://github.com/r-lib/fs",
+ "BugReports": "https://github.com/r-lib/fs/issues",
+ "Depends": [
+ "R (>= 4.1)"
+ ],
+ "Imports": [
+ "methods"
+ ],
+ "Suggests": [
+ "covr",
+ "crayon",
+ "knitr",
+ "pillar (>= 1.0.0)",
+ "rmarkdown",
+ "spelling",
+ "testthat (>= 3.0.0)",
+ "tibble (>= 1.1.0)",
+ "vctrs (>= 0.3.0)",
+ "withr"
+ ],
+ "VignetteBuilder": "knitr",
+ "SystemRequirements": "libuv: libuv-devel (rpm) or libuv1-dev (deb). Alternatively to build the vendored libuv 'cmake' is required. GNU make.",
+ "Config/Needs/website": "tidyverse/tidytemplate",
+ "Config/testthat/edition": "3",
+ "Config/usethis/last-upkeep": "2025-04-23",
+ "Copyright": "file COPYRIGHTS",
+ "Encoding": "UTF-8",
+ "Language": "en-US",
+ "RoxygenNote": "7.3.3",
+ "NeedsCompilation": "yes",
+ "Author": "Jim Hester [aut], Hadley Wickham [aut], Gábor Csárdi [aut], Jeroen Ooms [cre], libuv project contributors [cph] (libuv library), Joyent, Inc. and other Node contributors [cph] (libuv library), Posit Software, PBC [cph, fnd] (ROR: )",
+ "Maintainer": "Jeroen Ooms ",
+ "Repository": "https://packagemanager.posit.co/cran/latest"
},
"gdtools": {
"Package": "gdtools",
@@ -3181,78 +4143,31 @@
"Package": "ggbeeswarm",
"Version": "0.7.3",
"Source": "Repository",
- "Type": "Package",
- "Title": "Categorical Scatter (Violin Point) Plots",
- "Date": "2025-11-28",
- "Authors@R": "c( person(given=\"Erik\", family=\"Clarke\", role=c(\"aut\", \"cre\"), email=\"erikclarke@gmail.com\"), person(given=\"Scott\", family=\"Sherrill-Mix\", role=c(\"aut\"), email=\"sherrillmix@gmail.com\"), person(given=\"Charlotte\", family=\"Dawson\", role=c(\"aut\"), email=\"csdaw@outlook.com\"))",
- "Description": "Provides two methods of plotting categorical scatter plots such that the arrangement of points within a category reflects the density of data at that region, and avoids over-plotting.",
- "URL": "https://github.com/eclarke/ggbeeswarm",
- "BugReports": "https://github.com/eclarke/ggbeeswarm/issues",
- "Encoding": "UTF-8",
- "License": "GPL (>= 3)",
- "Depends": [
- "R (>= 3.5.0)",
- "ggplot2 (>= 3.3.0)"
- ],
- "Imports": [
+ "Requirements": [
"beeswarm",
+ "cli",
+ "ggplot2",
"lifecycle",
- "vipor",
- "cli"
- ],
- "Suggests": [
- "gridExtra"
- ],
- "RoxygenNote": "7.3.3",
- "NeedsCompilation": "no",
- "Author": "Erik Clarke [aut, cre], Scott Sherrill-Mix [aut], Charlotte Dawson [aut]",
- "Maintainer": "Erik Clarke ",
- "Repository": "CRAN"
+ "R",
+ "vipor"
+ ]
},
"ggh4x": {
"Package": "ggh4x",
"Version": "0.3.1",
"Source": "Repository",
- "Title": "Hacks for 'ggplot2'",
- "Authors@R": "person(given = \"Teun\", family = \"van den Brand\", role = c(\"aut\", \"cre\"), email = \"tahvdbrand@gmail.com\", comment = c(ORCID = \"0000-0002-9335-7468\"))",
- "Description": "A 'ggplot2' extension that does a variety of little helpful things. The package extends 'ggplot2' facets through customisation, by setting individual scales per panel, resizing panels and providing nested facets. Also allows multiple colour and fill scales per plot. Also hosts a smaller collection of stats, geoms and axis guides.",
- "License": "MIT + file LICENSE",
- "URL": "https://github.com/teunbrand/ggh4x, https://teunbrand.github.io/ggh4x/",
- "BugReports": "https://github.com/teunbrand/ggh4x/issues",
- "Depends": [
- "ggplot2 (>= 3.5.2)"
- ],
- "Imports": [
+ "Requirements": [
+ "cli",
+ "ggplot2",
"grid",
"gtable",
- "scales",
- "vctrs (>= 0.5.0)",
- "rlang (>= 1.1.0)",
"lifecycle",
+ "rlang",
+ "S7",
+ "scales",
"stats",
- "cli",
- "S7"
- ],
- "Suggests": [
- "covr",
- "fitdistrplus",
- "ggdendro",
- "vdiffr",
- "knitr",
- "MASS",
- "rmarkdown",
- "testthat (>= 3.0.0)",
- "utils"
- ],
- "VignetteBuilder": "knitr",
- "Encoding": "UTF-8",
- "RoxygenNote": "7.3.2",
- "Config/testthat/edition": "3",
- "Collate": "'at_panel.R' 'borrowed_ggplot2.R' 'conveniences.R' 'ggh4x_extensions.R' 'coord_axes_inside.R' 'deprecated.R' 'element_part_rect.R' 'facet_grid2.R' 'facet_wrap2.R' 'facet_manual.R' 'facet_nested.R' 'facet_nested_wrap.R' 'facetted_pos_scales.R' 'force_panelsize.R' 'geom_box.R' 'geom_outline_point.R' 'geom_pointpath.R' 'geom_polygonraster.R' 'geom_rectrug.R' 'geom_text_aimed.R' 'ggh4x-package.R' 'guide_stringlegend.R' 'help_secondary.R' 'position_disjoint_ranges.R' 'position_lineartrans.R' 'scale_facet.R' 'scale_listed.R' 'scale_manual.R' 'scale_multi.R' 'stat_difference.R' 'stat_funxy.R' 'stat_rle.R' 'stat_roll.R' 'stat_theodensity.R' 'strip_vanilla.R' 'strip_themed.R' 'strip_nested.R' 'strip_split.R' 'strip_tag.R' 'themes.R' 'utils.R' 'utils_grid.R' 'utils_gtable.R'",
- "NeedsCompilation": "no",
- "Author": "Teun van den Brand [aut, cre] (ORCID: )",
- "Maintainer": "Teun van den Brand ",
- "Repository": "RSPM"
+ "vctrs"
+ ]
},
"ggplot2": {
"Package": "ggplot2",
@@ -3273,79 +4188,33 @@
"grid",
"gtable (>= 0.3.6)",
"isoband",
- "lifecycle (> 1.0.1)",
- "rlang (>= 1.1.0)",
+ "lifecycle",
+ "R",
+ "rlang",
"S7",
- "scales (>= 1.4.0)",
+ "scales",
"stats",
- "vctrs (>= 0.6.0)",
- "withr (>= 2.5.0)"
- ],
- "Suggests": [
- "broom",
- "covr",
- "dplyr",
- "ggplot2movies",
- "hexbin",
- "Hmisc",
- "hms",
- "knitr",
- "mapproj",
- "maps",
- "MASS",
- "mgcv",
- "multcomp",
- "munsell",
- "nlme",
- "profvis",
- "quantreg",
- "quarto",
- "ragg (>= 1.2.6)",
- "RColorBrewer",
- "roxygen2",
- "rpart",
- "sf (>= 0.7-3)",
- "svglite (>= 2.1.2)",
- "testthat (>= 3.1.5)",
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- "NeedsCompilation": "no",
- "Author": "Hadley Wickham [aut] (ORCID: ), Winston Chang [aut] (ORCID: ), Lionel Henry [aut], Thomas Lin Pedersen [aut, cre] (ORCID: ), Kohske Takahashi [aut], Claus Wilke [aut] (ORCID: ), Kara Woo [aut] (ORCID: ), Hiroaki Yutani [aut] (ORCID: ), Dewey Dunnington [aut] (ORCID: ), Teun van den Brand [aut] (ORCID: ), Posit, PBC [cph, fnd] (ROR: )",
- "Maintainer": "Thomas Lin Pedersen ",
- "Repository": "CRAN"
+ "vctrs",
+ "withr"
+ ]
},
"ggpp": {
"Package": "ggpp",
"Version": "0.6.0",
"Source": "Repository",
- "Type": "Package",
- "Title": "Grammar Extensions to 'ggplot2'",
- "Date": "2026-01-18",
- "Authors@R": "c( person(\"Pedro J.\", \"Aphalo\", email = \"pedro.aphalo@helsinki.fi\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-3385-972X\")), person(\"Kamil\", \"Slowikowski\", role = \"ctb\", comment = c(ORCID = \"0000-0002-2843-6370\")), person(\"Michał\", \"Krassowski\", role = \"ctb\", comment = c(ORCID = \"0000-0002-9638-7785\")), person(\"Daniel\", \"Sabanés Bové\", role = \"ctb\", comment = c(ORCID = \"0000-0002-0176-9239\")), person(\"Stella\", \"Banjo\", role = \"ctb\") )",
- "Maintainer": "Pedro J. Aphalo ",
- "Description": "Extensions to 'ggplot2' respecting the grammar of graphics paradigm. Geometries: geom_table(), geom_plot() and geom_grob() add insets to plots using native data coordinates, while geom_table_npc(), geom_plot_npc() and geom_grob_npc() do the same using \"npc\" coordinates through new aesthetics \"npcx\" and \"npcy\". Statistics: select observations based on 2D density. Positions: radial nudging away from a center point and nudging away from a line or curve; combined stacking and nudging; combined dodging and nudging.",
- "License": "GPL (>= 2)",
- "LazyData": "TRUE",
- "LazyLoad": "TRUE",
- "ByteCompile": "TRUE",
- "Depends": [
- "R (>= 4.1.0)",
- "ggplot2 (>= 3.5.0)"
- ],
- "Imports": [
+ "Requirements": [
+ "dplyr",
+ "ggplot2",
+ "glue",
+ "grDevices",
+ "grid",
+ "gridExtra",
+ "lubridate",
+ "MASS",
+ "polynom",
+ "R",
+ "rlang",
+ "scales",
"stats",
"grid",
"grDevices",
@@ -3432,22 +4301,67 @@
"NeedsCompilation": "no",
"Author": "Alboukadel Kassambara [aut, cre], Laszlo Erdey [ctb] (Faculty of Economics and Business, University of Debrecen, Hungary)",
"Maintainer": "Alboukadel Kassambara ",
- "Repository": "RSPM"
+ "Repository": "https://packagemanager.posit.co/cran/latest"
},
- "ggrain": {
- "Package": "ggrain",
- "Version": "0.1.2",
+ "ggpubr": {
+ "Package": "ggpubr",
+ "Version": "0.6.3",
"Source": "Repository",
- "Title": "A Rainclouds Geom for 'ggplot2'",
- "Authors@R": "c( person(\"Nicholas\", \"Judd\", , \"nickkjudd@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-0196-9871\")), person(\"Jordy\", \"van Langen\", , \"jordyvanlangen@gmail.com\", role = c(\"aut\"), comment = c(ORCID = \"0000-0003-2504-2381\")), person(\"Micah\", \"Allen\", , \"\", role = c(\"ctb\"), comment = c(ORCID = \"0000-0001-9399-4179\")), person(\"Rogier\", \"Kievit\", , \"\", role = c(\"aut\"), comment = c(ORCID = \"0000-0003-0700-4568\")))",
- "Description": "The 'geom_rain()' function adds different geoms together using 'ggplot2' to create raincloud plots.",
- "License": "MIT + file LICENSE",
+ "Type": "Package",
+ "Title": "'ggplot2' Based Publication Ready Plots",
+ "Authors@R": "c( person(\"Alboukadel\", \"Kassambara\", role = c(\"aut\", \"cre\"), email = \"alboukadel.kassambara@gmail.com\"), person(\"Laszlo\", \"Erdey\", role = \"ctb\", email = \"erdey.laszlo@econ.unideb.hu\", comment = \"Faculty of Economics and Business, University of Debrecen, Hungary\"))",
+ "Description": "The 'ggplot2' package is excellent and flexible for elegant data visualization in R. However the default generated plots requires some formatting before we can send them for publication. Furthermore, to customize a 'ggplot', the syntax is opaque and this raises the level of difficulty for researchers with no advanced R programming skills. 'ggpubr' provides some easy-to-use functions for creating and customizing 'ggplot2'- based publication ready plots.",
+ "License": "GPL (>= 2)",
+ "LazyData": "TRUE",
"Encoding": "UTF-8",
"Depends": [
- "ggplot2 (>= 4.0.0)",
- "R (>= 3.4.0)"
+ "R (>= 4.1.0)",
+ "ggplot2 (>= 3.5.2)"
],
"Imports": [
+ "ggrepel (>= 0.9.2)",
+ "grid",
+ "ggsci",
+ "stats",
+ "utils",
+ "tidyr (>= 1.3.0)",
+ "purrr",
+ "dplyr (>= 1.1.0)",
+ "cowplot (>= 1.1.1)",
+ "ggsignif",
+ "scales",
+ "gridExtra",
+ "glue",
+ "polynom",
+ "rlang (>= 0.4.6)",
+ "rstatix (>= 0.7.2)",
+ "tibble",
+ "magrittr"
+ ],
+ "Suggests": [
+ "grDevices",
+ "knitr",
+ "RColorBrewer",
+ "gtable",
+ "testthat"
+ ],
+ "URL": "https://rpkgs.datanovia.com/ggpubr/",
+ "BugReports": "https://github.com/kassambara/ggpubr/issues",
+ "RoxygenNote": "7.3.3",
+ "Collate": "'utilities_color.R' 'utilities_base.R' 'desc_statby.R' 'utilities.R' 'add_summary.R' 'annotate_figure.R' 'as_ggplot.R' 'as_npc.R' 'axis_scale.R' 'background_image.R' 'bgcolor.R' 'border.R' 'compare_means.R' 'create_aes.R' 'diff_express.R' 'facet.R' 'font.R' 'gene_citation.R' 'gene_expression.R' 'geom_bracket.R' 'geom_exec.R' 'utils-aes.R' 'utils_stat_test_label.R' 'geom_pwc.R' 'get_breaks.R' 'get_coord.R' 'get_legend.R' 'get_palette.R' 'ggadd.R' 'ggadjust_pvalue.R' 'ggarrange.R' 'ggballoonplot.R' 'ggpar.R' 'ggbarplot.R' 'ggboxplot.R' 'ggdensity.R' 'ggpie.R' 'ggdonutchart.R' 'stat_conf_ellipse.R' 'stat_chull.R' 'ggdotchart.R' 'ggdotplot.R' 'ggecdf.R' 'ggerrorplot.R' 'ggexport.R' 'gghistogram.R' 'ggline.R' 'ggmaplot.R' 'ggpaired.R' 'ggparagraph.R' 'ggpubr-package.R' 'ggpubr_args.R' 'ggpubr_options.R' 'ggqqplot.R' 'utilities_label.R' 'stat_cor.R' 'stat_stars.R' 'ggscatter.R' 'ggscatterhist.R' 'ggstripchart.R' 'ggsummarystats.R' 'ggtext.R' 'ggtexttable.R' 'ggviolin.R' 'gradient_color.R' 'grids.R' 'npc_to_data_coord.R' 'reexports.R' 'rotate.R' 'rotate_axis_text.R' 'rremove.R' 'set_palette.R' 'shared_docs.R' 'show_line_types.R' 'show_point_shapes.R' 'stat_anova_test.R' 'stat_central_tendency.R' 'stat_compare_means.R' 'stat_friedman_test.R' 'stat_kruskal_test.R' 'stat_mean.R' 'stat_overlay_normal_density.R' 'stat_pvalue_manual.R' 'stat_regline_equation.R' 'stat_welch_anova_test.R' 'text_grob.R' 'theme_pubr.R' 'theme_transparent.R' 'utils-geom-signif.R' 'utils-pipe.R' 'utils-tidyr.R'",
+ "NeedsCompilation": "no",
+ "Author": "Alboukadel Kassambara [aut, cre], Laszlo Erdey [ctb] (Faculty of Economics and Business, University of Debrecen, Hungary)",
+ "Maintainer": "Alboukadel Kassambara ",
+ "Repository": "https://packagemanager.posit.co/cran/latest"
+ },
+ "ggrain": {
+ "Package": "ggrain",
+ "Version": "0.1.2",
+ "Source": "Repository",
+ "Requirements": [
+ "cli",
+ "ggplot2",
+ "ggpp",
"grid",
"ggpp (>= 0.5.6)",
"rlang",
@@ -3465,7 +4379,43 @@
"NeedsCompilation": "no",
"Author": "Nicholas Judd [aut, cre] (ORCID: ), Jordy van Langen [aut] (ORCID: ), Micah Allen [ctb] (ORCID: ), Rogier Kievit [aut] (ORCID: )",
"Maintainer": "Nicholas Judd ",
- "Repository": "RSPM"
+ "Repository": "CRAN"
+ },
+ "ggrastr": {
+ "Package": "ggrastr",
+ "Version": "1.0.2",
+ "Source": "Repository",
+ "Type": "Package",
+ "Title": "Rasterize Layers for 'ggplot2'",
+ "Authors@R": "c(person(\"Viktor\", \"Petukhov\", email = \"viktor.s.petukhov@ya.ru\", role = c(\"aut\", \"cph\")), person(\"Teun\", \"van den Brand\", email = \"t.vd.brand@nki.nl\", role=c(\"aut\")), person(\"Evan\", \"Biederstedt\", email = \"evan.biederstedt@gmail.com\", role=c(\"cre\", \"aut\")))",
+ "Description": "Rasterize only specific layers of a 'ggplot2' plot while simultaneously keeping all labels and text in vector format. This allows users to keep plots within the reasonable size limit without loosing vector properties of the scale-sensitive information.",
+ "License": "MIT + file LICENSE",
+ "Encoding": "UTF-8",
+ "Imports": [
+ "ggplot2 (>= 2.1.0)",
+ "Cairo (>= 1.5.9)",
+ "ggbeeswarm",
+ "grid",
+ "png",
+ "ragg"
+ ],
+ "Depends": [
+ "R (>= 3.2.2)"
+ ],
+ "RoxygenNote": "7.2.3",
+ "Suggests": [
+ "knitr",
+ "maps",
+ "rmarkdown",
+ "sf"
+ ],
+ "VignetteBuilder": "knitr",
+ "URL": "https://github.com/VPetukhov/ggrastr",
+ "BugReports": "https://github.com/VPetukhov/ggrastr/issues",
+ "NeedsCompilation": "no",
+ "Author": "Viktor Petukhov [aut, cph], Teun van den Brand [aut], Evan Biederstedt [cre, aut]",
+ "Maintainer": "Evan Biederstedt ",
+ "Repository": "CRAN"
},
"ggrastr": {
"Package": "ggrastr",
@@ -3517,44 +4467,11 @@
"Imports": [
"grid",
"Rcpp",
- "rlang (>= 1.1.6)",
+ "rlang",
"S7",
- "scales (>= 1.4.0)",
- "withr (>= 3.0.2)"
- ],
- "Suggests": [
- "knitr",
- "rmarkdown",
- "testthat",
- "svglite",
- "vdiffr",
- "gridExtra",
- "ggpp",
- "patchwork",
- "devtools",
- "prettydoc",
- "ggbeeswarm",
- "dplyr",
- "magrittr",
- "readr",
- "stringr",
- "marquee",
- "rsvg",
- "sf"
- ],
- "VignetteBuilder": "knitr",
- "License": "GPL-3 | file LICENSE",
- "URL": "https://ggrepel.slowkow.com/, https://github.com/slowkow/ggrepel",
- "BugReports": "https://github.com/slowkow/ggrepel/issues",
- "RoxygenNote": "7.3.3",
- "LinkingTo": [
- "Rcpp"
- ],
- "Encoding": "UTF-8",
- "NeedsCompilation": "yes",
- "Author": "Kamil Slowikowski [aut, cre] (ORCID: ), Teun van den Brand [ctb] (ORCID: ), Alicia Schep [ctb] (ORCID: ), Sean Hughes [ctb] (ORCID: ), Trung Kien Dang [ctb] (ORCID: ), Saulius Lukauskas [ctb], Jean-Olivier Irisson [ctb] (ORCID: ), Zhian N Kamvar [ctb] (ORCID: ), Thompson Ryan [ctb] (ORCID: ), Dervieux Christophe [ctb] (ORCID: ), Yutani Hiroaki [ctb], Pierre Gramme [ctb], Amir Masoud Abdol [ctb], Malcolm Barrett [ctb] (ORCID: ), Robrecht Cannoodt [ctb] (ORCID: ), Michał Krassowski [ctb] (ORCID: ), Michael Chirico [ctb] (ORCID: ), Pedro Aphalo [ctb] (ORCID: ), Francis Barton [ctb]",
- "Maintainer": "Kamil Slowikowski ",
- "Repository": "RSPM"
+ "scales",
+ "withr"
+ ]
},
"ggsci": {
"Package": "ggsci",
@@ -3574,6 +4491,7 @@
"Imports": [
"ggplot2 (>= 2.0.0)",
"grDevices",
+ "R",
"rlang",
"scales"
],
@@ -3620,6 +4538,36 @@
"Maintainer": "Constantin Ahlmann-Eltze ",
"Repository": "CRAN"
},
+ "ggsignif": {
+ "Package": "ggsignif",
+ "Version": "0.6.4",
+ "Source": "Repository",
+ "Type": "Package",
+ "Title": "Significance Brackets for 'ggplot2'",
+ "Authors@R": "c( person(given = \"Constantin\", family = \"Ahlmann-Eltze\", role = c(\"aut\", \"cre\", \"ctb\"), email = \"artjom31415@googlemail.com\", comment = c(ORCID = \"0000-0002-3762-068X\", Twitter = \"@const_ae\")), person(given = \"Indrajeet\", family = \"Patil\", role = c(\"aut\", \"ctb\"), email = \"patilindrajeet.science@gmail.com\", comment = c(ORCID = \"0000-0003-1995-6531\", Twitter = \"@patilindrajeets\")) )",
+ "Description": "Enrich your 'ggplots' with group-wise comparisons. This package provides an easy way to indicate if two groups are significantly different. Commonly this is shown by a bracket on top connecting the groups of interest which itself is annotated with the level of significance (NS, *, **, ***). The package provides a single layer (geom_signif()) that takes the groups for comparison and the test (t.test(), wilcox.text() etc.) as arguments and adds the annotation to the plot.",
+ "License": "GPL-3 | file LICENSE",
+ "URL": "https://const-ae.github.io/ggsignif/, https://github.com/const-ae/ggsignif",
+ "VignetteBuilder": "knitr",
+ "Encoding": "UTF-8",
+ "Language": "en-US",
+ "Imports": [
+ "ggplot2 (>= 3.3.5)"
+ ],
+ "Suggests": [
+ "knitr",
+ "rmarkdown",
+ "testthat",
+ "vdiffr (>= 1.0.2)"
+ ],
+ "RoxygenNote": "7.2.1",
+ "Config/testthat/edition": "3",
+ "Config/testthat/parallel": "true",
+ "NeedsCompilation": "no",
+ "Author": "Constantin Ahlmann-Eltze [aut, cre, ctb] (, @const_ae), Indrajeet Patil [aut, ctb] (, @patilindrajeets)",
+ "Maintainer": "Constantin Ahlmann-Eltze ",
+ "Repository": "CRAN"
+ },
"ggtext": {
"Package": "ggtext",
"Version": "0.1.2",
@@ -3697,7 +4645,7 @@
"NeedsCompilation": "yes",
"Author": "Jim Hester [aut] (ORCID: ), Jennifer Bryan [aut, cre] (ORCID: ), Posit Software, PBC [cph, fnd] (ROR: )",
"Maintainer": "Jennifer Bryan ",
- "Repository": "RSPM"
+ "Repository": "https://packagemanager.posit.co/cran/latest"
},
"gmp": {
"Package": "gmp",
@@ -3726,7 +4674,8 @@
"NeedsCompilation": "yes",
"URL": "https://forgemia.inra.fr/sylvain.jasson/gmp",
"Author": "Antoine Lucas [aut, cre] (ORCID: ), Immanuel Scholz [aut], Rainer Boehme [ctb], Sylvain Jasson [ctb], Martin Maechler [ctb]",
- "Repository": "CRAN"
+ "Repository": "RSPM",
+ "Encoding": "UTF-8"
},
"goftest": {
"Package": "goftest",
@@ -3847,7 +4796,45 @@
"NeedsCompilation": "yes",
"Author": "Claus O. Wilke [aut] (ORCID: ), Brenton M. Wiernik [aut, cre] (ORCID: , Twitter: @bmwiernik)",
"Maintainer": "Brenton M. Wiernik ",
- "Repository": "RSPM"
+ "Repository": "https://packagemanager.posit.co/cran/latest"
+ },
+ "gsl": {
+ "Package": "gsl",
+ "Version": "2.1-9",
+ "Source": "Repository",
+ "Depends": [
+ "R (>= 4.5.0)"
+ ],
+ "Title": "Wrapper for the Gnu Scientific Library",
+ "Authors@R": "c(person(given=c(\"Robin\", \"K. S.\"), family=\"Hankin\", role = c(\"aut\",\"cre\"), email=\"hankin.robin@gmail.com\", comment = c(ORCID = \"0000-0001-5982-0415\")), person(given=\"Andrew\",family=\"Clausen\",role=\"ctb\",comment=\"multimin functionality\"), person(given=\"Duncan\",family=\"Murdoch\",role=\"ctb\",comment=\"qrng functions\"))",
+ "SystemRequirements": "Gnu Scientific Library version >= 2.5",
+ "Description": "An R wrapper for some of the functionality of the Gnu Scientific Library.",
+ "Maintainer": "Robin K. S. Hankin ",
+ "License": "GPL-3",
+ "URL": "https://github.com/RobinHankin/gsl",
+ "BugReports": "https://github.com/RobinHankin/gsl/issues",
+ "NeedsCompilation": "yes",
+ "Author": "Robin K. S. Hankin [aut, cre] (ORCID: ), Andrew Clausen [ctb] (multimin functionality), Duncan Murdoch [ctb] (qrng functions)",
+ "Repository": "CRAN"
+ },
+ "gsl": {
+ "Package": "gsl",
+ "Version": "2.1-9",
+ "Source": "Repository",
+ "Depends": [
+ "R (>= 4.5.0)"
+ ],
+ "Title": "Wrapper for the Gnu Scientific Library",
+ "Authors@R": "c(person(given=c(\"Robin\", \"K. S.\"), family=\"Hankin\", role = c(\"aut\",\"cre\"), email=\"hankin.robin@gmail.com\", comment = c(ORCID = \"0000-0001-5982-0415\")), person(given=\"Andrew\",family=\"Clausen\",role=\"ctb\",comment=\"multimin functionality\"), person(given=\"Duncan\",family=\"Murdoch\",role=\"ctb\",comment=\"qrng functions\"))",
+ "SystemRequirements": "Gnu Scientific Library version >= 2.5",
+ "Description": "An R wrapper for some of the functionality of the Gnu Scientific Library.",
+ "Maintainer": "Robin K. S. Hankin ",
+ "License": "GPL-3",
+ "URL": "https://github.com/RobinHankin/gsl",
+ "BugReports": "https://github.com/RobinHankin/gsl/issues",
+ "NeedsCompilation": "yes",
+ "Author": "Robin K. S. Hankin [aut, cre] (ORCID: ), Andrew Clausen [ctb] (multimin functionality), Duncan Murdoch [ctb] (qrng functions)",
+ "Repository": "CRAN"
},
"gtable": {
"Package": "gtable",
@@ -3917,27 +4904,57 @@
"NeedsCompilation": "no",
"Author": "Yihui Xie [aut, cre] (ORCID: ), Yixuan Qiu [aut], Christopher Gandrud [ctb], Qiang Li [ctb]",
"Maintainer": "Yihui Xie ",
- "Repository": "RSPM"
+ "Repository": "CRAN"
},
- "htmlTable": {
- "Package": "htmlTable",
- "Version": "2.5.0",
+ "highr": {
+ "Package": "highr",
+ "Version": "0.12",
"Source": "Repository",
- "Title": "Advanced Tables for Markdown/HTML",
- "Authors@R": "c( person(\"Max\", \"Gordon\", email = \"max@gforge.se\", role = c(\"aut\", \"cre\")), person(\"Stephen\", \"Gragg\", role=c(\"aut\")), person(\"Peter\", \"Konings\", role=c(\"aut\")))",
- "Maintainer": "Max Gordon ",
- "Description": "Tables with state-of-the-art layout elements such as row spanners, column spanners, table spanners, zebra striping, and more. While allowing advanced layout, the underlying css-structure is simple in order to maximize compatibility with common word processors. The package also contains a few text formatting functions that help outputting text compatible with HTML/LaTeX.",
- "License": "GPL (>= 3)",
- "URL": "https://gforge.se/packages/",
- "BugReports": "https://github.com/gforge/htmlTable/issues",
- "Biarch": "yes",
+ "Type": "Package",
+ "Title": "Syntax Highlighting for R Source Code",
+ "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Yixuan\", \"Qiu\", role = \"aut\"), person(\"Christopher\", \"Gandrud\", role = \"ctb\"), person(\"Qiang\", \"Li\", role = \"ctb\") )",
+ "Description": "Provides syntax highlighting for R source code. Currently it supports LaTeX and HTML output. Source code of other languages is supported via Andre Simon's highlight package ().",
"Depends": [
- "R (>= 4.1)"
+ "R (>= 3.3.0)"
],
"Imports": [
- "stringr",
- "knitr (>= 1.6)",
- "magrittr (>= 1.5)",
+ "xfun (>= 0.18)"
+ ],
+ "Suggests": [
+ "knitr",
+ "markdown",
+ "testit"
+ ],
+ "License": "GPL",
+ "URL": "https://github.com/yihui/highr",
+ "BugReports": "https://github.com/yihui/highr/issues",
+ "VignetteBuilder": "knitr",
+ "Encoding": "UTF-8",
+ "RoxygenNote": "7.3.3",
+ "NeedsCompilation": "no",
+ "Author": "Yihui Xie [aut, cre] (ORCID: ), Yixuan Qiu [aut], Christopher Gandrud [ctb], Qiang Li [ctb]",
+ "Maintainer": "Yihui Xie ",
+ "Repository": "CRAN"
+ },
+ "htmlTable": {
+ "Package": "htmlTable",
+ "Version": "2.5.0",
+ "Source": "Repository",
+ "Title": "Advanced Tables for Markdown/HTML",
+ "Authors@R": "c( person(\"Max\", \"Gordon\", email = \"max@gforge.se\", role = c(\"aut\", \"cre\")), person(\"Stephen\", \"Gragg\", role=c(\"aut\")), person(\"Peter\", \"Konings\", role=c(\"aut\")))",
+ "Maintainer": "Max Gordon ",
+ "Description": "Tables with state-of-the-art layout elements such as row spanners, column spanners, table spanners, zebra striping, and more. While allowing advanced layout, the underlying css-structure is simple in order to maximize compatibility with common word processors. The package also contains a few text formatting functions that help outputting text compatible with HTML/LaTeX.",
+ "License": "GPL (>= 3)",
+ "URL": "https://gforge.se/packages/",
+ "BugReports": "https://github.com/gforge/htmlTable/issues",
+ "Biarch": "yes",
+ "Depends": [
+ "R (>= 4.1)"
+ ],
+ "Imports": [
+ "stringr",
+ "knitr (>= 1.6)",
+ "magrittr (>= 1.5)",
"methods",
"checkmate",
"htmlwidgets",
@@ -3965,7 +4982,55 @@
"VignetteBuilder": "knitr",
"RoxygenNote": "7.3.3",
"Author": "Max Gordon [aut, cre], Stephen Gragg [aut], Peter Konings [aut]",
- "Repository": "CRAN"
+ "Repository": "https://packagemanager.posit.co/cran/latest"
+ },
+ "htmlTable": {
+ "Package": "htmlTable",
+ "Version": "2.5.0",
+ "Source": "Repository",
+ "Title": "Advanced Tables for Markdown/HTML",
+ "Authors@R": "c( person(\"Max\", \"Gordon\", email = \"max@gforge.se\", role = c(\"aut\", \"cre\")), person(\"Stephen\", \"Gragg\", role=c(\"aut\")), person(\"Peter\", \"Konings\", role=c(\"aut\")))",
+ "Maintainer": "Max Gordon ",
+ "Description": "Tables with state-of-the-art layout elements such as row spanners, column spanners, table spanners, zebra striping, and more. While allowing advanced layout, the underlying css-structure is simple in order to maximize compatibility with common word processors. The package also contains a few text formatting functions that help outputting text compatible with HTML/LaTeX.",
+ "License": "GPL (>= 3)",
+ "URL": "https://gforge.se/packages/",
+ "BugReports": "https://github.com/gforge/htmlTable/issues",
+ "Biarch": "yes",
+ "Depends": [
+ "R (>= 4.1)"
+ ],
+ "Imports": [
+ "stringr",
+ "knitr (>= 1.6)",
+ "magrittr (>= 1.5)",
+ "methods",
+ "checkmate",
+ "htmlwidgets",
+ "htmltools",
+ "rstudioapi (>= 0.6)"
+ ],
+ "Suggests": [
+ "testthat",
+ "XML",
+ "xml2",
+ "Hmisc",
+ "rmarkdown",
+ "chron",
+ "lubridate",
+ "tibble",
+ "purrr",
+ "tidyselect",
+ "glue",
+ "rlang",
+ "tidyr (>= 0.7.2)",
+ "dplyr (>= 0.7.4)"
+ ],
+ "Encoding": "UTF-8",
+ "NeedsCompilation": "no",
+ "VignetteBuilder": "knitr",
+ "RoxygenNote": "7.3.3",
+ "Author": "Max Gordon [aut, cre], Stephen Gragg [aut], Peter Konings [aut]",
+ "Repository": "https://packagemanager.posit.co/cran/latest"
},
"htmltools": {
"Package": "htmltools",
@@ -4008,6 +5073,39 @@
"NeedsCompilation": "yes",
"Author": "Joe Cheng [aut], Carson Sievert [aut, cre] (ORCID: ), Barret Schloerke [aut] (ORCID: ), Winston Chang [aut] (ORCID: ), Yihui Xie [aut], Jeff Allen [aut], Posit Software, PBC [cph, fnd]",
"Maintainer": "Carson Sievert ",
+ "Repository": "https://packagemanager.posit.co/cran/latest"
+ },
+ "htmlwidgets": {
+ "Package": "htmlwidgets",
+ "Version": "1.6.4",
+ "Source": "Repository",
+ "Type": "Package",
+ "Title": "HTML Widgets for R",
+ "Authors@R": "c( person(\"Ramnath\", \"Vaidyanathan\", role = c(\"aut\", \"cph\")), person(\"Yihui\", \"Xie\", role = \"aut\"), person(\"JJ\", \"Allaire\", role = \"aut\"), person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Carson\", \"Sievert\", , \"carson@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Kenton\", \"Russell\", role = c(\"aut\", \"cph\")), person(\"Ellis\", \"Hughes\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
+ "Description": "A framework for creating HTML widgets that render in various contexts including the R console, 'R Markdown' documents, and 'Shiny' web applications.",
+ "License": "MIT + file LICENSE",
+ "URL": "https://github.com/ramnathv/htmlwidgets",
+ "BugReports": "https://github.com/ramnathv/htmlwidgets/issues",
+ "Imports": [
+ "grDevices",
+ "htmltools (>= 0.5.7)",
+ "jsonlite (>= 0.9.16)",
+ "knitr (>= 1.8)",
+ "rmarkdown",
+ "yaml"
+ ],
+ "Suggests": [
+ "testthat"
+ ],
+ "Enhances": [
+ "shiny (>= 1.1)"
+ ],
+ "VignetteBuilder": "knitr",
+ "Encoding": "UTF-8",
+ "RoxygenNote": "7.2.3",
+ "NeedsCompilation": "no",
+ "Author": "Ramnath Vaidyanathan [aut, cph], Yihui Xie [aut], JJ Allaire [aut], Joe Cheng [aut], Carson Sievert [aut, cre] (), Kenton Russell [aut, cph], Ellis Hughes [ctb], Posit Software, PBC [cph, fnd]",
+ "Maintainer": "Carson Sievert ",
"Repository": "CRAN"
},
"htmlwidgets": {
@@ -4081,7 +5179,47 @@
"NeedsCompilation": "no",
"Author": "Hadley Wickham [aut, cre], Posit Software, PBC [cph, fnd]",
"Maintainer": "Hadley Wickham ",
- "Repository": "RSPM"
+ "Repository": "https://packagemanager.posit.co/cran/latest"
+ },
+ "httr": {
+ "Package": "httr",
+ "Version": "1.4.8",
+ "Source": "Repository",
+ "Title": "Tools for Working with URLs and HTTP",
+ "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
+ "Description": "Useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configuration functions make it easy to control additional request components (authenticate(), add_headers() and so on).",
+ "License": "MIT + file LICENSE",
+ "URL": "https://httr.r-lib.org/, https://github.com/r-lib/httr",
+ "BugReports": "https://github.com/r-lib/httr/issues",
+ "Depends": [
+ "R (>= 3.6)"
+ ],
+ "Imports": [
+ "curl (>= 5.1.0)",
+ "jsonlite",
+ "mime",
+ "openssl (>= 0.8)",
+ "R6"
+ ],
+ "Suggests": [
+ "covr",
+ "httpuv",
+ "jpeg",
+ "knitr",
+ "png",
+ "readr",
+ "rmarkdown",
+ "testthat (>= 0.8.0)",
+ "xml2"
+ ],
+ "VignetteBuilder": "knitr",
+ "Config/Needs/website": "tidyverse/tidytemplate",
+ "Encoding": "UTF-8",
+ "RoxygenNote": "7.3.3",
+ "NeedsCompilation": "no",
+ "Author": "Hadley Wickham [aut, cre], Posit Software, PBC [cph, fnd]",
+ "Maintainer": "Hadley Wickham ",
+ "Repository": "https://packagemanager.posit.co/cran/latest"
},
"hypergeo": {
"Package": "hypergeo",
@@ -4106,7 +5244,7 @@
},
"igraph": {
"Package": "igraph",
- "Version": "2.3.1",
+ "Version": "2.3.2",
"Source": "Repository",
"Title": "Network Analysis and Visualization",
"Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0001-7098-9676\")), person(\"Tamás\", \"Nepusz\", , \"ntamas@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-1451-338X\")), person(\"Vincent\", \"Traag\", role = \"aut\", comment = c(ORCID = \"0000-0003-3170-3879\")), person(\"Szabolcs\", \"Horvát\", , \"szhorvat@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-3100-523X\")), person(\"Fabio\", \"Zanini\", , \"fabio.zanini@unsw.edu.au\", role = \"aut\", comment = c(ORCID = \"0000-0001-7097-8539\")), person(\"Daniel\", \"Noom\", role = \"aut\"), person(\"Kirill\", \"Müller\", , \"kirill@cynkra.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-1416-3412\")), person(\"Michael\", \"Antonov\", role = \"ctb\"), person(\"Chan Zuckerberg Initiative\", role = \"fnd\", comment = c(ROR = \"02qenvm24\")), person(\"David\", \"Schoch\", , \"david.schoch@cynkra.com\", role = \"aut\", comment = c(ORCID = \"0000-0003-2952-4812\")), person(\"Maëlle\", \"Salmon\", , \"maelle@cynkra.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-2815-0399\")), person(\"R Consortium\", role = \"fnd\", comment = c(ROR = \"01z833950\")) )",
@@ -4170,38 +5308,73 @@
"NeedsCompilation": "yes",
"Author": "Gábor Csárdi [aut] (ORCID: ), Tamás Nepusz [aut] (ORCID: ), Vincent Traag [aut] (ORCID: