From aea299ac4a3bd9453a769c48f455dddd66f8f3a4 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Tue, 24 Jun 2025 22:48:00 -0700 Subject: [PATCH 01/94] Adding class sero_mod_output to run_mod output --- R/Run_Mod.R | 2 ++ 1 file changed, 2 insertions(+) diff --git a/R/Run_Mod.R b/R/Run_Mod.R index 98e904c3..78310318 100644 --- a/R/Run_Mod.R +++ b/R/Run_Mod.R @@ -196,4 +196,6 @@ run_mod <- function(data, structure(jags.post = jags_post_final) } jags_out + class(jags_out) <- "sero_mod_output" + } From a13db942c5e590e8fabf26a64426da37d6b51424 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Tue, 24 Jun 2025 23:21:27 -0700 Subject: [PATCH 02/94] Specifying class in run_mod --- R/Run_Mod.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/Run_Mod.R b/R/Run_Mod.R index 78310318..2f0ed78f 100644 --- a/R/Run_Mod.R +++ b/R/Run_Mod.R @@ -195,7 +195,7 @@ run_mod <- function(data, jags_out <- jags_out |> structure(jags.post = jags_post_final) } - jags_out class(jags_out) <- "sero_mod_output" + jags_out } From eef3d8ed527cbef310098b7b06c386e1910e871d Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Tue, 24 Jun 2025 23:21:53 -0700 Subject: [PATCH 03/94] creating default print function method for sero_mod_output objects --- R/print_sero_mod_output.R | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 R/print_sero_mod_output.R diff --git a/R/print_sero_mod_output.R b/R/print_sero_mod_output.R new file mode 100644 index 00000000..dc950058 --- /dev/null +++ b/R/print_sero_mod_output.R @@ -0,0 +1,32 @@ +#' @title Default print method for run_mod output +#' @author Sam Schildhauer +#' @description +#' Will print a default output for a run_mod object that specifies the median +#' value of the posterior distribution for serokinetic curve parameters (y0, +#' y1, t1, alpha, shape) by stratification (if specified) and antigen/iso type. +#' @param obj A [serodynamics::sero_mod_output] object. +#' @returns A [dplyr::tbl_df] that contains the median value of the posterior +#' distribution of stratifications (if any specified), antigen/iso type, and +#' parameter value. +#' @export +#' @example inst/examples/run_mod-examples.R + +print.sero_mod_output <- function(obj) { + + # Summarizing results + df_obj <- data.frame("Parameter" = obj$Parameter, "Iso_type" = obj$Iso_type, + "Stratification" = obj$Stratification, + "Value" = obj$value) + if (unique(df_obj$Stratification == "None")) { + to_print <- df_obj |> + dplyr::group_by(Iso_type, Parameter) |> + dplyr::summarize(median = median(Value)) |> + tidyr::spread(Parameter, median) + } else { + to_print <- df_obj |> + dplyr::group_by(Stratification, Iso_type, Parameter) |> + dplyr::summarize(median = median(Value)) |> + tidyr::spread(Parameter, median) + } + to_print +} From 147ae9ec1e9b240dd2f2563c3f43ddc8b9f14036 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Tue, 24 Jun 2025 23:22:53 -0700 Subject: [PATCH 04/94] Adding S3 method to NameSpace --- NAMESPACE | 1 + 1 file changed, 1 insertion(+) diff --git a/NAMESPACE b/NAMESPACE index 09e6f3bd..022010b0 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,6 +1,7 @@ # Generated by roxygen2: do not edit by hand S3method(autoplot,case_data) +S3method(print,sero_mod_output) export(as_case_data) export(autoplot) export(get_biomarker_levels) From ea74517c908b6c366c07dfe0e9fc96011be284a7 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Tue, 24 Jun 2025 23:23:07 -0700 Subject: [PATCH 05/94] Documentation for default print method --- man/print.sero_mod_output.Rd | 50 ++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 man/print.sero_mod_output.Rd diff --git a/man/print.sero_mod_output.Rd b/man/print.sero_mod_output.Rd new file mode 100644 index 00000000..0dd8540f --- /dev/null +++ b/man/print.sero_mod_output.Rd @@ -0,0 +1,50 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/print_sero_mod_output.R +\name{print.sero_mod_output} +\alias{print.sero_mod_output} +\title{Default print method for run_mod output} +\usage{ +\method{print}{sero_mod_output}(obj) +} +\arguments{ +\item{obj}{A \link{sero_mod_output} object.} +} +\value{ +A \link[dplyr:tbl_df]{dplyr::tbl_df} that contains the median value of the posterior +distribution of stratifications (if any specified), antigen/iso type, and +parameter value. +} +\description{ +Will print a default output for a run_mod object that specifies the median +value of the posterior distribution for serokinetic curve parameters (y0, +y1, t1, alpha, shape) by stratification (if specified) and antigen/iso type. +} +\examples{ +if (!is.element(runjags::findjags(), c("", NULL))) { + library(runjags) + set.seed(1) + library(dplyr) + strat1 <- serocalculator::typhoid_curves_nostrat_100 |> + sim_case_data(n = 100) |> + mutate(strat = "stratum 2") + strat2 <- serocalculator::typhoid_curves_nostrat_100 |> + sim_case_data(n = 100) |> + mutate(strat = "stratum 1") + + dataset <- bind_rows(strat1, strat2) + + fitted_model <- run_mod( + data = dataset, # The data set input + file_mod = serodynamics_example("model.jags"), + nchain = 4, # Number of mcmc chains to run + nadapt = 100, # Number of adaptations to run + nburn = 100, # Number of unrecorded samples before sampling begins + nmc = 1000, + niter = 2000, # Number of iterations + strat = "strat" + ) # Variable to be stratified +} +} +\author{ +Sam Schildhauer +} From 102cb808b695691268eeb1622ada71c2cea46d97 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Tue, 8 Jul 2025 23:12:24 -0700 Subject: [PATCH 06/94] Creating default print for run_mod objects --- R/print.sr_model.R | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 R/print.sr_model.R diff --git a/R/print.sr_model.R b/R/print.sr_model.R new file mode 100644 index 00000000..0ba453b6 --- /dev/null +++ b/R/print.sr_model.R @@ -0,0 +1,29 @@ +#' @title Default print for run_mod object of class sr_model +#' @author Sam Schildhauer +#' @description +#' A default print method for class `sr_model` that includes the mean posterior +#' distribution for antibody kinetic curve parameters by `Iso_type` and +#' `Stratification` (if specified). +#' @param data A [serodynamics::sr_model] object output from the +#' [serodynamics::run_mod()] function. +#' @returns A [dplyr::grouped_df] that +#' contains the mean posterior distribution for antibody kinetic curve +#' parameters by `Iso_type` and `Stratification` (if specified). +#' @export +#' @example +#' print.sr_model(nepal_sees_output) +print.sr_model <- function(data) { + data_group <- data |> + dplyr::group_by(Stratification, Iso_type, Parameter) |> + dplyr::summarise(mean_val = mean(value)) |> + tidyr::spread(Parameter, mean_val) + # Taking out stratification column if not specified + if(unique(data$Stratification == "None")) { + data_group <- data_group[,2:7] + } + data_group +} + + + + \ No newline at end of file From 7323fda893e188968f65ef1a0b00f0e061996e90 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Tue, 8 Jul 2025 23:15:51 -0700 Subject: [PATCH 07/94] Creating a test for default run_mod object print --- tests/testthat/test-print.sr_model.R | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 tests/testthat/test-print.sr_model.R diff --git a/tests/testthat/test-print.sr_model.R b/tests/testthat/test-print.sr_model.R new file mode 100644 index 00000000..3f0d0e11 --- /dev/null +++ b/tests/testthat/test-print.sr_model.R @@ -0,0 +1,9 @@ +test_that( + desc = "results are consistent with printed output for sr_model class", + code = { + withr::local_seed(1) + results <- print(nepal_sees_jags_output) |> + ssdtools:::expect_snapshot_data("default-print-runmod-object") + + } +) From 88b96aff66c11de4f1f3831e2eec69cfe67c3aba Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Tue, 8 Jul 2025 23:16:23 -0700 Subject: [PATCH 08/94] Updating example for print default --- R/print.sr_model.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index 0ba453b6..2b48f933 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -11,7 +11,7 @@ #' parameters by `Iso_type` and `Stratification` (if specified). #' @export #' @example -#' print.sr_model(nepal_sees_output) +#' print.sr_model(nepal_sees_jags_output) print.sr_model <- function(data) { data_group <- data |> dplyr::group_by(Stratification, Iso_type, Parameter) |> From 91a887f03e7ecfb64933b20ad9e3f4b49051fa25 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Tue, 8 Jul 2025 23:16:46 -0700 Subject: [PATCH 09/94] Updating documentation for default print --- NAMESPACE | 1 + man/print.sr_model.Rd | 25 +++++++++++++++++++++++++ 2 files changed, 26 insertions(+) create mode 100644 man/print.sr_model.Rd diff --git a/NAMESPACE b/NAMESPACE index 022010b0..0bd66d02 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -2,6 +2,7 @@ S3method(autoplot,case_data) S3method(print,sero_mod_output) +S3method(print,sr_model) export(as_case_data) export(autoplot) export(get_biomarker_levels) diff --git a/man/print.sr_model.Rd b/man/print.sr_model.Rd new file mode 100644 index 00000000..6b14d968 --- /dev/null +++ b/man/print.sr_model.Rd @@ -0,0 +1,25 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/print.sr_model.R +\name{print.sr_model} +\alias{print.sr_model} +\title{Default print for run_mod object of class sr_model} +\usage{ +\method{print}{sr_model}(data) +} +\arguments{ +\item{data}{A \link{sr_model} object output from the +\code{\link[=run_mod]{run_mod()}} function.} +} +\value{ +A \link[dplyr:grouped_df]{dplyr::grouped_df} that +contains the mean posterior distribution for antibody kinetic curve +parameters by \code{Iso_type} and \code{Stratification} (if specified). +} +\description{ +A default print method for class \code{sr_model} that includes the mean posterior +distribution for antibody kinetic curve parameters by \code{Iso_type} and +\code{Stratification} (if specified). +} +\author{ +Sam Schildhauer +} From a7afd630bdaf134d4ac27c9a89570e8f586dcb59 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Tue, 8 Jul 2025 23:20:26 -0700 Subject: [PATCH 10/94] Arranging data by Iso_type to allow for easy comparison between stratifications --- R/print.sr_model.R | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index 2b48f933..90c47bf7 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -16,7 +16,8 @@ print.sr_model <- function(data) { data_group <- data |> dplyr::group_by(Stratification, Iso_type, Parameter) |> dplyr::summarise(mean_val = mean(value)) |> - tidyr::spread(Parameter, mean_val) + tidyr::spread(Parameter, mean_val) |> + dplyr::arrange(Iso_type) # Taking out stratification column if not specified if(unique(data$Stratification == "None")) { data_group <- data_group[,2:7] From f5be2b33313b844cea051a8c74ece9559989087e Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Tue, 8 Jul 2025 23:21:42 -0700 Subject: [PATCH 11/94] Adding test snap for run_mod object default print --- .../_snaps/print.sr_model/default-print-runmod-object.csv | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 tests/testthat/_snaps/print.sr_model/default-print-runmod-object.csv diff --git a/tests/testthat/_snaps/print.sr_model/default-print-runmod-object.csv b/tests/testthat/_snaps/print.sr_model/default-print-runmod-object.csv new file mode 100644 index 00000000..75d8a137 --- /dev/null +++ b/tests/testthat/_snaps/print.sr_model/default-print-runmod-object.csv @@ -0,0 +1,5 @@ +Stratification,Iso_type,alpha,shape,t1,y0,y1 +paratyphi,HlyE_IgA,0.00228672,1.66482,3.85028,2.55072,1024.3 +typhi,HlyE_IgA,0.00290543,1.61299,7.3068,2.9673,1031.9 +paratyphi,HlyE_IgG,0.00256872,1.36053,4.7794,1.72131,833.105 +typhi,HlyE_IgG,0.00153667,1.40846,8.72891,2.31451,338.572 From ba5973fa2f5f84a028787030b0c5c9ca2ccc7391 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Tue, 8 Jul 2025 23:25:53 -0700 Subject: [PATCH 12/94] Updating default sr_model print documentation --- R/print.sr_model.R | 6 +++--- man/print.sr_model.Rd | 8 +++----- 2 files changed, 6 insertions(+), 8 deletions(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index 90c47bf7..f4c6f40b 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -1,10 +1,10 @@ -#' @title Default print for run_mod object of class sr_model -#' @author Sam Schildhauer +#' @title Default print for [serodynamics::run_mod()] output object of class +#' `sr_model` #' @description #' A default print method for class `sr_model` that includes the mean posterior #' distribution for antibody kinetic curve parameters by `Iso_type` and #' `Stratification` (if specified). -#' @param data A [serodynamics::sr_model] object output from the +#' @param data An `sr_model` output object from the #' [serodynamics::run_mod()] function. #' @returns A [dplyr::grouped_df] that #' contains the mean posterior distribution for antibody kinetic curve diff --git a/man/print.sr_model.Rd b/man/print.sr_model.Rd index 6b14d968..847320bb 100644 --- a/man/print.sr_model.Rd +++ b/man/print.sr_model.Rd @@ -2,12 +2,13 @@ % Please edit documentation in R/print.sr_model.R \name{print.sr_model} \alias{print.sr_model} -\title{Default print for run_mod object of class sr_model} +\title{Default print for \code{\link[=run_mod]{run_mod()}} output object of class +\code{sr_model}} \usage{ \method{print}{sr_model}(data) } \arguments{ -\item{data}{A \link{sr_model} object output from the +\item{data}{An \code{sr_model} output object from the \code{\link[=run_mod]{run_mod()}} function.} } \value{ @@ -20,6 +21,3 @@ A default print method for class \code{sr_model} that includes the mean posterio distribution for antibody kinetic curve parameters by \code{Iso_type} and \code{Stratification} (if specified). } -\author{ -Sam Schildhauer -} From 4ed27e68009a4c0c21b41ef1eacd3a89a7db499e Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Tue, 8 Jul 2025 23:28:08 -0700 Subject: [PATCH 13/94] Updating example for print.sr_model --- R/print.sr_model.R | 4 ++-- man/print.sr_model.Rd | 3 +++ 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index f4c6f40b..887ddabf 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -10,8 +10,8 @@ #' contains the mean posterior distribution for antibody kinetic curve #' parameters by `Iso_type` and `Stratification` (if specified). #' @export -#' @example -#' print.sr_model(nepal_sees_jags_output) +#' @examples +#' print(nepal_sees_jags_output) print.sr_model <- function(data) { data_group <- data |> dplyr::group_by(Stratification, Iso_type, Parameter) |> diff --git a/man/print.sr_model.Rd b/man/print.sr_model.Rd index 847320bb..eb91c2a4 100644 --- a/man/print.sr_model.Rd +++ b/man/print.sr_model.Rd @@ -21,3 +21,6 @@ A default print method for class \code{sr_model} that includes the mean posterio distribution for antibody kinetic curve parameters by \code{Iso_type} and \code{Stratification} (if specified). } +\examples{ +print(nepal_sees_jags_output) +} From 8e5eba79442677d5f39502d2d20cee1da9cf5a35 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Tue, 8 Jul 2025 23:28:21 -0700 Subject: [PATCH 14/94] Increment version number to 0.0.0.9035 --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index bb07d694..5409ade5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: serodynamics Title: What the Package Does (One Line, Title Case) -Version: 0.0.0.9034 +Version: 0.0.0.9035 Authors@R: c( person("Peter", "Teunis", , "p.teunis@emory.edu", role = c("aut", "cph"), comment = "Author of the method and original code."), From f377d5c9e55be420f4b59a1e0ccfca5171348e4b Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Tue, 8 Jul 2025 23:29:03 -0700 Subject: [PATCH 15/94] Updating news --- NEWS.md | 1 + 1 file changed, 1 insertion(+) diff --git a/NEWS.md b/NEWS.md index 1867fca0..a51dca5d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -4,6 +4,7 @@ ## New features +* Creating default print.sr_model function for sr_model class (#) * Replacing old data object with new run_mod output (#102) * Adding class assignment to run_mod output (#76) * Making prep_priors modifiable (#78) From 9711df67d111cd291ead51bfbaa02b8e49af949c Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Tue, 8 Jul 2025 23:29:32 -0700 Subject: [PATCH 16/94] Adding print.sr_model to pkgdown --- pkgdown/_pkgdown.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml index 39698daf..1c1ef43b 100644 --- a/pkgdown/_pkgdown.yml +++ b/pkgdown/_pkgdown.yml @@ -41,6 +41,7 @@ reference: - title: Summarize seroresponse model estimates contents: - post_summ + - print.sr_model - title: Example data sets contents: - serodynamics_example From ff9ee850044a34b340d32e0d46322d9d1b6f6644 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Tue, 8 Jul 2025 23:33:18 -0700 Subject: [PATCH 17/94] Deleting a previous default print method that was being created --- R/print_sero_mod_output.R | 32 -------------------------------- 1 file changed, 32 deletions(-) delete mode 100644 R/print_sero_mod_output.R diff --git a/R/print_sero_mod_output.R b/R/print_sero_mod_output.R deleted file mode 100644 index dc950058..00000000 --- a/R/print_sero_mod_output.R +++ /dev/null @@ -1,32 +0,0 @@ -#' @title Default print method for run_mod output -#' @author Sam Schildhauer -#' @description -#' Will print a default output for a run_mod object that specifies the median -#' value of the posterior distribution for serokinetic curve parameters (y0, -#' y1, t1, alpha, shape) by stratification (if specified) and antigen/iso type. -#' @param obj A [serodynamics::sero_mod_output] object. -#' @returns A [dplyr::tbl_df] that contains the median value of the posterior -#' distribution of stratifications (if any specified), antigen/iso type, and -#' parameter value. -#' @export -#' @example inst/examples/run_mod-examples.R - -print.sero_mod_output <- function(obj) { - - # Summarizing results - df_obj <- data.frame("Parameter" = obj$Parameter, "Iso_type" = obj$Iso_type, - "Stratification" = obj$Stratification, - "Value" = obj$value) - if (unique(df_obj$Stratification == "None")) { - to_print <- df_obj |> - dplyr::group_by(Iso_type, Parameter) |> - dplyr::summarize(median = median(Value)) |> - tidyr::spread(Parameter, median) - } else { - to_print <- df_obj |> - dplyr::group_by(Stratification, Iso_type, Parameter) |> - dplyr::summarize(median = median(Value)) |> - tidyr::spread(Parameter, median) - } - to_print -} From 8eed4a7c768d4813421c4390e44f18258f97d8a7 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Tue, 8 Jul 2025 23:34:27 -0700 Subject: [PATCH 18/94] Updating function for pivot_wider --- R/print.sr_model.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index 887ddabf..00780c98 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -16,7 +16,7 @@ print.sr_model <- function(data) { data_group <- data |> dplyr::group_by(Stratification, Iso_type, Parameter) |> dplyr::summarise(mean_val = mean(value)) |> - tidyr::spread(Parameter, mean_val) |> + pivot_wider(Parameter, mean_val) |> dplyr::arrange(Iso_type) # Taking out stratification column if not specified if(unique(data$Stratification == "None")) { From 7a5ec6266efb9f9e3491ea5476e4759522f6dd1a Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Tue, 8 Jul 2025 23:35:14 -0700 Subject: [PATCH 19/94] Updating documentation to take out old print function --- NAMESPACE | 1 - man/print.sero_mod_output.Rd | 50 ------------------------------------ 2 files changed, 51 deletions(-) delete mode 100644 man/print.sero_mod_output.Rd diff --git a/NAMESPACE b/NAMESPACE index 0bd66d02..c45e1ccf 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,7 +1,6 @@ # Generated by roxygen2: do not edit by hand S3method(autoplot,case_data) -S3method(print,sero_mod_output) S3method(print,sr_model) export(as_case_data) export(autoplot) diff --git a/man/print.sero_mod_output.Rd b/man/print.sero_mod_output.Rd deleted file mode 100644 index 0dd8540f..00000000 --- a/man/print.sero_mod_output.Rd +++ /dev/null @@ -1,50 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/print_sero_mod_output.R -\name{print.sero_mod_output} -\alias{print.sero_mod_output} -\title{Default print method for run_mod output} -\usage{ -\method{print}{sero_mod_output}(obj) -} -\arguments{ -\item{obj}{A \link{sero_mod_output} object.} -} -\value{ -A \link[dplyr:tbl_df]{dplyr::tbl_df} that contains the median value of the posterior -distribution of stratifications (if any specified), antigen/iso type, and -parameter value. -} -\description{ -Will print a default output for a run_mod object that specifies the median -value of the posterior distribution for serokinetic curve parameters (y0, -y1, t1, alpha, shape) by stratification (if specified) and antigen/iso type. -} -\examples{ -if (!is.element(runjags::findjags(), c("", NULL))) { - library(runjags) - set.seed(1) - library(dplyr) - strat1 <- serocalculator::typhoid_curves_nostrat_100 |> - sim_case_data(n = 100) |> - mutate(strat = "stratum 2") - strat2 <- serocalculator::typhoid_curves_nostrat_100 |> - sim_case_data(n = 100) |> - mutate(strat = "stratum 1") - - dataset <- bind_rows(strat1, strat2) - - fitted_model <- run_mod( - data = dataset, # The data set input - file_mod = serodynamics_example("model.jags"), - nchain = 4, # Number of mcmc chains to run - nadapt = 100, # Number of adaptations to run - nburn = 100, # Number of unrecorded samples before sampling begins - nmc = 1000, - niter = 2000, # Number of iterations - strat = "strat" - ) # Variable to be stratified -} -} -\author{ -Sam Schildhauer -} From eb4e282c2f32fd4a93b8b8cb4d7b9f0e9a213fb9 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 9 Jul 2025 17:34:54 -0700 Subject: [PATCH 20/94] Updating wordlist --- inst/WORDLIST | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/inst/WORDLIST b/inst/WORDLIST index 12b8fafc..ba6d083d 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -1,6 +1,8 @@ +Biomarker CMD CodeFactor Codecov +Hyperpriors JAGs Lifecycle Postprocess @@ -9,6 +11,8 @@ Traceplots behaviour biomarker biomarkers +bmatrix +cdot dobson dotplots geoms @@ -16,21 +20,27 @@ ggproto hyp hyperprior hyperpriors +ij iso isotype isotypes +mathcal mcmc nmc +overfit params prec +pred rhat sd seroconversion serocourse seroresponse seroresponses +sr strat stratifications tbl +tibble unstratified wishdf From 141ba3c7aebfc6fa4b9a9fc5d1dd1b7b61db507d Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 9 Jul 2025 17:46:37 -0700 Subject: [PATCH 21/94] Updating lint --- R/print.sr_model.R | 17 +++++++---------- 1 file changed, 7 insertions(+), 10 deletions(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index 00780c98..a5dff189 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -14,17 +14,14 @@ #' print(nepal_sees_jags_output) print.sr_model <- function(data) { data_group <- data |> - dplyr::group_by(Stratification, Iso_type, Parameter) |> - dplyr::summarise(mean_val = mean(value)) |> - pivot_wider(Parameter, mean_val) |> - dplyr::arrange(Iso_type) + dplyr::group_by(.data$Stratification, .data$Iso_type, .data$Parameter) |> + dplyr::summarise(mean_val = mean(.data$value)) |> + tidyr::pivot_wider(names_from = .data$Parameter, + values_from = .data$mean_val) |> + dplyr::arrange(.data$Iso_type) # Taking out stratification column if not specified - if(unique(data$Stratification == "None")) { - data_group <- data_group[,2:7] + if (unique(data$Stratification == "None")) { + data_group <- data_group[, 2:7] } data_group } - - - - \ No newline at end of file From f95a88aa4b0323d8a901e055ff01b55862321926 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 9 Jul 2025 20:29:47 -0700 Subject: [PATCH 22/94] Fixing no lint. --- R/print.sr_model.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index a5dff189..33a3fed2 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -12,7 +12,7 @@ #' @export #' @examples #' print(nepal_sees_jags_output) -print.sr_model <- function(data) { +print.sr_model <- function(data) { # nolint data_group <- data |> dplyr::group_by(.data$Stratification, .data$Iso_type, .data$Parameter) |> dplyr::summarise(mean_val = mean(.data$value)) |> From 4dcd890514bcf6fec80a3a040595c778a6f6d30a Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Sun, 13 Jul 2025 19:32:41 -0700 Subject: [PATCH 23/94] Updating test lint --- tests/testthat/test-print.sr_model.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/testthat/test-print.sr_model.R b/tests/testthat/test-print.sr_model.R index 3f0d0e11..1a523b39 100644 --- a/tests/testthat/test-print.sr_model.R +++ b/tests/testthat/test-print.sr_model.R @@ -3,7 +3,7 @@ test_that( code = { withr::local_seed(1) results <- print(nepal_sees_jags_output) |> - ssdtools:::expect_snapshot_data("default-print-runmod-object") + ssdtools:::expect_snapshot_data("default-print-runmod-object") } ) From ee0a73c934f0266f10feea147e79761aaac9a71c Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Sun, 13 Jul 2025 19:36:59 -0700 Subject: [PATCH 24/94] Changing review recommended test code --- R/print.sr_model.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index 33a3fed2..86aee141 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -17,7 +17,7 @@ print.sr_model <- function(data) { # nolint dplyr::group_by(.data$Stratification, .data$Iso_type, .data$Parameter) |> dplyr::summarise(mean_val = mean(.data$value)) |> tidyr::pivot_wider(names_from = .data$Parameter, - values_from = .data$mean_val) |> + values_from = mean_val) |> dplyr::arrange(.data$Iso_type) # Taking out stratification column if not specified if (unique(data$Stratification == "None")) { From 0dbc9a2e811a37566f1050b08cf9e29fba32dfcd Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Sun, 13 Jul 2025 19:38:03 -0700 Subject: [PATCH 25/94] Updating test code based on review recommendations --- R/print.sr_model.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index 86aee141..675acad5 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -16,7 +16,7 @@ print.sr_model <- function(data) { # nolint data_group <- data |> dplyr::group_by(.data$Stratification, .data$Iso_type, .data$Parameter) |> dplyr::summarise(mean_val = mean(.data$value)) |> - tidyr::pivot_wider(names_from = .data$Parameter, + tidyr::pivot_wider(names_from = Parameter, values_from = mean_val) |> dplyr::arrange(.data$Iso_type) # Taking out stratification column if not specified From a22ed27c47ec4093deaf5b157bb0997d1ea95844 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Sun, 13 Jul 2025 20:13:05 -0700 Subject: [PATCH 26/94] Adding .data$ back in to code --- R/print.sr_model.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index 675acad5..33a3fed2 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -16,8 +16,8 @@ print.sr_model <- function(data) { # nolint data_group <- data |> dplyr::group_by(.data$Stratification, .data$Iso_type, .data$Parameter) |> dplyr::summarise(mean_val = mean(.data$value)) |> - tidyr::pivot_wider(names_from = Parameter, - values_from = mean_val) |> + tidyr::pivot_wider(names_from = .data$Parameter, + values_from = .data$mean_val) |> dplyr::arrange(.data$Iso_type) # Taking out stratification column if not specified if (unique(data$Stratification == "None")) { From 29ec557dcc461c794fd95eefc5f47047b7f19ebe Mon Sep 17 00:00:00 2001 From: Samuel Schildhauer <165851188+sschildhauer@users.noreply.github.com> Date: Tue, 15 Jul 2025 18:18:44 -0700 Subject: [PATCH 27/94] Update NEWS.md Co-authored-by: Douglas Ezra Morrison --- NEWS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index a51dca5d..3d2dedea 100644 --- a/NEWS.md +++ b/NEWS.md @@ -4,7 +4,7 @@ ## New features -* Creating default print.sr_model function for sr_model class (#) +* Creating default print.sr_model function for sr_model class (#114) * Replacing old data object with new run_mod output (#102) * Adding class assignment to run_mod output (#76) * Making prep_priors modifiable (#78) From 9de64b06cfe30434bac93abe35ec3001e8688418 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 16 Jul 2025 20:29:10 -0700 Subject: [PATCH 28/94] Updating parameter inputs to refelct x, ... --- R/print.sr_model.R | 7 ++++--- man/print.sr_model.Rd | 6 ++++-- 2 files changed, 8 insertions(+), 5 deletions(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index 33a3fed2..d71fcbe3 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -4,7 +4,8 @@ #' A default print method for class `sr_model` that includes the mean posterior #' distribution for antibody kinetic curve parameters by `Iso_type` and #' `Stratification` (if specified). -#' @param data An `sr_model` output object from the +#' @param x An `sr_model` output object from [run_mod()]. +#' @param ... Additional arguments affecting the summary produced. #' [serodynamics::run_mod()] function. #' @returns A [dplyr::grouped_df] that #' contains the mean posterior distribution for antibody kinetic curve @@ -12,8 +13,8 @@ #' @export #' @examples #' print(nepal_sees_jags_output) -print.sr_model <- function(data) { # nolint - data_group <- data |> +print.sr_model <- function(x, ...) { # nolint + data_group <- x |> dplyr::group_by(.data$Stratification, .data$Iso_type, .data$Parameter) |> dplyr::summarise(mean_val = mean(.data$value)) |> tidyr::pivot_wider(names_from = .data$Parameter, diff --git a/man/print.sr_model.Rd b/man/print.sr_model.Rd index eb91c2a4..7f4d0fee 100644 --- a/man/print.sr_model.Rd +++ b/man/print.sr_model.Rd @@ -5,10 +5,12 @@ \title{Default print for \code{\link[=run_mod]{run_mod()}} output object of class \code{sr_model}} \usage{ -\method{print}{sr_model}(data) +\method{print}{sr_model}(x, ...) } \arguments{ -\item{data}{An \code{sr_model} output object from the +\item{x}{An \code{sr_model} output object from \code{\link[=run_mod]{run_mod()}}.} + +\item{...}{Additional arguments affecting the summary produced. \code{\link[=run_mod]{run_mod()}} function.} } \value{ From b1d15c48a72dbfe2760052edbec12f976b9d9341 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 16 Jul 2025 20:32:13 -0700 Subject: [PATCH 29/94] Fixing column call for taking out Stratification --- R/print.sr_model.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index d71fcbe3..da8abbbf 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -22,7 +22,7 @@ print.sr_model <- function(x, ...) { # nolint dplyr::arrange(.data$Iso_type) # Taking out stratification column if not specified if (unique(data$Stratification == "None")) { - data_group <- data_group[, 2:7] + data_group <- data_group |> select(-c(Stratification)) } data_group } From 0dcac1899160dd16f9bfcca60c3271d77d596fb2 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 16 Jul 2025 20:33:09 -0700 Subject: [PATCH 30/94] Fixing column Stratification exclusion --- R/print.sr_model.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index da8abbbf..5c4b4c6f 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -22,7 +22,7 @@ print.sr_model <- function(x, ...) { # nolint dplyr::arrange(.data$Iso_type) # Taking out stratification column if not specified if (unique(data$Stratification == "None")) { - data_group <- data_group |> select(-c(Stratification)) + data_group <- data_group |> select(-all_of(Stratification)) } data_group } From 86e9965108ecc6ca870d3c86b459b3028ed3d191 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 16 Jul 2025 20:36:01 -0700 Subject: [PATCH 31/94] Changing object call in function to "x" --- R/print.sr_model.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index 5c4b4c6f..46bf5d26 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -14,7 +14,7 @@ #' @examples #' print(nepal_sees_jags_output) print.sr_model <- function(x, ...) { # nolint - data_group <- x |> + x <- x |> dplyr::group_by(.data$Stratification, .data$Iso_type, .data$Parameter) |> dplyr::summarise(mean_val = mean(.data$value)) |> tidyr::pivot_wider(names_from = .data$Parameter, @@ -22,7 +22,7 @@ print.sr_model <- function(x, ...) { # nolint dplyr::arrange(.data$Iso_type) # Taking out stratification column if not specified if (unique(data$Stratification == "None")) { - data_group <- data_group |> select(-all_of(Stratification)) + x <- x |> select(-all_of(Stratification)) } - data_group + invisible(x) } From d97e4b2e750d3913cc7593464704b05fdae3dc9f Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 16 Jul 2025 20:46:07 -0700 Subject: [PATCH 32/94] Updating test for default print --- tests/testthat/test-print.sr_model.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/testthat/test-print.sr_model.R b/tests/testthat/test-print.sr_model.R index 1a523b39..440b820b 100644 --- a/tests/testthat/test-print.sr_model.R +++ b/tests/testthat/test-print.sr_model.R @@ -3,7 +3,7 @@ test_that( code = { withr::local_seed(1) results <- print(nepal_sees_jags_output) |> - ssdtools:::expect_snapshot_data("default-print-runmod-object") + ssdtools:::expect_snapshot("default-print-runmod-object") } ) From 42b181013acd8ce2c63ff31bbeb8f8d709453c0c Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 16 Jul 2025 20:59:15 -0700 Subject: [PATCH 33/94] Increment version number to 0.0.0.9036 --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index eac0b2cf..a5726c00 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: serodynamics Title: What the Package Does (One Line, Title Case) -Version: 0.0.0.9035 +Version: 0.0.0.9036 Authors@R: c( person("Peter", "Teunis", , "p.teunis@emory.edu", role = c("aut", "cph"), comment = "Author of the method and original code."), From 5c9fe1c125f97c996fb400b1b254476c2a9229f8 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 16 Jul 2025 21:10:23 -0700 Subject: [PATCH 34/94] Updating visible binding --- R/print.sr_model.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index 46bf5d26..356501c6 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -22,7 +22,7 @@ print.sr_model <- function(x, ...) { # nolint dplyr::arrange(.data$Iso_type) # Taking out stratification column if not specified if (unique(data$Stratification == "None")) { - x <- x |> select(-all_of(Stratification)) + x <- x |> select(-all_of(.data$Stratification)) } invisible(x) } From 1252e18ec751ff8b89d7e3e8058a45589be44a25 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Thu, 31 Jul 2025 16:12:25 +0700 Subject: [PATCH 35/94] Merged origin/main into default_print --- NEWS.md | 1 + R/ab.R | 11 +++++------ tests/testthat/_snaps/ab.md | 6 +++--- tests/testthat/test-ab.R | 6 +++--- 4 files changed, 12 insertions(+), 12 deletions(-) diff --git a/NEWS.md b/NEWS.md index 5b444e15..b854db07 100644 --- a/NEWS.md +++ b/NEWS.md @@ -47,6 +47,7 @@ None yet ## Developer-facing changes +* vectorized `ab()` function (#116) * Added `lintr::undesirable_function_linter()` to `.lintr.R` (#81) * Reformatted `.lintr` as R file (following https://github.com/r-lib/lintr/issues/2844#issuecomment-2776725389) (#81) diff --git a/R/ab.R b/R/ab.R index 10d2d585..652995c1 100644 --- a/R/ab.R +++ b/R/ab.R @@ -1,10 +1,9 @@ ab <- function(t, y0, y1, t1, alpha, shape) { beta <- bt(y0, y1, t1) - yt <- 0 - if (t <= t1) { - yt <- y0 * exp(beta * t) - } else { - yt <- (y1^(1 - shape) - (1 - shape) * alpha * (t - t1))^(1 / (1 - shape)) - } + yt <- ifelse( + t <= t1, + y0 * exp(beta * t), + (y1^(1 - shape) - (1 - shape) * alpha * (t - t1))^(1 / (1 - shape)) + ) return(yt) } diff --git a/tests/testthat/_snaps/ab.md b/tests/testthat/_snaps/ab.md index 70d5f3c2..cdacb76b 100644 --- a/tests/testthat/_snaps/ab.md +++ b/tests/testthat/_snaps/ab.md @@ -1,8 +1,8 @@ # results are consistent Code - do.call(dplyr::mutate(dplyr::select(params, -c(antigen_iso, iter), shape = r), - t = 10), what = ab) + do.call(dplyr::mutate(dplyr::rename(dplyr::select(params, -c(antigen_iso, iter)), + shape = r), t = 10), what = ab) Output - [1] 63.09329 + [1] 63.09329 157.74561 diff --git a/tests/testthat/test-ab.R b/tests/testthat/test-ab.R index f9407dae..51f388f2 100644 --- a/tests/testthat/test-ab.R +++ b/tests/testthat/test-ab.R @@ -1,11 +1,11 @@ test_that("results are consistent", { params <- serocalculator::typhoid_curves_nostrat_100 |> - head(1) + head(2) params |> - dplyr::select(-c(antigen_iso, iter), - shape = r) |> + dplyr::select(-c(antigen_iso, iter)) |> + dplyr::rename(shape = r) |> dplyr::mutate(t = 10) |> do.call(what = ab) |> expect_snapshot() From 9a6931eb04c65cfbc3bc8f7539c53a340207b832 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Thu, 31 Jul 2025 22:00:15 +0700 Subject: [PATCH 36/94] Updating output description and documentation --- R/print.sr_model.R | 7 ++++++- man/print.sr_model.Rd | 2 +- 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index 356501c6..861e43c6 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -7,13 +7,17 @@ #' @param x An `sr_model` output object from [run_mod()]. #' @param ... Additional arguments affecting the summary produced. #' [serodynamics::run_mod()] function. -#' @returns A [dplyr::grouped_df] that +#' @returns A data summary that #' contains the mean posterior distribution for antibody kinetic curve #' parameters by `Iso_type` and `Stratification` (if specified). #' @export #' @examples #' print(nepal_sees_jags_output) print.sr_model <- function(x, ...) { # nolint + + cat("An sr_model with the following mean values:") + cat("\n") + cat("\n") x <- x |> dplyr::group_by(.data$Stratification, .data$Iso_type, .data$Parameter) |> dplyr::summarise(mean_val = mean(.data$value)) |> @@ -24,5 +28,6 @@ print.sr_model <- function(x, ...) { # nolint if (unique(data$Stratification == "None")) { x <- x |> select(-all_of(.data$Stratification)) } + print(data.frame(x)) invisible(x) } diff --git a/man/print.sr_model.Rd b/man/print.sr_model.Rd index 7f4d0fee..49fc5db4 100644 --- a/man/print.sr_model.Rd +++ b/man/print.sr_model.Rd @@ -14,7 +14,7 @@ \code{\link[=run_mod]{run_mod()}} function.} } \value{ -A \link[dplyr:grouped_df]{dplyr::grouped_df} that +A data summary that contains the mean posterior distribution for antibody kinetic curve parameters by \code{Iso_type} and \code{Stratification} (if specified). } From 6dda0ca8f74cd2e7238d3caf73381047a821c2ee Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Thu, 31 Jul 2025 22:12:30 +0700 Subject: [PATCH 37/94] Increment version number to 0.0.0.9037 --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index a5726c00..44d2af08 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: serodynamics Title: What the Package Does (One Line, Title Case) -Version: 0.0.0.9036 +Version: 0.0.0.9037 Authors@R: c( person("Peter", "Teunis", , "p.teunis@emory.edu", role = c("aut", "cph"), comment = "Author of the method and original code."), From 26c78000fd23d35b884f078c4625a8e7393701c6 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Thu, 31 Jul 2025 22:27:30 +0700 Subject: [PATCH 38/94] Updating test and snapshot --- tests/testthat/_snaps/print.sr_model.md | 27 +++++++++++++++++++++++++ tests/testthat/test-print.sr_model.R | 5 +---- 2 files changed, 28 insertions(+), 4 deletions(-) create mode 100644 tests/testthat/_snaps/print.sr_model.md diff --git a/tests/testthat/_snaps/print.sr_model.md b/tests/testthat/_snaps/print.sr_model.md new file mode 100644 index 00000000..a235ba65 --- /dev/null +++ b/tests/testthat/_snaps/print.sr_model.md @@ -0,0 +1,27 @@ +# results are consistent with printed output for sr_model class + + Code + print(nepal_sees_jags_output) + Output + An sr_model with the following mean values: + + Condition + Warning: + Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. + i Please use `"Parameter"` instead of `.data$Parameter` + Warning: + Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. + i Please use `"mean_val"` instead of `.data$mean_val` + Warning: + Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. + i Please use `"Parameter"` instead of `.data$Parameter` + Warning: + Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. + i Please use `"mean_val"` instead of `.data$mean_val` + Output + Stratification Iso_type alpha shape t1 y0 y1 + 1 paratyphi HlyE_IgA 0.002286716 1.664825 3.850284 2.550720 1024.2988 + 2 typhi HlyE_IgA 0.002905432 1.612991 7.306797 2.967301 1031.8956 + 3 paratyphi HlyE_IgG 0.002568724 1.360532 4.779399 1.721313 833.1053 + 4 typhi HlyE_IgG 0.001536668 1.408457 8.728905 2.314505 338.5723 + diff --git a/tests/testthat/test-print.sr_model.R b/tests/testthat/test-print.sr_model.R index 440b820b..50966cd5 100644 --- a/tests/testthat/test-print.sr_model.R +++ b/tests/testthat/test-print.sr_model.R @@ -1,9 +1,6 @@ test_that( desc = "results are consistent with printed output for sr_model class", code = { - withr::local_seed(1) - results <- print(nepal_sees_jags_output) |> - ssdtools:::expect_snapshot("default-print-runmod-object") - + expect_snapshot(print(nepal_sees_jags_output)) } ) From 27b1c52b3872b226a07d63461a9f0f68b3bf7283 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Fri, 1 Aug 2025 11:47:49 +0700 Subject: [PATCH 39/94] Fixing lint in test --- tests/testthat/test-print.sr_model.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/testthat/test-print.sr_model.R b/tests/testthat/test-print.sr_model.R index 50966cd5..d0b248c6 100644 --- a/tests/testthat/test-print.sr_model.R +++ b/tests/testthat/test-print.sr_model.R @@ -1,6 +1,6 @@ test_that( desc = "results are consistent with printed output for sr_model class", code = { - expect_snapshot(print(nepal_sees_jags_output)) + expect_snapshot(print(nepal_sees_jags_output)) } ) From e6b54c1c57dcc402d6bdd16f4df8e78c56506f15 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Fri, 1 Aug 2025 11:49:09 +0700 Subject: [PATCH 40/94] Fixing for closure --- R/print.sr_model.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index 861e43c6..3d18e6b0 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -25,7 +25,7 @@ print.sr_model <- function(x, ...) { # nolint values_from = .data$mean_val) |> dplyr::arrange(.data$Iso_type) # Taking out stratification column if not specified - if (unique(data$Stratification == "None")) { + if (unique(.data$Stratification == "None")) { x <- x |> select(-all_of(.data$Stratification)) } print(data.frame(x)) From 1657ff1ad6c00ecae7e5fbcec0ccb82901fbf046 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Fri, 1 Aug 2025 11:59:46 +0700 Subject: [PATCH 41/94] Fixing data call in if statement --- R/print.sr_model.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index 3d18e6b0..90edf098 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -25,8 +25,8 @@ print.sr_model <- function(x, ...) { # nolint values_from = .data$mean_val) |> dplyr::arrange(.data$Iso_type) # Taking out stratification column if not specified - if (unique(.data$Stratification == "None")) { - x <- x |> select(-all_of(.data$Stratification)) + if (unique(x$Stratification == "None")) { + x <- x |> select(-c(.data$Stratification)) } print(data.frame(x)) invisible(x) From 571bf165e8f31de981d793903280b96b026fe265 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Fri, 1 Aug 2025 13:38:56 +0700 Subject: [PATCH 42/94] Updating snap. --- R/print.sr_model.R | 7 ++++--- tests/testthat/_snaps/print.sr_model.md | 21 ++++++++++++++++----- 2 files changed, 20 insertions(+), 8 deletions(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index 90edf098..2fe15be5 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -19,8 +19,9 @@ print.sr_model <- function(x, ...) { # nolint cat("\n") cat("\n") x <- x |> - dplyr::group_by(.data$Stratification, .data$Iso_type, .data$Parameter) |> - dplyr::summarise(mean_val = mean(.data$value)) |> + dplyr::summarise(.by = c(.data$Stratification, .data$Iso_type, + .data$Parameter), + mean_val = mean(.data$value)) |> tidyr::pivot_wider(names_from = .data$Parameter, values_from = .data$mean_val) |> dplyr::arrange(.data$Iso_type) @@ -28,6 +29,6 @@ print.sr_model <- function(x, ...) { # nolint if (unique(x$Stratification == "None")) { x <- x |> select(-c(.data$Stratification)) } - print(data.frame(x)) + print(x) invisible(x) } diff --git a/tests/testthat/_snaps/print.sr_model.md b/tests/testthat/_snaps/print.sr_model.md index a235ba65..7da7bdd4 100644 --- a/tests/testthat/_snaps/print.sr_model.md +++ b/tests/testthat/_snaps/print.sr_model.md @@ -6,6 +6,15 @@ An sr_model with the following mean values: Condition + Warning: + Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. + i Please use `"Stratification"` instead of `.data$Stratification` + Warning: + Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. + i Please use `"Iso_type"` instead of `.data$Iso_type` + Warning: + Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. + i Please use `"Parameter"` instead of `.data$Parameter` Warning: Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. i Please use `"Parameter"` instead of `.data$Parameter` @@ -19,9 +28,11 @@ Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. i Please use `"mean_val"` instead of `.data$mean_val` Output - Stratification Iso_type alpha shape t1 y0 y1 - 1 paratyphi HlyE_IgA 0.002286716 1.664825 3.850284 2.550720 1024.2988 - 2 typhi HlyE_IgA 0.002905432 1.612991 7.306797 2.967301 1031.8956 - 3 paratyphi HlyE_IgG 0.002568724 1.360532 4.779399 1.721313 833.1053 - 4 typhi HlyE_IgG 0.001536668 1.408457 8.728905 2.314505 338.5723 + # A tibble: 4 x 7 + Stratification Iso_type alpha shape t1 y0 y1 + + 1 typhi HlyE_IgA 0.00291 1.61 7.31 2.97 1032. + 2 paratyphi HlyE_IgA 0.00229 1.66 3.85 2.55 1024. + 3 typhi HlyE_IgG 0.00154 1.41 8.73 2.31 339. + 4 paratyphi HlyE_IgG 0.00257 1.36 4.78 1.72 833. From 95a91c9843bf911288e8595a145c97681c9c022e Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Sun, 3 Aug 2025 22:30:27 +0700 Subject: [PATCH 43/94] making output table a dataframe to get rid of tibble descriptors --- R/print.sr_model.R | 2 +- tests/testthat/_snaps/print.sr_model.md | 12 +++++------- 2 files changed, 6 insertions(+), 8 deletions(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index 2fe15be5..cb9e8cd9 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -29,6 +29,6 @@ print.sr_model <- function(x, ...) { # nolint if (unique(x$Stratification == "None")) { x <- x |> select(-c(.data$Stratification)) } - print(x) + print(as.data.frame(x)) invisible(x) } diff --git a/tests/testthat/_snaps/print.sr_model.md b/tests/testthat/_snaps/print.sr_model.md index 7da7bdd4..db291607 100644 --- a/tests/testthat/_snaps/print.sr_model.md +++ b/tests/testthat/_snaps/print.sr_model.md @@ -28,11 +28,9 @@ Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. i Please use `"mean_val"` instead of `.data$mean_val` Output - # A tibble: 4 x 7 - Stratification Iso_type alpha shape t1 y0 y1 - - 1 typhi HlyE_IgA 0.00291 1.61 7.31 2.97 1032. - 2 paratyphi HlyE_IgA 0.00229 1.66 3.85 2.55 1024. - 3 typhi HlyE_IgG 0.00154 1.41 8.73 2.31 339. - 4 paratyphi HlyE_IgG 0.00257 1.36 4.78 1.72 833. + Stratification Iso_type alpha shape t1 y0 y1 + 1 typhi HlyE_IgA 0.002905432 1.612991 7.306797 2.967301 1031.8956 + 2 paratyphi HlyE_IgA 0.002286716 1.664825 3.850284 2.550720 1024.2988 + 3 typhi HlyE_IgG 0.001536668 1.408457 8.728905 2.314505 338.5723 + 4 paratyphi HlyE_IgG 0.002568724 1.360532 4.779399 1.721313 833.1053 From 3915ec2a24fcf199c080847692776fdf3656ce5d Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Mon, 4 Aug 2025 15:50:31 +0700 Subject: [PATCH 44/94] Updating print test --- tests/testthat/_snaps/print.sr_model.md | 2 +- tests/testthat/test-print.sr_model.R | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/testthat/_snaps/print.sr_model.md b/tests/testthat/_snaps/print.sr_model.md index db291607..bbc55ae3 100644 --- a/tests/testthat/_snaps/print.sr_model.md +++ b/tests/testthat/_snaps/print.sr_model.md @@ -1,7 +1,7 @@ # results are consistent with printed output for sr_model class Code - print(nepal_sees_jags_output) + nepal_sees_jags_output Output An sr_model with the following mean values: diff --git a/tests/testthat/test-print.sr_model.R b/tests/testthat/test-print.sr_model.R index d0b248c6..a3f99df4 100644 --- a/tests/testthat/test-print.sr_model.R +++ b/tests/testthat/test-print.sr_model.R @@ -1,6 +1,6 @@ test_that( desc = "results are consistent with printed output for sr_model class", code = { - expect_snapshot(print(nepal_sees_jags_output)) + expect_snapshot(nepal_sees_jags_output) } ) From 4233b52596183e23806d4724598d56729119cece Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Mon, 4 Aug 2025 16:14:42 +0700 Subject: [PATCH 45/94] Updating snap --- tests/testthat/_snaps/print.sr_model.md | 2 +- tests/testthat/test-print.sr_model.R | 4 +++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/tests/testthat/_snaps/print.sr_model.md b/tests/testthat/_snaps/print.sr_model.md index bbc55ae3..13a362ad 100644 --- a/tests/testthat/_snaps/print.sr_model.md +++ b/tests/testthat/_snaps/print.sr_model.md @@ -1,7 +1,7 @@ # results are consistent with printed output for sr_model class Code - nepal_sees_jags_output + suppressWarnings(nepal_sees_jags_output) Output An sr_model with the following mean values: diff --git a/tests/testthat/test-print.sr_model.R b/tests/testthat/test-print.sr_model.R index a3f99df4..820bd268 100644 --- a/tests/testthat/test-print.sr_model.R +++ b/tests/testthat/test-print.sr_model.R @@ -1,6 +1,8 @@ test_that( desc = "results are consistent with printed output for sr_model class", code = { - expect_snapshot(nepal_sees_jags_output) + nepal_sees_jags_output |> + suppressWarnings() |> + expect_snapshot() } ) From 37f451e33ccc6fe940814aa6d56e5e5e9c0d7fe4 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Thu, 7 Aug 2025 13:10:20 +0700 Subject: [PATCH 46/94] Making model output median value --- R/print.sr_model.R | 10 +++++----- man/print.sr_model.Rd | 6 +++--- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index cb9e8cd9..980904be 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -1,9 +1,9 @@ #' @title Default print for [serodynamics::run_mod()] output object of class #' `sr_model` #' @description -#' A default print method for class `sr_model` that includes the mean posterior -#' distribution for antibody kinetic curve parameters by `Iso_type` and -#' `Stratification` (if specified). +#' A default print method for class `sr_model` that includes the median +#' posterior distribution for antibody kinetic curve parameters by `Iso_type` +#' and `Stratification` (if specified). #' @param x An `sr_model` output object from [run_mod()]. #' @param ... Additional arguments affecting the summary produced. #' [serodynamics::run_mod()] function. @@ -15,13 +15,13 @@ #' print(nepal_sees_jags_output) print.sr_model <- function(x, ...) { # nolint - cat("An sr_model with the following mean values:") + cat("An sr_model with the following median values:") cat("\n") cat("\n") x <- x |> dplyr::summarise(.by = c(.data$Stratification, .data$Iso_type, .data$Parameter), - mean_val = mean(.data$value)) |> + median_val = stats::median(.data$value)) |> tidyr::pivot_wider(names_from = .data$Parameter, values_from = .data$mean_val) |> dplyr::arrange(.data$Iso_type) diff --git a/man/print.sr_model.Rd b/man/print.sr_model.Rd index 49fc5db4..67be9223 100644 --- a/man/print.sr_model.Rd +++ b/man/print.sr_model.Rd @@ -19,9 +19,9 @@ contains the mean posterior distribution for antibody kinetic curve parameters by \code{Iso_type} and \code{Stratification} (if specified). } \description{ -A default print method for class \code{sr_model} that includes the mean posterior -distribution for antibody kinetic curve parameters by \code{Iso_type} and -\code{Stratification} (if specified). +A default print method for class \code{sr_model} that includes the median +posterior distribution for antibody kinetic curve parameters by \code{Iso_type} +and \code{Stratification} (if specified). } \examples{ print(nepal_sees_jags_output) From 3f8c7066ef5f106ed3811a65a86eb7d6bcaa0f3d Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Thu, 7 Aug 2025 13:11:32 +0700 Subject: [PATCH 47/94] Updating test snap --- R/print.sr_model.R | 2 +- tests/testthat/_snaps/print.sr_model.md | 16 ++++++++-------- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index 980904be..c7eca62c 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -23,7 +23,7 @@ print.sr_model <- function(x, ...) { # nolint .data$Parameter), median_val = stats::median(.data$value)) |> tidyr::pivot_wider(names_from = .data$Parameter, - values_from = .data$mean_val) |> + values_from = .data$median_val) |> dplyr::arrange(.data$Iso_type) # Taking out stratification column if not specified if (unique(x$Stratification == "None")) { diff --git a/tests/testthat/_snaps/print.sr_model.md b/tests/testthat/_snaps/print.sr_model.md index 13a362ad..01b63ff3 100644 --- a/tests/testthat/_snaps/print.sr_model.md +++ b/tests/testthat/_snaps/print.sr_model.md @@ -3,7 +3,7 @@ Code suppressWarnings(nepal_sees_jags_output) Output - An sr_model with the following mean values: + An sr_model with the following median values: Condition Warning: @@ -20,17 +20,17 @@ i Please use `"Parameter"` instead of `.data$Parameter` Warning: Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. - i Please use `"mean_val"` instead of `.data$mean_val` + i Please use `"median_val"` instead of `.data$median_val` Warning: Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. i Please use `"Parameter"` instead of `.data$Parameter` Warning: Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. - i Please use `"mean_val"` instead of `.data$mean_val` + i Please use `"median_val"` instead of `.data$median_val` Output - Stratification Iso_type alpha shape t1 y0 y1 - 1 typhi HlyE_IgA 0.002905432 1.612991 7.306797 2.967301 1031.8956 - 2 paratyphi HlyE_IgA 0.002286716 1.664825 3.850284 2.550720 1024.2988 - 3 typhi HlyE_IgG 0.001536668 1.408457 8.728905 2.314505 338.5723 - 4 paratyphi HlyE_IgG 0.002568724 1.360532 4.779399 1.721313 833.1053 + Stratification Iso_type alpha shape t1 y0 y1 + 1 typhi HlyE_IgA 0.001788800 1.538820 6.235540 2.405515 342.565 + 2 paratyphi HlyE_IgA 0.001272495 1.614535 3.700500 2.406050 153.787 + 3 typhi HlyE_IgG 0.001140990 1.346445 7.025800 2.073250 252.156 + 4 paratyphi HlyE_IgG 0.001742340 1.321350 4.370495 1.537045 288.325 From ff21aa331d984005c6e6ee786f3da8c94e370993 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Fri, 8 Aug 2025 14:26:49 +0700 Subject: [PATCH 48/94] Increment version number to 0.0.0.9038 --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 44d2af08..65983bda 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: serodynamics Title: What the Package Does (One Line, Title Case) -Version: 0.0.0.9037 +Version: 0.0.0.9038 Authors@R: c( person("Peter", "Teunis", , "p.teunis@emory.edu", role = c("aut", "cph"), comment = "Author of the method and original code."), From 47ab5b07d3193e95fd77f58f148035f9edf8c204 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Fri, 8 Aug 2025 14:33:51 +0700 Subject: [PATCH 49/94] Redoing snap --- tests/testthat/_snaps/print.sr_model.md | 36 ------------------------- 1 file changed, 36 deletions(-) delete mode 100644 tests/testthat/_snaps/print.sr_model.md diff --git a/tests/testthat/_snaps/print.sr_model.md b/tests/testthat/_snaps/print.sr_model.md deleted file mode 100644 index 01b63ff3..00000000 --- a/tests/testthat/_snaps/print.sr_model.md +++ /dev/null @@ -1,36 +0,0 @@ -# results are consistent with printed output for sr_model class - - Code - suppressWarnings(nepal_sees_jags_output) - Output - An sr_model with the following median values: - - Condition - Warning: - Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. - i Please use `"Stratification"` instead of `.data$Stratification` - Warning: - Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. - i Please use `"Iso_type"` instead of `.data$Iso_type` - Warning: - Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. - i Please use `"Parameter"` instead of `.data$Parameter` - Warning: - Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. - i Please use `"Parameter"` instead of `.data$Parameter` - Warning: - Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. - i Please use `"median_val"` instead of `.data$median_val` - Warning: - Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. - i Please use `"Parameter"` instead of `.data$Parameter` - Warning: - Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. - i Please use `"median_val"` instead of `.data$median_val` - Output - Stratification Iso_type alpha shape t1 y0 y1 - 1 typhi HlyE_IgA 0.001788800 1.538820 6.235540 2.405515 342.565 - 2 paratyphi HlyE_IgA 0.001272495 1.614535 3.700500 2.406050 153.787 - 3 typhi HlyE_IgG 0.001140990 1.346445 7.025800 2.073250 252.156 - 4 paratyphi HlyE_IgG 0.001742340 1.321350 4.370495 1.537045 288.325 - From 0c2a6bd403bd0a9f4145d51824dc5ab4cd0715b3 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Fri, 8 Aug 2025 14:35:15 +0700 Subject: [PATCH 50/94] Updating snap to suppress warnings --- R/print.sr_model.R | 3 ++- tests/testthat/_snaps/print.sr_model.md | 36 +++++++++++++++++++++++++ 2 files changed, 38 insertions(+), 1 deletion(-) create mode 100644 tests/testthat/_snaps/print.sr_model.md diff --git a/R/print.sr_model.R b/R/print.sr_model.R index c7eca62c..a10f930b 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -24,7 +24,8 @@ print.sr_model <- function(x, ...) { # nolint median_val = stats::median(.data$value)) |> tidyr::pivot_wider(names_from = .data$Parameter, values_from = .data$median_val) |> - dplyr::arrange(.data$Iso_type) + dplyr::arrange(.data$Iso_type) |> + suppressWarnings() # Taking out stratification column if not specified if (unique(x$Stratification == "None")) { x <- x |> select(-c(.data$Stratification)) diff --git a/tests/testthat/_snaps/print.sr_model.md b/tests/testthat/_snaps/print.sr_model.md new file mode 100644 index 00000000..01b63ff3 --- /dev/null +++ b/tests/testthat/_snaps/print.sr_model.md @@ -0,0 +1,36 @@ +# results are consistent with printed output for sr_model class + + Code + suppressWarnings(nepal_sees_jags_output) + Output + An sr_model with the following median values: + + Condition + Warning: + Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. + i Please use `"Stratification"` instead of `.data$Stratification` + Warning: + Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. + i Please use `"Iso_type"` instead of `.data$Iso_type` + Warning: + Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. + i Please use `"Parameter"` instead of `.data$Parameter` + Warning: + Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. + i Please use `"Parameter"` instead of `.data$Parameter` + Warning: + Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. + i Please use `"median_val"` instead of `.data$median_val` + Warning: + Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. + i Please use `"Parameter"` instead of `.data$Parameter` + Warning: + Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. + i Please use `"median_val"` instead of `.data$median_val` + Output + Stratification Iso_type alpha shape t1 y0 y1 + 1 typhi HlyE_IgA 0.001788800 1.538820 6.235540 2.405515 342.565 + 2 paratyphi HlyE_IgA 0.001272495 1.614535 3.700500 2.406050 153.787 + 3 typhi HlyE_IgG 0.001140990 1.346445 7.025800 2.073250 252.156 + 4 paratyphi HlyE_IgG 0.001742340 1.321350 4.370495 1.537045 288.325 + From 04c720002ca5cb39520e0ce06f51cdfa654d75bf Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Fri, 8 Aug 2025 14:35:27 +0700 Subject: [PATCH 51/94] Updating snap --- tests/testthat/_snaps/print.sr_model.md | 23 ----------------------- 1 file changed, 23 deletions(-) diff --git a/tests/testthat/_snaps/print.sr_model.md b/tests/testthat/_snaps/print.sr_model.md index 01b63ff3..e796e1c9 100644 --- a/tests/testthat/_snaps/print.sr_model.md +++ b/tests/testthat/_snaps/print.sr_model.md @@ -5,29 +5,6 @@ Output An sr_model with the following median values: - Condition - Warning: - Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. - i Please use `"Stratification"` instead of `.data$Stratification` - Warning: - Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. - i Please use `"Iso_type"` instead of `.data$Iso_type` - Warning: - Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. - i Please use `"Parameter"` instead of `.data$Parameter` - Warning: - Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. - i Please use `"Parameter"` instead of `.data$Parameter` - Warning: - Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. - i Please use `"median_val"` instead of `.data$median_val` - Warning: - Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. - i Please use `"Parameter"` instead of `.data$Parameter` - Warning: - Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0. - i Please use `"median_val"` instead of `.data$median_val` - Output Stratification Iso_type alpha shape t1 y0 y1 1 typhi HlyE_IgA 0.001788800 1.538820 6.235540 2.405515 342.565 2 paratyphi HlyE_IgA 0.001272495 1.614535 3.700500 2.406050 153.787 From 87dd5c7351870aa0b4bcf0f406ed819078bdfdb2 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Fri, 8 Aug 2025 14:49:45 +0700 Subject: [PATCH 52/94] troubleshooting snap --- tests/testthat/_snaps/print.sr_model.md | 2 +- tests/testthat/test-print.sr_model.R | 4 +--- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/tests/testthat/_snaps/print.sr_model.md b/tests/testthat/_snaps/print.sr_model.md index e796e1c9..634ff26c 100644 --- a/tests/testthat/_snaps/print.sr_model.md +++ b/tests/testthat/_snaps/print.sr_model.md @@ -1,7 +1,7 @@ # results are consistent with printed output for sr_model class Code - suppressWarnings(nepal_sees_jags_output) + nepal_sees_jags_output Output An sr_model with the following median values: diff --git a/tests/testthat/test-print.sr_model.R b/tests/testthat/test-print.sr_model.R index 820bd268..b835db0e 100644 --- a/tests/testthat/test-print.sr_model.R +++ b/tests/testthat/test-print.sr_model.R @@ -1,8 +1,6 @@ test_that( desc = "results are consistent with printed output for sr_model class", code = { - nepal_sees_jags_output |> - suppressWarnings() |> - expect_snapshot() + testthat::expect_snapshot(nepal_sees_jags_output) } ) From 9f2fd61a1b038df496865eff79455458bd91e41d Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Fri, 8 Aug 2025 15:14:49 +0700 Subject: [PATCH 53/94] Fixing lint --- tests/testthat/test-print.sr_model.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/testthat/test-print.sr_model.R b/tests/testthat/test-print.sr_model.R index b835db0e..c1715a0d 100644 --- a/tests/testthat/test-print.sr_model.R +++ b/tests/testthat/test-print.sr_model.R @@ -1,6 +1,6 @@ test_that( desc = "results are consistent with printed output for sr_model class", code = { - testthat::expect_snapshot(nepal_sees_jags_output) + testthat::expect_snapshot(nepal_sees_jags_output) } ) From 55c97aa8f283436054f2f44cc53f9d8d488d3575 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Fri, 12 Sep 2025 14:27:54 -0700 Subject: [PATCH 54/94] Merging with main --- DESCRIPTION | 4 ---- 1 file changed, 4 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 54a18405..742a6116 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,10 +1,6 @@ Package: serodynamics Title: What the Package Does (One Line, Title Case) -<<<<<<< HEAD -Version: 0.0.0.9038 -======= Version: 0.0.0.9041 ->>>>>>> d0c5aec9a60c1db30076e15b404f82261354cd3a Authors@R: c( person("Peter", "Teunis", , "p.teunis@emory.edu", role = c("aut", "cph"), comment = "Author of the method and original code."), From 058ed6119da66aa14475fa65847c884936fce7fa Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 1 Oct 2025 16:14:20 -0700 Subject: [PATCH 55/94] Updating autoplot documentation --- man/autoplot.case_data.Rd | 14 +++----------- 1 file changed, 3 insertions(+), 11 deletions(-) diff --git a/man/autoplot.case_data.Rd b/man/autoplot.case_data.Rd index 0dd118f6..4526b7ae 100644 --- a/man/autoplot.case_data.Rd +++ b/man/autoplot.case_data.Rd @@ -36,7 +36,7 @@ will be used as the layer data. A \code{function} can be created from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{\code{stat}}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used to override the default coupling between geoms and +argument can be used the override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. @@ -64,19 +64,11 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display. To include legend keys for all levels, even -when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, -but unobserved levels are omitted.} +display.} \item{\code{inherit.aes}}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from -the default plot specification, e.g. \code{\link[ggplot2:annotation_borders]{annotation_borders()}}.} - \item{\code{arrow}}{Arrow specification, as created by \code{\link[grid:arrow]{grid::arrow()}}.} - \item{\code{arrow.fill}}{fill colour to use for the arrow head (if closed). \code{NULL} -means use \code{colour} aesthetic.} - \item{\code{lineend}}{Line end style (round, butt, square).} - \item{\code{linejoin}}{Line join style (round, mitre, bevel).} - \item{\code{linemitre}}{Line mitre limit (number greater than 1).} +the default plot specification, e.g. \code{\link[ggplot2:borders]{borders()}}.} \item{\code{orientation}}{The orientation of the layer. The default (\code{NA}) automatically determines the orientation from the aesthetic mapping. In the rare event that this fails it can be given explicitly by setting \code{orientation} From a24fc41c219c1e34611c63b2388f196833668a7a Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 1 Oct 2025 16:17:15 -0700 Subject: [PATCH 56/94] Updating plot_predictive_curve snaps --- .../predicted-curve-linear.svg | 3 +-- .../predicted-curve-log.svg | 3 +-- .../predicted-curve-logx.svg | 3 +-- .../predicted-curve-multi-id-2.svg | 3 +-- .../predicted-curve-multi-id-3.svg | 21 +++++++++++++++++-- .../predicted-curve-multi-id-4.svg | 3 +-- .../predicted-curve-xlim.svg | 3 +-- 7 files changed, 25 insertions(+), 14 deletions(-) diff --git a/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-linear.svg b/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-linear.svg index 44bf0eec..ba78c0e6 100644 --- a/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-linear.svg +++ b/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-linear.svg @@ -18,7 +18,6 @@ - @@ -1076,7 +1075,7 @@ Median prediction Observed data Posterior samples - + 95% credible interval diff --git a/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-log.svg b/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-log.svg index f88e1393..574233f1 100644 --- a/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-log.svg +++ b/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-log.svg @@ -18,7 +18,6 @@ - @@ -1078,7 +1077,7 @@ Median prediction Observed data Posterior samples - + 95% credible interval diff --git a/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-logx.svg b/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-logx.svg index b4cd7d3b..2401c132 100644 --- a/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-logx.svg +++ b/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-logx.svg @@ -18,7 +18,6 @@ - @@ -1073,7 +1072,7 @@ Median prediction Observed data Posterior samples - + 95% credible interval diff --git a/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-multi-id-2.svg b/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-multi-id-2.svg index c6a5410c..51b97d17 100644 --- a/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-multi-id-2.svg +++ b/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-multi-id-2.svg @@ -18,7 +18,6 @@ - @@ -2144,7 +2143,7 @@ Median prediction Observed data Posterior samples - + 95% credible interval diff --git a/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-multi-id-3.svg b/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-multi-id-3.svg index 773e33bc..dc2cfaf9 100644 --- a/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-multi-id-3.svg +++ b/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-multi-id-3.svg @@ -18,7 +18,6 @@ - @@ -3129,6 +3128,15 @@ + + + + + + + + + @@ -3139,6 +3147,15 @@ + + + + + + + + + @@ -3186,7 +3203,7 @@ Median prediction Observed data Posterior samples - + 95% credible interval diff --git a/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-multi-id-4.svg b/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-multi-id-4.svg index 214e06f8..f1ccd4fc 100644 --- a/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-multi-id-4.svg +++ b/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-multi-id-4.svg @@ -18,7 +18,6 @@ - @@ -4237,7 +4236,7 @@ Median prediction Observed data Posterior samples - + 95% credible interval diff --git a/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-xlim.svg b/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-xlim.svg index 8d494e9c..18c2ac51 100644 --- a/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-xlim.svg +++ b/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-xlim.svg @@ -18,7 +18,6 @@ - @@ -1076,7 +1075,7 @@ Median prediction Observed data Posterior samples - + 95% credible interval From 1b90556c40c70fe0df4be71956a84abc08f85515 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 1 Oct 2025 16:17:47 -0700 Subject: [PATCH 57/94] Increment version number to 0.0.0.9043 --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 5307401d..32f96b5a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: serodynamics Title: What the Package Does (One Line, Title Case) -Version: 0.0.0.9042 +Version: 0.0.0.9043 Authors@R: c( person("Peter", "Teunis", , "p.teunis@emory.edu", role = c("aut", "cph"), comment = "Author of the method and original code."), From 2cad837b30eb33ab20590521334751cf168ab8b3 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 1 Oct 2025 16:41:04 -0700 Subject: [PATCH 58/94] Changing the median function to try and fix the snap issue --- R/print.sr_model.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index a10f930b..c5416580 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -21,7 +21,7 @@ print.sr_model <- function(x, ...) { # nolint x <- x |> dplyr::summarise(.by = c(.data$Stratification, .data$Iso_type, .data$Parameter), - median_val = stats::median(.data$value)) |> + median_val = median(.data$value)) |> tidyr::pivot_wider(names_from = .data$Parameter, values_from = .data$median_val) |> dplyr::arrange(.data$Iso_type) |> From 97f293138bfce070182486a9eb01c9cc94c5bf68 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Thu, 2 Oct 2025 15:30:21 -0700 Subject: [PATCH 59/94] Updating plot_predicted curve snaps after ggplot update --- .../predicted-curve-linear.svg | 3 ++- .../predicted-curve-log.svg | 3 ++- .../predicted-curve-logx.svg | 3 ++- .../predicted-curve-multi-id-2.svg | 3 ++- .../predicted-curve-multi-id-3.svg | 21 ++----------------- .../predicted-curve-multi-id-4.svg | 3 ++- .../predicted-curve-xlim.svg | 3 ++- 7 files changed, 14 insertions(+), 25 deletions(-) diff --git a/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-linear.svg b/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-linear.svg index ba78c0e6..44bf0eec 100644 --- a/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-linear.svg +++ b/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-linear.svg @@ -18,6 +18,7 @@ + @@ -1075,7 +1076,7 @@ Median prediction Observed data Posterior samples - + 95% credible interval diff --git a/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-log.svg b/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-log.svg index 574233f1..f88e1393 100644 --- a/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-log.svg +++ b/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-log.svg @@ -18,6 +18,7 @@ + @@ -1077,7 +1078,7 @@ Median prediction Observed data Posterior samples - + 95% credible interval diff --git a/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-logx.svg b/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-logx.svg index 2401c132..b4cd7d3b 100644 --- a/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-logx.svg +++ b/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-logx.svg @@ -18,6 +18,7 @@ + @@ -1072,7 +1073,7 @@ Median prediction Observed data Posterior samples - + 95% credible interval diff --git a/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-multi-id-2.svg b/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-multi-id-2.svg index 51b97d17..c6a5410c 100644 --- a/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-multi-id-2.svg +++ b/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-multi-id-2.svg @@ -18,6 +18,7 @@ + @@ -2143,7 +2144,7 @@ Median prediction Observed data Posterior samples - + 95% credible interval diff --git a/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-multi-id-3.svg b/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-multi-id-3.svg index dc2cfaf9..773e33bc 100644 --- a/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-multi-id-3.svg +++ b/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-multi-id-3.svg @@ -18,6 +18,7 @@ + @@ -3128,15 +3129,6 @@ - - - - - - - - - @@ -3147,15 +3139,6 @@ - - - - - - - - - @@ -3203,7 +3186,7 @@ Median prediction Observed data Posterior samples - + 95% credible interval diff --git a/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-multi-id-4.svg b/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-multi-id-4.svg index f1ccd4fc..214e06f8 100644 --- a/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-multi-id-4.svg +++ b/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-multi-id-4.svg @@ -18,6 +18,7 @@ + @@ -4236,7 +4237,7 @@ Median prediction Observed data Posterior samples - + 95% credible interval diff --git a/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-xlim.svg b/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-xlim.svg index 18c2ac51..8d494e9c 100644 --- a/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-xlim.svg +++ b/tests/testthat/_snaps/plot_predicted_curve/predicted-curve-xlim.svg @@ -18,6 +18,7 @@ + @@ -1075,7 +1076,7 @@ Median prediction Observed data Posterior samples - + 95% credible interval From f9a3f53ff7c5b4350cb9d0c9bcf0da2d58cdc426 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Thu, 2 Oct 2025 15:31:04 -0700 Subject: [PATCH 60/94] Updating autoplot documentation --- man/autoplot.case_data.Rd | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/man/autoplot.case_data.Rd b/man/autoplot.case_data.Rd index 4526b7ae..0dd118f6 100644 --- a/man/autoplot.case_data.Rd +++ b/man/autoplot.case_data.Rd @@ -36,7 +36,7 @@ will be used as the layer data. A \code{function} can be created from a \code{formula} (e.g. \code{~ head(.x, 10)}).} \item{\code{stat}}{The statistical transformation to use on the data for this layer. When using a \verb{geom_*()} function to construct a layer, the \code{stat} -argument can be used the override the default coupling between geoms and +argument can be used to override the default coupling between geoms and stats. The \code{stat} argument accepts the following: \itemize{ \item A \code{Stat} ggproto subclass, for example \code{StatCount}. @@ -64,11 +64,19 @@ a warning. If \code{TRUE}, missing values are silently removed.} \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes. It can also be a named logical vector to finely select the aesthetics to -display.} +display. To include legend keys for all levels, even +when no data exists, use \code{TRUE}. If \code{NA}, all levels are shown in legend, +but unobserved levels are omitted.} \item{\code{inherit.aes}}{If \code{FALSE}, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from -the default plot specification, e.g. \code{\link[ggplot2:borders]{borders()}}.} +the default plot specification, e.g. \code{\link[ggplot2:annotation_borders]{annotation_borders()}}.} + \item{\code{arrow}}{Arrow specification, as created by \code{\link[grid:arrow]{grid::arrow()}}.} + \item{\code{arrow.fill}}{fill colour to use for the arrow head (if closed). \code{NULL} +means use \code{colour} aesthetic.} + \item{\code{lineend}}{Line end style (round, butt, square).} + \item{\code{linejoin}}{Line join style (round, mitre, bevel).} + \item{\code{linemitre}}{Line mitre limit (number greater than 1).} \item{\code{orientation}}{The orientation of the layer. The default (\code{NA}) automatically determines the orientation from the aesthetic mapping. In the rare event that this fails it can be given explicitly by setting \code{orientation} From 597d6138dd4caacfc42fa53d28d1114efcc494ae Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 8 Oct 2025 15:35:23 -0700 Subject: [PATCH 61/94] Merged origin/main into default_print --- DESCRIPTION | 5 ++--- NEWS.md | 1 + inst/WORDLIST | 2 ++ 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 32f96b5a..84539943 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -20,7 +20,7 @@ Imports: cli, coda, dplyr, - ggmcmc (>= 1.5.1.1), + ggmcmc (>= 1.5.1.2), ggplot2, purrr, rlang, @@ -62,8 +62,7 @@ Config/needs/test: rlist Config/needs/check: commonmark, xml2 Remotes: - ucd-serg/serocalculator, - xfim/ggmcmc + ucd-serg/serocalculator Depends: R (>= 4.1.0) LazyData: true diff --git a/NEWS.md b/NEWS.md index b94623f5..b2371a73 100644 --- a/NEWS.md +++ b/NEWS.md @@ -49,6 +49,7 @@ None yet ## Developer-facing changes +* Switched ggmcmc dependency from GitHub dev version to CRAN v1.5.1.2 (#135) * vectorized `ab()` function (#116) * Added `lintr::undesirable_function_linter()` to `.lintr.R` (#81) * Reformatted `.lintr` as R file (following diff --git a/inst/WORDLIST b/inst/WORDLIST index 7e1af870..e408d40e 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -24,6 +24,7 @@ cdot cdots colour ddots +dev dobson dotplots dt @@ -31,6 +32,7 @@ dy epidemiologic frac geoms +ggmcmc ggproto hyp hyperprior From 64d7ea4a8a071d7b5ee8cf881e3fdc62e31f50d1 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 8 Oct 2025 18:03:49 -0700 Subject: [PATCH 62/94] Increment version number to 0.0.0.9044 --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 84539943..251af531 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: serodynamics Title: What the Package Does (One Line, Title Case) -Version: 0.0.0.9043 +Version: 0.0.0.9044 Authors@R: c( person("Peter", "Teunis", , "p.teunis@emory.edu", role = c("aut", "cph"), comment = "Author of the method and original code."), From 2985fc6c52fbf08e75dfe4483e07037670c690e3 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 8 Oct 2025 18:16:41 -0700 Subject: [PATCH 63/94] Adding option to print output as tibble --- R/print.sr_model.R | 10 +++++++++- man/print.sr_model.Rd | 4 +++- 2 files changed, 12 insertions(+), 2 deletions(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index c5416580..af223fa2 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -5,6 +5,7 @@ #' posterior distribution for antibody kinetic curve parameters by `Iso_type` #' and `Stratification` (if specified). #' @param x An `sr_model` output object from [run_mod()]. +#' @param print_tbl A [logical] indicator to print in style of [dplyr::tbl_df]. #' @param ... Additional arguments affecting the summary produced. #' [serodynamics::run_mod()] function. #' @returns A data summary that @@ -13,8 +14,14 @@ #' @export #' @examples #' print(nepal_sees_jags_output) -print.sr_model <- function(x, ...) { # nolint +print.sr_model <- function(x, + print_tbl = FALSE, + ...) { # nolint + if (print_tbl == FALSE) { + x <- as_tibble(x) + print(x) + } else { cat("An sr_model with the following median values:") cat("\n") cat("\n") @@ -32,4 +39,5 @@ print.sr_model <- function(x, ...) { # nolint } print(as.data.frame(x)) invisible(x) + } } diff --git a/man/print.sr_model.Rd b/man/print.sr_model.Rd index 67be9223..f3e2b8c2 100644 --- a/man/print.sr_model.Rd +++ b/man/print.sr_model.Rd @@ -5,11 +5,13 @@ \title{Default print for \code{\link[=run_mod]{run_mod()}} output object of class \code{sr_model}} \usage{ -\method{print}{sr_model}(x, ...) +\method{print}{sr_model}(x, print_tbl = FALSE, ...) } \arguments{ \item{x}{An \code{sr_model} output object from \code{\link[=run_mod]{run_mod()}}.} +\item{print_tbl}{A \link{logical} indicator to print in style of \link[dplyr:tbl_df]{dplyr::tbl_df}.} + \item{...}{Additional arguments affecting the summary produced. \code{\link[=run_mod]{run_mod()}} function.} } From 46d53a34294b6fc3b9f71b4e90d5cbdae234c9e4 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 8 Oct 2025 18:23:51 -0700 Subject: [PATCH 64/94] Updating lint and structure of logical indicator --- R/print.sr_model.R | 37 ++++++++++++++++++------------------- 1 file changed, 18 insertions(+), 19 deletions(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index af223fa2..7a474e99 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -17,27 +17,26 @@ print.sr_model <- function(x, print_tbl = FALSE, ...) { # nolint - - if (print_tbl == FALSE) { + if (print_tbl) { x <- as_tibble(x) print(x) } else { - cat("An sr_model with the following median values:") - cat("\n") - cat("\n") - x <- x |> - dplyr::summarise(.by = c(.data$Stratification, .data$Iso_type, - .data$Parameter), - median_val = median(.data$value)) |> - tidyr::pivot_wider(names_from = .data$Parameter, - values_from = .data$median_val) |> - dplyr::arrange(.data$Iso_type) |> - suppressWarnings() - # Taking out stratification column if not specified - if (unique(x$Stratification == "None")) { - x <- x |> select(-c(.data$Stratification)) + cat("An sr_model with the following median values:") + cat("\n") + cat("\n") + x <- x |> + dplyr::summarise(.by = c(.data$Stratification, .data$Iso_type, + .data$Parameter), + median_val = median(.data$value)) |> + tidyr::pivot_wider(names_from = .data$Parameter, + values_from = .data$median_val) |> + dplyr::arrange(.data$Iso_type) |> + suppressWarnings() + # Taking out stratification column if not specified + if (unique(x$Stratification == "None")) { + x <- x |> select(-c(.data$Stratification)) + } + print(as.data.frame(x)) + invisible(x) } - print(as.data.frame(x)) - invisible(x) - } } From f0bf0680ba5e28a5ecbf0ce758f5c12c4345c939 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 8 Oct 2025 18:32:18 -0700 Subject: [PATCH 65/94] Updating tests for print --- tests/testthat/_snaps/print.sr_model.md | 13 ------------- tests/testthat/test-print.sr_model.R | 14 +++++++++++++- 2 files changed, 13 insertions(+), 14 deletions(-) delete mode 100644 tests/testthat/_snaps/print.sr_model.md diff --git a/tests/testthat/_snaps/print.sr_model.md b/tests/testthat/_snaps/print.sr_model.md deleted file mode 100644 index 2a559f5e..00000000 --- a/tests/testthat/_snaps/print.sr_model.md +++ /dev/null @@ -1,13 +0,0 @@ -# results are consistent with printed output for sr_model class - - Code - nepal_sees_jags_output - Output - An sr_model with the following median values: - - Stratification Iso_type alpha shape t1 y0 y1 - 1 typhi HlyE_IgA 0.000869201 1.587970 6.41418 2.486935 317.1110 - 2 paratyphi HlyE_IgA 0.001556295 1.561960 3.90369 2.852925 191.8805 - 3 typhi HlyE_IgG 0.001337480 1.304980 5.88293 1.805900 297.7720 - 4 paratyphi HlyE_IgG 0.001432405 1.386685 4.72698 2.330555 272.8455 - diff --git a/tests/testthat/test-print.sr_model.R b/tests/testthat/test-print.sr_model.R index c1715a0d..71440d96 100644 --- a/tests/testthat/test-print.sr_model.R +++ b/tests/testthat/test-print.sr_model.R @@ -1,6 +1,18 @@ test_that( desc = "results are consistent with printed output for sr_model class", code = { - testthat::expect_snapshot(nepal_sees_jags_output) + results <- print(nepal_sees_jags_output) + results |> + testthat::expect_snapshot("as summary") + } +) + +test_that( + desc = "results are consistent with printed output for sr_model class + as a tbl", + code = { + results <- print(nepal_sees_jags_output, print_tbl = TRUE) + results |> + testthat::expect_snapshot_data("as tbl") } ) From c25630c7a18ceca61bee26d25f3350187d5f6648 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 8 Oct 2025 18:42:46 -0700 Subject: [PATCH 66/94] Updadting snaps for default print to test a tbl output --- tests/testthat/_snaps/print.sr_model.md | 33 +++++++++++++++++++++++++ tests/testthat/test-print.sr_model.R | 12 +++------ 2 files changed, 37 insertions(+), 8 deletions(-) create mode 100644 tests/testthat/_snaps/print.sr_model.md diff --git a/tests/testthat/_snaps/print.sr_model.md b/tests/testthat/_snaps/print.sr_model.md new file mode 100644 index 00000000..fec78019 --- /dev/null +++ b/tests/testthat/_snaps/print.sr_model.md @@ -0,0 +1,33 @@ +# results are consistent with printed output for sr_model class + + Code + nepal_sees_jags_output + Output + An sr_model with the following median values: + + Stratification Iso_type alpha shape t1 y0 y1 + 1 typhi HlyE_IgA 0.000869201 1.587970 6.41418 2.486935 317.1110 + 2 paratyphi HlyE_IgA 0.001556295 1.561960 3.90369 2.852925 191.8805 + 3 typhi HlyE_IgG 0.001337480 1.304980 5.88293 1.805900 297.7720 + 4 paratyphi HlyE_IgG 0.001432405 1.386685 4.72698 2.330555 272.8455 + +# results are consistent with printed output for sr_model class as tbl + + Code + print(nepal_sees_jags_output, print_tbl = TRUE) + Output + # A tibble: 70,000 x 7 + Iteration Chain Parameter Iso_type Stratification Subject value + + 1 1 1 alpha HlyE_IgA typhi sees_npl_1 0.00757 + 2 2 1 alpha HlyE_IgA typhi sees_npl_1 0.00794 + 3 3 1 alpha HlyE_IgA typhi sees_npl_1 0.00794 + 4 4 1 alpha HlyE_IgA typhi sees_npl_1 0.0103 + 5 5 1 alpha HlyE_IgA typhi sees_npl_1 0.00925 + 6 6 1 alpha HlyE_IgA typhi sees_npl_1 0.00925 + 7 7 1 alpha HlyE_IgA typhi sees_npl_1 0.00950 + 8 8 1 alpha HlyE_IgA typhi sees_npl_1 0.00950 + 9 9 1 alpha HlyE_IgA typhi sees_npl_1 0.00852 + 10 10 1 alpha HlyE_IgA typhi sees_npl_1 0.00852 + # i 69,990 more rows + diff --git a/tests/testthat/test-print.sr_model.R b/tests/testthat/test-print.sr_model.R index 71440d96..3b18debe 100644 --- a/tests/testthat/test-print.sr_model.R +++ b/tests/testthat/test-print.sr_model.R @@ -1,18 +1,14 @@ test_that( desc = "results are consistent with printed output for sr_model class", code = { - results <- print(nepal_sees_jags_output) - results |> - testthat::expect_snapshot("as summary") + testthat::expect_snapshot(nepal_sees_jags_output) } ) test_that( - desc = "results are consistent with printed output for sr_model class - as a tbl", + desc = "results are consistent with printed output for sr_model class as tbl", code = { - results <- print(nepal_sees_jags_output, print_tbl = TRUE) - results |> - testthat::expect_snapshot_data("as tbl") + testthat::expect_snapshot(print(nepal_sees_jags_output, print_tbl = TRUE)) } ) + From 4a14365557ccda57e647f7e925927d439b316a9c Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 8 Oct 2025 18:49:14 -0700 Subject: [PATCH 67/94] Fixing lint --- R/print.sr_model.R | 2 +- tests/testthat/test-print.sr_model.R | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index 7a474e99..5ebf1499 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -18,7 +18,7 @@ print.sr_model <- function(x, print_tbl = FALSE, ...) { # nolint if (print_tbl) { - x <- as_tibble(x) + x <- dplyr::as_tibble(x) print(x) } else { cat("An sr_model with the following median values:") diff --git a/tests/testthat/test-print.sr_model.R b/tests/testthat/test-print.sr_model.R index 3b18debe..1e54993a 100644 --- a/tests/testthat/test-print.sr_model.R +++ b/tests/testthat/test-print.sr_model.R @@ -11,4 +11,3 @@ test_that( testthat::expect_snapshot(print(nepal_sees_jags_output, print_tbl = TRUE)) } ) - From 89e5bf527c1856182eefa5d3eac58b7fa56dc7d8 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 8 Oct 2025 20:12:14 -0700 Subject: [PATCH 68/94] Updating stats::median call --- R/print.sr_model.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index 5ebf1499..8b4e964e 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -27,7 +27,7 @@ print.sr_model <- function(x, x <- x |> dplyr::summarise(.by = c(.data$Stratification, .data$Iso_type, .data$Parameter), - median_val = median(.data$value)) |> + median_val = stats::median(.data$value)) |> tidyr::pivot_wider(names_from = .data$Parameter, values_from = .data$median_val) |> dplyr::arrange(.data$Iso_type) |> From a2be02254c309eb9c44176d601aae7ca47695239 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Sat, 11 Oct 2025 08:44:48 -0700 Subject: [PATCH 69/94] Merged origin/main into default_print --- .lintr.R | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.lintr.R b/.lintr.R index e7bb380c..2983ad8c 100644 --- a/.lintr.R +++ b/.lintr.R @@ -73,6 +73,9 @@ exclusions <- list( vignettes = list( undesirable_function_linter = Inf ), + "inst/examples" = list( + undesirable_function_linter = Inf + ), "inst/analyses" = list( undesirable_function_linter = Inf ), From c9847dc7c56e66ba304b1a6595f032ed215f399f Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Sun, 26 Oct 2025 17:31:23 -0700 Subject: [PATCH 70/94] Updating print documentation --- R/print.sr_model.R | 2 +- man/print.sr_model.Rd | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index 8b4e964e..439da5e6 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -9,7 +9,7 @@ #' @param ... Additional arguments affecting the summary produced. #' [serodynamics::run_mod()] function. #' @returns A data summary that -#' contains the mean posterior distribution for antibody kinetic curve +#' contains the median posterior distribution for antibody kinetic curve #' parameters by `Iso_type` and `Stratification` (if specified). #' @export #' @examples diff --git a/man/print.sr_model.Rd b/man/print.sr_model.Rd index f3e2b8c2..cc61b69b 100644 --- a/man/print.sr_model.Rd +++ b/man/print.sr_model.Rd @@ -17,7 +17,7 @@ } \value{ A data summary that -contains the mean posterior distribution for antibody kinetic curve +contains the median posterior distribution for antibody kinetic curve parameters by \code{Iso_type} and \code{Stratification} (if specified). } \description{ From e160b395b41bc1a3dd5df6ce3dda6ff54513c466 Mon Sep 17 00:00:00 2001 From: Samuel Schildhauer <165851188+sschildhauer@users.noreply.github.com> Date: Sun, 26 Oct 2025 17:49:57 -0700 Subject: [PATCH 71/94] Update R/print.sr_model.R Co-authored-by: Kwan-Jenny <68584166+Kwan-Jenny@users.noreply.github.com> --- R/print.sr_model.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index 439da5e6..9374ff9a 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -33,9 +33,9 @@ print.sr_model <- function(x, dplyr::arrange(.data$Iso_type) |> suppressWarnings() # Taking out stratification column if not specified - if (unique(x$Stratification == "None")) { - x <- x |> select(-c(.data$Stratification)) - } + if (!"Stratification" %in% names(x) || all(x$Stratification == "None", na.rm = TRUE)) { + x <- dplyr::select(x, -dplyr::any_of("Stratification")) +} print(as.data.frame(x)) invisible(x) } From 7fdb0d4ea19d129a1a9ae0ff9a0e1dec7339f77f Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Sun, 26 Oct 2025 17:56:59 -0700 Subject: [PATCH 72/94] Updating lint for print --- R/print.sr_model.R | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index 9374ff9a..6ebf6081 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -33,9 +33,10 @@ print.sr_model <- function(x, dplyr::arrange(.data$Iso_type) |> suppressWarnings() # Taking out stratification column if not specified - if (!"Stratification" %in% names(x) || all(x$Stratification == "None", na.rm = TRUE)) { - x <- dplyr::select(x, -dplyr::any_of("Stratification")) -} + if (!"Stratification" %in% names(x) || all(x$Stratification == "None", + na.rm = TRUE)) { + x <- dplyr::select(x, -dplyr::any_of("Stratification")) + } print(as.data.frame(x)) invisible(x) } From 2eb9a2978b55d14434ca96eee93133c452a1a6f1 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 24 Dec 2025 09:16:37 -0800 Subject: [PATCH 73/94] Merged origin/main into default_print --- R/expect_snapshot_data.R | 4 +++- man/expect_snapshot_data.Rd | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/R/expect_snapshot_data.R b/R/expect_snapshot_data.R index 28e76445..e6091a0d 100644 --- a/R/expect_snapshot_data.R +++ b/R/expect_snapshot_data.R @@ -11,7 +11,9 @@ #' @export #' @keywords internal #' @examples -#' expect_snapshot_data(iris, name = iris) +#' \dontrun{ +#' expect_snapshot_data(iris, name = "iris") +#' } expect_snapshot_data <- function(x, name, digits = 6) { fun <- function(x) signif(x, digits = digits) lapply_fun <- function(x) I(lapply(x, fun)) diff --git a/man/expect_snapshot_data.Rd b/man/expect_snapshot_data.Rd index 98fb0d3a..7e86c956 100644 --- a/man/expect_snapshot_data.Rd +++ b/man/expect_snapshot_data.Rd @@ -21,6 +21,8 @@ copied from \url{https://github.com/bcgov/ssdtools} with permission (\url{https://github.com/bcgov/ssdtools/issues/379}) } \examples{ -expect_snapshot_data(iris, name = iris) +\dontrun{ +expect_snapshot_data(iris, name = "iris") +} } \keyword{internal} From dee362d6d8cf9b00ba36ad70219e7ccdcb0ec068 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Mon, 30 Mar 2026 10:21:42 +0700 Subject: [PATCH 74/94] Increment version number to 0.0.0.9048 --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index ea5d92de..a46b1417 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: serodynamics Title: What the Package Does (One Line, Title Case) -Version: 0.0.0.9047 +Version: 0.0.0.9048 Authors@R: c( person("Peter", "Teunis", , "p.teunis@emory.edu", role = c("aut", "cph"), comment = "Author of the method and original code."), From 822b1e3d02c1994d3bc7d55420ff4809db92c563 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Tue, 31 Mar 2026 16:22:24 +0700 Subject: [PATCH 75/94] Updating expect snapshot --- man/expect_snapshot_data.Rd | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/man/expect_snapshot_data.Rd b/man/expect_snapshot_data.Rd index 740e3781..1be69751 100644 --- a/man/expect_snapshot_data.Rd +++ b/man/expect_snapshot_data.Rd @@ -25,14 +25,9 @@ often rely on minor details of dependencies.} text from the output. Should take a character vector of lines as input and return a modified character vector as output.} \item{\code{variant}}{If not-\code{NULL}, results will be saved in -\verb{_snaps/{variant}/{test}/{name}}. This allows you to create +\verb{_snaps/{variant}/{test}/{name}.{ext}}. This allows you to create different snapshots for different scenarios, like different operating -systems or different R versions. - -Note that there's no way to declare all possible variants up front which -means that as soon as you start using variants, you are responsible for -deleting snapshot variants that are no longer used. (testthat will still -delete all variants if you delete the test.)} +systems or different R versions.} }} } \value{ From d4115431935e3fabda79ce85f3a3a191956f2750 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 8 Apr 2026 12:05:26 +0700 Subject: [PATCH 76/94] Note in expect_snapshot_data --- man/expect_snapshot_data.Rd | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/man/expect_snapshot_data.Rd b/man/expect_snapshot_data.Rd index 1be69751..740e3781 100644 --- a/man/expect_snapshot_data.Rd +++ b/man/expect_snapshot_data.Rd @@ -25,9 +25,14 @@ often rely on minor details of dependencies.} text from the output. Should take a character vector of lines as input and return a modified character vector as output.} \item{\code{variant}}{If not-\code{NULL}, results will be saved in -\verb{_snaps/{variant}/{test}/{name}.{ext}}. This allows you to create +\verb{_snaps/{variant}/{test}/{name}}. This allows you to create different snapshots for different scenarios, like different operating -systems or different R versions.} +systems or different R versions. + +Note that there's no way to declare all possible variants up front which +means that as soon as you start using variants, you are responsible for +deleting snapshot variants that are no longer used. (testthat will still +delete all variants if you delete the test.)} }} } \value{ From 9546eefced80d8a30c40ebfa20f018f9eef51891 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 8 Apr 2026 13:45:48 +0700 Subject: [PATCH 77/94] Adding a test for default print with no stratification --- tests/testthat/_snaps/print.sr_model.md | 11 +++++++++++ tests/testthat/test-print.sr_model.R | 20 ++++++++++++++++++++ 2 files changed, 31 insertions(+) diff --git a/tests/testthat/_snaps/print.sr_model.md b/tests/testthat/_snaps/print.sr_model.md index fec78019..f2aeba9f 100644 --- a/tests/testthat/_snaps/print.sr_model.md +++ b/tests/testthat/_snaps/print.sr_model.md @@ -31,3 +31,14 @@ 10 10 1 alpha HlyE_IgA typhi sees_npl_1 0.00852 # i 69,990 more rows +# results are consistent with printed output for sr_model class as tbl with no stratification + + Code + print(results) + Output + An sr_model with the following median values: + + Iso_type alpha shape t1 y0 y1 + 1 HlyE_IgA 0.01831560 1.36788 2.71828 2.71828 1099.35 + 2 HlyE_IgG 0.00965289 1.30665 2.76880 2.71828 1099.35 + diff --git a/tests/testthat/test-print.sr_model.R b/tests/testthat/test-print.sr_model.R index 1e54993a..62b026fd 100644 --- a/tests/testthat/test-print.sr_model.R +++ b/tests/testthat/test-print.sr_model.R @@ -11,3 +11,23 @@ test_that( testthat::expect_snapshot(print(nepal_sees_jags_output, print_tbl = TRUE)) } ) + +test_that( + desc = "results are consistent with printed output for sr_model class as tbl + with no stratification", + code = { +dataset <- serodynamics::nepal_sees +results <- run_mod( + data = dataset, # The data set input + file_mod = serodynamics_example("model.jags"), + nchain = 2, # Number of mcmc chains to run + nadapt = 10, # Number of adaptations to run + nburn = 10, # Number of unrecorded samples before sampling begins + nmc = 100, + niter = 100, # Number of iterations +) |> + suppressWarnings() + +testthat::expect_snapshot(print(results)) + } +) From 6f19b4ee474a3be84a02b1fa9d849ba9d863e5ad Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 8 Apr 2026 13:49:22 +0700 Subject: [PATCH 78/94] filtering to newperson --- R/print.sr_model.R | 1 + tests/testthat/_snaps/print.sr_model.md | 16 ++++++++-------- 2 files changed, 9 insertions(+), 8 deletions(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index 6ebf6081..72f576ce 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -25,6 +25,7 @@ print.sr_model <- function(x, cat("\n") cat("\n") x <- x |> + dplyr::filter(Subject == "newperson") |> dplyr::summarise(.by = c(.data$Stratification, .data$Iso_type, .data$Parameter), median_val = stats::median(.data$value)) |> diff --git a/tests/testthat/_snaps/print.sr_model.md b/tests/testthat/_snaps/print.sr_model.md index f2aeba9f..631778d0 100644 --- a/tests/testthat/_snaps/print.sr_model.md +++ b/tests/testthat/_snaps/print.sr_model.md @@ -5,11 +5,11 @@ Output An sr_model with the following median values: - Stratification Iso_type alpha shape t1 y0 y1 - 1 typhi HlyE_IgA 0.000869201 1.587970 6.41418 2.486935 317.1110 - 2 paratyphi HlyE_IgA 0.001556295 1.561960 3.90369 2.852925 191.8805 - 3 typhi HlyE_IgG 0.001337480 1.304980 5.88293 1.805900 297.7720 - 4 paratyphi HlyE_IgG 0.001432405 1.386685 4.72698 2.330555 272.8455 + Stratification Iso_type alpha shape t1 y0 y1 + 1 typhi HlyE_IgA 0.001508265 1.673340 6.358405 2.340330 258.1235 + 2 paratyphi HlyE_IgA 0.001556295 1.561960 3.903690 2.852925 191.8805 + 3 typhi HlyE_IgG 0.001393980 1.385280 6.019110 1.788035 243.9110 + 4 paratyphi HlyE_IgG 0.001432405 1.386685 4.726980 2.330555 272.8455 # results are consistent with printed output for sr_model class as tbl @@ -38,7 +38,7 @@ Output An sr_model with the following median values: - Iso_type alpha shape t1 y0 y1 - 1 HlyE_IgA 0.01831560 1.36788 2.71828 2.71828 1099.35 - 2 HlyE_IgG 0.00965289 1.30665 2.76880 2.71828 1099.35 + Iso_type alpha shape t1 y0 y1 + 1 HlyE_IgA 0.01637070 1.352345 2.74673 2.68448 968.6465 + 2 HlyE_IgG 0.00938515 1.288250 2.97289 2.61949 1099.8900 From deb74e8dd0fa064bbcd89ff737240fc2fd4c45ca Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 8 Apr 2026 13:52:34 +0700 Subject: [PATCH 79/94] Changing documentation and taking out ... as recommended by copilot --- R/print.sr_model.R | 5 +---- man/print.sr_model.Rd | 5 +---- 2 files changed, 2 insertions(+), 8 deletions(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index 72f576ce..f0ff0702 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -6,8 +6,6 @@ #' and `Stratification` (if specified). #' @param x An `sr_model` output object from [run_mod()]. #' @param print_tbl A [logical] indicator to print in style of [dplyr::tbl_df]. -#' @param ... Additional arguments affecting the summary produced. -#' [serodynamics::run_mod()] function. #' @returns A data summary that #' contains the median posterior distribution for antibody kinetic curve #' parameters by `Iso_type` and `Stratification` (if specified). @@ -15,8 +13,7 @@ #' @examples #' print(nepal_sees_jags_output) print.sr_model <- function(x, - print_tbl = FALSE, - ...) { # nolint + print_tbl = FALSE) { # nolint if (print_tbl) { x <- dplyr::as_tibble(x) print(x) diff --git a/man/print.sr_model.Rd b/man/print.sr_model.Rd index cc61b69b..2cf40f9d 100644 --- a/man/print.sr_model.Rd +++ b/man/print.sr_model.Rd @@ -5,15 +5,12 @@ \title{Default print for \code{\link[=run_mod]{run_mod()}} output object of class \code{sr_model}} \usage{ -\method{print}{sr_model}(x, print_tbl = FALSE, ...) +\method{print}{sr_model}(x, print_tbl = FALSE) } \arguments{ \item{x}{An \code{sr_model} output object from \code{\link[=run_mod]{run_mod()}}.} \item{print_tbl}{A \link{logical} indicator to print in style of \link[dplyr:tbl_df]{dplyr::tbl_df}.} - -\item{...}{Additional arguments affecting the summary produced. -\code{\link[=run_mod]{run_mod()}} function.} } \value{ A data summary that From 3ef9db14ad8d3b5897370f5827a9ac422e7ee4f7 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 8 Apr 2026 13:54:29 +0700 Subject: [PATCH 80/94] Adding an invisibile command --- R/print.sr_model.R | 1 + 1 file changed, 1 insertion(+) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index f0ff0702..f82d54ac 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -17,6 +17,7 @@ print.sr_model <- function(x, if (print_tbl) { x <- dplyr::as_tibble(x) print(x) + invisible(x) } else { cat("An sr_model with the following median values:") cat("\n") From a7ddcc043417609cff1e4b4bf1b996a3f4078b36 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 8 Apr 2026 14:15:06 +0700 Subject: [PATCH 81/94] Fixing lint --- R/print.sr_model.R | 2 +- tests/testthat/test-print.sr_model.R | 24 ++++++++++++------------ 2 files changed, 13 insertions(+), 13 deletions(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index f82d54ac..0e2a2741 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -23,7 +23,7 @@ print.sr_model <- function(x, cat("\n") cat("\n") x <- x |> - dplyr::filter(Subject == "newperson") |> + dplyr::filter(.data$Subject == "newperson") |> dplyr::summarise(.by = c(.data$Stratification, .data$Iso_type, .data$Parameter), median_val = stats::median(.data$value)) |> diff --git a/tests/testthat/test-print.sr_model.R b/tests/testthat/test-print.sr_model.R index 62b026fd..42191e36 100644 --- a/tests/testthat/test-print.sr_model.R +++ b/tests/testthat/test-print.sr_model.R @@ -16,18 +16,18 @@ test_that( desc = "results are consistent with printed output for sr_model class as tbl with no stratification", code = { -dataset <- serodynamics::nepal_sees -results <- run_mod( - data = dataset, # The data set input - file_mod = serodynamics_example("model.jags"), - nchain = 2, # Number of mcmc chains to run - nadapt = 10, # Number of adaptations to run - nburn = 10, # Number of unrecorded samples before sampling begins - nmc = 100, - niter = 100, # Number of iterations -) |> - suppressWarnings() + dataset <- serodynamics::nepal_sees + results <- run_mod( + data = dataset, # The data set input + file_mod = serodynamics_example("model.jags"), + nchain = 2, # Number of mcmc chains to run + nadapt = 10, # Number of adaptations to run + nburn = 10, # Number of unrecorded samples before sampling begins + nmc = 100, + niter = 100, # Number of iterations + ) |> + suppressWarnings() -testthat::expect_snapshot(print(results)) + testthat::expect_snapshot(print(results)) } ) From 61b802d1c9a1f150b71d84785a6b097e4d4da791 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 8 Apr 2026 16:25:11 +0700 Subject: [PATCH 82/94] Fixing title for default print test --- tests/testthat/_snaps/print.sr_model.md | 2 +- tests/testthat/test-print.sr_model.R | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/tests/testthat/_snaps/print.sr_model.md b/tests/testthat/_snaps/print.sr_model.md index 631778d0..e867693d 100644 --- a/tests/testthat/_snaps/print.sr_model.md +++ b/tests/testthat/_snaps/print.sr_model.md @@ -31,7 +31,7 @@ 10 10 1 alpha HlyE_IgA typhi sees_npl_1 0.00852 # i 69,990 more rows -# results are consistent with printed output for sr_model class as tbl with no stratification +# results are consistent with printed output for sr_model class as tbl with no stratification Code print(results) diff --git a/tests/testthat/test-print.sr_model.R b/tests/testthat/test-print.sr_model.R index 42191e36..2f371a7e 100644 --- a/tests/testthat/test-print.sr_model.R +++ b/tests/testthat/test-print.sr_model.R @@ -13,8 +13,7 @@ test_that( ) test_that( - desc = "results are consistent with printed output for sr_model class as tbl - with no stratification", + desc = "results are consistent with printed output for sr_model class as tbl with no stratification", code = { dataset <- serodynamics::nepal_sees results <- run_mod( From 76225d235ad996927a29a528fbf759dadc0a5dc9 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 8 Apr 2026 16:26:55 +0700 Subject: [PATCH 83/94] changing snap to darwin variant --- .../print.sr_model/nostrat-defaultprint.csv | 378001 +++++++++++++++ tests/testthat/_snaps/print.sr_model.md | 11 - tests/testthat/test-print.sr_model.R | 9 +- 3 files changed, 378007 insertions(+), 14 deletions(-) create mode 100644 tests/testthat/_snaps/darwin/print.sr_model/nostrat-defaultprint.csv diff --git a/tests/testthat/_snaps/darwin/print.sr_model/nostrat-defaultprint.csv b/tests/testthat/_snaps/darwin/print.sr_model/nostrat-defaultprint.csv new file mode 100644 index 00000000..61c3bd24 --- /dev/null +++ b/tests/testthat/_snaps/darwin/print.sr_model/nostrat-defaultprint.csv @@ -0,0 +1,378001 @@ +Iteration,Chain,Parameter,Iso_type,Stratification,Subject,value +1,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 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+56,2,y1,HlyE_IgG,None,newperson,267.317 +57,2,y1,HlyE_IgG,None,newperson,542.034 +58,2,y1,HlyE_IgG,None,newperson,1988.6 +59,2,y1,HlyE_IgG,None,newperson,2788.69 +60,2,y1,HlyE_IgG,None,newperson,1420.23 +61,2,y1,HlyE_IgG,None,newperson,559.84 +62,2,y1,HlyE_IgG,None,newperson,769.351 +63,2,y1,HlyE_IgG,None,newperson,1008.91 +64,2,y1,HlyE_IgG,None,newperson,280.789 +65,2,y1,HlyE_IgG,None,newperson,687.073 +66,2,y1,HlyE_IgG,None,newperson,737.836 +67,2,y1,HlyE_IgG,None,newperson,2958.17 +68,2,y1,HlyE_IgG,None,newperson,2739.06 +69,2,y1,HlyE_IgG,None,newperson,756.505 +70,2,y1,HlyE_IgG,None,newperson,679.761 +71,2,y1,HlyE_IgG,None,newperson,1510.23 +72,2,y1,HlyE_IgG,None,newperson,4332.79 +73,2,y1,HlyE_IgG,None,newperson,917.108 +74,2,y1,HlyE_IgG,None,newperson,1260.66 +75,2,y1,HlyE_IgG,None,newperson,2544.96 +76,2,y1,HlyE_IgG,None,newperson,479.541 +77,2,y1,HlyE_IgG,None,newperson,253.026 +78,2,y1,HlyE_IgG,None,newperson,1795.34 +79,2,y1,HlyE_IgG,None,newperson,118.751 +80,2,y1,HlyE_IgG,None,newperson,3822.38 +81,2,y1,HlyE_IgG,None,newperson,27.8291 +82,2,y1,HlyE_IgG,None,newperson,1047.64 +83,2,y1,HlyE_IgG,None,newperson,77.8833 +84,2,y1,HlyE_IgG,None,newperson,4282.08 +85,2,y1,HlyE_IgG,None,newperson,200.7 +86,2,y1,HlyE_IgG,None,newperson,733.883 +87,2,y1,HlyE_IgG,None,newperson,1470.34 +88,2,y1,HlyE_IgG,None,newperson,23.9 +89,2,y1,HlyE_IgG,None,newperson,194.65 +90,2,y1,HlyE_IgG,None,newperson,4088.92 +91,2,y1,HlyE_IgG,None,newperson,657.126 +92,2,y1,HlyE_IgG,None,newperson,865.124 +93,2,y1,HlyE_IgG,None,newperson,88.9675 +94,2,y1,HlyE_IgG,None,newperson,4773.51 +95,2,y1,HlyE_IgG,None,newperson,220.485 +96,2,y1,HlyE_IgG,None,newperson,347.584 +97,2,y1,HlyE_IgG,None,newperson,1988.19 +98,2,y1,HlyE_IgG,None,newperson,691.887 +99,2,y1,HlyE_IgG,None,newperson,895.466 +100,2,y1,HlyE_IgG,None,newperson,1254.34 diff --git a/tests/testthat/_snaps/print.sr_model.md b/tests/testthat/_snaps/print.sr_model.md index e867693d..22e72404 100644 --- a/tests/testthat/_snaps/print.sr_model.md +++ b/tests/testthat/_snaps/print.sr_model.md @@ -31,14 +31,3 @@ 10 10 1 alpha HlyE_IgA typhi sees_npl_1 0.00852 # i 69,990 more rows -# results are consistent with printed output for sr_model class as tbl with no stratification - - Code - print(results) - Output - An sr_model with the following median values: - - Iso_type alpha shape t1 y0 y1 - 1 HlyE_IgA 0.01637070 1.352345 2.74673 2.68448 968.6465 - 2 HlyE_IgG 0.00938515 1.288250 2.97289 2.61949 1099.8900 - diff --git a/tests/testthat/test-print.sr_model.R b/tests/testthat/test-print.sr_model.R index 2f371a7e..1c19ad6a 100644 --- a/tests/testthat/test-print.sr_model.R +++ b/tests/testthat/test-print.sr_model.R @@ -15,6 +15,7 @@ test_that( test_that( desc = "results are consistent with printed output for sr_model class as tbl with no stratification", code = { + withr::local_seed(1) dataset <- serodynamics::nepal_sees results <- run_mod( data = dataset, # The data set input @@ -25,8 +26,10 @@ test_that( nmc = 100, niter = 100, # Number of iterations ) |> - suppressWarnings() - - testthat::expect_snapshot(print(results)) + suppressWarnings()|> + expect_snapshot_data( + "nostrat-defaultprint", + variant = darwin_variant() + ) } ) From 0e52f43ef291b044257652422906e26a535d1c24 Mon Sep 17 00:00:00 2001 From: Samuel Hisaji Schildhauer <165851188+sschildhauer@users.noreply.github.com> Date: Wed, 8 Apr 2026 16:30:37 +0700 Subject: [PATCH 84/94] Update R/print.sr_model.R Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- R/print.sr_model.R | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index 0e2a2741..cac99001 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -22,15 +22,16 @@ print.sr_model <- function(x, cat("An sr_model with the following median values:") cat("\n") cat("\n") - x <- x |> - dplyr::filter(.data$Subject == "newperson") |> - dplyr::summarise(.by = c(.data$Stratification, .data$Iso_type, - .data$Parameter), - median_val = stats::median(.data$value)) |> - tidyr::pivot_wider(names_from = .data$Parameter, - values_from = .data$median_val) |> - dplyr::arrange(.data$Iso_type) |> - suppressWarnings() + x <- suppressWarnings({ + x |> + dplyr::filter(.data$Subject == "newperson") |> + dplyr::summarise(.by = c(.data$Stratification, .data$Iso_type, + .data$Parameter), + median_val = stats::median(.data$value)) |> + tidyr::pivot_wider(names_from = .data$Parameter, + values_from = .data$median_val) |> + dplyr::arrange(.data$Iso_type) + }) # Taking out stratification column if not specified if (!"Stratification" %in% names(x) || all(x$Stratification == "None", na.rm = TRUE)) { From 215e02b14dcdf7d7ec69a0fa8d0f3717fdbd5f0a Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 8 Apr 2026 16:35:47 +0700 Subject: [PATCH 85/94] Adding ... back in to allow for additional arguments --- R/print.sr_model.R | 5 ++++- man/print.sr_model.Rd | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index 0e2a2741..e210da6c 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -6,6 +6,8 @@ #' and `Stratification` (if specified). #' @param x An `sr_model` output object from [run_mod()]. #' @param print_tbl A [logical] indicator to print in style of [dplyr::tbl_df]. +#' @param ... Additional arguments affecting the summary produced. +#' [serodynamics::run_mod()] function. #' @returns A data summary that #' contains the median posterior distribution for antibody kinetic curve #' parameters by `Iso_type` and `Stratification` (if specified). @@ -13,7 +15,8 @@ #' @examples #' print(nepal_sees_jags_output) print.sr_model <- function(x, - print_tbl = FALSE) { # nolint + print_tbl = FALSE, + ...) { # nolint if (print_tbl) { x <- dplyr::as_tibble(x) print(x) diff --git a/man/print.sr_model.Rd b/man/print.sr_model.Rd index 2cf40f9d..cc61b69b 100644 --- a/man/print.sr_model.Rd +++ b/man/print.sr_model.Rd @@ -5,12 +5,15 @@ \title{Default print for \code{\link[=run_mod]{run_mod()}} output object of class \code{sr_model}} \usage{ -\method{print}{sr_model}(x, print_tbl = FALSE) +\method{print}{sr_model}(x, print_tbl = FALSE, ...) } \arguments{ \item{x}{An \code{sr_model} output object from \code{\link[=run_mod]{run_mod()}}.} \item{print_tbl}{A \link{logical} indicator to print in style of \link[dplyr:tbl_df]{dplyr::tbl_df}.} + +\item{...}{Additional arguments affecting the summary produced. +\code{\link[=run_mod]{run_mod()}} function.} } \value{ A data summary that From 06d8d538b4b67328c8de8c29241a6ccb20b26ada Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 8 Apr 2026 16:41:58 +0700 Subject: [PATCH 86/94] Clarifying in documentation that we are printing the predictive distribution --- R/print.sr_model.R | 4 ++-- man/print.sr_model.Rd | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index cccbf160..89e61ab7 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -2,8 +2,8 @@ #' `sr_model` #' @description #' A default print method for class `sr_model` that includes the median -#' posterior distribution for antibody kinetic curve parameters by `Iso_type` -#' and `Stratification` (if specified). +#' predictive posterior distribution for antibody kinetic curve parameters +#' by `Iso_type` and `Stratification` (if specified). #' @param x An `sr_model` output object from [run_mod()]. #' @param print_tbl A [logical] indicator to print in style of [dplyr::tbl_df]. #' @param ... Additional arguments affecting the summary produced. diff --git a/man/print.sr_model.Rd b/man/print.sr_model.Rd index cc61b69b..b7727a34 100644 --- a/man/print.sr_model.Rd +++ b/man/print.sr_model.Rd @@ -22,8 +22,8 @@ parameters by \code{Iso_type} and \code{Stratification} (if specified). } \description{ A default print method for class \code{sr_model} that includes the median -posterior distribution for antibody kinetic curve parameters by \code{Iso_type} -and \code{Stratification} (if specified). +predictive posterior distribution for antibody kinetic curve parameters +by \code{Iso_type} and \code{Stratification} (if specified). } \examples{ print(nepal_sees_jags_output) From 5d086afa28ed137db3b8bbed7695d9192cbaedef Mon Sep 17 00:00:00 2001 From: Samuel Hisaji Schildhauer <165851188+sschildhauer@users.noreply.github.com> Date: Wed, 8 Apr 2026 16:46:28 +0700 Subject: [PATCH 87/94] Update tests/testthat/test-print.sr_model.R Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- tests/testthat/test-print.sr_model.R | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/tests/testthat/test-print.sr_model.R b/tests/testthat/test-print.sr_model.R index 1c19ad6a..b6555b3b 100644 --- a/tests/testthat/test-print.sr_model.R +++ b/tests/testthat/test-print.sr_model.R @@ -26,10 +26,11 @@ test_that( nmc = 100, niter = 100, # Number of iterations ) |> - suppressWarnings()|> - expect_snapshot_data( - "nostrat-defaultprint", - variant = darwin_variant() - ) + suppressWarnings() + + testthat::expect_snapshot( + print(results, print_tbl = TRUE), + variant = darwin_variant() + ) } ) From 8145cc9c97995d9d88006ebaec9d4d99ba14c93b Mon Sep 17 00:00:00 2001 From: Samuel Hisaji Schildhauer <165851188+sschildhauer@users.noreply.github.com> Date: Wed, 8 Apr 2026 16:47:31 +0700 Subject: [PATCH 88/94] Update tests/testthat/test-print.sr_model.R Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- tests/testthat/test-print.sr_model.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/testthat/test-print.sr_model.R b/tests/testthat/test-print.sr_model.R index b6555b3b..03360082 100644 --- a/tests/testthat/test-print.sr_model.R +++ b/tests/testthat/test-print.sr_model.R @@ -24,7 +24,7 @@ test_that( nadapt = 10, # Number of adaptations to run nburn = 10, # Number of unrecorded samples before sampling begins nmc = 100, - niter = 100, # Number of iterations + niter = 100 # Number of iterations ) |> suppressWarnings() From 60acbd4bc8c3474c14027aacab5379b98c8dbe3c Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 8 Apr 2026 16:57:54 +0700 Subject: [PATCH 89/94] Updating non-stratified results to be a snap of the print, not a tbl --- .../testthat/_snaps/darwin/print.sr_model.md | 11 + .../print.sr_model/nostrat-defaultprint.csv | 378001 --------------- tests/testthat/test-print.sr_model.R | 2 +- 3 files changed, 12 insertions(+), 378002 deletions(-) create mode 100644 tests/testthat/_snaps/darwin/print.sr_model.md delete mode 100644 tests/testthat/_snaps/darwin/print.sr_model/nostrat-defaultprint.csv diff --git a/tests/testthat/_snaps/darwin/print.sr_model.md b/tests/testthat/_snaps/darwin/print.sr_model.md new file mode 100644 index 00000000..f7803b62 --- /dev/null +++ b/tests/testthat/_snaps/darwin/print.sr_model.md @@ -0,0 +1,11 @@ +# results are consistent with printed output for sr_model class as tbl with no stratification + + Code + print(results) + Output + An sr_model with the following median values: + + Iso_type alpha shape t1 y0 y1 + 1 HlyE_IgA 0.01637070 1.352345 2.74673 2.68448 968.6465 + 2 HlyE_IgG 0.00938515 1.288250 2.97289 2.61949 1099.8900 + diff --git a/tests/testthat/_snaps/darwin/print.sr_model/nostrat-defaultprint.csv b/tests/testthat/_snaps/darwin/print.sr_model/nostrat-defaultprint.csv deleted file mode 100644 index 61c3bd24..00000000 --- a/tests/testthat/_snaps/darwin/print.sr_model/nostrat-defaultprint.csv +++ /dev/null @@ -1,378001 +0,0 @@ -Iteration,Chain,Parameter,Iso_type,Stratification,Subject,value -1,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -2,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -3,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -4,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -5,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -6,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -7,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -8,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -9,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -10,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -11,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -12,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -13,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -14,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -15,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -16,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -17,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -18,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -19,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -20,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -21,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -22,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -23,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -24,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -25,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -26,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -27,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -28,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -29,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -30,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -31,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -32,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -33,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -34,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -35,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -36,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -37,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -38,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -39,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 -40,1,alpha,HlyE_IgA,None,sees_npl_1,0.0183156 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-99,2,y1,HlyE_IgA,None,sees_npl_74,1115.54 -100,2,y1,HlyE_IgA,None,sees_npl_74,1115.54 -1,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -2,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -3,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -4,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -5,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -6,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -7,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -8,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -9,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -10,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -11,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -12,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -13,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -14,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -15,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -16,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -17,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -18,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -19,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -20,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -21,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -22,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -23,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -24,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -25,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -26,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -27,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -28,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -29,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -30,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -31,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -32,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -33,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -34,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -35,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -36,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -37,1,y1,HlyE_IgG,None,sees_npl_74,1099.35 -38,1,y1,HlyE_IgG,None,sees_npl_74,995.963 -39,1,y1,HlyE_IgG,None,sees_npl_74,995.963 -40,1,y1,HlyE_IgG,None,sees_npl_74,995.963 -41,1,y1,HlyE_IgG,None,sees_npl_74,995.963 -42,1,y1,HlyE_IgG,None,sees_npl_74,995.963 -43,1,y1,HlyE_IgG,None,sees_npl_74,995.963 -44,1,y1,HlyE_IgG,None,sees_npl_74,995.963 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-19,1,y1,HlyE_IgG,None,sees_npl_82,565.207 -20,1,y1,HlyE_IgG,None,sees_npl_82,565.207 -21,1,y1,HlyE_IgG,None,sees_npl_82,565.207 -22,1,y1,HlyE_IgG,None,sees_npl_82,565.207 -23,1,y1,HlyE_IgG,None,sees_npl_82,565.207 -24,1,y1,HlyE_IgG,None,sees_npl_82,1370.85 -25,1,y1,HlyE_IgG,None,sees_npl_82,1370.85 -26,1,y1,HlyE_IgG,None,sees_npl_82,1370.85 -27,1,y1,HlyE_IgG,None,sees_npl_82,1370.85 -28,1,y1,HlyE_IgG,None,sees_npl_82,1370.85 -29,1,y1,HlyE_IgG,None,sees_npl_82,1370.85 -30,1,y1,HlyE_IgG,None,sees_npl_82,1393.33 -31,1,y1,HlyE_IgG,None,sees_npl_82,1393.33 -32,1,y1,HlyE_IgG,None,sees_npl_82,1393.33 -33,1,y1,HlyE_IgG,None,sees_npl_82,1393.33 -34,1,y1,HlyE_IgG,None,sees_npl_82,1393.33 -35,1,y1,HlyE_IgG,None,sees_npl_82,1393.33 -36,1,y1,HlyE_IgG,None,sees_npl_82,1393.33 -37,1,y1,HlyE_IgG,None,sees_npl_82,1393.33 -38,1,y1,HlyE_IgG,None,sees_npl_82,1393.33 -39,1,y1,HlyE_IgG,None,sees_npl_82,1393.33 -40,1,y1,HlyE_IgG,None,sees_npl_82,1393.33 -41,1,y1,HlyE_IgG,None,sees_npl_82,3326 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-86,2,y1,HlyE_IgA,None,sees_npl_140,1099.35 -87,2,y1,HlyE_IgA,None,sees_npl_140,1099.35 -88,2,y1,HlyE_IgA,None,sees_npl_140,1099.35 -89,2,y1,HlyE_IgA,None,sees_npl_140,1099.35 -90,2,y1,HlyE_IgA,None,sees_npl_140,1099.35 -91,2,y1,HlyE_IgA,None,sees_npl_140,1099.35 -92,2,y1,HlyE_IgA,None,sees_npl_140,1099.35 -93,2,y1,HlyE_IgA,None,sees_npl_140,1099.35 -94,2,y1,HlyE_IgA,None,sees_npl_140,1099.35 -95,2,y1,HlyE_IgA,None,sees_npl_140,1099.35 -96,2,y1,HlyE_IgA,None,sees_npl_140,1099.35 -97,2,y1,HlyE_IgA,None,sees_npl_140,1099.35 -98,2,y1,HlyE_IgA,None,sees_npl_140,1099.35 -99,2,y1,HlyE_IgA,None,sees_npl_140,1099.35 -100,2,y1,HlyE_IgA,None,sees_npl_140,1099.35 -1,1,y1,HlyE_IgG,None,sees_npl_140,1361.77 -2,1,y1,HlyE_IgG,None,sees_npl_140,1361.77 -3,1,y1,HlyE_IgG,None,sees_npl_140,1361.77 -4,1,y1,HlyE_IgG,None,sees_npl_140,1361.77 -5,1,y1,HlyE_IgG,None,sees_npl_140,1361.77 -6,1,y1,HlyE_IgG,None,sees_npl_140,1361.77 -7,1,y1,HlyE_IgG,None,sees_npl_140,2550.72 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-8,2,y1,HlyE_IgG,None,newperson,612.548 -9,2,y1,HlyE_IgG,None,newperson,2256.12 -10,2,y1,HlyE_IgG,None,newperson,1603.02 -11,2,y1,HlyE_IgG,None,newperson,1278.47 -12,2,y1,HlyE_IgG,None,newperson,4726.13 -13,2,y1,HlyE_IgG,None,newperson,2675.74 -14,2,y1,HlyE_IgG,None,newperson,1322.05 -15,2,y1,HlyE_IgG,None,newperson,6951.96 -16,2,y1,HlyE_IgG,None,newperson,4098.81 -17,2,y1,HlyE_IgG,None,newperson,79.6868 -18,2,y1,HlyE_IgG,None,newperson,218.601 -19,2,y1,HlyE_IgG,None,newperson,334.071 -20,2,y1,HlyE_IgG,None,newperson,293.336 -21,2,y1,HlyE_IgG,None,newperson,2929.06 -22,2,y1,HlyE_IgG,None,newperson,3715 -23,2,y1,HlyE_IgG,None,newperson,1902.36 -24,2,y1,HlyE_IgG,None,newperson,888.618 -25,2,y1,HlyE_IgG,None,newperson,223.095 -26,2,y1,HlyE_IgG,None,newperson,463.761 -27,2,y1,HlyE_IgG,None,newperson,1168.22 -28,2,y1,HlyE_IgG,None,newperson,445.309 -29,2,y1,HlyE_IgG,None,newperson,1108.68 -30,2,y1,HlyE_IgG,None,newperson,997.142 -31,2,y1,HlyE_IgG,None,newperson,622.13 -32,2,y1,HlyE_IgG,None,newperson,472.211 -33,2,y1,HlyE_IgG,None,newperson,3749.69 -34,2,y1,HlyE_IgG,None,newperson,3150.01 -35,2,y1,HlyE_IgG,None,newperson,665.677 -36,2,y1,HlyE_IgG,None,newperson,979.954 -37,2,y1,HlyE_IgG,None,newperson,474.641 -38,2,y1,HlyE_IgG,None,newperson,292.682 -39,2,y1,HlyE_IgG,None,newperson,2871.66 -40,2,y1,HlyE_IgG,None,newperson,191.761 -41,2,y1,HlyE_IgG,None,newperson,777.589 -42,2,y1,HlyE_IgG,None,newperson,949.111 -43,2,y1,HlyE_IgG,None,newperson,471.657 -44,2,y1,HlyE_IgG,None,newperson,432.629 -45,2,y1,HlyE_IgG,None,newperson,348.568 -46,2,y1,HlyE_IgG,None,newperson,686.684 -47,2,y1,HlyE_IgG,None,newperson,174.059 -48,2,y1,HlyE_IgG,None,newperson,2442.09 -49,2,y1,HlyE_IgG,None,newperson,856.649 -50,2,y1,HlyE_IgG,None,newperson,2746.71 -51,2,y1,HlyE_IgG,None,newperson,1627.92 -52,2,y1,HlyE_IgG,None,newperson,1146.35 -53,2,y1,HlyE_IgG,None,newperson,1342.76 -54,2,y1,HlyE_IgG,None,newperson,135.427 -55,2,y1,HlyE_IgG,None,newperson,1920.96 -56,2,y1,HlyE_IgG,None,newperson,267.317 -57,2,y1,HlyE_IgG,None,newperson,542.034 -58,2,y1,HlyE_IgG,None,newperson,1988.6 -59,2,y1,HlyE_IgG,None,newperson,2788.69 -60,2,y1,HlyE_IgG,None,newperson,1420.23 -61,2,y1,HlyE_IgG,None,newperson,559.84 -62,2,y1,HlyE_IgG,None,newperson,769.351 -63,2,y1,HlyE_IgG,None,newperson,1008.91 -64,2,y1,HlyE_IgG,None,newperson,280.789 -65,2,y1,HlyE_IgG,None,newperson,687.073 -66,2,y1,HlyE_IgG,None,newperson,737.836 -67,2,y1,HlyE_IgG,None,newperson,2958.17 -68,2,y1,HlyE_IgG,None,newperson,2739.06 -69,2,y1,HlyE_IgG,None,newperson,756.505 -70,2,y1,HlyE_IgG,None,newperson,679.761 -71,2,y1,HlyE_IgG,None,newperson,1510.23 -72,2,y1,HlyE_IgG,None,newperson,4332.79 -73,2,y1,HlyE_IgG,None,newperson,917.108 -74,2,y1,HlyE_IgG,None,newperson,1260.66 -75,2,y1,HlyE_IgG,None,newperson,2544.96 -76,2,y1,HlyE_IgG,None,newperson,479.541 -77,2,y1,HlyE_IgG,None,newperson,253.026 -78,2,y1,HlyE_IgG,None,newperson,1795.34 -79,2,y1,HlyE_IgG,None,newperson,118.751 -80,2,y1,HlyE_IgG,None,newperson,3822.38 -81,2,y1,HlyE_IgG,None,newperson,27.8291 -82,2,y1,HlyE_IgG,None,newperson,1047.64 -83,2,y1,HlyE_IgG,None,newperson,77.8833 -84,2,y1,HlyE_IgG,None,newperson,4282.08 -85,2,y1,HlyE_IgG,None,newperson,200.7 -86,2,y1,HlyE_IgG,None,newperson,733.883 -87,2,y1,HlyE_IgG,None,newperson,1470.34 -88,2,y1,HlyE_IgG,None,newperson,23.9 -89,2,y1,HlyE_IgG,None,newperson,194.65 -90,2,y1,HlyE_IgG,None,newperson,4088.92 -91,2,y1,HlyE_IgG,None,newperson,657.126 -92,2,y1,HlyE_IgG,None,newperson,865.124 -93,2,y1,HlyE_IgG,None,newperson,88.9675 -94,2,y1,HlyE_IgG,None,newperson,4773.51 -95,2,y1,HlyE_IgG,None,newperson,220.485 -96,2,y1,HlyE_IgG,None,newperson,347.584 -97,2,y1,HlyE_IgG,None,newperson,1988.19 -98,2,y1,HlyE_IgG,None,newperson,691.887 -99,2,y1,HlyE_IgG,None,newperson,895.466 -100,2,y1,HlyE_IgG,None,newperson,1254.34 diff --git a/tests/testthat/test-print.sr_model.R b/tests/testthat/test-print.sr_model.R index 03360082..0c809ea1 100644 --- a/tests/testthat/test-print.sr_model.R +++ b/tests/testthat/test-print.sr_model.R @@ -29,7 +29,7 @@ test_that( suppressWarnings() testthat::expect_snapshot( - print(results, print_tbl = TRUE), + print(results), variant = darwin_variant() ) } From 129adceb078e0413530188801587cafe46c9a832 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 8 Apr 2026 17:08:19 +0700 Subject: [PATCH 90/94] Updating lint in test --- tests/testthat/test-print.sr_model.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/testthat/test-print.sr_model.R b/tests/testthat/test-print.sr_model.R index 0c809ea1..87afa4d5 100644 --- a/tests/testthat/test-print.sr_model.R +++ b/tests/testthat/test-print.sr_model.R @@ -13,7 +13,7 @@ test_that( ) test_that( - desc = "results are consistent with printed output for sr_model class as tbl with no stratification", + desc = "results consistent with printed output for sr_model as tbl no strat", code = { withr::local_seed(1) dataset <- serodynamics::nepal_sees From ec7f1edadd2b9a28965af2f63006c8dde1f0ade8 Mon Sep 17 00:00:00 2001 From: sschildhauer Date: Wed, 8 Apr 2026 17:17:50 +0700 Subject: [PATCH 91/94] Updating test snap --- tests/testthat/_snaps/darwin/print.sr_model.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/testthat/_snaps/darwin/print.sr_model.md b/tests/testthat/_snaps/darwin/print.sr_model.md index f7803b62..3948ad19 100644 --- a/tests/testthat/_snaps/darwin/print.sr_model.md +++ b/tests/testthat/_snaps/darwin/print.sr_model.md @@ -1,4 +1,4 @@ -# results are consistent with printed output for sr_model class as tbl with no stratification +# results consistent with printed output for sr_model as tbl no strat Code print(results) From 0be057f1d30dc379eec9c326e791888c1ee190fa Mon Sep 17 00:00:00 2001 From: Samuel Hisaji Schildhauer <165851188+sschildhauer@users.noreply.github.com> Date: Wed, 8 Apr 2026 17:27:36 +0700 Subject: [PATCH 92/94] Update R/print.sr_model.R Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- R/print.sr_model.R | 23 ++++++++++++++--------- 1 file changed, 14 insertions(+), 9 deletions(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index 89e61ab7..3ff3aaee 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -1,16 +1,21 @@ #' @title Default print for [serodynamics::run_mod()] output object of class #' `sr_model` #' @description -#' A default print method for class `sr_model` that includes the median -#' predictive posterior distribution for antibody kinetic curve parameters -#' by `Iso_type` and `Stratification` (if specified). +#' A default print method for class `sr_model` that prints posterior medians +#' for antibody kinetic curve parameters by `Iso_type` and +#' `Stratification` (if specified). #' @param x An `sr_model` output object from [run_mod()]. -#' @param print_tbl A [logical] indicator to print in style of [dplyr::tbl_df]. -#' @param ... Additional arguments affecting the summary produced. -#' [serodynamics::run_mod()] function. -#' @returns A data summary that -#' contains the median posterior distribution for antibody kinetic curve -#' parameters by `Iso_type` and `Stratification` (if specified). +#' @param print_tbl A [logical] indicator to print `x` in the style of a +#' [dplyr::tbl_df]. +#' @param ... Additional arguments passed to the print method. +#' @returns Invisibly returns either: +#' \itemize{ +#' \item when `print_tbl = TRUE`, a tibble containing the raw `sr_model` +#' draws; +#' \item otherwise, a data summary containing posterior medians for +#' antibody kinetic curve parameters by `Iso_type` and `Stratification` +#' (if specified). +#' } #' @export #' @examples #' print(nepal_sees_jags_output) From 1a97278a6577893ac9ebdd420a96eb3fe9216e7e Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Wed, 8 Apr 2026 11:04:18 +0000 Subject: [PATCH 93/94] Fix .data in tidyselect contexts, regenerate docs, add missing snapshot Agent-Logs-Url: https://github.com/ucdavis/serodynamics/sessions/9e5d11ac-b621-49bc-9420-165105d24b90 Co-authored-by: sschildhauer <165851188+sschildhauer@users.noreply.github.com> --- R/print.sr_model.R | 7 +++---- man/nepal_sees_jags_output.Rd | 2 +- man/plot_predicted_curve.Rd | 2 +- man/print.sr_model.Rd | 23 ++++++++++++++--------- man/run_mod.Rd | 2 +- man/use_att_names.Rd | 2 +- tests/testthat/_snaps/print.sr_model.md | 11 +++++++++++ 7 files changed, 32 insertions(+), 17 deletions(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index 3ff3aaee..809292b4 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -33,11 +33,10 @@ print.sr_model <- function(x, x <- suppressWarnings({ x |> dplyr::filter(.data$Subject == "newperson") |> - dplyr::summarise(.by = c(.data$Stratification, .data$Iso_type, - .data$Parameter), + dplyr::summarise(.by = c("Stratification", "Iso_type", "Parameter"), median_val = stats::median(.data$value)) |> - tidyr::pivot_wider(names_from = .data$Parameter, - values_from = .data$median_val) |> + tidyr::pivot_wider(names_from = "Parameter", + values_from = "median_val") |> dplyr::arrange(.data$Iso_type) }) # Taking out stratification column if not specified diff --git a/man/nepal_sees_jags_output.Rd b/man/nepal_sees_jags_output.Rd index 2bd13915..4ea195d1 100644 --- a/man/nepal_sees_jags_output.Rd +++ b/man/nepal_sees_jags_output.Rd @@ -5,7 +5,7 @@ \alias{nepal_sees_jags_output} \title{SEES Typhoid run_mod jags output} \format{ -An S3 object of class \code{sr_model}: A \link[dplyr:tbl_df]{dplyr::tbl_df} that contains the +An S3 object of class \code{sr_model}: A \link[dplyr:defunct]{dplyr::tbl_df} that contains the posterior predictive distribution of the person-specific parameters for a "new person" with no observed data (\code{Subject = "newperson"}) and posterior distributions of the person-specific parameters for two arbitrarily-chosen diff --git a/man/plot_predicted_curve.Rd b/man/plot_predicted_curve.Rd index 7e2fabde..b5638b88 100644 --- a/man/plot_predicted_curve.Rd +++ b/man/plot_predicted_curve.Rd @@ -31,7 +31,7 @@ samples from the posterior distribution of the model parameters.} \item{antigen_iso}{The antigen isotype to plot; for example, "HlyE_IgA" or "HlyE_IgG".} -\item{dataset}{(Optional) A \link[dplyr:tbl_df]{dplyr::tbl_df} with observed antibody response +\item{dataset}{(Optional) A \link[dplyr:defunct]{dplyr::tbl_df} with observed antibody response data. Must contain: \itemize{ diff --git a/man/print.sr_model.Rd b/man/print.sr_model.Rd index b7727a34..e030629d 100644 --- a/man/print.sr_model.Rd +++ b/man/print.sr_model.Rd @@ -10,20 +10,25 @@ \arguments{ \item{x}{An \code{sr_model} output object from \code{\link[=run_mod]{run_mod()}}.} -\item{print_tbl}{A \link{logical} indicator to print in style of \link[dplyr:tbl_df]{dplyr::tbl_df}.} +\item{print_tbl}{A \link{logical} indicator to print \code{x} in the style of a +\link[dplyr:defunct]{dplyr::tbl_df}.} -\item{...}{Additional arguments affecting the summary produced. -\code{\link[=run_mod]{run_mod()}} function.} +\item{...}{Additional arguments passed to the print method.} } \value{ -A data summary that -contains the median posterior distribution for antibody kinetic curve -parameters by \code{Iso_type} and \code{Stratification} (if specified). +Invisibly returns either: +\itemize{ +\item when \code{print_tbl = TRUE}, a tibble containing the raw \code{sr_model} +draws; +\item otherwise, a data summary containing posterior medians for +antibody kinetic curve parameters by \code{Iso_type} and \code{Stratification} +(if specified). +} } \description{ -A default print method for class \code{sr_model} that includes the median -predictive posterior distribution for antibody kinetic curve parameters -by \code{Iso_type} and \code{Stratification} (if specified). +A default print method for class \code{sr_model} that prints posterior medians +for antibody kinetic curve parameters by \code{Iso_type} and +\code{Stratification} (if specified). } \examples{ print(nepal_sees_jags_output) diff --git a/man/run_mod.Rd b/man/run_mod.Rd index 08f91427..585210ae 100644 --- a/man/run_mod.Rd +++ b/man/run_mod.Rd @@ -93,7 +93,7 @@ If specified, must be 2 values long: }} } \value{ -An \code{sr_model} class object: a subclass of \link[dplyr:tbl_df]{dplyr::tbl_df} that +An \code{sr_model} class object: a subclass of \link[dplyr:defunct]{dplyr::tbl_df} that contains MCMC samples from the joint posterior distribution of the model parameters, conditional on the provided input \code{data}, including the following: diff --git a/man/use_att_names.Rd b/man/use_att_names.Rd index f43fcef0..9a2151e0 100644 --- a/man/use_att_names.Rd +++ b/man/use_att_names.Rd @@ -16,7 +16,7 @@ The input \link{data.frame} with columns named after attributes. \description{ \code{use_att_names} takes prepared longitudinal data for antibody kinetic modeling and names columns using attribute values to allow merging -with a modeled \code{\link[=run_mod]{run_mod()}} output \link[dplyr:tbl_df]{dplyr::tbl_df}. The column names include +with a modeled \code{\link[=run_mod]{run_mod()}} output \link[dplyr:defunct]{dplyr::tbl_df}. The column names include \code{Subject}, \code{Iso_type}, \code{t}, and \code{result}. } \keyword{internal} diff --git a/tests/testthat/_snaps/print.sr_model.md b/tests/testthat/_snaps/print.sr_model.md index 22e72404..9aa9ff03 100644 --- a/tests/testthat/_snaps/print.sr_model.md +++ b/tests/testthat/_snaps/print.sr_model.md @@ -31,3 +31,14 @@ 10 10 1 alpha HlyE_IgA typhi sees_npl_1 0.00852 # i 69,990 more rows +# results consistent with printed output for sr_model as tbl no strat + + Code + print(results) + Output + An sr_model with the following median values: + + Iso_type alpha shape t1 y0 y1 + 1 HlyE_IgA 0.01718040 1.368230 2.755075 2.646905 1184.585 + 2 HlyE_IgG 0.01005685 1.293325 2.910905 2.641075 817.486 + From ec88ab11b6aad31696145fc07d4262a235809531 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Wed, 8 Apr 2026 11:06:52 +0000 Subject: [PATCH 94/94] Fix dplyr::tbl_df reference to tibble::tbl_df in documentation Agent-Logs-Url: https://github.com/ucdavis/serodynamics/sessions/9e5d11ac-b621-49bc-9420-165105d24b90 Co-authored-by: sschildhauer <165851188+sschildhauer@users.noreply.github.com> --- R/print.sr_model.R | 2 +- man/print.sr_model.Rd | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/R/print.sr_model.R b/R/print.sr_model.R index 809292b4..1bddcc69 100644 --- a/R/print.sr_model.R +++ b/R/print.sr_model.R @@ -6,7 +6,7 @@ #' `Stratification` (if specified). #' @param x An `sr_model` output object from [run_mod()]. #' @param print_tbl A [logical] indicator to print `x` in the style of a -#' [dplyr::tbl_df]. +#' [tibble::tbl_df]. #' @param ... Additional arguments passed to the print method. #' @returns Invisibly returns either: #' \itemize{ diff --git a/man/print.sr_model.Rd b/man/print.sr_model.Rd index e030629d..b302a5a1 100644 --- a/man/print.sr_model.Rd +++ b/man/print.sr_model.Rd @@ -11,7 +11,7 @@ \item{x}{An \code{sr_model} output object from \code{\link[=run_mod]{run_mod()}}.} \item{print_tbl}{A \link{logical} indicator to print \code{x} in the style of a -\link[dplyr:defunct]{dplyr::tbl_df}.} +\link[tibble:tbl_df-class]{tibble::tbl_df}.} \item{...}{Additional arguments passed to the print method.} }