v0.1.1

DESCRIPTION

@@ -1,9 +1,14 @@
 Package: vmxr
 Title: VeloMetrix R Client
-Version: 0.1.0
+Version: 0.1.1
 Authors@R: c(
-    person("Eric", "Novik", , "eric@generable.com", role = c("aut", "cre")),
-    person("Generable", role = c("cph", "fnd")))
+    person(given = "Eric", family = "Novik", email = "eric@generable.com", role = c("aut", "cre")),
+    person(given = "Juho", family = "Timonen", role = "ctb"),
+    person(given = "Generable", role = c("cph", "fnd")))
+Author: Eric Novik [aut, cre],
+    Juho Timonen [ctb],
+    Generable [cph, fnd]
+Maintainer: Eric Novik <eric@generable.com>
 Description: A native R client for the VeloMetrix REST API (vmx-api). Wraps the
     treatment-to-simulation analysis workflow in ergonomic, pipe-friendly verbs
     that block-and-poll for asynchronous server jobs and return native R objects
@@ -36,3 +41,4 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 Config/roxygen2/version: 8.0.0
+RoxygenNote: 7.3.3

NAMESPACE

@@ -27,6 +27,7 @@ export(vmx_dataset_files)
 export(vmx_dataset_tags)
 export(vmx_datasets)
 export(vmx_dosing_input)
+export(vmx_dosing_input_status)
 export(vmx_fit_global_estimates)
 export(vmx_fit_obs_vs_pred)
 export(vmx_fit_subject_estimates)
@@ -39,13 +40,15 @@ export(vmx_model_build_events)
 export(vmx_model_build_export)
 export(vmx_model_build_logs)
 export(vmx_model_build_report)
+export(vmx_model_build_report_create)
 export(vmx_model_build_results)
 export(vmx_model_build_runs)
 export(vmx_model_build_status)
 export(vmx_model_catalog)
 export(vmx_model_data)
 export(vmx_model_describe)
 export(vmx_model_fit)
+export(vmx_model_fit_postprocessor_status)
 export(vmx_model_fits)
 export(vmx_modeling_options)
 export(vmx_nca)
@@ -60,8 +63,12 @@ export(vmx_prep_questions)
 export(vmx_prep_status)
 export(vmx_sim_cancel)
 export(vmx_sim_existing_subject)
+export(vmx_sim_existing_subject_from_text)
 export(vmx_sim_hypothetical_subject)
+export(vmx_sim_hypothetical_subject_from_text)
+export(vmx_sim_jobs)
 export(vmx_sim_population)
+export(vmx_sim_population_from_text)
 export(vmx_sim_result)
 export(vmx_sim_status)
 export(vmx_studies)

NEWS.md

@@ -1,3 +1,13 @@
+# vmxr 0.1.1
+
+* Send upload `config_yaml` as inline YAML text, matching the current API form
+  contract.
+* Add wrappers for report creation, model-fit postprocessor status,
+  dosing-input status, fit simulation-job listing, and simulation `from-text`
+  creation endpoints.
+* Fix examples to use valid time bases and clarify that OpenAPI codegen is not
+  shipped yet.
+
 # vmxr 0.1.0
 
 First broadly functional release: the client now covers the full analysis

R/datasets.R

@@ -37,7 +37,13 @@ vmx_upload <- function(study, files,
 
   parts <- list(treatment_id = tmt_id, study_id = std_id, mode = mode)
   if (!is.null(config)) {
-    parts$config_yaml <- curl::form_file(config, type = "application/yaml")
+    if (!file.exists(config)) {
+      vmx_abort(
+        sprintf("Config file not found: %s", config),
+        class = "vmx_usage_error"
+      )
+    }
+    parts$config_yaml <- paste(readLines(config, warn = FALSE), collapse = "\n")
   }
   # Repeated `files` form field — a list with duplicate names, spliced in.
   file_parts <- stats::setNames(

R/generated/README.md

@@ -1,11 +1,8 @@
-# Generated bindings (do not hand-edit)
+# Generated constants
 
-Files in this directory are produced by [`data-raw/codegen.R`](../../data-raw/codegen.R)
-from the vendored OpenAPI spec at
-[`inst/openapi/openapi.json`](../../inst/openapi/openapi.json).
+This directory is reserved for generated constants from
+[`data-raw/codegen.R`](../../data-raw/codegen.R) once the vendored OpenAPI
+snapshot and contract test are implemented.
 
-Per the design (section 3, path b), codegen emits **enum/type constants only**;
-the HTTP calls are hand-written in `R/*.R` and a contract test
-(`tests/testthat/test-contract.R`) asserts the hand-written layer has not
-drifted from the spec. Do not edit generated files by hand — re-run codegen
-instead.
+Per the design (section 3, path b), codegen will emit **enum/type constants
+only**; the HTTP calls are hand-written in `R/*.R`.

R/modeling.R

@@ -171,6 +171,25 @@ vmx_model_build_report <- function(run, client = vmx_client()) {
   vmx_get(client, paste0("/model-build-runs/", vmx_id(run, "run"), "/report"))
 }
 
+#' Request build-run report generation
+#'
+#' `POST /model-build-runs/{run_id}/report` queues HTML report generation.
+#'
+#' @param run A build-run id or object.
+#' @param subject_plot_mode One of `"all"` or `"none"`.
+#' @param client A `vmx_client`.
+#' @return A list with report status.
+#' @export
+vmx_model_build_report_create <- function(run, subject_plot_mode = c("all", "none"),
+                                          client = vmx_client()) {
+  subject_plot_mode <- match.arg(subject_plot_mode)
+  vmx_post(
+    client,
+    paste0("/model-build-runs/", vmx_id(run, "run"), "/report"),
+    list(subject_plot_mode = subject_plot_mode)
+  )
+}
+
 #' Cancel a build run
 #' @param run A build-run id or object.
 #' @param client A `vmx_client`.
@@ -232,6 +251,15 @@ vmx_model_fit <- function(id, client = vmx_client()) {
   new_vmx_resource(data, "vmx_model_fit", "model_fit_id")
 }
 
+#' Model-fit postprocessor status
+#' @param fit A fit id or `vmx_model_fit`.
+#' @param client A `vmx_client`.
+#' @return A list with postprocessor status.
+#' @export
+vmx_model_fit_postprocessor_status <- function(fit, client = vmx_client()) {
+  vmx_get(client, paste0("/model-fits/", vmx_id(fit, "mf"), "/postprocessor-status"))
+}
+
 #' Subject-level parameter estimates (tidy, long)
 #'
 #' One row per subject x parameter, with the posterior point estimate (`value`)

R/simulation.R

@@ -18,6 +18,16 @@ vmx_dosing_input <- function(fit, dosing_text, scenario_name,
   new_vmx_resource(data, "vmx_dosing_input", "dosing_input_id")
 }
 
+#' Dosing-input status
+#' @param dosing_input A dosing-input id or `vmx_dosing_input`.
+#' @param client A `vmx_client`.
+#' @return A `vmx_dosing_input`.
+#' @export
+vmx_dosing_input_status <- function(dosing_input, client = vmx_client()) {
+  data <- vmx_get(client, paste0("/simulation-dosing-inputs/", vmx_dosing_input_id(dosing_input)))
+  new_vmx_resource(data, "vmx_dosing_input", "dosing_input_id")
+}
+
 #' Simulate existing (observed) subjects
 #'
 #' `POST /model-fits/{mf_id}/existing-subject-simulation-jobs`.
@@ -26,6 +36,7 @@ vmx_dosing_input <- function(fit, dosing_text, scenario_name,
 #' @param dosing_input A dosing-input id or `vmx_dosing_input`.
 #' @param subjects Subjects to simulate: a data.frame/tibble with
 #'   `gen_subject_uuid` + `subject_name` columns, or a list of such records.
+#' @param min_timepoints Optional minimum number of simulated timepoints.
 #' @param idempotency_key,retried_from Optional create fields.
 #' @param wait If `TRUE`, block until the job settles.
 #' @param ... Polling controls forwarded to [vmx_wait()].
@@ -34,16 +45,40 @@ vmx_dosing_input <- function(fit, dosing_text, scenario_name,
 #' @export
 vmx_sim_existing_subject <- function(fit, dosing_input, subjects,
                                      idempotency_key = NULL, retried_from = NULL,
+                                     min_timepoints = NULL,
                                      wait = FALSE, ..., client = vmx_client()) {
   body <- vmx_compact(list(
     dosing_input_id = vmx_dosing_input_id(dosing_input),
     subjects = vmx_rows_to_records(subjects, c("gen_subject_uuid", "subject_name")),
+    min_timepoints = min_timepoints,
     idempotency_key = idempotency_key,
     retried_from = retried_from
   ))
   vmx_create_sim_job(fit, "existing-subject-simulation-jobs", body, wait, client, ...)
 }
 
+#' Simulate existing subjects from dosing text
+#'
+#' `POST /model-fits/{mf_id}/existing-subject-simulation-jobs/from-text`.
+#'
+#' @inheritParams vmx_sim_existing_subject
+#' @param dosing_text The dosing regimen text.
+#' @return A `vmx_simulation_job`.
+#' @export
+vmx_sim_existing_subject_from_text <- function(fit, dosing_text, subjects,
+                                               idempotency_key = NULL, retried_from = NULL,
+                                               min_timepoints = NULL,
+                                               wait = FALSE, ..., client = vmx_client()) {
+  body <- vmx_compact(list(
+    dosing_text = dosing_text,
+    subjects = vmx_rows_to_records(subjects, c("gen_subject_uuid", "subject_name")),
+    min_timepoints = min_timepoints,
+    idempotency_key = idempotency_key,
+    retried_from = retried_from
+  ))
+  vmx_create_sim_job(fit, "existing-subject-simulation-jobs/from-text", body, wait, client, ...)
+}
+
 #' Simulate hypothetical subjects
 #'
 #' `POST /model-fits/{mf_id}/hypothetical-subject-simulation-jobs`.
@@ -52,6 +87,7 @@ vmx_sim_existing_subject <- function(fit, dosing_input, subjects,
 #' @param dosing_input A dosing-input id or `vmx_dosing_input`.
 #' @param subjects A data.frame/tibble with a `subject_name` column plus one
 #'   column per covariate, or a list of `{subject_name, covariates}` records.
+#' @param min_timepoints Optional minimum number of simulated timepoints.
 #' @param idempotency_key,retried_from Optional create fields.
 #' @param wait If `TRUE`, block until the job settles.
 #' @param ... Polling controls forwarded to [vmx_wait()].
@@ -60,23 +96,48 @@ vmx_sim_existing_subject <- function(fit, dosing_input, subjects,
 #' @export
 vmx_sim_hypothetical_subject <- function(fit, dosing_input, subjects,
                                          idempotency_key = NULL, retried_from = NULL,
+                                         min_timepoints = NULL,
                                          wait = FALSE, ..., client = vmx_client()) {
   body <- vmx_compact(list(
     dosing_input_id = vmx_dosing_input_id(dosing_input),
     subjects = vmx_hypothetical_records(subjects),
+    min_timepoints = min_timepoints,
     idempotency_key = idempotency_key,
     retried_from = retried_from
   ))
   vmx_create_sim_job(fit, "hypothetical-subject-simulation-jobs", body, wait, client, ...)
 }
 
+#' Simulate hypothetical subjects from dosing text
+#'
+#' `POST /model-fits/{mf_id}/hypothetical-subject-simulation-jobs/from-text`.
+#'
+#' @inheritParams vmx_sim_hypothetical_subject
+#' @param dosing_text The dosing regimen text.
+#' @return A `vmx_simulation_job`.
+#' @export
+vmx_sim_hypothetical_subject_from_text <- function(fit, dosing_text, subjects,
+                                                   idempotency_key = NULL, retried_from = NULL,
+                                                   min_timepoints = NULL,
+                                                   wait = FALSE, ..., client = vmx_client()) {
+  body <- vmx_compact(list(
+    dosing_text = dosing_text,
+    subjects = vmx_hypothetical_records(subjects),
+    min_timepoints = min_timepoints,
+    idempotency_key = idempotency_key,
+    retried_from = retried_from
+  ))
+  vmx_create_sim_job(fit, "hypothetical-subject-simulation-jobs/from-text", body, wait, client, ...)
+}
+
 #' Simulate a population scenario
 #'
 #' `POST /model-fits/{mf_id}/population-simulation-jobs`.
 #'
 #' @param fit A fit id or `vmx_model_fit`.
 #' @param dosing_input A dosing-input id or `vmx_dosing_input`.
 #' @param scenario_name The population scenario name.
+#' @param min_timepoints Optional minimum number of simulated timepoints.
 #' @param idempotency_key,retried_from Optional create fields.
 #' @param wait If `TRUE`, block until the job settles.
 #' @param ... Polling controls forwarded to [vmx_wait()].
@@ -85,16 +146,49 @@ vmx_sim_hypothetical_subject <- function(fit, dosing_input, subjects,
 #' @export
 vmx_sim_population <- function(fit, dosing_input, scenario_name,
                                idempotency_key = NULL, retried_from = NULL,
+                               min_timepoints = NULL,
                                wait = FALSE, ..., client = vmx_client()) {
   body <- vmx_compact(list(
     dosing_input_id = vmx_dosing_input_id(dosing_input),
     scenario_name = scenario_name,
+    min_timepoints = min_timepoints,
     idempotency_key = idempotency_key,
     retried_from = retried_from
   ))
   vmx_create_sim_job(fit, "population-simulation-jobs", body, wait, client, ...)
 }
 
+#' Simulate a population scenario from dosing text
+#'
+#' `POST /model-fits/{mf_id}/population-simulation-jobs/from-text`.
+#'
+#' @inheritParams vmx_sim_population
+#' @param dosing_text The dosing regimen text.
+#' @return A `vmx_simulation_job`.
+#' @export
+vmx_sim_population_from_text <- function(fit, dosing_text, scenario_name,
+                                         idempotency_key = NULL, retried_from = NULL,
+                                         min_timepoints = NULL,
+                                         wait = FALSE, ..., client = vmx_client()) {
+  body <- vmx_compact(list(
+    dosing_text = dosing_text,
+    scenario_name = scenario_name,
+    min_timepoints = min_timepoints,
+    idempotency_key = idempotency_key,
+    retried_from = retried_from
+  ))
+  vmx_create_sim_job(fit, "population-simulation-jobs/from-text", body, wait, client, ...)
+}
+
+#' List simulation jobs for a model fit
+#' @param fit A fit id or `vmx_model_fit`.
+#' @param client A `vmx_client`.
+#' @return A tibble.
+#' @export
+vmx_sim_jobs <- function(fit, client = vmx_client()) {
+  vmx_items_to_tibble(vmx_paginate(client, paste0("/model-fits/", vmx_id(fit, "mf", "fit"), "/simulation-jobs")))
+}
+
 #' Simulation job status
 #' @param job A job id (`simjob_...`) or `vmx_simulation_job`.
 #' @param client A `vmx_client`.

README.md

@@ -12,7 +12,7 @@ modeling → simulation workflow in ergonomic, pipe-friendly verbs that
 Our users are pharmacometricians who work in R/RStudio; `vmxr` keeps the whole
 analysis next to their data instead of shuttling files and IDs through a shell.
 
-> **Status: functional (v0.1.0), pre-CRAN.** The client covers the full analysis
+> **Status: functional (v0.1.1), pre-CRAN.** The client covers the full analysis
 > workflow end to end — treatments, studies, datasets & prep, data-versions,
 > modeling-data tables, NCA, modeling (build runs, fits, estimates), simulation,
 > and the study analysis log — validated against the live API on staging.
@@ -61,18 +61,16 @@ tmt   <- vmx_treatment_create("Compound XYZ", indication = "atrial fibrillation"
 study <- vmx_study_create(tmt, "Phase 1 SAD", phase = "1")
 ds    <- vmx_upload(study, c("conc.csv", "dosing.csv"), mode = "initial", wait = TRUE)
 dv    <- vmx_data_version(vmx_prep_status(ds)$data_version_id)
-nca   <- vmx_nca(dv, time_basis = "actual")
+nca   <- vmx_nca(dv, time_basis = "observed")
 vmx_nca_result(nca)
 ```
 
 ## Design
 
-The package has two layers (see the design doc):
-
-1. **Low-level bindings** (`R/generated/`) — one function per OpenAPI operation,
-   generated from a vendored `openapi.json` snapshot. Users rarely call these.
-2. **Ergonomic layer** (`R/*.R`) — the curated, hand-written public API that adds
-   polling, pagination, multipart upload, and tibble/S3 conversion.
+The package exposes a curated, hand-written public API in `R/*.R` that adds
+polling, pagination, multipart upload, and tibble/S3 conversion. The OpenAPI
+snapshot/codegen path is still a development task, not a shipped generated
+binding layer.
 
 The client holds **no business logic**: the API is the single source of truth.
 

data-raw/codegen.R

@@ -9,8 +9,8 @@
 # Steps:
 #   1. Download the published spec to inst/openapi/openapi.json.
 #   2. Emit enum/type constants into R/generated/.
-#   3. Leave the hand-written calls in R/*.R untouched; the contract test
-#      (tests/testthat/test-contract.R) verifies they still match the spec.
+#   3. Leave the hand-written calls in R/*.R untouched. A future contract test
+#      should verify that they still match the spec.
 
 # Published artifact (see inst/openapi/README.md).
 OPENAPI_URL <- Sys.getenv(