Tweaks for cran (#278)

Author: mattsecrest

.github/workflows/R-CMD-check.yaml

@@ -17,7 +17,7 @@ jobs:
       matrix:
         config:
           - {os: macOS-latest,   r: 'release'}
-          - {os: windows-latest, r: 'release'}
+          #- {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -38,6 +38,7 @@ jobs:
         with:
           extra-packages: rcmdcheck, survival, flexsurv, testthat, usethis, vdiffr, tibble, xml2, knitr, rmarkdown, bayesplot, matrixcalc, WeightIt, MatchIt, BayesPPD, ggsurvfit, gbm, ggplot2, cobalt, table1, gt, gtsummary
           dependencies: '"hard"'
+          cache: false
 
       - name: Install system dependencies on Linux
         if: runner.os == 'Linux'

DESCRIPTION

@@ -27,17 +27,19 @@ Authors@R: c(
 Description: Bayesian dynamic borrowing is an approach to incorporating external
    data to supplement a randomized, controlled trial analysis in which
    external data are incorporated in a dynamic way (e.g., based on similarity
-   of outcomes); see Viele 2013 \doi{10.1002/pst.1589} for an overview.
+   of outcomes); see Viele 2013 <doi:10.1002/pst.1589> for an overview.
    This package implements the hierarchical commensurate prior approach to dynamic borrowing
-   as described in Hobbes 2011 \doi{10.1111/j.1541-0420.2011.01564.x}.
+   as described in Hobbes 2011 <doi:10.1111/j.1541-0420.2011.01564.x>.
    There are three main functionalities. First, 'psborrow2' provides a user-friendly 
    interface for applying dynamic borrowing on the study results handles the Markov Chain
    Monte Carlo sampling on behalf of the user. Second, 'psborrow2' provides a 
    simulation framework to compare different borrowing parameters (e.g. full borrowing, no
    borrowing, dynamic borrowing) and other trial and borrowing characteristics
    (e.g. sample size, covariates) in a unified way. Third, 'psborrow2' provides
    a set of functions to generate data for simulation studies, and also allows
-   the user to specify their own data generation process.
+   the user to specify their own data generation process. This package is designed to 
+   use the sampling functions from 'cmdstanr' which can be installed from
+   <https://mc-stan.org/r-packages/>.
 URL: https://github.com/Genentech/psborrow2, https://genentech.github.io/psborrow2/index.html
 BugReports: https://github.com/Genentech/psborrow2/issues
 License: Apache License 2.0

NAMESPACE

@@ -18,21 +18,18 @@ export(check_cmdstanr)
 export(check_data_matrix_has_columns)
 export(cont_var)
 export(covariance_matrix)
-export(create_alpha_string)
 export(create_analysis_obj)
 export(create_baseline_object)
 export(create_data_matrix)
 export(create_data_simulation)
 export(create_event_dist)
 export(create_simulation_obj)
-export(create_tau_string)
 export(custom_enrollment)
 export(cut_off_after_events)
 export(cut_off_after_first)
 export(cut_off_after_last)
 export(cut_off_none)
 export(enrollment_constant)
-export(eval_constraints)
 export(exp_surv_dist)
 export(exponential_prior)
 export(gamma_prior)
@@ -81,11 +78,10 @@ export(sim_outcome_list)
 export(sim_samplesize)
 export(sim_treatment_list)
 export(treatment_details)
-export(trim_cols)
-export(trim_rows)
 export(uniform_prior)
 export(variable_dictionary)
 export(weib_ph_surv_dist)
+exportMethods(c)
 exportMethods(generate)
 exportMethods(mcmc_sample)
 exportMethods(set_transformations)

R/borrowing_details.R

@@ -1,11 +1,18 @@
 #' Legacy function for specifying borrowing details
 #'
-#' Please use one of `hierarchical_commensurate_borrowing()`, `no_borrowing()`, or `full_borrowing()` instead.
+#' Please use one of `borrowing_hierarchical_commensurate()`, `borrowing_none()`, or `borrowing_full()` instead.
 #' @export
+#' 
+#' @return
+#' This function does not return a value. When called, it triggers an error 
+#' message indicating that `borrowing_details()` is deprecated and that 
+#' one of `borrowing_hierarchical_commensurate()`, `borrowing_none()`, or
+#' `borrowing_full()` should be used instead.
+#' 
 #' @param ... Deprecated arguments to `borrowing_details`.
 borrowing_details <- function(...) {
   .Defunct(
-    "hierarchical_commensurate_borrowing()",
+    "borrowing_hierarchical_commensurate()",
     "psborrow2",
     paste(
       "`borrowing_details()` is deprecated. Use `borrowing_hierarchical_commensurate()` for dynamic borrowing,",

R/check_data_matrix_has_columns.R

@@ -7,7 +7,7 @@
 #' @return `stop()` if some columns are missing.
 #' @export
 #' @examples
-#' anls <- psborrow2:::.analysis_obj(
+#' anls <- create_analysis_obj(
 #'   data_matrix = example_matrix,
 #'   covariates = add_covariates(
 #'     covariates = c("cov1", "cov2"),
@@ -25,8 +25,7 @@
 #'   treatment = treatment_details(
 #'     "trt",
 #'     prior_normal(0, 1000)
-#'   ),
-#'   ready_to_sample = FALSE
+#'   )
 #' )
 #'
 #' check_data_matrix_has_columns(anls)

R/generics.R

@@ -10,14 +10,13 @@
 #' @param y Not used.
 #' @param add logical. Add density to existing plot.
 #' @param ... Optional arguments for plotting.
-#'
+#' @return No return value, this function generates a plot in the current graphics device.
 #' @export
 #' @details
 #' Plot ranges are selected by default to show 99% of the density for unbounded distributions.
 #' The limits can be changed by specifying `xlim = c(lower, upper)`.
 #'
 #' Colors, line types, and other typical [par()] parameters can be used.
-#'
 if (!isGeneric("plot")) setGeneric("plot", function(x, y, ...) standardGeneric("plot"))
 
 
@@ -29,7 +28,7 @@ if (!isGeneric("plot")) setGeneric("plot", function(x, y, ...) standardGeneric("
 #' @aliases get_vars
 #'
 #' @param object Object
-#' @returns A `character` vector containing variable names
+#' @return A `character` vector containing variable names
 #' @export
 #'
 setGeneric("get_vars", function(object) standardGeneric("get_vars"))
@@ -57,6 +56,8 @@ setGeneric("mcmc_sample", function(x, ...) standardGeneric("mcmc_sample"))
 #'
 #' @rdname show_guide
 #'
+#' @return A `data.frame` showing all simulation scenarios.
+#' 
 #' @export
 #'
 setGeneric("show_guide", function(object) standardGeneric("show_guide"))
@@ -68,6 +69,8 @@ setGeneric("show_guide", function(object) standardGeneric("show_guide"))
 #' @param object `MCMCSimulationResults` object
 #'
 #' @rdname get_results
+#' 
+#' @return data.frame with simulation results.
 #'
 #' @export
 #'
@@ -80,6 +83,8 @@ setGeneric("get_results", function(object) standardGeneric("get_results"))
 #' @param object `MCMCSimulationResults` object
 #'
 #' @rdname get_cmd_stan_models
+#' 
+#' @return List of lists of `CmdStanModel` objects for each model.
 #'
 #' @export
 #'
@@ -92,6 +97,8 @@ setGeneric("get_cmd_stan_models", function(object) standardGeneric("get_cmd_stan
 #'
 #' @rdname generate
 #'
+#' @return Object of class [`SimDataList`][SimDataList-class].
+#' 
 #' @export
 setGeneric("generate", function(x, ...) standardGeneric("generate"))
 
@@ -101,8 +108,6 @@ setGeneric("generate", function(x, ...) standardGeneric("generate"))
 #' @param analysis_object analysis object
 #'
 #' @rdname trim_rows
-#'
-#' @export
 setGeneric("trim_rows", function(borrowing_object, analysis_object) standardGeneric("trim_rows"))
 
 #' Trim columns from Data Matrix Based on Borrowing object type
@@ -111,8 +116,6 @@ setGeneric("trim_rows", function(borrowing_object, analysis_object) standardGene
 #' @param analysis_object analysis object
 #'
 #' @rdname trim_cols
-#'
-#' @export
 setGeneric("trim_cols", function(borrowing_object, analysis_object) standardGeneric("trim_cols"))
 
 #' Create alpha string
@@ -121,20 +124,15 @@ setGeneric("trim_cols", function(borrowing_object, analysis_object) standardGene
 #' @param outcome_object outcome object
 #'
 #' @rdname create_alpha_string
-#'
-#' @export
 setGeneric("create_alpha_string", function(borrowing_object, outcome_object) standardGeneric("create_alpha_string"))
 
 #' Create tau string
 #'
 #' @param borrowing_object borrowing object
 #'
 #' @rdname create_tau_string
-#'
-#' @export
 setGeneric("create_tau_string", function(borrowing_object) standardGeneric("create_tau_string"))
 
-
 #' Create Stan Code for Model
 #'
 #' @param borrowing borrowing object
@@ -145,12 +143,26 @@ setGeneric("create_tau_string", function(borrowing_object) standardGeneric("crea
 #' @return `glue` `character` containing the Stan code for the data block.
 #' @export
 #' @examples
-#' anls_obj <- psborrow2:::.analysis_obj(
-#'   data_matrix = example_matrix,
-#'   outcome = outcome_surv_exponential("time", "cnsr", prior_normal(0, 100)),
-#'   borrowing = borrowing_full("ext"),
-#'   treatment = treatment_details("trt", prior_normal(0, 100))
-#' )
+#' anls_obj <- create_analysis_obj(
+#'     data_matrix = example_matrix,
+#'     outcome = outcome_surv_exponential(
+#'       "time",
+#'       "cnsr",
+#'       baseline_prior = prior_normal(0, 1000)
+#'     ),
+#'     borrowing = borrowing_hierarchical_commensurate(
+#'       "ext",
+#'       prior_exponential(.001)
+#'     ),
+#'     treatment = treatment_details(
+#'       "trt",
+#'       prior_normal(0, 1000)
+#'     ),
+#'     covariates = add_covariates(
+#'       covariates = c("cov1", "cov2"),
+#'       priors = prior_normal(0, 1000)
+#'     )
+#'   )
 #' make_model_string_model(anls_obj@borrowing, anls_obj@outcome, anls_obj)
 setGeneric("make_model_string_model", function(borrowing, outcome, analysis_obj) {
   standardGeneric("make_model_string_model")
@@ -164,7 +176,7 @@ setGeneric("make_model_string_model", function(borrowing, outcome, analysis_obj)
 #'
 #' @param x object of type: [BaselineDataList-class]
 #' @param ... Optional arguments for passed to [data.frame]
-#' @returns A `data.frame`
+#' @return A `data.frame`
 NULL
 
 #' @title Combine objects in `psborrow2`
@@ -173,7 +185,7 @@ NULL
 #' @name c
 #' @param x object of type: [SimDataList-class]
 #' @param ... additional objects to combine
-#' @returns A combined object
+#' @return A combined object
 NULL
 
 #' Get Simulated Data from `SimDataList` object
@@ -183,7 +195,7 @@ NULL
 #' @param object `SimDataList` object
 #' @param index the index of the scenario (see guide with print(`SimDataList`))
 #' @param dataset the dataset out of `n_datasets_per_param`
-#' @returns Simulated data as a data frame if the index is specified, else as a list
+#' @return Simulated data as a data frame if the index is specified, else as a list
 #' @export
 setGeneric("get_data", function(object, index = 1, dataset = 1) standardGeneric("get_data"))
 
@@ -192,12 +204,12 @@ setGeneric("get_data", function(object, index = 1, dataset = 1) standardGeneric(
 #' @param object `BaselineObject` object
 #' @param ... Additional arguments passed to methods
 #' @param overwrite logical. Overwrite existing transformations?
-#' @returns `BaselineObject` object with transformations
+#' @return `BaselineObject` object with transformations
 #' @export
 setGeneric("set_transformations", function(object, ..., overwrite = FALSE) standardGeneric("set_transformations"))
 
 #' Get method for Stan model
 #' @param object `Analysis` object
-#' @returns String containing the Stan model
+#' @return String containing the Stan model
 #' @export
 setGeneric("get_stan_code", function(object) standardGeneric("get_stan_code"))

R/helpers.R

@@ -6,8 +6,11 @@
 #'
 #' Plots the density values as a curve with the lower vertical limit set to 0.
 #'
-#' @export
+#' 
+#' @return No return value, this function generates a plot in the current graphics device.
 #'
+#' @export
+#' 
 #' @examples
 #' x <- seq(-2, 2, len = 100)
 #' y <- dnorm(x)
@@ -36,6 +39,8 @@ plot_pdf <- function(x, y, ...) {
 #'
 #' Plots the probability values as a barplot.
 #'
+#' @return No return value, this function generates a plot in the current graphics device.
+#'
 #' @export
 #'
 #' @examples
@@ -73,12 +78,12 @@ plot_pmf <- function(x, y, ..., col = "grey", add = FALSE) {
 #' @param collapse_sep string. A character string to separate the original strings in the collapsed string.
 #'
 #' @return A character (of class `glue`).
-#' @noRd
 #' @examples
 #' name <- "Tom"
 #' psborrow2:::h_glue("hello, my name is {{name}}.")
 #' name <- c("Tom", "Fred")
 #' psborrow2:::h_glue("hello, my name is {{name}}.", collapse = TRUE)
+#' @noRd
 h_glue <- function(..., collapse = FALSE, collapse_sep = "\n") {
   result <- glue::glue(..., .open = "{{", .close = "}}", .envir = parent.frame())
   if (isTRUE(collapse)) {
@@ -94,7 +99,7 @@ h_glue <- function(..., collapse = FALSE, collapse_sep = "\n") {
 #'
 #' @return A `matrix` with columns "lower" and "upper" with rows for each `Prior`.
 #' @examples
-#' psborrow2:::get_covariate_constraints(
+#' get_covariate_constraints(
 #'   add_covariates(
 #'     c("cov1", "cov2", "cov3"),
 #'     list(
@@ -104,7 +109,7 @@ h_glue <- function(..., collapse = FALSE, collapse_sep = "\n") {
 #'     )
 #'   )
 #' )
-#'
+#' @noRd
 get_covariate_constraints <- function(cov_obj) {
   n_covs <- length(cov_obj@covariates)
   if (is(cov_obj@priors, "Prior")) {
@@ -125,7 +130,8 @@ get_covariate_constraints <- function(cov_obj) {
 #' A list with upper and lower bounds. Any unspecified bounds are set to `-Inf` or `Inf`.
 #' @examples
 #' np <- prior_normal(0, 100)
-#' psborrow2:::parse_constraint(np)
+#' parse_constraint(np)
+#' @noRd
 parse_constraint <- function(object) {
   assert_class(object, "Prior")
   s <- eval_constraints(object)
@@ -214,7 +220,8 @@ variable_dictionary <- function(analysis_obj) {
 #'
 #' @return A string containing the Stan code sampling from specified distribution.
 #' @examples
-#' psborrow2:::get_prior_string(prior_normal(0, 100))
+#' get_prior_string(prior_normal(0, 100))
+#' @noRd
 get_prior_string <- function(object) {
   assert_multi_class(object, c("Prior", "list"))
   if (is(object, "list")) {

R/make_model_string_data.R

@@ -3,20 +3,20 @@
 #' Create the Stan string encompassed by data `{}`
 #'
 #' @param analysis_obj `Analysis`. Object of class [`Analysis`][Analysis-class] created by
-#' `psborrow2:::.analysis_obj()`.
+#' `.analysis_obj()`.
 #'
 #' @return `glue` `character` containing the text for the data block.
 #'
 #' @examples
-#' anls_obj <- psborrow2:::.analysis_obj(
+#' anls_obj <- .analysis_obj(
 #'   data_matrix = example_matrix,
 #'   outcome = outcome_surv_exponential("time", "cnsr", prior_normal(0, 100)),
 #'   borrowing = borrowing_full("ext"),
 #'   treatment = treatment_details("trt", prior_normal(0, 100))
 #' )
-#'
-#' psborrow2:::make_model_string_data(anls_obj)
-#'
+#' 
+#' make_model_string_data(anls_obj)
+#' @noRd
 make_model_string_data <- function(analysis_obj) {
   outcome_string <- analysis_obj@outcome@data_stan_code