baseline data simulation

.pre-commit-config.yaml

@@ -3,13 +3,15 @@
 # R specific hooks: https://github.com/lorenzwalthert/precommit
 repos:
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.3.2.9003
+    rev: v0.3.2.9019
     hooks:
       - id: style-files
         args: []
       - id: roxygenize
         additional_dependencies:
           - knitr
+          - stan-dev/cmdstanr@*release
+          - mvtnorm
       # codemeta must be above use-tidy-description when both are used
       # -   id: codemeta-description-updated
       - id: use-tidy-description
@@ -49,11 +51,11 @@ repos:
       - id: no-browser-statement
       - id: deps-in-desc
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.0-alpha.3
+    rev: v3.0.1
     hooks:
       - id: prettier
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v4.4.0
     hooks:
       - id: check-added-large-files
         args: ["--maxkb=200"]
@@ -79,7 +81,7 @@ repos:
         files: '\.Rhistory|\.RData|\.Rds|\.rds$'
         # `exclude: <regex>` to allow committing specific files.
   - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.32.2
+    rev: v0.34.0
     hooks:
       - id: markdownlint
         args:

DESCRIPTION

@@ -42,7 +42,10 @@ Imports:
     glue,
     methods,
     graphics,
-    posterior
+    posterior,
+    generics,
+    Matrix,
+    mvtnorm
 Suggests:
     survival,
     flexsurv,
@@ -121,6 +124,7 @@ Collate:
     'sim_is_null_effect_covered.R'
     'sim_is_true_effect_covered.R'
     'sim_samplesize.R'
+    'simulate_data.R'
     'simvar_class.R'
     'trim_data_matrix.R'
     'uniform_prior.R'

NAMESPACE

@@ -1,22 +1,28 @@
 # Generated by roxygen2: do not edit by hand
 
 export(add_covariates)
+export(baseline_covariates)
 export(bernoulli_prior)
 export(beta_prior)
 export(bin_var)
+export(binary_cutoff)
 export(borrowing_details)
 export(cauchy_prior)
 export(check_cmdstanr)
 export(check_data_matrix_has_columns)
 export(cont_var)
+export(covariance_matrix)
 export(create_analysis_obj)
+export(create_baseline_object)
 export(create_data_matrix)
 export(create_simulation_obj)
 export(eval_constraints)
 export(exp_surv_dist)
 export(exponential_prior)
 export(gamma_prior)
+export(generate)
 export(get_cmd_stan_models)
+export(get_quantiles)
 export(get_results)
 export(get_vars)
 export(half_cauchy_prior)
@@ -41,9 +47,12 @@ export(treatment_details)
 export(uniform_prior)
 export(variable_dictionary)
 export(weib_ph_surv_dist)
+exportMethods(generate)
 exportMethods(mcmc_sample)
 import(checkmate)
 import(cmdstanr)
+importFrom(Matrix,nearPD)
+importFrom(generics,generate)
 importFrom(graphics,axis)
 importFrom(graphics,lines)
 importFrom(graphics,par)
@@ -53,7 +62,9 @@ importFrom(methods,callNextMethod)
 importFrom(methods,is)
 importFrom(methods,new)
 importFrom(methods,show)
+importFrom(mvtnorm,rmvnorm)
 importFrom(stats,complete.cases)
 importFrom(stats,formula)
 importFrom(stats,model.matrix)
+importFrom(stats,pnorm)
 importFrom(stats,setNames)

R/cmdstan.R

@@ -1,18 +1,21 @@
 #' Check Stan
 #'
 #' @description Check whether `cmdstanr` is available and prints version and logistic example.
+#' @param check_sampling Compile and sample from the "logistic" example model.
 #'
 #' @export
 #'
 #' @examples
 #' check_cmdstanr()
-check_cmdstanr <- function() {
+check_cmdstanr <- function(check_sampling = FALSE) {
   cat("cmdstan version: \n")
   print(cmdstan_version())
 
   cat("Example program:\n")
   print_example_program(example = c("logistic"))
 
-  cat("Example program results:\n")
-  cmdstanr_example("logistic", quiet = FALSE, chains = 1)
+  if (check_sampling) {
+    cat("Example program results:\n")
+    cmdstanr_example("logistic", quiet = FALSE, chains = 1)
+  }
 }

R/generics.R

@@ -1,4 +1,3 @@
-
 #' Plot Prior Objects
 #'
 #' Plot prior distributions as densities. Continuous distributions are plotted as curves and
@@ -85,3 +84,13 @@ setGeneric("get_results", function(object) standardGeneric("get_results"))
 #' @export
 #'
 setGeneric("get_cmd_stan_models", function(object) standardGeneric("get_cmd_stan_models"))
+
+#' Generate Data from Object
+#'
+#' @param x object
+#' @param ... Other arguments passed to methods
+#'
+#' @rdname generate
+#'
+#' @export
+setGeneric("generate", function(x, ...) standardGeneric("generate"))