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Global option for turning off warning for partial initial values #913

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merged 3 commits into from
Feb 28, 2024
Merged

Global option for turning off warning for partial initial values #913

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9e3a39c
Global option for turning off warning for partial initial values
jgabry Jan 31, 2024
231d5c5
Update args.R
jgabry Jan 31, 2024
6bf9b3d
Merge branch 'master' into cmdstanr_warn_inits-global-option
jgabry Feb 26, 2024
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9 changes: 7 additions & 2 deletions R/args.R
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Original file line number Diff line number Diff line change
Expand Up @@ -1021,8 +1021,12 @@ validate_exe_file <- function(exe_file) {
#' @param num_procs Number of CmdStan processes.
#' @param model_variables A list of all parameters with their types and
#' number of dimensions. Typically the output of model$variables().
#' @param warn_partial Should a warning be thrown if inits are only specified
#' for a subset of parameters? Can be controlled by global option
#' `cmdstanr_warn_inits`.
#' @return A character vector of file paths.
process_init_list <- function(init, num_procs, model_variables = NULL) {
process_init_list <- function(init, num_procs, model_variables = NULL,
warn_partial = getOption("cmdstanr_warn_inits", TRUE)) {
if (!all(sapply(init, function(x) is.list(x) && !is.data.frame(x)))) {
stop("If 'init' is a list it must be a list of lists.", call. = FALSE)
}
Expand All @@ -1048,7 +1052,7 @@ process_init_list <- function(init, num_procs, model_variables = NULL) {
}
}
}
if (length(missing_parameter_values) > 0) {
if (length(missing_parameter_values) > 0 && isTRUE(warn_partial)) {
warning_message <- c(
"Init values were only set for a subset of parameters. \nMissing init values for the following parameters:\n"
)
Expand All @@ -1062,6 +1066,7 @@ process_init_list <- function(init, num_procs, model_variables = NULL) {
warning_message <- c(warning_message, paste0(line_text, paste0(missing_parameter_values[[i]], collapse = ", "), "\n"))
}
}
warning_message <- c(warning_message, "\nTo disable this message use options(cmdstanr_warn_inits = FALSE).\n")
message(warning_message)
}
}
Expand Down
18 changes: 18 additions & 0 deletions tests/testthat/test-model-init.R
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Expand Up @@ -240,6 +240,7 @@ test_that("error if init function specified incorrectly", {
})

test_that("print message if not all parameters are initialized", {
options(cmdstanr_warn_inits = NULL) # should default to TRUE
init_list <- list(
list(
alpha = 1
Expand Down Expand Up @@ -271,6 +272,23 @@ test_that("print message if not all parameters are initialized", {
)
})

test_that("No message printed if options(cmdstanr_warn_inits=FALSE)", {
options(cmdstanr_warn_inits = FALSE)
expect_message(
utils::capture.output(mod_logistic$optimize(data = data_list_logistic, init = list(list(a = 0)), seed = 123)),
regexp = NA
)
expect_message(
utils::capture.output(mod_logistic$optimize(data = data_list_logistic, init = list(list(alpha = 1)), seed = 123)),
regexp = NA
)
expect_message(
utils::capture.output(mod_logistic$sample(data = data_list_logistic, init = list(list(alpha = 1),list(alpha = 1)), chains = 2, seed = 123)),
regexp = NA
)
options(cmdstanr_warn_inits = TRUE)
})

test_that("Initial values for single-element containers treated correctly", {
modcode <- "
data {
Expand Down
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