Replace get_prior_names with get_param_names (related to #3)

bodkan · Dec 8, 2023 · 9d4c914 · 9d4c914
1 parent 26216a5
commit 9d4c914
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Showing 3 changed files with 7 additions and 7 deletions.
diff --git a/R/plot_prior.R b/R/plot_prior.R
@@ -17,7 +17,7 @@
 plot_prior <- function(x, param = NULL, facets = FALSE, file = NULL,
                        replicates = 10000, geom = ggplot2::geom_density, ...) {
   priors <- if (inherits(x, "demografr_abc.abc")) attr(x, "priors") else x
-  all_params <- get_prior_names(priors); names(priors) <- all_params
+  all_params <- get_param_names(priors); names(priors) <- all_params
   subset_params <- subset_parameters(subset = param, all = all_params)
   priors <- priors[subset_params]; unname(priors)
 
@@ -42,7 +42,7 @@ plot_prior <- function(x, param = NULL, facets = FALSE, file = NULL,
 simulate_priors <- function(priors, replicates = 1000) {
   if (!is.list(priors)) priors <- list(priors)
 
-  vars <- get_prior_names(priors)
+  vars <- get_param_names(priors)
 
   samples_list <- lapply(
     seq_along(priors), \(i)

diff --git a/R/validate_abc.R b/R/validate_abc.R
@@ -56,7 +56,7 @@ validate_abc <- function(model, priors, functions, observed,
 
   prior_samples <- list()
 
-  prior_names <- get_prior_names(priors)
+  prior_names <- get_param_names(priors)
 
   cat("Testing sampling of each prior parameter:\n")
 
@@ -110,13 +110,13 @@ validate_abc <- function(model, priors, functions, observed,
 
     # first expand any generic "..." prior sampling expressions (if needed)
     priors <- tryCatch(
-      expand_priors(model, priors, model_args),
+      expand_formulas(priors, model, model_args),
       error = function(e) {
         cat(" \u274C\n\n")
         stop(e$message, call. = FALSE)
     })
     # prior names generated above have to be re-generated after templating
-    prior_names <- get_prior_names(priors)
+    prior_names <- get_param_names(priors)
 
     missing_priors <- setdiff(prior_names, methods::formalArgs(model))
     if (length(missing_priors) > 0) {
@@ -142,7 +142,7 @@ validate_abc <- function(model, priors, functions, observed,
 
     cat("The model is a custom user-defined", script_engine, "script\n")
 
-    prior_names <- get_prior_names(priors)
+    prior_names <- get_param_names(priors)
     template_priors <- grepl("\\.\\.\\.", prior_names)
     if (any(template_priors)) {
       cat(" \u274C\n\n")

diff --git a/tests/testthat/test-prior-expansion.R b/tests/testthat/test-prior-expansion.R
@@ -66,7 +66,7 @@ test_that("Templated prior sampling expressions validate correctly", {
 
 test_that("expand_fromulas() produces parameters equal to formal arguments of a model", {
   expanded_priors <- expand_formulas(templated_priors, model)
-  expect_true(all(get_prior_names(expanded_priors) == names(formals(model))))
+  expect_true(all(get_param_names(expanded_priors) == names(formals(model))))
 })
 
 test_that("With the same seed, both sets of priors give the same tree sequence", {