export loglik_array generic

NAMESPACE

@@ -4,11 +4,11 @@ S3method(as_draws,measrfit)
 S3method(as_measrfit,default)
 S3method(c,measrprior)
 S3method(fit_m2,measrdcm)
+S3method(loglik_array,measrdcm)
 S3method(loo,measrfit)
 S3method(loo_compare,measrfit)
 S3method(measr_extract,measrdcm)
 S3method(predict,measrdcm)
-S3method(prep_loglik_array,measrdcm)
 S3method(reliability,measrdcm)
 S3method(waic,measrfit)
 export("%>%")
@@ -32,6 +32,7 @@ export(fit_m2)
 export(fit_ppmc)
 export(get_parameters)
 export(is.measrprior)
+export(loglik_array)
 export(loo)
 export(loo_compare)
 export(measr_dcm)

R/loo-methods.R

@@ -38,7 +38,7 @@ loo.measrfit <- function(x, ..., r_eff = NA, force = FALSE) { #nolint
                                       "estimated with `method = \"mcmc\"`."))
   }
 
-  log_lik_array <- prep_loglik_array(model)
+  log_lik_array <- loglik_array(model)
 
   loo::loo(log_lik_array, r_eff = r_eff, ...)
 }
@@ -70,7 +70,7 @@ waic.measrfit <- function(x, ..., force = FALSE) { #nolint
                                       "estimated with `method = \"mcmc\"`."))
   }
 
-  log_lik_array <- prep_loglik_array(model)
+  log_lik_array <- loglik_array(model)
 
   loo::waic(log_lik_array, ...)
 }

R/model-evaluation.R

@@ -139,7 +139,7 @@ add_criterion <- function(x, criterion = c("loo", "waic"), overwrite = FALSE,
   all_criteria <- c(new_criteria, redo_criteria)
 
   if (length(all_criteria) > 0) {
-    log_lik_array <- prep_loglik_array(model)
+    log_lik_array <- loglik_array(model)
   }
 
   if ("loo" %in% all_criteria) {

R/utils-loo.R

@@ -1,9 +1,21 @@
-prep_loglik_array <- function(model) {
-  UseMethod("prep_loglik_array")
+#' Extract the log-likelihood of an estimated model
+#'
+#' The `loglik_array()` methods for [measrfit] objects calculates the
+#' log-likelihood for an estimated model via the generated quantities
+#' functionality in *Stan* and returns the draws of the `log_lik` parameter.
+#'
+#' @param model A [measrfit] object.
+#'
+#' @return A "[`draws_array`][posterior::draws_array()]" object containing the
+#'   log-likelihood estimates for the model.
+#' @export
+loglik_array <- function(model) {
+  UseMethod("loglik_array")
 }
 
+#' @rdname loglik_array
 #' @export
-prep_loglik_array.measrdcm <- function(model) {
+loglik_array.measrdcm <- function(model) {
   score_data <- model$data$data
   clean_qmatrix <- model$data$qmatrix %>%
     dplyr::select(-"item_id") %>%

pkgdown/_pkgdown.yml

@@ -106,6 +106,7 @@ reference:
   - loo_compare.measrfit
   - loo.measrfit
   - waic.measrfit
+  - loglik_array
 
 - subtitle: Add evaluations to model objects
   desc: >

tests/testthat/test-mcmc.R

@@ -73,7 +73,7 @@ test_that("get_mcmc_draws works as expected", {
 test_that("log_lik is calculated correctly", {
   skip_on_cran()
 
-  log_lik <- prep_loglik_array(cmds_mdm_lcdm)
+  log_lik <- loglik_array(cmds_mdm_lcdm)
 
   # expected value from 2-class LCA fit in Mplus
   expect_equal(sum(apply(log_lik, c(3), mean)), -331.764, tolerance = 1.000)