Merge branch '29-brms-style-stancode-method-for-readability' into main

Merge branch '29-brms-style-stancode-method-for-readability'

# Conflicts:
#	NAMESPACE
#	tests/testthat/test-coev_fit.R

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: coevolve
 Title: Fit Bayesian Dynamic Coevolutionary Models using 'Stan'
-Version: 0.0.0.9010
+Version: 0.0.0.9011
 Authors@R: 
     c(person("Scott", "Claessens", , "scott.claessens@gmail.com", 
              role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3562-6981")),

NAMESPACE

@@ -3,6 +3,8 @@
 S3method(extract_samples,coevfit)
 S3method(print,coevfit)
 S3method(print,coevsummary)
+S3method(stancode,coevfit)
+S3method(standata,coevfit)
 S3method(summary,coevfit)
 export(coev_calculate_delta_theta)
 export(coev_calculate_theta)
@@ -15,4 +17,6 @@ export(coev_plot_predictive_check)
 export(coev_plot_selection_gradient)
 export(coev_simulate_coevolution)
 export(extract_samples)
+export(stancode)
+export(standata)
 importFrom(rlang,.data)

R/stancode.R

@@ -0,0 +1,14 @@
+#' Expose the Stan code of a fitted model represented by a \code{coevfit} object
+#'
+#' @param object An object of class \code{coevfit}.
+#'
+#' @return Printed Stan code
+#' @export
+stancode <- function(object){
+  UseMethod("stancode")
+}
+
+#' @export
+stancode.coevfit <- function(object){
+  cat(object$stan_code)
+}

R/standata.R

@@ -0,0 +1,15 @@
+#' Expose the Stan data list for a fitted model represented by a \code{coevfit}
+#'   object
+#'
+#' @param object An object of class \code{coevfit}.
+#'
+#' @return Named list of data for Stan
+#' @export
+standata <- function(object){
+  UseMethod("standata")
+}
+
+#' @export
+standata.coevfit <- function(object){
+  object$stan_data
+}

tests/testthat/test-coev_fit.R

@@ -536,6 +536,23 @@ test_that("coev_fit() fits the model without error", {
   expect_true(SW(methods::is(extract_samples(m2), "list")))
   expect_true(SW(methods::is(extract_samples(m3), "list")))
   expect_true(SW(methods::is(extract_samples(m4), "list")))
+  # expect no error for stancode and standata methods
+  expect_no_error(SW(stancode(m1)))
+  expect_no_error(SW(stancode(m2)))
+  expect_no_error(SW(stancode(m3)))
+  expect_no_error(SW(stancode(m4)))
+  expect_no_error(SW(standata(m1)))
+  expect_no_error(SW(standata(m2)))
+  expect_no_error(SW(standata(m3)))
+  expect_no_error(SW(standata(m4)))
+  expect_output(SW(stancode(m1)))
+  expect_output(SW(stancode(m2)))
+  expect_output(SW(stancode(m3)))
+  expect_output(SW(stancode(m4)))
+  expect_true(SW(methods::is(standata(m1), "list")))
+  expect_true(SW(methods::is(standata(m2), "list")))
+  expect_true(SW(methods::is(standata(m3), "list")))
+  expect_true(SW(methods::is(standata(m4), "list")))
 })
 
 test_that("effects_mat argument to coev_fit() works as expected", {
@@ -552,6 +569,11 @@ test_that("effects_mat argument to coev_fit() works as expected", {
   # expect no errors for extract_samples method
   expect_no_error(SW(extract_samples(m)))
   expect_true(SW(methods::is(extract_samples(m), "list")))
+  # expect no errors for stancode or standata methods
+  expect_no_error(SW(stancode(m)))
+  expect_no_error(SW(standata(m)))
+  expect_output(SW(stancode(m)))
+  expect_true(SW(methods::is(standata(m), "list")))
   # expect effects_mat correct in model output
   effects_mat <- matrix(
     c(TRUE, TRUE,
@@ -586,6 +608,11 @@ test_that("coev_fit() works with missing data", {
   # expect no errors for extract_samples method
   expect_no_error(SW(extract_samples(m)))
   expect_true(SW(methods::is(extract_samples(m), "list")))
+  # expect no errors for stancode or standata methods
+  expect_no_error(SW(stancode(m)))
+  expect_no_error(SW(standata(m)))
+  expect_output(SW(stancode(m)))
+  expect_true(SW(methods::is(standata(m), "list")))
   # expect warning in summary output
   capture.output(
     SW(
@@ -612,4 +639,9 @@ test_that("coev_fit() works with repeated observations", {
   expect_no_error(SW(summary(m)))
   expect_output(SW(print(m)))
   expect_output(SW(print(summary(m))))
+  # expect no errors for stancode or standata methods
+  expect_no_error(SW(stancode(m)))
+  expect_no_error(SW(standata(m)))
+  expect_output(SW(stancode(m)))
+  expect_true(SW(methods::is(standata(m), "list")))
 })