Small tweaks for CRAN (#277)

* missed one DOI

* edge case tests

* hide other misc folders

.Rbuildignore

@@ -18,6 +18,7 @@ README.*
 coverage.*
 ^codemeta\.json$
 devel
+develop
 ^design$
 ^data-raw$
 ^doc$

.gitignore

@@ -14,6 +14,7 @@
 /.project
 articles
 devel/*
+develop/
 doc
 docs
 inst/outputs/*

R/borrowing_hierarchical_commensurate.R

@@ -42,10 +42,9 @@
 #' In Bayesian dynamic borrowing using the hierarchical commensurate prior approach,
 #' external control information is borrowed to the extent that the
 #' outcomes (i.e., log hazard rates or log odds) are similar between
-#' external and internal control populations. See
-#' \href{https://doi.org/10.1002/pst.1589}{Viele et. al. 2014} and
-#' \href{https://doi.org/10.1111/j.1541-0420.2011.01564.x}{Hobbs et. al. 2011}
-#' for details.
+#' external and internal control populations. See Viele 2014
+#' \doi{10.1002/pst.1589} and Hobbs 2011
+#' \doi{10.1111/j.1541-0420.2011.01564.x} for details.
 #'
 #' ## External Control
 #'
@@ -56,7 +55,7 @@
 #'
 #' The `tau_prior` argument specifies the hyperprior on the precision parameter
 #' commonly referred to as the commensurability parameter.
-#' See \href{https://doi.org/10.1002/pst.1589}{Viele et. al. 2014} for more
+#' See Viele 2014 \doi{10.1002/pst.1589} for more
 #' details.
 #' This hyperprior determines (along with the comparability of the outcomes
 #' between internal and external controls) how much borrowing of the external

R/cmdstan.R

@@ -14,7 +14,7 @@ is_cmdstanr_available <- function() {
 #' check_cmdstanr()
 check_cmdstanr <- function(check_sampling = FALSE) {
   if (!is_cmdstanr_available()) {
-    cat("cmdstanr is not installed. \n")
+    cat("cmdstanr is not installed or is installed but not configured. \n")
   } else {
     cat("cmdstanr is installed.\n")
     cat("cmdstanr version: \n")

R/create_analysis_obj.R

@@ -117,7 +117,7 @@ create_analysis_obj <- function(data_matrix,
   analysis_obj@model_string <- stan_model_string
 
   # Compile model
-  if (is_cmdstanr_available()) {
+  if (check_cmdstan()) {
     stan_file <- cmdstanr::write_stan_file(analysis_obj@model_string)
     if (!quiet) {
       analysis_obj@model <- cmdstanr::cmdstan_model(stan_file)

tests/testthat/test-analysis_class.R

@@ -88,7 +88,7 @@ test_that("show works with no borrowing", {
 
 
 test_that("get_stan_code works when cmdstanr isn't available", {
-  skip_if(is_cmdstanr_available())
+  skip_if(check_cmdstan())
   expect_warning(
     object <- create_analysis_obj(
       data_matrix = example_matrix,
@@ -162,7 +162,7 @@ beta[2] ~ normal(0, 1000) ;
 
 
 test_that("get_stan_code works when cmdstanr is available", {
-  skip_if(!is_cmdstanr_available())
+  skip_if_not(check_cmdstan())
   object <- create_analysis_obj(
     data_matrix = example_matrix,
     covariates = add_covariates(