From 7f6ac55ae22137d286883115814be71abc86115c Mon Sep 17 00:00:00 2001
From: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Date: Fri, 2 Feb 2024 13:51:22 +0000
Subject: [PATCH] updates in response to lintr

---
 .github/workflows/lint-only-changed-files.yaml |  1 +
 R/estimate_infections.R                        |  8 ++++----
 R/extract.R                                    |  2 +-
 R/opts.R                                       | 12 +++++-------
 R/stan.R                                       |  2 +-
 5 files changed, 12 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/lint-only-changed-files.yaml b/.github/workflows/lint-only-changed-files.yaml
index 8af5572bc..605b2db69 100644
--- a/.github/workflows/lint-only-changed-files.yaml
+++ b/.github/workflows/lint-only-changed-files.yaml
@@ -23,6 +23,7 @@ jobs:
         with:
           dependencies: NA
           extra-packages: |
+            stan-dev/cmdstanr
             any::gh
             any::lintr
             any::purrr
diff --git a/R/estimate_infections.R b/R/estimate_infections.R
index 52c376a62..2a2c68020 100644
--- a/R/estimate_infections.R
+++ b/R/estimate_infections.R
@@ -333,7 +333,7 @@ init_cumulative_fit <- function(args, samples = 50, warmup = 50,
       open_progress = FALSE,
       show_messages = FALSE
     ),
-    data = args$data, init = args$init,
+    data = args$data, init = args$init
   )
   # change observations to be cumulative in order to protect against noise and
   # give an approximate fit (though for Rt constrained to be > 1)
@@ -450,10 +450,10 @@ fit_model_with_nuts <- function(args, future = FALSE, max_execution_time = Inf,
       )
     }
 
-    if (!inherits(fit, c("stanfit", "CmdStanMCMC"))) {
-      return(NULL)
-    } else {
+    if (inherits(fit, c("stanfit", "CmdStanMCMC"))) {
       return(fit)
+    } else {
+      return(NULL)
     }
   }
 
diff --git a/R/extract.R b/R/extract.R
index 2c1d2ad9c..d4b7fbc33 100644
--- a/R/extract.R
+++ b/R/extract.R
@@ -102,7 +102,7 @@ extract_samples <- function(stan_fit, pars = NULL, include = TRUE) {
     )
     df <- df[, new_draw := permutation[.draw]]
     setkey(df, new_draw)
-    max_indices <- strsplit(tail(df$index, 1), split = ",")[[1]]
+    max_indices <- strsplit(tail(df$index, 1), split = ",", fixed = TRUE)[[1]]
     if (any(grepl("[^0-9]", max_indices))) {
       max_indices <- 1
     } else {
diff --git a/R/opts.R b/R/opts.R
index 7d79c50ca..9ad675dff 100644
--- a/R/opts.R
+++ b/R/opts.R
@@ -791,13 +791,11 @@ stan_opts <- function(object = NULL,
                       ...) {
   method <- arg_match(method, values = c("sampling", "vb"))
   backend <- arg_match(backend, values = c("rstan", "cmdstanr"))
-  if (backend == "cmdstanr") {
-    if (!requireNamespace("cmdstanr", quietly = TRUE)) {
-      stop(paste0(
-        "The `cmdstanr` package needs to be installed for using the ",
-        "\"cmdstanr\" backend."
-      ))
-    }
+  if (backend == "cmdstanr" && !requireNamespace("cmdstanr", quietly = TRUE)) {
+    stop(
+      "The `cmdstanr` package needs to be installed for using the ",
+      "\"cmdstanr\" backend."
+    )
   }
   opts <- list()
   if (!is.null(object) && !missing(backend)) {
diff --git a/R/stan.R b/R/stan.R
index 7db30a692..102b265ae 100644
--- a/R/stan.R
+++ b/R/stan.R
@@ -35,7 +35,7 @@ package_model <- function(model = "estimate_infections",
   )
   if (verbose) {
     message(sprintf("Using model %s.", model))
-    message(sprintf("include is %s.", paste(include, collapse = ", ")))
+    message(sprintf("include is %s.", toString(include)))
   }
 
   monitor <- suppressMessages