From bd5cec3b27a2f890770096764b5f2baf74663be3 Mon Sep 17 00:00:00 2001
From: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Date: Wed, 22 Nov 2023 15:22:01 +0000
Subject: [PATCH] linting

---
 R/adjust.R    | 8 +++-----
 R/dist.R      | 6 +++---
 R/get.R       | 2 +-
 R/report.R    | 2 +-
 R/utilities.R | 4 ++--
 5 files changed, 10 insertions(+), 12 deletions(-)

diff --git a/R/adjust.R b/R/adjust.R
index d22b05a8b..5ff7d6ed1 100644
--- a/R/adjust.R
+++ b/R/adjust.R
@@ -148,12 +148,10 @@ adjust_infection_to_report <- function(infections, delay_defs,
     deprecate_warn(
       "2.0.0",
       "adjust_infection_to_report(delay_defs = 'should be a dist_spec')",
-      details = c(
-        "Specifying this as a list of data tables is deprecated."
-      )
+      details = "Specifying this as a list of data tables is deprecated."
     )
     report <- sample_single_dist(infections, delay_defs[[1]])
-    if (length(delay_defs ) > 1) {
+    if (length(delay_defs) > 1) {
       for (def in 2:length(delay_defs)) {
         report <- sample_single_dist(report, delay_defs[[def]])
       }
@@ -181,7 +179,7 @@ adjust_infection_to_report <- function(infections, delay_defs,
   }
 
   ## Truncate reported cases by maximum infection date
-  if (type %in% "sample" && truncate_future) {
+  if (type == "sample" && truncate_future) {
     report <- report[date <= max(infections$date)]
   }
   return(report)
diff --git a/R/dist.R b/R/dist.R
index 1b05b956e..cfca88dd1 100644
--- a/R/dist.R
+++ b/R/dist.R
@@ -127,7 +127,7 @@ dist_skel <- function(n, dist = FALSE, cum = TRUE, model,
         plnorm(n, params[["meanlog"]], params[["sdlog"]])) /
         plnorm(max_value + 1, params[["meanlog"]], params[["sdlog"]])
     }
-  } else if (model %in% "normal") {
+  } else if (model == "normal") {
     rdist <- function(n) {
       rnorm(n, params[["mean"]], params[["sd"]])
     }
@@ -903,7 +903,7 @@ dist_spec <- function(distribution = c(
       "dist_spec(fixed)",
       "fix_dist()"
     )
-    params_sd <- c()
+    params_sd <- NULL
   }
   ## check for deprecated parameters
   if (!all(missing(mean), missing(sd), missing(mean_sd), missing(sd_sd)) &&
@@ -941,7 +941,7 @@ dist_spec <- function(distribution = c(
       params_sd <- c(mean = mean_sd, sd = sd_sd)
     } else if (distribution == "fixed") {
       params_mean <- mean
-      params_sd <- c()
+      params_sd <- NULL
     }
   }
   return(.dist_spec(distribution, params_mean, params_sd, max, pmf))
diff --git a/R/get.R b/R/get.R
index f05161dc7..b3a284734 100644
--- a/R/get.R
+++ b/R/get.R
@@ -16,7 +16,7 @@ get_regions <- function(results_dir) {
   )
 
   # put into alphabetical order
-  regions <- regions[!(regions %in% "runtimes.csv")]
+  regions <- regions[!(regions == "runtimes.csv")]
   regions <- sort(regions)
   names(regions) <- regions
   return(regions)
diff --git a/R/report.R b/R/report.R
index 21ae87af0..a055118b1 100644
--- a/R/report.R
+++ b/R/report.R
@@ -201,7 +201,7 @@ report_summary <- function(summarised_estimates,
   }
 
   if (!is.null(target_folder)) {
-    saveRDS(summary, paste0(target_folder, "/summary.rds"))
+    saveRDS(summary, file.path(target_folder, "summary.rds"))
   }
   return(summary)
 }
diff --git a/R/utilities.R b/R/utilities.R
index a095e62ef..e15c65bf7 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -62,8 +62,8 @@ make_conf <- function(value, CrI = 90, reverse = FALSE) {
   )
   conf <- paste0(
     value$median, " (",
-    ifelse(!reverse, CrI$lower, CrI$upper), " -- ",
-    ifelse(!reverse, CrI$upper, CrI$lower), ")"
+    ifelse(reverse, CrI$upper, CrI$lower), " -- ",
+    ifelse(reverse, CrI$lower, CrI$upper), ")"
   )
   return(conf)
 }