Update to the latest lintr version and remove some nolint comments

.lintr

@@ -1,14 +1,39 @@
-linters: linters_with_tags(
-    tags = NULL, # include all linters
+linters: all_linters(
+    packages = c("lintr", "etdev"),
+    pipe_consistency_linter(pipe = "%>%"),
     object_name_linter = NULL,
-    undesirable_function_linter = NULL,
     implicit_integer_linter = NULL,
-    extraction_operator_linter = NULL,
     todo_comment_linter = NULL,
-    function_argument_linter = NULL
+    library_call_linter = NULL,
+    undesirable_function_linter(
+      modify_defaults(
+        default_undesirable_functions,
+        citEntry = "use the more modern bibentry() function",
+        library = NULL # too many false positive in too many files
+      )
+    ),
+    function_argument_linter = NULL,
+    object_overwrite_linter = NULL,
+    return_linter = NULL,
     # Use minimum R declared in DESCRIPTION or fall back to current R version.
     # Install etdev package from https://github.com/epiverse-trace/etdev
+    backport_linter(if (length(x <- etdev::extract_min_r_version())) x else getRversion())
   )
 exclusions: list(
-    "tests/testthat.R" = list(unused_import_linter = Inf)
+    "tests/testthat.R" = list(
+      unused_import_linter = Inf
+    ),
+    "tests" = list(
+      undesirable_function_linter = Inf
+    ),
+    "data-raw" = list(
+      missing_package_linter = Inf,
+      namespace_linter = Inf
+    ),
+    # RcppExports.R is auto-generated and will not pass many linters. In
+    # particular, it can create very long lines.
+    "R/RcppExports.R",
+    # R/stanmodels.R is auto-generated and will not pass many linters. In
+    # particular, it uses `sapply()`.
+    "R/stanmodels.R"
   )

R/coh_data_wrangling.R

@@ -113,7 +113,7 @@ truncate_from_start_cohort <- function(data_set,
     " the mininimum immunization date. \n",
     n0 - nf, " registers were removed with outcomes before the start date.\n"
   )
-  warning(msg)
+  warning(msg, call. = FALSE)
 
   return(data_set)
 }

R/coh_eff_utils.R

@@ -102,7 +102,7 @@ cox_model <- function(data_set,
   # Cox model time to event, outcome ~ vaccine status
   # Regression
   model <- survival::coxph(
-    survival::Surv( # nolint
+    survival::Surv(
       data_set[[time_to_event_col]], data_set[[outcome_status_col]]
     ) ~ data_set[[vacc_status_col]]
   )

R/coh_immunization.R

@@ -167,13 +167,12 @@ get_immunization_date <- function(data_set,
       #(i.e. the max delta). If take_firt = FALSE it returns the
       #closest date to the event (i.e. the min delta).
       if (all(is.na(x))) {
-        NA_real_
+        return(NA_real_)
+      }
+      if (take_first) {
+        max(x, na.rm = TRUE)
       } else {
-        if (take_first) {
-          max(x, na.rm = TRUE)
-        } else {
-          min(x, na.rm = TRUE)
-        }
+        min(x, na.rm = TRUE)
       }
     }
   )

R/coh_match_iterate.R

@@ -63,15 +63,16 @@ rematch_ <- function(all,
           start_cohort = start_cohort,
           end_cohort = end_cohort
         )
-        warning("Iteration ", im, " for ", rematch_status)
-        warning(" - New: ", nrow(adjusted_i_s), "\n")
+        warning("Iteration ", im, " for ", rematch_status, call. = FALSE)
+        warning(" - New: ", nrow(adjusted_i_s), "\n", call. = FALSE)
       },
       error = function(e) {
         # MatchIt returns error if there are no enough individuals
         # from both groups to match
         warning(
           "Error at iteration ", im, " for ", rematch_status, ": ",
-          e$message, "- skipping to next \n"
+          e$message, "- skipping to next \n",
+          call. = FALSE
         )
       }
     )

R/coh_match_static.R

@@ -100,7 +100,7 @@ static_match <- function(data_set,
   adjusted_f <- adjusted_f[, -which(names(adjusted_f) == "match_id")]
 
   warning(
-    warning_1, warning_2, warning_3, warning_4
+    warning_1, warning_2, warning_3, warning_4, call. = FALSE
   )
 
   # Match object

R/coh_match_utils.R

@@ -57,12 +57,12 @@ match_pair_info <- function(data_set,
       function(x) {
         if (all(is.na(x))) {
           return(NA)
-        } else {
-          if (criteria == "min") {
-            return(as.character(min(x, na.rm = TRUE)))
-          } else if (criteria == "max") {
-            return(as.character(max(x, na.rm = TRUE)))
-          }
+        }
+        if (criteria == "min") {
+          return(as.character(min(x, na.rm = TRUE)))
+        }
+        if (criteria == "max") {
+          return(as.character(max(x, na.rm = TRUE)))
         }
       }
     )

R/handler_validations.R

@@ -105,7 +105,8 @@ check_vaccineff_inputs <- function(data_set,
       sprintf(
         "`end_cohort` has a date with year > %s, please check the date!",
         as.character(max_year)
-      )
+      ),
+      call. = FALSE
     )
   }
 
@@ -119,7 +120,8 @@ check_vaccineff_inputs <- function(data_set,
     # Check if both 'exact' and 'nearest' are NULL or missing
     if (is.null(nearest) && is.null(exact)) {
       stop(
-        "`exact` and `nearest` cannot be NULL. At least one must be provided"
+        "`exact` and `nearest` cannot be NULL. At least one must be provided",
+        call. = FALSE
       )
     }
 

R/utils_get_age_group.R

@@ -64,7 +64,7 @@ get_age_group <- function(data_set, col_age, max_val, min_val = 0, step) {
     war_msg <- "(max_val - min_val) must be an integer multiple of step.
     The last interval will be truncated to "
     war_msg <- paste0(war_msg, lim_labels[length(lim_labels)])
-    warning(war_msg)
+    warning(war_msg, call. = FALSE)
   }
 
   # cut the age data and apply labels

inst/WORDLIST

@@ -27,30 +27,19 @@ VE
 WIP
 Zulma
 anonymised
-codecov
-confounders
 cumincidence
 de
 disaggregated
 eq
 frac
 funder
 ggplot
-gh
-github
-https
 img
 invokeRestart
-io
 lifecycle
 muffleWarning
 packagename
-repo
 rmarkdown
 surv
-svg
-unadjusted
 unvaccinated
-www
-yaml
 Érika

tests/testthat/test-coh_data_wrangling.R

@@ -75,7 +75,7 @@ test_that("`set_status`: Correctness", {
     cohortdata[, c("death_date", "vaccine_date_1")],
     MARGIN = 1,
     FUN = function(x) {
-      all(!is.na(x)) # nolint
+      all(!is.na(x))
     }
   )
   expect_identical(
@@ -88,7 +88,7 @@ test_that("`set_status`: Correctness", {
     cohortdata[, c("death_date", "vaccine_date_1")],
     MARGIN = 1,
     FUN = function(x) {
-      any(!is.na(x)) # nolint
+      any(!is.na(x))
     }
   )
   expect_identical(

tests/testthat/test-coh_match.R

@@ -50,7 +50,7 @@ test_that("`match_cohort`: basic expectations", {
 })
 
 # Snapshot for summary
-test_that("`match_cohort`: summary snapshot", { # nolint
+test_that("`match_cohort`: summary snapshot", {
   for (column in c("balance_all", "balance_match", "summary")) {
     expect_snapshot_value(matching[column], style = "json2", tolerance = 1e-1)
   }

tests/testthat/test-handler_warnings.R

@@ -2,8 +2,8 @@
 
 # Example function that generates warnings
 example_function <- function() {
-  warning("This is warning 1")
-  warning("This is warning 2")
+  warning("This is warning 1", call. = FALSE)
+  warning("This is warning 2", call. = FALSE)
   return("Function completed")
 }
 

vaccineff.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: 88426aa9-8cf3-4db4-aaf2-686ba4a249cd
 
 RestoreWorkspace: Default
 SaveWorkspace: Default