lintr fix

Author: smasongarrison

.lintr

@@ -3,6 +3,7 @@ linters: linters_with_defaults(
   commented_code_linter = NULL,
   whitespace_linter = NULL,
   indentation_linter = NULL,
+  return_linter = NULL,
   object_name_linter= NULL) # see vignette("lintr")
 encoding: "UTF-8"
 exclusions: list(

tests/testthat/test-constructAdjacency.R

@@ -16,8 +16,8 @@ test_that("computeParentAdjacency matches across all methods for additive compon
     verbose = FALSE, lastComputed = 0, checkpoint_files = checkpoint_files,
     update_rate = 10, parList = init_list, lens = init_lens, save_rate_parlist = 20,
     config = config
-  ) %>%
-    as.data.frame() %>% # sort by iss and jss to ensure consistent ordering
+  ) |>
+    as.data.frame() |> # sort by iss and jss to ensure consistent ordering
     dplyr::arrange(iss, jss)
 
   adj_indexed <- computeParentAdjacency(
@@ -26,8 +26,8 @@ test_that("computeParentAdjacency matches across all methods for additive compon
     verbose = FALSE, lastComputed = 0, checkpoint_files = checkpoint_files,
     update_rate = 10, parList = init_list, lens = init_lens, save_rate_parlist = 20,
     config = config
-  ) %>%
-    as.data.frame() %>% # sort by iss and jss to ensure consistent ordering
+  ) |>
+    as.data.frame() |> # sort by iss and jss to ensure consistent ordering
     dplyr::arrange(iss, jss)
 
   adj_direct <- computeParentAdjacency(
@@ -36,8 +36,8 @@ test_that("computeParentAdjacency matches across all methods for additive compon
     verbose = FALSE, lastComputed = 0, checkpoint_files = checkpoint_files,
     update_rate = 10, parList = init_list, lens = init_lens, save_rate_parlist = 20,
     config = config
-  ) %>%
-    as.data.frame() %>% # sort by iss and jss to ensure consistent ordering
+  ) |>
+    as.data.frame() |> # sort by iss and jss to ensure consistent ordering
     dplyr::arrange(iss, jss)
 
   expect_equal(adj_loop, adj_indexed, tolerance = tolerance)
@@ -55,17 +55,17 @@ test_that("adjBeta matches .adjDirect for common nuclear component", {
     parList = NULL, lens = NULL, lastComputed = 0, saveable = FALSE, resume = FALSE,
     save_path = NULL, verbose = FALSE, save_rate_parlist = NULL, update_rate = NULL,
     checkpoint_files = NULL, config = config
-  ) %>%
-    as.data.frame() %>% # sort by iss and jss to ensure consistent ordering
+  ) |>
+    as.data.frame() |> # sort by iss and jss to ensure consistent ordering
     dplyr::arrange(iss, jss)
 
   direct <- .adjDirect(
     ped = hazard, component = "common nuclear", saveable = FALSE, resume = FALSE,
     save_path = NULL, verbose = FALSE, lastComputed = 0, checkpoint_files = NULL,
     update_rate = NULL, parList = NULL, lens = NULL, save_rate_parlist = NULL,
     config = config
-  ) %>%
-    as.data.frame() %>% # sort by iss and jss to ensure consistent ordering
+  ) |>
+    as.data.frame() |> # sort by iss and jss to ensure consistent ordering
     dplyr::arrange(iss, jss)
 
   expect_equal(beta_5, direct, tolerance = tolerance)

tests/testthat/test-simulatePedigree.R

@@ -4,7 +4,7 @@ test_that("simulated pedigree generates expected data structure", {
   kpc <- 4
   sexR <- .50
   marR <- .7
-  beta_options <- c(F, T)
+  beta_options <- c(FALSE, TRUE)
   strict_tolerance <- 1e-8
   sex_tolerance <- .035
   base_length <- 57
@@ -49,7 +49,7 @@ test_that("simulated pedigree generates expected data structure when sexR is imb
   kpc <- 4
   sexR <- .55
   marR <- .7
-  beta_options <- c(F, T)
+  beta_options <- c(FALSE, TRUE)
   strict_tolerance <- 1e-8
   sex_tolerance <- .03
   base_length <- 154
@@ -96,7 +96,7 @@ test_that("simulated pedigree generates expected data structure when sexR is imb
   kpc <- 4
   sexR <- .45
   marR <- .7
-  beta_options <- c(F, T)
+  beta_options <- c(FALSE, TRUE)
   strict_tolerance <- 1e-8
   sex_tolerance <- .03
   # Optimized version needs wider tolerance for sex ratios on large pedigrees
@@ -158,11 +158,11 @@ test_that("simulated pedigree generates expected data structure but supply var n
   code_male <- "M"
   code_female <- "Fe"
   personID <- "Id"
-  beta_options <- c(F, T)
+  beta_options <- c(FALSE, TRUE)
   strict_tolerance <- 1e-8
   sex_tolerance <- .03
   sex_tolerance_opt <- .07
-  # beta_options <- T
+  # beta_options <- TRUE
   base_length <- 57
   base_length_tol <- 0.2 * base_length
   beta_match_base <- FALSE
@@ -221,9 +221,9 @@ test_that("simulatePedigree verbose prints updates", {
   kpc <- 4
   sexR <- .50
   marR <- .7
-  beta_options <- c(F, T)
+  beta_options <- c(FALSE, TRUE)
 
-  # beta_options <- T
+  # beta_options <- TRUE
   for (beta in beta_options) {
     set.seed(seed)
     message("Beta option Starting: ", beta)