Apply styler to all remaining tern code (#833)

Closes #832
insightsengineering · Feb 21, 2023 · a285716 · a285716
1 parent e27cca2
commit a285716
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diff --git a/R/abnormal_by_marked.R b/R/abnormal_by_marked.R
@@ -47,12 +47,13 @@ NULL
 #' )
 #'
 #' df <- df %>%
-#'   mutate(abn_dir = factor(case_when(
-#'     ANRIND == "LOW LOW" ~ "Low",
-#'     ANRIND == "HIGH HIGH" ~ "High",
-#'     TRUE ~ ""
-#'   ),
-#'   levels = c("Low", "High")
+#'   mutate(abn_dir = factor(
+#'     case_when(
+#'       ANRIND == "LOW LOW" ~ "Low",
+#'       ANRIND == "HIGH HIGH" ~ "High",
+#'       TRUE ~ ""
+#'     ),
+#'     levels = c("Low", "High")
 #'   ))
 #'
 #' # Select only post-baseline records.

diff --git a/R/abnormal_by_worst_grade_worsen.R b/R/abnormal_by_worst_grade_worsen.R
@@ -111,7 +111,6 @@ h_adlb_worsen <- function(adlb,
 
   # extract data with worst lab
   if (!is.null(worst_flag_high) && !is.null(worst_flag_low)) {
-
     # change H to High, L to Low
     adlb_f_h[[direction_var]] <- rep("High", nrow(adlb_f_h))
     adlb_f_l[[direction_var]] <- rep("Low", nrow(adlb_f_l))

diff --git a/R/cox_regression_inter.R b/R/cox_regression_inter.R
@@ -1,4 +1,3 @@
-
 #' Cox Regression Helper: Interactions
 #'
 #' @description `r lifecycle::badge("stable")`

diff --git a/R/coxph.R b/R/coxph.R
@@ -391,7 +391,7 @@ s_cox_multivariate <- function(formula, data,
   y <- fit_n_aov(
     formula = formula,
     data = data,
-    conf_level  = conf_level,
+    conf_level = conf_level,
     pval_method = pval_method,
     ...
   )

diff --git a/R/d_pkparam.R b/R/d_pkparam.R
diff --git a/R/estimate_proportion.R b/R/estimate_proportion.R
@@ -93,27 +93,27 @@ s_proportion <- function(df,
   p_hat <- mean(rsp)
 
   prop_ci <- switch(method,
-                    "clopper-pearson" = prop_clopper_pearson(rsp, conf_level),
-                    "wilson" = prop_wilson(rsp, conf_level),
-                    "wilsonc" = prop_wilson(rsp, conf_level, correct = TRUE),
-                    "strat_wilson" = prop_strat_wilson(rsp,
-                                                       strata,
-                                                       weights,
-                                                       conf_level,
-                                                       max_iterations,
-                                                       correct = FALSE
-                    )$conf_int,
-                    "strat_wilsonc" = prop_strat_wilson(rsp,
-                                                        strata,
-                                                        weights,
-                                                        conf_level,
-                                                        max_iterations,
-                                                        correct = TRUE
-                    )$conf_int,
-                    "wald" = prop_wald(rsp, conf_level),
-                    "waldcc" = prop_wald(rsp, conf_level, correct = TRUE),
-                    "agresti-coull" = prop_agresti_coull(rsp, conf_level),
-                    "jeffreys" = prop_jeffreys(rsp, conf_level)
+    "clopper-pearson" = prop_clopper_pearson(rsp, conf_level),
+    "wilson" = prop_wilson(rsp, conf_level),
+    "wilsonc" = prop_wilson(rsp, conf_level, correct = TRUE),
+    "strat_wilson" = prop_strat_wilson(rsp,
+      strata,
+      weights,
+      conf_level,
+      max_iterations,
+      correct = FALSE
+    )$conf_int,
+    "strat_wilsonc" = prop_strat_wilson(rsp,
+      strata,
+      weights,
+      conf_level,
+      max_iterations,
+      correct = TRUE
+    )$conf_int,
+    "wald" = prop_wald(rsp, conf_level),
+    "waldcc" = prop_wald(rsp, conf_level, correct = TRUE),
+    "agresti-coull" = prop_agresti_coull(rsp, conf_level),
+    "jeffreys" = prop_jeffreys(rsp, conf_level)
   )
 
   list(

diff --git a/R/h_biomarkers_subgroups.R b/R/h_biomarkers_subgroups.R
@@ -41,7 +41,6 @@ h_tab_one_biomarker <- function(df,
 
   # If there is any subgroup variables, we extend the layout accordingly.
   if ("analysis" %in% df$row_type) {
-
     # Now only continue with the subgroup rows.
     lyt <- split_rows_by(
       lyt = lyt,

diff --git a/R/h_response_subgroups.R b/R/h_response_subgroups.R
@@ -182,7 +182,6 @@ h_odds_ratio_df <- function(rsp, arm, strata_data = NULL, conf_level = 0.95, met
   l_df <- split(df_rsp, arm)
 
   if (nrow(l_df[[1]]) > 0 && nrow(l_df[[2]]) > 0) {
-
     # Odds ratio and CI.
     result_odds_ratio <- s_odds_ratio(
       df = l_df[[2]],
@@ -206,7 +205,6 @@ h_odds_ratio_df <- function(rsp, arm, strata_data = NULL, conf_level = 0.95, met
     )
 
     if (!is.null(method)) {
-
       # Test for difference.
       result_test <- s_test_proportion_diff(
         df = l_df[[2]],

diff --git a/R/h_stack_by_baskets.R b/R/h_stack_by_baskets.R
@@ -64,7 +64,6 @@ h_stack_by_baskets <- function(df,
                                keys = c("STUDYID", "USUBJID", "ASTDTM", "AEDECOD", "AESEQ"),
                                aag_summary = NULL,
                                na_level = "<Missing>") {
-
   # Use of df_explicit_na() in case the user has not previously used
   df <- df_explicit_na(df, na_level = na_level)
 
@@ -103,7 +102,6 @@ h_stack_by_baskets <- function(df,
   if (all(is.na(df[, baskets]))) { # in case there is no level for the target baskets
     df_long <- df[-seq_len(nrow(df)), keys] # we just need an empty dataframe keeping all factor levels
   } else {
-
     # Concatenate SMQxxxNAM with corresponding SMQxxxSC
     df_cnct <- df[, c(keys, baskets[startsWith(baskets, "CQ")])]
 

diff --git a/R/h_survival_duration_subgroups.R b/R/h_survival_duration_subgroups.R
@@ -203,7 +203,6 @@ h_coxph_df <- function(tte, is_event, arm, strata_data = NULL, control = control
   l_df <- split(df_tte, arm)
 
   if (nrow(l_df[[1]]) > 0 && nrow(l_df[[2]]) > 0) {
-
     # Hazard ratio and CI.
     result <- s_coxph_pairwise(
       df = l_df[[2]],

diff --git a/R/prop_diff.R b/R/prop_diff.R
@@ -98,26 +98,26 @@ s_proportion_diff <- function(df,
     }
 
     y <- switch(method,
-                "wald" = prop_diff_wald(rsp, grp, conf_level, correct = FALSE),
-                "waldcc" = prop_diff_wald(rsp, grp, conf_level, correct = TRUE),
-                "ha" = prop_diff_ha(rsp, grp, conf_level),
-                "newcombe" = prop_diff_nc(rsp, grp, conf_level, correct = FALSE),
-                "newcombecc" = prop_diff_nc(rsp, grp, conf_level, correct = TRUE),
-                "strat_newcombe" = prop_diff_strat_nc(rsp,
-                                                      grp,
-                                                      strata,
-                                                      weights_method,
-                                                      conf_level,
-                                                      correct = FALSE
-                ),
-                "strat_newcombecc" = prop_diff_strat_nc(rsp,
-                                                        grp,
-                                                        strata,
-                                                        weights_method,
-                                                        conf_level,
-                                                        correct = TRUE
-                ),
-                "cmh" = prop_diff_cmh(rsp, grp, strata, conf_level)[c("diff", "diff_ci")]
+      "wald" = prop_diff_wald(rsp, grp, conf_level, correct = FALSE),
+      "waldcc" = prop_diff_wald(rsp, grp, conf_level, correct = TRUE),
+      "ha" = prop_diff_ha(rsp, grp, conf_level),
+      "newcombe" = prop_diff_nc(rsp, grp, conf_level, correct = FALSE),
+      "newcombecc" = prop_diff_nc(rsp, grp, conf_level, correct = TRUE),
+      "strat_newcombe" = prop_diff_strat_nc(rsp,
+        grp,
+        strata,
+        weights_method,
+        conf_level,
+        correct = FALSE
+      ),
+      "strat_newcombecc" = prop_diff_strat_nc(rsp,
+        grp,
+        strata,
+        weights_method,
+        conf_level,
+        correct = TRUE
+      ),
+      "cmh" = prop_diff_cmh(rsp, grp, strata, conf_level)[c("diff", "diff_ci")]
     )
 
     y$diff <- y$diff * 100
@@ -149,7 +149,7 @@ s_proportion_diff <- function(df,
 #' @export
 a_proportion_diff <- make_afun(
   s_proportion_diff,
-  .formats =  c(diff = "xx.x", diff_ci = "(xx.x, xx.x)"),
+  .formats = c(diff = "xx.x", diff_ci = "(xx.x, xx.x)"),
   .indent_mods = c(diff = 0L, diff_ci = 1L)
 )
 

diff --git a/R/response_subgroups.R b/R/response_subgroups.R
@@ -157,19 +157,20 @@ a_response_subgroups <- function(.formats = list(
     c("n", "n_rsp", "prop", "n_tot", "or", "ci", "pval")
   )
 
-  afun_lst <- Map(function(stat, fmt) {
-    if (stat == "ci") {
-      function(df, labelstr = "", ...) {
-        in_rows(.list = combine_vectors(df$lcl, df$ucl), .labels = as.character(df$subgroup), .formats = fmt)
+  afun_lst <- Map(
+    function(stat, fmt) {
+      if (stat == "ci") {
+        function(df, labelstr = "", ...) {
+          in_rows(.list = combine_vectors(df$lcl, df$ucl), .labels = as.character(df$subgroup), .formats = fmt)
+        }
+      } else {
+        function(df, labelstr = "", ...) {
+          in_rows(.list = as.list(df[[stat]]), .labels = as.character(df$subgroup), .formats = fmt)
+        }
       }
-    } else {
-      function(df, labelstr = "", ...) {
-        in_rows(.list = as.list(df[[stat]]), .labels = as.character(df$subgroup), .formats = fmt)
-      }
-    }
-  },
-  stat = names(.formats),
-  fmt = .formats
+    },
+    stat = names(.formats),
+    fmt = .formats
   )
 
   afun_lst

diff --git a/R/rtables_access.R b/R/rtables_access.R
@@ -40,9 +40,8 @@ NULL
 #'
 #' @export
 h_row_first_values <- function(table_row,
-                         col_names = NULL,
-                         col_indices = NULL) {
-
+                               col_names = NULL,
+                               col_indices = NULL) {
   col_indices <- check_names_indices(table_row, col_names, col_indices)
   checkmate::assert_integerish(col_indices)
   checkmate::assert_subset(col_indices, seq_len(ncol(table_row)))
@@ -71,7 +70,7 @@ h_row_first_values <- function(table_row,
 #' # Using values with integers
 #' tree_row_elem <- collect_leaves(tbl[3, ])[[1]]
 #' result <- h_row_counts(tree_row_elem)
-#' #result
+#' # result
 #'
 #' @export
 h_row_counts <- function(table_row,
@@ -140,8 +139,10 @@ check_names_indices <- function(table_row,
                                 col_indices = NULL) {
   if (!is.null(col_names)) {
     if (!is.null(col_indices)) {
-      stop("Inserted both col_names and col_indices when selecting row values. ",
-           "Please choose one.")
+      stop(
+        "Inserted both col_names and col_indices when selecting row values. ",
+        "Please choose one."
+      )
     }
     col_indices <- h_col_indices(table_row, col_names)
   }

diff --git a/R/summarize_patients_exposure_in_cols.R b/R/summarize_patients_exposure_in_cols.R
@@ -124,14 +124,15 @@ summarize_patients_exposure_in_cols <- function(lyt, # nolintr
                                                 .labels = c(n_patients = "Patients", sum_exposure = "Person time"),
                                                 .indent_mods = NULL,
                                                 col_split = TRUE) {
-  afun_list <- Map(function(stat) {
-    make_afun(
-      s_count_patients_sum_exposure,
-      .stats = stat,
-      .formats = ifelse(stat == "n_patients", "xx (xx.x%)", "xx")
-    )
-  },
-  stat = .stats
+  afun_list <- Map(
+    function(stat) {
+      make_afun(
+        s_count_patients_sum_exposure,
+        .stats = stat,
+        .formats = ifelse(stat == "n_patients", "xx (xx.x%)", "xx")
+      )
+    },
+    stat = .stats
   )
 
   if (col_split) {

diff --git a/R/survival_duration_subgroups.R b/R/survival_duration_subgroups.R
@@ -178,27 +178,28 @@ a_survival_subgroups <- function(.formats = list(
     c("n", "n_events", "median", "n_tot", "n_tot_events", "hr", "ci", "pval")
   )
 
-  afun_lst <- Map(function(stat, fmt) {
-    if (stat == "ci") {
-      function(df, labelstr = "", ...) {
-        in_rows(
-          .list = combine_vectors(df$lcl, df$ucl),
-          .labels = as.character(df$subgroup),
-          .formats = fmt
-        )
+  afun_lst <- Map(
+    function(stat, fmt) {
+      if (stat == "ci") {
+        function(df, labelstr = "", ...) {
+          in_rows(
+            .list = combine_vectors(df$lcl, df$ucl),
+            .labels = as.character(df$subgroup),
+            .formats = fmt
+          )
+        }
+      } else {
+        function(df, labelstr = "", ...) {
+          in_rows(
+            .list = as.list(df[[stat]]),
+            .labels = as.character(df$subgroup),
+            .formats = fmt
+          )
+        }
       }
-    } else {
-      function(df, labelstr = "", ...) {
-        in_rows(
-          .list = as.list(df[[stat]]),
-          .labels = as.character(df$subgroup),
-          .formats = fmt
-        )
-      }
-    }
-  },
-  stat = names(.formats),
-  fmt = .formats
+    },
+    stat = names(.formats),
+    fmt = .formats
   )
 
   afun_lst

diff --git a/R/utils_checkmate.R b/R/utils_checkmate.R
@@ -18,7 +18,6 @@
 NULL
 
 check_list_of_variables <- function(x) {
-
   # drop NULL elements in list
   x <- Filter(Negate(is.null), x)
 

diff --git a/man/abnormal_by_marked.Rd b/man/abnormal_by_marked.Rd
diff --git a/man/rtables_access.Rd b/man/rtables_access.Rd
diff --git a/tests/testthat/test-coxreg.R b/tests/testthat/test-coxreg.R
@@ -23,7 +23,8 @@ dta_bladder_raw <- local({
       armcd = formatters::with_label(as.factor(rx), "ARM"),
       covar1 = formatters::with_label(as.factor(enum), "A Covariate Label"),
       covar2 = formatters::with_label(
-        factor(sample(as.factor(enum)), levels = 1:4, labels = c("F", "F", "M", "M")), "Sex (F/M)"),
+        factor(sample(as.factor(enum)), levels = 1:4, labels = c("F", "F", "M", "M")), "Sex (F/M)"
+      ),
       age = sample(20:60, size = 340, replace = TRUE)
     )
   )

diff --git a/tests/testthat/test-estimate_proportion.R b/tests/testthat/test-estimate_proportion.R
@@ -337,4 +337,5 @@ testthat::test_that(
 
     res <- testthat::expect_silent(result)
     testthat::expect_snapshot(res)
-})
+  }
+)
diff --git a/tests/testthat/test-fit_rsp_step.R b/tests/testthat/test-fit_rsp_step.R
@@ -19,7 +19,7 @@ testthat::test_that("fit_rsp_step works as expected with default options", {
     covariates = "AGE",
     response = "RSP"
   )
- suppressWarnings(testthat::expect_warning(result <- fit_rsp_step(
+  suppressWarnings(testthat::expect_warning(result <- fit_rsp_step(
     variables = variables,
     data = data
   )))