Lintr (#869)

* Lintr * Merge branch 'main' into lintr2 * fix * fix
easystats · Apr 29, 2024 · 5446137 · 5446137
1 parent a3769f0
commit 5446137
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Showing 8 changed files with 104 additions and 99 deletions.
diff --git a/R/format_bf.R b/R/format_bf.R
@@ -42,7 +42,7 @@ format_bf <- function(bf,
 
   digits <- ifelse(is.na(bf), 0, ifelse(bf < 1, 3, 2)) # nolint
 
-  text <- paste0(
+  bf_text <- paste0(
     "= ",
     ifelse(is_small, "1/", ""),
     format_value(bf, digits = digits)
@@ -52,37 +52,37 @@ format_bf <- function(bf,
   is_extreme <- bf_orig > 1000 | bf_orig < 1 / 1000
   if (any(is_extreme)) {
     if (exact) {
-      text[is_extreme] <- ifelse(bf_orig[is_extreme] > 1000,
+      bf_text[is_extreme] <- ifelse(bf_orig[is_extreme] > 1000,
         sprintf("= %.2e", bf_orig[is_extreme]),
-        text[is_extreme]
+        bf_text[is_extreme]
       )
-      text[is_extreme] <- ifelse(bf_orig[is_extreme] < 1 / 1000,
+      bf_text[is_extreme] <- ifelse(bf_orig[is_extreme] < 1 / 1000,
         ifelse(is_small[is_extreme], # nolint
           sprintf("= 1/%.2e", bf[is_extreme]),
           sprintf("= %.2e", bf_orig[is_extreme])
         ),
-        text[is_extreme]
+        bf_text[is_extreme]
       )
     } else {
-      text[is_extreme] <- ifelse(bf_orig[is_extreme] > 1000,
+      bf_text[is_extreme] <- ifelse(bf_orig[is_extreme] > 1000,
         "> 1000",
-        text[is_extreme]
+        bf_text[is_extreme]
       )
-      text[is_extreme] <- ifelse(bf_orig[is_extreme] < 1 / 1000,
+      bf_text[is_extreme] <- ifelse(bf_orig[is_extreme] < 1 / 1000,
         ifelse(is_small[is_extreme], "< 1/1000", "< 0.001"), # nolint
-        text[is_extreme]
+        bf_text[is_extreme]
       )
     }
   }
 
   ## Add stars
-  text <- ifelse(bf_orig > 30, paste0(text, "***"),
-    ifelse(bf_orig > 10, paste0(text, "**"), # nolint
-      ifelse(bf_orig > 3, paste0(text, "*"), text) # nolint
+  bf_text <- ifelse(bf_orig > 30, paste0(bf_text, "***"),
+    ifelse(bf_orig > 10, paste0(bf_text, "**"), # nolint
+      ifelse(bf_orig > 3, paste0(bf_text, "*"), bf_text) # nolint
     )
   )
 
-  out <- .add_prefix_and_remove_stars(text, stars, stars_only, name)
+  out <- .add_prefix_and_remove_stars(p_text = bf_text, stars, stars_only, name)
   if (is.na(na_reference)) out[bad_bf] <- ""
   out
 }
diff --git a/R/format_p.R b/R/format_p.R
@@ -43,14 +43,12 @@ format_p <- function(p,
   # only convert p if it's a valid numeric, or at least coercible to
   # valid numeric values...
   if (!is.numeric(p)) {
-    if (.is_numeric_character(p)) {
-      p <- .factor_to_numeric(p)
-    } else {
+    if (!.is_numeric_character(p)) {
       return(p)
     }
+    p <- .factor_to_numeric(p)
   }
 
-
   if (identical(stars, "only")) {
     stars <- TRUE
     stars_only <- TRUE
@@ -67,7 +65,7 @@ format_p <- function(p,
     if (is.na(digits)) {
       digits <- 5
     }
-    text <- ifelse(is.na(p), NA,
+    p_text <- ifelse(is.na(p), NA,
       ifelse(p < 0.001, sprintf("= %.*e***", digits, p), # nolint
         ifelse(p < 0.01, sprintf("= %.*e**", digits, p), # nolint
           ifelse(p < 0.05, sprintf("= %.*e*", digits, p), # nolint
@@ -79,7 +77,7 @@ format_p <- function(p,
       )
     )
   } else if (digits <= 3) {
-    text <- ifelse(is.na(p), NA,
+    p_text <- ifelse(is.na(p), NA,
       ifelse(p < 0.001, "< .001***", # nolint
         ifelse(p < 0.01, paste0("= ", format_value(p, digits), "**"), # nolint
           ifelse(p < 0.05, paste0("= ", format_value(p, digits), "*"), # nolint
@@ -91,7 +89,7 @@ format_p <- function(p,
       )
     )
   } else {
-    text <- ifelse(is.na(p), NA,
+    p_text <- ifelse(is.na(p), NA,
       ifelse(p < 0.001, paste0("= ", format_value(p, digits), "***"), # nolint
         ifelse(p < 0.01, paste0("= ", format_value(p, digits), "**"), # nolint
           ifelse(p < 0.05, paste0("= ", format_value(p, digits), "*"), # nolint
@@ -102,38 +100,44 @@ format_p <- function(p,
     )
   }
 
-  .add_prefix_and_remove_stars(text, stars, stars_only, name, missing, whitespace, decimal_separator)
+  .add_prefix_and_remove_stars(p_text, stars, stars_only, name, missing, whitespace, decimal_separator)
 }
 
 
 #' @keywords internal
-.add_prefix_and_remove_stars <- function(text, stars, stars_only, name, missing = "", whitespace = TRUE, decimal_separator = NULL) {
-  missing_index <- is.na(text)
+.add_prefix_and_remove_stars <- function(p_text,
+                                         stars,
+                                         stars_only,
+                                         name,
+                                         missing = "",
+                                         whitespace = TRUE,
+                                         decimal_separator = NULL) {
+  missing_index <- is.na(p_text)
 
   if (is.null(name)) {
-    text <- gsub("= ", "", text, fixed = TRUE)
+    p_text <- gsub("= ", "", p_text, fixed = TRUE)
   } else {
-    text <- paste(name, text)
+    p_text <- paste(name, p_text)
   }
 
   if (stars_only) {
-    text <- gsub("[^\\*]", "", text)
+    p_text <- gsub("[^\\*]", "", p_text)
   } else if (!stars) {
-    text <- gsub("*", "", text, fixed = TRUE)
+    p_text <- gsub("*", "", p_text, fixed = TRUE)
   }
 
   # replace missing with related string
-  text[missing_index] <- missing
+  p_text[missing_index] <- missing
 
   # remove whitespace around < and >
   if (isFALSE(whitespace)) {
-    text <- gsub(" ", "", text, fixed = TRUE)
+    p_text <- gsub(" ", "", p_text, fixed = TRUE)
   }
 
   # replace decimal separator
   if (!is.null(decimal_separator)) {
-    text <- gsub(".", decimal_separator, text, fixed = TRUE)
+    p_text <- gsub(".", decimal_separator, p_text, fixed = TRUE)
   }
 
-  text
+  p_text
 }
diff --git a/R/format_pd.R b/R/format_pd.R
@@ -10,7 +10,7 @@
 #' format_pd(c(0.12, 1, 0.9999, 0.98, 0.995, 0.96), stars = TRUE)
 #' @export
 format_pd <- function(pd, stars = FALSE, stars_only = FALSE, name = "pd") {
-  text <- ifelse(pd >= 1, "= 100%***",
+  p_text <- ifelse(pd >= 1, "= 100%***",
     ifelse(pd > 0.999, paste0("= ", format_value(pd * 100), "%***"), # nolint
       ifelse(pd > 0.99, paste0("= ", format_value(pd * 100), "%**"), # nolint
         ifelse(pd > 0.97, paste0("= ", format_value(pd * 100), "%*"), # nolint
@@ -20,5 +20,5 @@ format_pd <- function(pd, stars = FALSE, stars_only = FALSE, name = "pd") {
     )
   )
 
-  .add_prefix_and_remove_stars(text, stars, stars_only, name)
+  .add_prefix_and_remove_stars(p_text, stars, stars_only, name)
 }
diff --git a/R/format_table.R b/R/format_table.R
@@ -390,22 +390,22 @@ format_table <- function(x,
   for (stats in c("t", "Chi2")) {
     if (stats %in% names(x) && "df" %in% names(x)) {
       if (is.character(x$df)) {
-        x$df[x$df == ""] <- NA_character_
+        x$df[x$df == ""] <- NA_character_ # nolint
       }
-      df <- unique(x$df)
-      df <- df[!is.na(df)]
-      if (length(df) == 1 && !all(is.infinite(df))) {
-        names(x)[names(x) == stats] <- paste0(stats, "(", df, ")")
+      dof <- unique(x$df)
+      dof <- dof[!is.na(dof)]
+      if (length(dof) == 1 && !all(is.infinite(dof))) {
+        names(x)[names(x) == stats] <- paste0(stats, "(", dof, ")")
         x$df <- NULL
       }
     } else if (stats %in% names(x) && "df_error" %in% names(x)) {
       if (is.character(x$df_error)) {
-        x$df_error[x$df_error == ""] <- NA_character_
+        x$df_error[x$df_error == ""] <- NA_character_ # nolint
       }
-      df <- unique(x$df_error)
-      df <- df[!is.na(df)]
-      if (length(df) == 1 && !all(is.infinite(df))) {
-        names(x)[names(x) == stats] <- paste0(stats, "(", df, ")")
+      dof <- unique(x$df_error)
+      dof <- dof[!is.na(dof)]
+      if (length(dof) == 1 && !all(is.infinite(dof))) {
+        names(x)[names(x) == stats] <- paste0(stats, "(", dof, ")")
         x$df_error <- NULL
       }
     }
@@ -414,10 +414,10 @@ format_table <- function(x,
   for (stats in c("Baseline", "Chi2")) {
     df_col <- paste0(stats, "_df")
     if (stats %in% names(x) && df_col %in% names(x)) {
-      df <- unique(x[[df_col]])
-      df <- df[!is.na(df)]
-      if (length(df) == 1 && !all(is.infinite(df))) {
-        names(x)[names(x) == stats] <- paste0(stats, "(", df, ")")
+      dof <- unique(x[[df_col]])
+      dof <- dof[!is.na(dof)]
+      if (length(dof) == 1 && !all(is.infinite(dof))) {
+        names(x)[names(x) == stats] <- paste0(stats, "(", dof, ")")
         x[[df_col]] <- NULL
       }
     }
@@ -831,10 +831,10 @@ format_table <- function(x,
 
 
 .additional_arguments <- function(x, value, default) {
-  args <- attributes(x)$additional_arguments
+  my_args <- attributes(x)$additional_arguments
 
-  if (length(args) > 0 && value %in% names(args)) {
-    out <- args[[value]]
+  if (length(my_args) > 0 && value %in% names(my_args)) {
+    out <- my_args[[value]]
   } else {
     out <- attributes(x)[[value]]
   }

diff --git a/R/get_loglikelihood.R b/R/get_loglikelihood.R
@@ -248,8 +248,8 @@ get_loglikelihood.afex_aov <- function(x, ...) {
       NA
     },
     gaussian = {
-      nobs <- length(resp)
-      -((log(dev / nobs * 2 * pi) + 1) - log(w)) / 2
+      model_nobs <- length(resp)
+      -((log(dev / model_nobs * 2 * pi) + 1) - log(w)) / 2
     },
     inverse.gaussian = {
       -((log(disp * 2 * pi) + 1) + 3 * log(resp)) / 2
@@ -475,7 +475,7 @@ get_loglikelihood.phyloglm <- get_loglikelihood.phylolm
     {
       trans <- find_transformation(x)
 
-      if (trans == "identity") {
+      if (trans == "identity") { # nolint
         .weighted_sum(log(get_response(x, as_proportion = TRUE)), w = model_weights)
       } else if (trans == "log") {
         .weighted_sum(log(1 / get_response(x, as_proportion = TRUE)), w = model_weights)