Format the package with Air (#660)

Author: etiennebacher

.Rbuildignore

@@ -50,3 +50,5 @@ docs
 ^.dev$
 ^vignettes/s.
 ^vignettes/t.
+^[\.]?air\.toml$
+^\.vscode$

R/adjust.R

@@ -64,17 +64,19 @@
 #' abline(lm(V2 ~ V1, data = adjusted_icpt), col = "red")
 #'
 #' @export
-adjust <- function(data,
-                   effect = NULL,
-                   select = is.numeric,
-                   exclude = NULL,
-                   multilevel = FALSE,
-                   additive = FALSE,
-                   bayesian = FALSE,
-                   keep_intercept = FALSE,
-                   ignore_case = FALSE,
-                   regex = FALSE,
-                   verbose = FALSE) {
+adjust <- function(
+  data,
+  effect = NULL,
+  select = is.numeric,
+  exclude = NULL,
+  multilevel = FALSE,
+  additive = FALSE,
+  bayesian = FALSE,
+  keep_intercept = FALSE,
+  ignore_case = FALSE,
+  regex = FALSE,
+  verbose = FALSE
+) {
   # make sure column names are syntactically valid
   .check_dataframe_names(data, action = "error")
 
@@ -92,7 +94,8 @@ adjust <- function(data,
     select <- is.numeric
   }
 
-  select <- .select_nse(select,
+  select <- .select_nse(
+    select,
     data,
     exclude,
     ignore_case,
@@ -105,9 +108,15 @@ adjust <- function(data,
   facs <- names(data[effect][!vapply(data[effect], is.numeric, logical(1L))])
   if (length(facs) >= 1 && multilevel) {
     if (additive) {
-      formula_random <- stats::as.formula(paste("~", paste(paste0("(1|", facs, ")"), collapse = " + ")))
+      formula_random <- stats::as.formula(paste(
+        "~",
+        paste(paste0("(1|", facs, ")"), collapse = " + ")
+      ))
     } else {
-      formula_random <- paste("+", paste(paste0("(1|", facs, ")"), collapse = " + "))
+      formula_random <- paste(
+        "+",
+        paste(paste0("(1|", facs, ")"), collapse = " + ")
+      )
     }
     effect <- effect[!effect %in% facs]
   }
@@ -117,8 +126,16 @@ adjust <- function(data,
   for (var in select) {
     predictors <- effect[effect != var]
     if (additive) {
-      predictors_num <- names(data[predictors][vapply(data[predictors], is.numeric, logical(1L))])
-      predictors[predictors == predictors_num] <- paste0("s(", predictors_num, ")")
+      predictors_num <- names(data[predictors][vapply(
+        data[predictors],
+        is.numeric,
+        logical(1L)
+      )])
+      predictors[predictors == predictors_num] <- paste0(
+        "s(",
+        predictors_num,
+        ")"
+      )
     }
     formula_predictors <- paste(c("1", predictors), collapse = " + ")
     model_formula <- paste(var, "~", formula_predictors)
@@ -134,7 +151,9 @@ adjust <- function(data,
     )
     out[var] <- x
   }
-  out[names(data)[!names(data) %in% names(out)]] <- data[names(data)[!names(data) %in% names(out)]]
+  out[names(data)[!names(data) %in% names(out)]] <- data[names(data)[
+    !names(data) %in% names(out)
+  ]]
   out[names(data)]
 }
 
@@ -144,31 +163,46 @@ data_adjust <- adjust
 
 
 #' @keywords internal
-.model_adjust_for <- function(data,
-                              model_formula,
-                              multilevel = FALSE,
-                              additive = FALSE,
-                              bayesian = FALSE,
-                              formula_random = NULL,
-                              keep_intercept = FALSE) {
+.model_adjust_for <- function(
+  data,
+  model_formula,
+  multilevel = FALSE,
+  additive = FALSE,
+  bayesian = FALSE,
+  formula_random = NULL,
+  keep_intercept = FALSE
+) {
   # Additive -----------------------
   if (additive) {
     # Bayesian
     if (bayesian) {
       insight::check_if_installed("rstanarm")
-      model <- rstanarm::stan_gamm4(stats::as.formula(model_formula), random = formula_random, data = data, refresh = 0)
+      model <- rstanarm::stan_gamm4(
+        stats::as.formula(model_formula),
+        random = formula_random,
+        data = data,
+        refresh = 0
+      )
       # Frequentist
     } else {
       insight::check_if_installed("gamm4")
-      model <- gamm4::gamm4(stats::as.formula(model_formula), random = formula_random, data = data)
+      model <- gamm4::gamm4(
+        stats::as.formula(model_formula),
+        random = formula_random,
+        data = data
+      )
     }
 
     # Linear -------------------------
   } else if (bayesian) {
     # Bayesian
     insight::check_if_installed("rstanarm")
     if (multilevel) {
-      model <- rstanarm::stan_lmer(paste(model_formula, formula_random), data = data, refresh = 0)
+      model <- rstanarm::stan_lmer(
+        paste(model_formula, formula_random),
+        data = data,
+        refresh = 0
+      )
     } else {
       model <- rstanarm::stan_glm(model_formula, data = data, refresh = 0)
     }
@@ -185,8 +219,12 @@ data_adjust <- adjust
   # Re-add intercept if need be
   if (keep_intercept) {
     intercept <- insight::get_intercept(model)
-    if (length(intercept) > 1) intercept <- stats::median(intercept) # For bayesian model
-    if (is.na(intercept)) intercept <- 0
+    if (length(intercept) > 1) {
+      intercept <- stats::median(intercept)
+    } # For bayesian model
+    if (is.na(intercept)) {
+      intercept <- 0
+    }
     adjusted <- adjusted + intercept
   }
 

R/assign_labels.R

@@ -64,7 +64,10 @@ assign_labels <- function(x, ...) {
 assign_labels.default <- function(x, verbose = TRUE, ...) {
   if (isTRUE(verbose)) {
     insight::format_alert(
-      sprintf("Adding labels currently not possible for variables of class `%s`.", class(x)[1])
+      sprintf(
+        "Adding labels currently not possible for variables of class `%s`.",
+        class(x)[1]
+      )
     )
   }
   x
@@ -98,7 +101,11 @@ assign_labels.numeric <- function(x, variable = NULL, values = NULL, ...) {
       } else {
         insight::format_error(
           "Cannot add labels. Number of unique values and number of value labels are not equal.",
-          sprintf("There are %i unique values and %i provided labels.", length(unique_values), length(values))
+          sprintf(
+            "There are %i unique values and %i provided labels.",
+            length(unique_values),
+            length(values)
+          )
         )
       }
     } else {
@@ -107,14 +114,25 @@ assign_labels.numeric <- function(x, variable = NULL, values = NULL, ...) {
       if (!all(matching_labels)) {
         insight::format_error(
           "Following labels were associated with values that don't exist:",
-          text_concatenate(paste0(values[!matching_labels], " (", names(values)[!matching_labels], ")"), enclose = "`")
+          text_concatenate(
+            paste0(
+              values[!matching_labels],
+              " (",
+              names(values)[!matching_labels],
+              ")"
+            ),
+            enclose = "`"
+          )
         )
       }
       values <- values[names(values) %in% unique_values]
 
       if (length(values)) {
         # we need to switch names and values
-        value_labels <- stats::setNames(coerce_to_numeric(names(values)), values)
+        value_labels <- stats::setNames(
+          coerce_to_numeric(names(values)),
+          values
+        )
       }
     }
 
@@ -132,23 +150,32 @@ assign_labels.character <- assign_labels.numeric
 
 #' @rdname assign_labels
 #' @export
-assign_labels.data.frame <- function(x,
-                                     select = NULL,
-                                     exclude = NULL,
-                                     values = NULL,
-                                     ignore_case = FALSE,
-                                     regex = FALSE,
-                                     verbose = TRUE,
-                                     ...) {
+assign_labels.data.frame <- function(
+  x,
+  select = NULL,
+  exclude = NULL,
+  values = NULL,
+  ignore_case = FALSE,
+  regex = FALSE,
+  verbose = TRUE,
+  ...
+) {
   # evaluate arguments
-  select <- .select_nse(select,
+  select <- .select_nse(
+    select,
     x,
     exclude,
     ignore_case,
     regex = regex,
     verbose = verbose
   )
 
-  x[select] <- lapply(x[select], assign_labels, values = values, verbose = verbose, ...)
+  x[select] <- lapply(
+    x[select],
+    assign_labels,
+    values = values,
+    verbose = verbose,
+    ...
+  )
   x
 }