Cleaning

R/SHARED.R

@@ -691,22 +691,24 @@ make_df <- function(ncol, nrow = 0, types = "numeric") {
             stop("'types' must be an acceptable type. For factors, use NA.")
         }
         if (length(types) == 1) types <- rep(types, ncol)
-        for (i in seq_len(ncol)) if (!is.na(types)[i] && types[i] != "numeric") df[[i]] <- get(types[i])(nrow)
+        for (i in seq_len(ncol)) if (!is.na(types)[i] && types[i] != "numeric") {
+            df[[i]] <- get(types[i])(nrow)
+        }
     }
 
     df
 }
 ifelse_ <- function(...) {
     dotlen <- ...length()
-    if (dotlen %% 2 == 0) stop("ifelse_ must have an odd number of arguments: pairs of test/yes, and one no.")
+    if (dotlen %% 2 == 0) stop("`ifelse_()` must have an odd number of arguments: pairs of test/yes, and one no.")
     out <- ...elt(dotlen)
 
     if (dotlen <= 1) {
-        if (!is.atomic(out)) stop("The first entry to ifelse_ must be atomic.")
+        if (!is.atomic(out)) stop("The first entry to `ifelse_()` must be atomic.")
     }
 
     if (!is.atomic(out)) {
-        stop("The last entry to ifelse_ must be atomic.")
+        stop("The last entry to `ifelse_()` must be atomic.")
     }
 
     if (length(out) == 1) out <- rep(out, length(..1))
@@ -716,8 +718,8 @@ ifelse_ <- function(...) {
         yes <- ...elt(2*i)
         if (length(yes) == 1) yes <- rep(yes, n)
         if (length(yes) != n || length(test) != n) stop("All entries must have the same length.")
-        if (!is.logical(test)) stop(paste("The", ordinal(2*i - 1), "entry to ifelse_ must be logical."))
-        if (!is.atomic(yes)) stop(paste("The", ordinal(2*i), "entry to ifelse_ must be atomic."))
+        if (!is.logical(test)) stop(paste("The", ordinal(2*i - 1), "entry to `ifelse_()` must be logical."))
+        if (!is.atomic(yes)) stop(paste("The", ordinal(2*i), "entry to `ifelse_()` must be atomic."))
         pos <- which(test)
         out[pos] <- yes[pos]
     }

R/functions_for_processing.R

@@ -2047,6 +2047,7 @@ get_covs_from_formula <- function(f, data = NULL, factor_sep = "_", int_sep = "
     #ex=names of variables to exclude in interactions and polynomials; a subset of df
     #int=whether to include interactions or not; currently only 2-way are supported
     #poly=degree of polynomials to include; will also include all below poly. If 1, no polynomial will be included
+    #orth=use orthogonal polynomials
     #nunder=number of underscores between variables
 
     cn <- is_not_null(co.names)

R/set.cobalt.options.R

@@ -65,11 +65,11 @@ set.cobalt.options <- function(..., default = FALSE) {
         opts <- opts[names(opts) %in% names(acceptable.options())]
     }
 
+    return.to.default <- NULL
     if (default) {
         return.to.default <- setdiff(names(acceptable.options()), names(opts))
     }
-    else return.to.default <- NULL
-
+
     multiple.opts <- NULL
     bad.opts <- NULL
     for (i in names(opts)) {
@@ -80,8 +80,11 @@ set.cobalt.options <- function(..., default = FALSE) {
         else {
             if (length(opts[[i]]) > 1 && i %nin% multiple.allowed) multiple.opts <- c(multiple.opts, i)
             if (mode(opts[[i]]) != mode(acceptable.options()[[i]]) || 
-                (!(is.character(opts[[i]]) && is.character(acceptable.options()[[i]]) && (i %in% any.string.allowed || !anyNA(pmatch(opts[[i]], acceptable.options()[[i]])))) &&
-                 !all(opts[[i]] %in% acceptable.options()[[i]]))) bad.opts <- c(bad.opts, i)
+                (!(is.character(opts[[i]]) && is.character(acceptable.options()[[i]]) &&
+                   (i %in% any.string.allowed || !anyNA(pmatch(opts[[i]], acceptable.options()[[i]])))) &&
+                 !all(opts[[i]] %in% acceptable.options()[[i]]))) {
+                bad.opts <- c(bad.opts, i)
+            }
         }
     }
 
@@ -167,6 +170,7 @@ acceptable.options <- function() {
          int_sep = " * ",
          factor_sep = "_",
          center = TF,
+         orth = TF,
          remove_perfect_col = TF,
          disp.call = TF)
 }