Merge pull request #301 from billdenney/299-simplify-the-setexcludeco…

…lumn-function

Simplify exclude column addition

R/class-PKNCAconc.R

@@ -58,7 +58,7 @@ PKNCAconc.tbl_df <- function(data, ...) {
 #' @rdname PKNCAconc
 #' @export
 PKNCAconc.data.frame <- function(data, formula, subject,
-                                 time.nominal, exclude, duration, volume,
+                                 time.nominal, exclude = NULL, duration, volume,
                                  exclude_half.life, include_half.life, sparse=FALSE, ...) {
   # The data must have... data
   if (nrow(data) == 0) {
@@ -132,11 +132,7 @@ PKNCAconc.data.frame <- function(data, formula, subject,
       )
   }
   class(ret) <- c("PKNCAconc", class(ret))
-  if (missing(exclude)) {
-    ret <- setExcludeColumn(ret, dataname=getDataName.PKNCAconc(ret))
-  } else {
-    ret <- setExcludeColumn(ret, exclude=exclude, dataname=getDataName.PKNCAconc(ret))
-  }
+  ret <- setExcludeColumn(ret, exclude = exclude, dataname = getDataName.PKNCAconc(ret))
   # Values must be unique (one value per measurement), check after the exclusion
   # column has been added to the object so that exclusions can be accounted for
   # in duplicate checking.

R/class-PKNCAdose.R

@@ -57,7 +57,7 @@ PKNCAdose.tbl_df <- function(data, ...) {
 #' @rdname PKNCAdose
 #' @export
 PKNCAdose.data.frame <- function(data, formula, route, rate, duration,
-                                 time.nominal, exclude, ...) {
+                                 time.nominal, exclude = NULL, ...) {
   # The data must have... data
   if (nrow(data) == 0) {
     stop("data must have at least one row.")
@@ -115,11 +115,7 @@ PKNCAdose.data.frame <- function(data, formula, route, rate, duration,
       columns = parsed_form
     )
   class(ret) <- c("PKNCAdose", class(ret))
-  if (missing(exclude)) {
-    ret <- setExcludeColumn(ret)
-  } else {
-    ret <- setExcludeColumn(ret, exclude=exclude)
-  }
+  ret <- setExcludeColumn(ret, exclude = exclude)
   # Values must be unique (one value per measurement), check after the exclusion
   # column has been added to the object so that exclusions can be accounted for
   # in duplicate checking.

R/class-PKNCAresults.R

@@ -14,16 +14,12 @@
 #' @returns A PKNCAresults object with each of the above within.
 #' @family PKNCA objects
 #' @export
-PKNCAresults <- function(result, data, exclude) {
-  result <- pknca_unit_conversion(result=result, units=data$units)
+PKNCAresults <- function(result, data, exclude = NULL) {
+  result <- pknca_unit_conversion(result = result, units = data$units)
   # Add all the parts into the object
   ret <- list(result=result,
               data=data)
-  if (missing(exclude)) {
-    ret <- setExcludeColumn(ret, dataname="result")
-  } else {
-    ret <- setExcludeColumn(ret, exclude=exclude, dataname="result")
-  }
+  ret <- setExcludeColumn(ret, exclude = exclude, dataname = "result")
   class(ret) <- c("PKNCAresults", class(ret))
   addProvenance(ret)
 }

R/exclude.R

@@ -120,9 +120,9 @@ exclude.default <- function(object, reason, mask, FUN) {
 #' @param dataname The name of the data.frame within the object to add the
 #'   exclude column to.
 #' @returns The object with an exclude column and attribute
-setExcludeColumn <- function(object, exclude, dataname="data") {
+setExcludeColumn <- function(object, exclude = NULL, dataname = "data") {
   add.exclude <- FALSE
-  if (missing(exclude)) {
+  if (missing(exclude) || is.null(exclude)) {
     # Exclude is not provided.
     if ("exclude" %in% names(object$columns)) {
       # If exclude is already given, then do nothing.
@@ -141,7 +141,7 @@ setExcludeColumn <- function(object, exclude, dataname="data") {
     add.exclude <- TRUE
   }
   if (add.exclude) {
-    if (missing(exclude)) {
+    if (missing(exclude) | is.null(exclude)) {
       # Generate the column name
       exclude <-
         setdiff(c("exclude", paste0("exclude.", max(names(object[[dataname]])))),