Document as.data.frame() methods

NAMESPACE

@@ -47,6 +47,7 @@ exportMethods("totals<-")
 exportMethods(aggregate)
 exportMethods(all_assigned)
 exportMethods(any_assigned)
+exportMethods(as.data.frame)
 exportMethods(as_amounts)
 exportMethods(as_composition)
 exportMethods(as_graph)

R/AllGenerics.R

@@ -183,8 +183,6 @@ setGeneric(
 )
 
 # Extract ======================================================================
-
-
 ## Subset ----------------------------------------------------------------------
 #' Extract or Replace Parts of an Object
 #'
@@ -272,6 +270,26 @@ setGeneric(
   def = function(object, value) standardGeneric("totals<-")
 )
 
+#' Coerce to a Data Frame
+#'
+#' @param x An \R object (typically, a [`CompositionMatrix-class`] object).
+#' @param row.names A [`character`] vector giving the row names for the data
+#'  frame, or `NULL`.
+#' @param optional A [`logical`] scalar: should the names of the variables in
+#'  the data frame be checked?
+#' @param group_var A [`character`] string specifying the name of the column to
+#'  create for group attribution.
+#' @param ... Currently not used.
+#' @return
+#'  A [`data.frame`].
+#' @example inst/examples/ex-coerce.R
+#' @author N. Frerebeau
+#' @docType methods
+#' @family mutators
+#' @name as.data.frame
+#' @rdname as.data.frame
+NULL
+
 #' Matrix Transpose
 #'
 #' @param x A [`CompositionMatrix-class`] object.

R/coerce.R

@@ -93,40 +93,74 @@ setMethod(
 # To data.frame ================================================================
 #' @method as.data.frame CompositionMatrix
 #' @export
-as.data.frame.CompositionMatrix <- function(x, ...) {
-  as.data.frame(methods::as(x, "matrix"), row.names = rownames(x))
+as.data.frame.CompositionMatrix <- function(x, row.names = rownames(x),
+                                            optional = FALSE, ...) {
+  as.data.frame(methods::as(x, "matrix"), row.names = row.names, optional = optional)
 }
 
+#' @export
+#' @rdname as.data.frame
+#' @aliases as.data.frame,CompositionMatrix-method
+setMethod("as.data.frame", "CompositionMatrix", as.data.frame.CompositionMatrix)
+
 #' @method as.data.frame GroupedComposition
 #' @export
-as.data.frame.GroupedComposition <- function(x, ..., group_var = ".group") {
+as.data.frame.GroupedComposition <- function(x, row.names = rownames(x),
+                                             optional = FALSE, ...,
+                                             group_var = ".group") {
   z <- data.frame(
     methods::as(x, "matrix"),
-    row.names = rownames(x)
+    row.names = row.names,
+    check.names = !optional
   )
   z[[group_var]] <- group_names(x)
   z
 }
 
+#' @export
+#' @rdname as.data.frame
+#' @aliases as.data.frame,GroupedComposition-method
+setMethod("as.data.frame", "GroupedComposition", as.data.frame.GroupedComposition)
+
 #' @method as.data.frame LogRatio
 #' @export
-as.data.frame.LogRatio <- function(x, ...) {
-  as.data.frame(methods::as(x, "matrix"), row.names = rownames(x))
+as.data.frame.LogRatio <- function(x, row.names = rownames(x),
+                                   optional = FALSE, ...) {
+  as.data.frame(methods::as(x, "matrix"), row.names = row.names, optional = optional)
 }
 
+#' @export
+#' @rdname as.data.frame
+#' @aliases as.data.frame,LogRatio-method
+setMethod("as.data.frame", "LogRatio", as.data.frame.LogRatio)
+
 #' @method as.data.frame GroupedLogRatio
 #' @export
-as.data.frame.GroupedLogRatio <- function(x, ..., group_var = ".group") {
+as.data.frame.GroupedLogRatio <- function(x, row.names = rownames(x),
+                                          optional = FALSE, ...,
+                                          group_var = ".group") {
   z <- data.frame(
     methods::as(x, "matrix"),
-    row.names = rownames(x)
+    row.names = row.names,
+    check.names = !optional
   )
   z[[group_var]] <- group_names(x)
   z
 }
 
+#' @export
+#' @rdname as.data.frame
+#' @aliases as.data.frame,GroupedLogRatio-method
+setMethod("as.data.frame", "GroupedLogRatio", as.data.frame.GroupedLogRatio)
+
 #' @method as.data.frame OutlierIndex
 #' @export
-as.data.frame.OutlierIndex <- function(x, ...) {
-  as.data.frame(x@standard, row.names = rownames(x))
+as.data.frame.OutlierIndex <- function(x, row.names = rownames(x),
+                                       optional = FALSE, ...) {
+  as.data.frame(x@standard, row.names = row.names, optional = optional)
 }
+
+#' @export
+#' @rdname as.data.frame
+#' @aliases as.data.frame,OutlierIndex-method
+setMethod("as.data.frame", "OutlierIndex", as.data.frame.OutlierIndex)

inst/examples/ex-coerce.R

@@ -11,5 +11,5 @@ totals(B)
 A2 <- as_amounts(B)
 
 ## Coerce to a data.frame
-X <- data.frame(B)
+X <- as.data.frame(B)
 head(X)