Rename as_features() to augment()

NAMESPACE

@@ -36,8 +36,8 @@ exportMethods("set_totals<-")
 exportMethods(aggregate)
 exportMethods(as_amounts)
 exportMethods(as_composition)
-exportMethods(as_features)
 exportMethods(as_graph)
+exportMethods(augment)
 exportMethods(barplot)
 exportMethods(closure)
 exportMethods(condense)
@@ -120,4 +120,5 @@ importFrom(utils,tail)
 importMethodsFrom(arkhe,describe)
 importMethodsFrom(arkhe,replace_NA)
 importMethodsFrom(arkhe,replace_zero)
+importMethodsFrom(dimensio,augment)
 importMethodsFrom(dimensio,pca)

R/AllGenerics.R

@@ -10,6 +10,7 @@ setGeneric("mahalanobis", package = "stats")
 #' @importMethodsFrom arkhe describe
 #' @importMethodsFrom arkhe replace_NA
 #' @importMethodsFrom arkhe replace_zero
+#' @importMethodsFrom dimensio augment
 #' @importMethodsFrom dimensio pca
 NULL
 
@@ -54,22 +55,20 @@ setGeneric(
   valueClass = "matrix"
 )
 
-#' Coerce to Features
+#' Augment Data with Extra Columns
 #'
-#' Converts an object to a collection of features.
-#' @param from A [`CompositionMatrix-class`] object.
+#' Adds columns from the original data.
+#' @param x A [`CompositionMatrix-class`] or [`LogRatio-class`] object.
 #' @param ... Currently not used.
 #' @return
 #'  A [`data.frame`].
-#' @example inst/examples/ex-coerce.R
+#' @example inst/examples/ex-augment.R
 #' @author N. Frerebeau
 #' @docType methods
 #' @family compositional data tools
-#' @aliases as_features-method
-setGeneric(
-  name = "as_features",
-  def = function(from, ...) standardGeneric("as_features")
-)
+#' @name augment
+#' @rdname augment
+NULL
 
 #' Data Description
 #'

R/coerce.R

@@ -75,7 +75,7 @@ setMethod(
   }
 )
 
-# To Amounts ===================================================================
+# To amounts ===================================================================
 #' @export
 #' @rdname as_amounts
 #' @aliases as_amounts,CompositionMatrix-method
@@ -87,33 +87,33 @@ setMethod(
   }
 )
 
-# To Features ==================================================================
+# To features ==================================================================
 #' @export
-#' @rdname as_features
-#' @aliases as_features,CompositionMatrix-method
+#' @rdname augment
+#' @aliases augment,CompositionMatrix-method
 setMethod(
-  f = "as_features",
-  signature = c(from = "CompositionMatrix"),
-  definition = function(from) {
-    if (has_extra(from)) {
-      data.frame(get_extra(from), from)
+  f = "augment",
+  signature = c(x = "CompositionMatrix"),
+  definition = function(x, ...) {
+    if (has_extra(x)) {
+      data.frame(get_extra(x), x)
     } else {
-      as.data.frame(from)
+      as.data.frame(x)
     }
   }
 )
 
 #' @export
-#' @rdname as_features
-#' @aliases as_features,LogRatio-method
+#' @rdname augment
+#' @aliases augment,LogRatio-method
 setMethod(
-  f = "as_features",
-  signature = c(from = "LogRatio"),
-  definition = function(from) {
-    if (has_extra(from)) {
-      data.frame(get_extra(from), from)
+  f = "augment",
+  signature = c(x = "LogRatio"),
+  definition = function(x, ...) {
+    if (has_extra(x)) {
+      data.frame(get_extra(x), x)
     } else {
-      as.data.frame(from)
+      as.data.frame(x)
     }
   }
 )

inst/examples/ex-augment.R

@@ -0,0 +1,11 @@
+## Data from Aitchison 1986
+data("arctic")
+
+## Coerce to compositional data
+coda <- as_composition(arctic, parts = 1:3)
+
+## Isometric log-ratio
+ilr <- transform_ilr(coda)
+
+## Add extra column
+augment(ilr)

inst/examples/ex-mutators.R

@@ -4,4 +4,4 @@ head(slides)
 
 ## Coerce to compositional data
 coda <- as_composition(slides)
-head(as_features(coda))
+head(augment(coda))

inst/tinytest/test_coerce.R

@@ -1,10 +1,10 @@
 # Data with groups =============================================================
 data("slides")
 coda <- as_composition(slides)
-expect_equal_to_reference(as_features(coda), file = "_snaps/features.rds")
+expect_equal_to_reference(augment(coda), file = "_snaps/augment_coda.rds")
 
 clr <- transform_clr(coda, weights = FALSE)
-expect_equal_to_reference(clr, file = "_snaps/features_clr.rds")
+expect_equal_to_reference(clr, file = "_snaps/augment_clr.rds")
 
 # Back transform to count ======================================================
 data("hongite")

inst/tinytest/test_outliers.R

@@ -4,7 +4,6 @@ coda <- as_composition(hongite)
 # Detect outliers ==============================================================
 out <- outliers(coda)
 # expect_equal_to_reference(out, file = "_snaps/outliers.rds")
-# expect_equal_to_reference(as_features(out), file = "_snaps/features_outliers.rds")
 
 # Plot =========================================================================
 if (at_home()) {