Add missing values replacement (#4)

NAMESPACE

@@ -53,6 +53,7 @@ exportMethods(pca)
 exportMethods(perturbation)
 exportMethods(plot)
 exportMethods(powering)
+exportMethods(replace_NA)
 exportMethods(replace_zero)
 exportMethods(scalar)
 exportMethods(transform_alr)

R/AllGenerics.R

@@ -935,15 +935,15 @@ NULL
 # Missign Values ===============================================================
 #' Zero-Replacement
 #'
-#' Multiplicative replacement of zeros in compositional data.
-#' @param x An \eqn{m \times p}{m x p} [`CompositionMatrix-class`] object.
-#' @param value A length-\eqn{p} [`numeric`] vector giving the detection limits
-#'  of each part (in \eqn{(0,1)}).
+#' Multiplicative replacement of zeros.
+#' @param x A [`CompositionMatrix-class`] object.
+#' @param value A [`numeric`] vector giving the detection limits of each part
+#'  (in \eqn{(0,1)}).
 #' @param delta A [`numeric`] vector specifying the fraction of the detection
 #'  limit to be used in replacement.
 #' @return
-#'  An \eqn{m \times p}{m x p} [`CompositionMatrix-class`] object, where all
-#'  zero values have been replaced.
+#'  An [`CompositionMatrix-class`] object, where all zero values have been
+#'  replaced.
 #' @references
 #'  Aitchison, J. (1986). *The Statistical Analysis of Compositional Data*.
 #'  London: Chapman and Hall. \doi{10.1007/978-94-009-4109-0}.
@@ -957,7 +957,28 @@ NULL
 #' @docType methods
 #' @family imputation methods
 #' @name zero
-#' @rdname zero
+#' @rdname replace_zero
+NULL
+
+#' Missing Values Replacement
+#'
+#' Multiplicative replacement of missing values.
+#' @param x A [`CompositionMatrix-class`] object.
+#' @param value A [`numeric`] vector giving the replacement values.
+#' @return
+#'  An [`CompositionMatrix-class`] object, where all missing values have been
+#'  replaced.
+#' @references
+#'  Martín-Fernández, J. A., Barceló-Vidal, C. & Pawlowsky-Glahn, V. (2003).
+#'  Dealing with Zeros and Missing Values in Compositional Data Sets Using
+#'  Nonparametric Imputation. *Mathematical Geology*, 35(3): 253-278.
+#'  \doi{10.1023/A:1023866030544}.
+#' @example inst/examples/ex-missing.R
+#' @author N. Frerebeau
+#' @docType methods
+#' @family imputation methods
+#' @name missing
+#' @rdname replace_NA
 NULL
 
 # Outliers =====================================================================

R/replace.R

@@ -1,25 +1,26 @@
-# REPLACE ZEROS
+# REPLACE
 #' @include AllGenerics.R
 NULL
 
+# Zeros ========================================================================
 #' @export
-#' @rdname zero
+#' @rdname replace_zero
 #' @aliases replace_zero,CompositionMatrix-method
 setMethod(
   f = "replace_zero",
   signature = c(x = "CompositionMatrix"),
-  definition = function(x, value = NULL, delta = 2/3) {
+  definition = function(x, value, delta = 2/3) {
     ## Validation
     D <- ncol(x)
     if (is.null(value)) return(x)
-    if (length(value) == 1) rep(value, D)
+    if (length(value) == 1) value <- rep(value, D)
     if (length(value) > 1) arkhe::assert_length(value, D)
     if (length(delta) > 1) arkhe::assert_length(delta, D)
 
     sigma <- value * delta
-    repl <- apply(X = x, MARGIN = 1, FUN = zero_multiplicative, sigma = sigma)
+    r <- apply(X = x, MARGIN = 1, FUN = zero_multiplicative, sigma = sigma)
 
-    methods::initialize(x, t(repl))
+    methods::initialize(x, t(r))
   }
 )
 
@@ -35,12 +36,35 @@ zero_additive <- function(x, sigma) {
   x
 }
 zero_multiplicative <- function(x, sigma) {
-  D <- length(x)
+  is_zero <- x == 0 & !is.na(x)
+  x[is_zero] <- sigma[is_zero]
+  x[!is_zero] <- x[!is_zero] * (1 - sum(sigma[is_zero]) / 1)
+  x
+}
 
-  is_zero <- x == 0
+# Missing values ===============================================================
+#' @export
+#' @rdname replace_NA
+#' @aliases replace_NA,CompositionMatrix-method
+setMethod(
+  f = "replace_NA",
+  signature = c(x = "CompositionMatrix"),
+  definition = function(x, value) {
+    ## Validation
+    D <- ncol(x)
+    if (is.null(value)) return(x)
+    if (length(value) == 1) value <- rep(value, D)
+    if (length(value) > 1) arkhe::assert_length(value, D)
 
-  x[is_zero] <- sigma[is_zero]
-  x[!is_zero] <- x[!is_zero] * (1 - (sum(sigma[is_zero])) / 1)
+    r <- apply(X = x, MARGIN = 1, FUN = missing_multiplicative, sigma = value)
+
+    methods::initialize(x, t(r))
+  }
+)
 
+missing_multiplicative <- function(x, sigma) {
+  is_missing <- is.na(x)
+  x[is_missing] <- sigma[is_missing]
+  x[!is_missing] <- x[!is_missing] * (1 - sum(sigma[is_missing])) / sum(x[!is_missing])
   x
 }

inst/examples/ex-missing.R

@@ -0,0 +1,15 @@
+## Data from Martín-Fernández et al. 2003
+X <- data.frame(
+  X1 = c(0.0000, 0.1304, 0.1963),
+  X2 = c(0.1250, 0.3151, NA),
+  X3 = c(0.1237, NA, NA),
+  X4 = c(0.7253, 0.2002, 0.0819),
+  X5 = c(0.0260, 0.3543, 0.0114)
+)
+
+## Coerce to a compositional matrix
+Y <- as_composition(X)
+
+## Replace zeros
+Z <- replace_NA(Y, value = 0.2)
+Z

inst/examples/ex-zero.R

@@ -1,13 +1,15 @@
-## Create a data.frame
+## Data from Martín-Fernández et al. 2003
 X <- data.frame(
-  Ca = c(7.72, 0, 3.11, 7.19, 7.41, 5, 0, 1, 4.51),
-  Fe = c(6.12, 5.88, 5.12, 0, 6.02, 0, 0, 5.28, 5.72),
-  Na = c(0.97, 1.59, 0, 0.86, 0.76, 0.51, 0.75, 0.52, 0.56)
+  X1 = c(0.0000, 0.1304, 0.1963),
+  X2 = c(0.1250, 0.3151, NA),
+  X3 = c(0.1237, NA, NA),
+  X4 = c(0.7253, 0.2002, 0.0819),
+  X5 = c(0.0260, 0.3543, 0.0114)
 )
 
 ## Coerce to a compositional matrix
 Y <- as_composition(X)
 
 ## Replace zeros
-Z <- replace_zero(Y, value = c(0.02, 0.1, 0.01), delta = 2/3)
+Z <- replace_zero(Y, value = 0.02, delta = 2/3)
 Z

inst/tinytest/test_zero.R → inst/tinytest/test_replace.R

@@ -9,3 +9,15 @@ Y <- as_composition(X)
 ## Multiplicative replacement
 Z <- replace_zero(Y, value = c(0.02, 0.1, 0.01), delta = 2/3)
 expect_equal_to_reference(Z, file = "_snaps/zero_multiplicative.rds")
+
+# Replace missing ==============================================================
+X <- data.frame(
+  Ca = c(7.72, NA, 3.11, 7.19, 7.41, 5, NA, 1, 4.51),
+  Fe = c(6.12, 5.88, 5.12, NA, 6.02, NA, NA, 5.28, 5.72),
+  Na = c(0.97, 1.59, NA, 0.86, 0.76, 0.51, 0.75, 0.52, 0.56)
+)
+Y <- as_composition(X)
+
+## Multiplicative replacement
+Z <- replace_NA(Y, value = 0.02)
+expect_equal_to_reference(Z, file = "_snaps/missing_multiplicative.rds")