Make it possible to deprecated argument 'center'; introduced option '…

…matrixStats.center.onUse'/env var 'MATRIXSTATS_CENTER_ONUSE' for controlling this [#187]

R/000.DEPRECATION.R

@@ -0,0 +1,27 @@
+centerOnUse <- function(fcnname, calls = sys.calls(), msg = NULL) {
+  value <- getOption("matrixStats.center.onUse")
+  if (is.null(value) || identical(value, "ignore")) return()
+
+  value <- match.arg(value, c("deprecated", "defunct"))
+  fcn <- switch(value, deprecated = .Deprecated, defunct = .Defunct)
+
+  if (is.null(msg)) {
+    msg <- sprintf("Argument 'center' of %s::%s() is %s: %s",
+                   .packageName, fcnname, value, deparse(calls[[1]]))
+  }
+
+  fcn(msg = msg, package = .packageName)
+}
+
+
+onLoadSetCenterOnUse <- function() {
+  ## Option is already set?
+  if (!is.null(getOption("matrixStats.center.onUse", NULL))) return()
+
+  ## Is environment variable set?
+  value <- Sys.getenv("MATRIXSTATS_CENTER_ONUSE", NA_character_)
+  if (is.na(value)) return()
+
+  value <- match.arg(value, c("ignore", "deprecated", "defunct"))
+  options(matrixStats.center.onUse = value)
+}

R/rowMads.R

@@ -12,8 +12,11 @@ rowMads <- function(x, rows = NULL, cols = NULL, center = NULL,
     has_nas <- TRUE
     x <- .Call(C_rowMads, x, dim., rows, cols, constant, na.rm, has_nas, TRUE)
   } else {
+    ## https://github.com/HenrikBengtsson/matrixStats/issues/187
+    centerOnUse("rowMads")
+
     if (is.vector(x)) dim(x) <- dim.
-
+    
     # Apply subset on 'center'
     if (length(center) != nrow(x)) {
       ## Scalar 'center'?
@@ -53,6 +56,9 @@ colMads <- function(x, rows = NULL, cols = NULL, center = NULL,
     has_nas <- TRUE
     x <- .Call(C_rowMads, x, dim., rows, cols, constant, na.rm, has_nas, FALSE)
   } else {
+    ## https://github.com/HenrikBengtsson/matrixStats/issues/187
+    centerOnUse("colMads")
+
     if (is.vector(x)) dim(x) <- dim.
 
     # Apply subset on 'center'

R/rowVars.R

@@ -46,6 +46,9 @@ rowVars <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, center = NULL,
     return(sigma2)
   }
 
+  ## https://github.com/HenrikBengtsson/matrixStats/issues/187
+  centerOnUse("rowVars")
+
   if (is.vector(x)) dim(x) <- dim.
 
   # Apply subset on 'center'
@@ -117,6 +120,9 @@ colVars <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, center = NULL,
     return(sigma2)
   }
 
+  ## https://github.com/HenrikBengtsson/matrixStats/issues/187
+  centerOnUse("colVars")
+
   if (is.vector(x)) dim(x) <- dim.
 
   # Apply subset on 'center'

R/weightedMad.R

@@ -133,6 +133,9 @@ weightedMad <- function(x, w = NULL, idxs = NULL, na.rm = FALSE,
   # Estimate the mean?
   if (is.null(center)) {
     center <- weightedMedian(x, w = w, na.rm = NA)
+  } else {
+    ## https://github.com/HenrikBengtsson/matrixStats/issues/187
+    centerOnUse("weightedMad")
   }
 
   # Estimate the standard deviation

R/weightedVar.R

@@ -132,6 +132,9 @@ weightedVar <- function(x, w = NULL, idxs = NULL, na.rm = FALSE,
   # Estimate the mean?
   if (is.null(center)) {
     center <- sum(w * x) / wsum
+  } else {
+    ## https://github.com/HenrikBengtsson/matrixStats/issues/187
+    centerOnUse("weightedVar")
   }
 
   # Estimate the variance

R/zzz.R

@@ -1,3 +1,8 @@
+.onLoad <- function(libname, pkgname) {
+  ## https://github.com/HenrikBengtsson/matrixStats/issues/187
+  onLoadSetCenterOnUse()
+}
+
 #' @useDynLib "matrixStats", .registration = TRUE, .fixes = "C_"
 .onUnload <- function(libpath) {
   library.dynam.unload("matrixStats", libpath)