@@ -11,7 +11,7 @@ Description: High performance functions for row and column operations on sparse

 License: MIT + file LICENSE

 Encoding: UTF-8

 LazyData: true

-RoxygenNote: 7.1.0

+RoxygenNote: 7.1.1

 LinkingTo: 

     Rcpp

 Imports: 

@@ -864,7 +864,7 @@ function(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L, trim = 0){

 #' @aliases colAvgsPerRowSet

 #' @export

 setMethod("colAvgsPerRowSet", signature(X = "xgCMatrix"),

-function(X, W = NULL, cols = NULL, S, FUN = colMeans2, ..., tFUN = FALSE){

+function(X, W = NULL, cols = NULL, S, FUN = colMeans2, ..., na.rm = NA, tFUN = FALSE){

   if(! is.null(W)) stop("the W parameter is not supported.")

   nbrOfSets <- ncol(S)

   setNames <- colnames(S)

@@ -876,6 +876,10 @@ function(X, W = NULL, cols = NULL, S, FUN = colMeans2, ..., tFUN = FALSE){

   }

   dimX <- dim(X)

   tFUN <- as.logical(tFUN)

+

+  # Check if missing values have to be excluded while averaging

+  if (is.na(na.rm)) na.rm <- (base::anyNA(X@x) || matrixStats::anyMissing(S))

+

   colnamesX <- colnames(X)

   dimnames(X) <- list(NULL, NULL)

@@ -886,7 +890,11 @@ function(X, W = NULL, cols = NULL, S, FUN = colMeans2, ..., tFUN = FALSE){

     if (tFUN) {

       Zjj <- t(Zjj)

     }

-    Zjj <- FUN(Zjj, ...)

+    tryCatch({

+      Zjj <- FUN(Zjj, ..., na.rm = na.rm)

+    }, error = function(err){

+      Zjj <<- FUN(as.matrix(Zjj), ..., na.rm = na.rm)

+    })

     if (length(Zjj) != dimX[2L])

       stop("Internal error: length(Zjj) != dimX[1L]")

     Zjj

@@ -559,8 +559,8 @@ setMethod("rowIQRDiffs", signature(x = "dgCMatrix"),

 #' @rdname colAvgsPerRowSet-xgCMatrix-method

 #' @export

 setMethod("rowAvgsPerColSet", signature(X = "xgCMatrix"),

-          function(X, W = NULL, rows = NULL, S, FUN = rowMeans2, ..., tFUN = FALSE){

-  tZ <- colAvgsPerRowSet(t(X), W = W, cols = rows, S = S, FUN  = FUN, ..., tFUN = ! tFUN)

+          function(X, W = NULL, rows = NULL, S, FUN = rowMeans2, ..., na.rm = NA, tFUN = FALSE){

+  tZ <- colAvgsPerRowSet(t(X), W = W, cols = rows, S = S, FUN  = FUN, ..., na.rm = na.rm, tFUN = ! tFUN)

   t(tZ)

 })

@@ -52,10 +52,9 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)

 }

 \seealso{

 \itemize{

-\item \code{matrixStats::\link[matrixStats]{rowAlls}()} and

-\code{matrixStats::\link[matrixStats:rowAlls]{colAlls}()} which are used

-when the input is a \code{\link{matrix}}, \code{\link{array}},

-or \code{\link{numeric}} vector.

+\item \code{matrixStats::\link[matrixStats:rowAlls]{rowAlls}()} and

+\code{matrixStats::\link[matrixStats:rowAlls]{colAlls}()} which are

+used when the input is a \code{matrix} or \code{numeric} vector.

 \item For checks if \emph{any} element is equal to a value, see

 \code{\link[MatrixGenerics]{rowAnys}()}.

 \item \code{base::\link{all}()}.

@@ -53,8 +53,10 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)

 \seealso{

 \itemize{

 \item \code{matrixStats::\link[matrixStats:rowAlls]{rowAnys}()} and

-\code{matrixStats::\link[matrixStats:rowAlls]{colAnys}()} which are used

-when the input is a \code{matrix} or \code{numeric} vector.

+\code{matrixStats::\link[matrixStats:rowAlls]{colAnys}()} which are

+used when the input is a \code{matrix} or \code{numeric} vector.

+\item For checks if \emph{all} elements are equal to a value, see

+\code{\link[MatrixGenerics]{rowAlls}()}.

 \item \code{base::\link{any}()}.

 }

 }

@@ -13,6 +13,7 @@

   S,

   FUN = colMeans2,

   ...,

+  na.rm = NA,

   tFUN = FALSE

 )

@@ -23,6 +24,7 @@

   S,

   FUN = rowMeans2,

   ...,

+  na.rm = NA,

   tFUN = FALSE

 )

 }

@@ -44,6 +46,10 @@ applied to to each column (row) subset of \code{X} that is specified by \code{S}

 \item{...}{Additional arguments passed to \code{FUN}.}

+\item{na.rm}{(logical) Argument passed to \code{FUN()} as \code{na.rm = na.rm}.

+If \code{NA} (default), then \code{na.rm = TRUE} is used if \code{X} or \code{S} holds missing values,

+otherwise \code{na.rm = FALSE}.}

+

 \item{tFUN}{If \code{TRUE}, \code{X} is transposed before it is passed to \code{FUN}.}

 \item{rows}{A \code{\link{vector}} indicating the subset (and/or

@@ -78,8 +84,8 @@ mat <- matrix(rnorm(20), nrow = 5, ncol = 4)

 }

 \seealso{

 \itemize{

-\item \code{matrixStats::\link[matrixStats]{rowAvgsPerColSet}()} and

-\code{matrixStats::\link[matrixStats:rowAvgsPerColSet]{colAvgsPerRowSet}()}

+\item \code{matrixStats::\link[matrixStats:rowAvgsPerColSet]{rowAvgsPerColSet}()}

+and \code{matrixStats::\link[matrixStats:rowAvgsPerColSet]{colAvgsPerRowSet}()}

 which are used when the input is a \code{matrix} or \code{numeric} vector.

 }

 }

@@ -50,8 +50,8 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)

 }

 \seealso{

 \itemize{

-\item \code{matrixStats::\link[matrixStats]{rowCollapse}()} and

-\code{matrixStats::\link[matrixStats:rowCollapse]{colCollapse}()}

+\item \code{matrixStats::\link[matrixStats:rowCollapse]{rowCollapse}()}

+and \code{matrixStats::\link[matrixStats:rowCollapse]{colCollapse}()}

 which are used when the input is a \code{matrix} or \code{numeric} vector.

 }

 }

@@ -41,13 +41,9 @@ done.}

 are excluded first, otherwise not.}

 \item{type}{An integer specifying the type of estimator. See

-\code{stats::\link[stats]{quantile}()}. for more details. Note, that this

-is not a generic argument and not all implementation of this function have

-to provide it.}

+\code{stats::\link[stats]{quantile}()}. for more details.}

-\item{drop}{If \code{TRUE} a vector is returned if \code{J == 1}.

-Note, that this is not a generic argument and not all implementation of

-this function have to provide it.}

+\item{drop}{If \code{TRUE} a vector is returned if \code{J == 1}.}

 }

 \value{

 a \code{\link{numeric}} \code{NxJ} (\code{KxJ})

@@ -404,12 +404,9 @@ for(idx in seq_along(matrix_list)){

   test_that("colAvgsPerRowSet works", {

     S <-  suppressWarnings(matrix(seq_len(nrow(mat)), ncol = 2))

-    expect_equal(colAvgsPerRowSet(sp_mat, S = S, na.rm = TRUE), matrixStats::colAvgsPerRowSet(mat, S = S))

-    expect_equal(colAvgsPerRowSet(sp_mat, S = S, FUN = colVarDiffs, na.rm = TRUE), matrixStats::colAvgsPerRowSet(mat, S = S, FUN = colVarDiffs))

-    if(ncol(mat) == 1 || length(col_subset) == 1){

-      skip("matrixStats has a bug in colAvgsPerRowSet if the input has exactly one column")

-    }

-    expect_equal(colAvgsPerRowSet(sp_mat, S = S, na.rm = TRUE, cols = col_subset), matrixStats::colAvgsPerRowSet(mat, S = S, cols = col_subset))

+    expect_equal(colAvgsPerRowSet(sp_mat, S = S), matrixStats::colAvgsPerRowSet(mat, S = S))

+    expect_equal(colAvgsPerRowSet(sp_mat, S = S, FUN = colVarDiffs, na.rm = FALSE), matrixStats::colAvgsPerRowSet(mat, S = S, FUN = colVarDiffs, na.rm = FALSE))

+    expect_equal(colAvgsPerRowSet(sp_mat, S = S, na.rm = FALSE, cols = col_subset), matrixStats::colAvgsPerRowSet(mat, S = S, na.rm = FALSE, cols = col_subset))

   })

 }

@@ -285,9 +285,9 @@ test_that("rowCollapse works", {

 test_that("rowAvgsPerColSet works", {

   S <-  suppressWarnings(matrix(seq_len(ncol(mat)), ncol = 2))

-  expect_equal(rowAvgsPerColSet(sp_mat, S = S, na.rm = TRUE), matrixStats::rowAvgsPerColSet(mat, S = S))

-  expect_equal(rowAvgsPerColSet(sp_mat, S = S, FUN = rowVarDiffs, na.rm = TRUE), matrixStats::rowAvgsPerColSet(mat, S = S, FUN = rowVarDiffs))

-  expect_equal(rowAvgsPerColSet(sp_mat, S = S, na.rm = TRUE, rows = row_subset), matrixStats::rowAvgsPerColSet(mat, S = S, rows = row_subset))

+  expect_equal(rowAvgsPerColSet(sp_mat, S = S, na.rm = TRUE), matrixStats::rowAvgsPerColSet(mat, S = S, na.rm = TRUE))

+  expect_equal(rowAvgsPerColSet(sp_mat, S = S, FUN = rowVarDiffs, na.rm = FALSE), matrixStats::rowAvgsPerColSet(mat, S = S, FUN = rowVarDiffs, na.rm = FALSE))

+  expect_equal(rowAvgsPerColSet(sp_mat, S = S, na.rm = FALSE, rows = row_subset), matrixStats::rowAvgsPerColSet(mat, S = S, na.rm = FALSE, rows = row_subset))

 })