STYLE: More lintr conformations

HenrikBengtsson · Mar 29, 2017 · 7e3dfa2 · 7e3dfa2
1 parent 4f7e45a
commit 7e3dfa2
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diff --git a/R/benchmark.R b/R/benchmark.R
@@ -1,4 +1,5 @@
-benchmark <- function(fcn, tags = NULL, path = NULL, workdir = "reports", envir = parent.frame(), ...) {
+benchmark <- function(fcn, tags = NULL, path = NULL, workdir = "reports",
+                      envir = parent.frame(), ...) {
   requireNamespace("R.rsp") || stop("R.rsp not installed.")
 
   if (is.function(fcn)) {

diff --git a/R/binCounts.R b/R/binCounts.R
@@ -12,9 +12,9 @@
 #' @param idxs A \code{\link[base]{vector}} indicating subset of elements to
 #' operate over. If \code{\link[base]{NULL}}, no subsetting is done.
 #'
-#' @param bx A \code{\link[base]{numeric}} \code{\link[base]{vector}} of B+1
+#' @param bx A \code{\link[base]{numeric}} \code{\link[base]{vector}} of B + 1
 #' ordered positions specifying the B > 0 bins \code{[bx[1], bx[2])},
-#' \code{[bx[2], bx[3])}, ..., \code{[bx[B], bx[B+1])}.
+#' \code{[bx[2], bx[3])}, ..., \code{[bx[B], bx[B + 1])}.
 #'
 #' @param right If \code{\link[base:logical]{TRUE}}, the bins are right-closed
 #' (left open), otherwise left-closed (right open).

diff --git a/R/binMeans.R b/R/binMeans.R
@@ -14,9 +14,9 @@
 #' @param idxs A \code{\link[base]{vector}} indicating subset of elements to
 #' operate over. If \code{\link[base]{NULL}}, no subsetting is done.
 #'
-#' @param bx A \code{\link[base]{numeric}} \code{\link[base]{vector}} of B+1
+#' @param bx A \code{\link[base]{numeric}} \code{\link[base]{vector}} of B + 1
 #' ordered positions specifying the B > 0 bins \code{[bx[1], bx[2])},
-#' \code{[bx[2], bx[3])}, ..., \code{[bx[B], bx[B+1])}.
+#' \code{[bx[2], bx[3])}, ..., \code{[bx[B], bx[B + 1])}.
 #'
 #' @param na.rm If \code{\link[base:logical]{TRUE}}, missing values in \code{y}
 #' are dropped before calculating the mean, otherwise not.
@@ -51,7 +51,8 @@
 #'
 #' @keywords univar
 #' @export
-binMeans <- function(y, x, idxs = NULL, bx, na.rm = TRUE, count = TRUE, right = FALSE, ...) {
+binMeans <- function(y, x, idxs = NULL, bx, na.rm = TRUE, count = TRUE,
+                     right = FALSE, ...) {
   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
   # Validate arguments
   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
@@ -69,7 +70,8 @@ binMeans <- function(y, x, idxs = NULL, bx, na.rm = TRUE, count = TRUE, right =
     stop("Argument 'x' is not numeric: ", mode(x))
   }
   if (length(x) != n) {
-    stop("Argument 'y' and 'x' are of different lengths: ", length(y), " != ", length(x))
+    stop("Argument 'y' and 'x' are of different lengths: ",
+         length(y), " != ", length(x))
   }
 
   # Argument 'bx':

diff --git a/R/rowAvgsPerColSet.R b/R/rowAvgsPerColSet.R
@@ -45,7 +45,8 @@
 #' @author Henrik Bengtsson
 #' @keywords internal utilities
 #' @export
-rowAvgsPerColSet <- function(X, W = NULL, rows = NULL, S, FUN = rowMeans, ..., tFUN = FALSE) {
+rowAvgsPerColSet <- function(X, W = NULL, rows = NULL, S,
+                             FUN = rowMeans, ..., tFUN = FALSE) {
   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
   # Validate arguments
   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
@@ -138,7 +139,8 @@ rowAvgsPerColSet <- function(X, W = NULL, rows = NULL, S, FUN = rowMeans, ..., t
 
 #' @rdname rowAvgsPerColSet
 #' @export
-colAvgsPerRowSet <- function(X, W = NULL, cols = NULL, S, FUN = colMeans, tFUN = FALSE, ...) {
+colAvgsPerRowSet <- function(X, W = NULL, cols = NULL, S,
+                             FUN = colMeans, tFUN = FALSE, ...) {
   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
   # Validate arguments
   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

diff --git a/R/rowCollapse.R b/R/rowCollapse.R
@@ -41,7 +41,7 @@ rowCollapse <- function(x, idxs, rows = NULL, dim. = dim(x), ...) {
   idxs <- rep(idxs, length.out = dim.[1L])
 
   # Columns of interest
-  cols <- 0:(dim.[2L]-1L)
+  cols <- 0:(dim.[2L] - 1L)
   cols <- cols[idxs]
 
   # Calculate column-based indices
@@ -70,7 +70,7 @@ colCollapse <- function(x, idxs, cols = NULL, dim. = dim(x), ...) {
   rows <- rows[idxs]
 
   # Calculate column-based indices
-  idxs <- dim.[1L] * 0:(dim.[2L]-1L) + rows
+  idxs <- dim.[1L] * 0:(dim.[2L] - 1L) + rows
   rows <- NULL # Not needed anymore
 
   x[idxs]

diff --git a/R/rowCounts.R b/R/rowCounts.R
@@ -9,7 +9,7 @@
 #' temporarily create/allocate a matrix, if only such is needed only for these
 #' calculations.
 #'
-#' @param x An NxK \code{\link[base]{matrix}} or an N*K
+#' @param x An NxK \code{\link[base]{matrix}} or an N * K
 #' \code{\link[base]{vector}}.
 #'
 #' @param idxs,rows,cols A \code{\link[base]{vector}} indicating subset of
@@ -37,7 +37,8 @@
 #' @author Henrik Bengtsson
 #' @keywords array logic iteration univar
 #' @export
-rowCounts <- function(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE, dim. = dim(x), ...) {
+rowCounts <- function(x, rows = NULL, cols = NULL, value = TRUE,
+                      na.rm = FALSE, dim. = dim(x), ...) {
   # Argument 'x':
   if (is.matrix(x)) {
   } else if (is.vector(x)) {
@@ -85,7 +86,8 @@ rowCounts <- function(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE,
 
 #' @rdname rowCounts
 #' @export
-colCounts <- function(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE, dim. = dim(x), ...) {
+colCounts <- function(x, rows = NULL, cols = NULL, value = TRUE,
+                      na.rm = FALSE, dim. = dim(x), ...) {
   # Argument 'x':
   if (is.matrix(x)) {
   } else if (is.vector(x)) {
@@ -121,9 +123,13 @@ colCounts <- function(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE,
     dim. <- dim(x)
 
     if (is.na(value)) {
-      counts <- apply(x, MARGIN = 2L, FUN = function(x) sum(is.na(x)))
+      counts <- apply(x, MARGIN = 2L, FUN = function(x)
+        sum(is.na(x))
+      )
     } else {
-      counts <- apply(x, MARGIN = 2L, FUN = function(x) sum(x == value, na.rm = na.rm))
+      counts <- apply(x, MARGIN = 2L, FUN = function(x)
+        sum(x == value, na.rm = na.rm)
+      )
     }
   }
 
@@ -171,7 +177,8 @@ count <- function(x, idxs = NULL, value = TRUE, na.rm = FALSE, ...) {
 
 #' @rdname rowCounts
 #' @export
-rowAlls <- function(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE, dim. = dim(x), ...) {
+rowAlls <- function(x, rows = NULL, cols = NULL, value = TRUE,
+                    na.rm = FALSE, dim. = dim(x), ...) {
   if (is.numeric(x) || is.logical(x)) {
     na.rm <- as.logical(na.rm)
     hasNAs <- TRUE
@@ -197,7 +204,8 @@ rowAlls <- function(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE, di
 
 #' @rdname rowCounts
 #' @export
-colAlls <- function(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE, dim. = dim(x), ...) {
+colAlls <- function(x, rows = NULL, cols = NULL, value = TRUE,
+                    na.rm = FALSE, dim. = dim(x), ...) {
   if (is.numeric(x) || is.logical(x)) {
     na.rm <- as.logical(na.rm)
     hasNAs <- TRUE
@@ -244,7 +252,8 @@ allValue <- function(x, idxs = NULL, value = TRUE, na.rm = FALSE, ...) {
 
 #' @rdname rowCounts
 #' @export
-rowAnys <- function(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE, dim. = dim(x), ...) {
+rowAnys <- function(x, rows = NULL, cols = NULL, value = TRUE,
+                    na.rm = FALSE, dim. = dim(x), ...) {
   if (is.numeric(x) || is.logical(x)) {
     na.rm <- as.logical(na.rm)
     hasNAs <- TRUE
@@ -270,7 +279,8 @@ rowAnys <- function(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE, di
 
 #' @rdname rowCounts
 #' @export
-colAnys <- function(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE, dim. = dim(x), ...) {
+colAnys <- function(x, rows = NULL, cols = NULL, value = TRUE,
+                    na.rm = FALSE, dim. = dim(x), ...) {
   if (is.numeric(x) || is.logical(x)) {
     na.rm <- as.logical(na.rm)
     hasNAs <- TRUE

diff --git a/R/rowDiffs.R b/R/rowDiffs.R
@@ -26,12 +26,16 @@
 #' @seealso See also \code{\link{diff2}}().
 #' @keywords array iteration robust univar
 #' @export
-rowDiffs <- function(x, rows = NULL, cols = NULL, lag = 1L, differences = 1L, ...) {
-  .Call(C_rowDiffs, x, dim(x), rows, cols, as.integer(lag), as.integer(differences), TRUE)
+rowDiffs <- function(x, rows = NULL, cols = NULL,
+                     lag = 1L, differences = 1L, ...) {
+  .Call(C_rowDiffs, x, dim(x), rows, cols,
+        as.integer(lag), as.integer(differences), TRUE)
 }
 
 #' @rdname rowDiffs
 #' @export
-colDiffs <- function(x, rows = NULL, cols = NULL, lag = 1L, differences = 1L, ...) {
-  .Call(C_rowDiffs, x, dim(x), rows, cols, as.integer(lag), as.integer(differences), FALSE)
+colDiffs <- function(x, rows = NULL, cols = NULL,
+                     lag = 1L, differences = 1L, ...) {
+  .Call(C_rowDiffs, x, dim(x), rows, cols,
+        as.integer(lag), as.integer(differences), FALSE)
 }
diff --git a/R/rowIQRs.R b/R/rowIQRs.R
@@ -32,7 +32,8 @@
 #' @importFrom stats quantile
 #' @export
 rowIQRs <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ...) {
-  Q <- rowQuantiles(x, rows = rows, cols = cols, probs = c(0.25, 0.75), na.rm = na.rm, drop = FALSE, ...)
+  Q <- rowQuantiles(x, rows = rows, cols = cols,
+                    probs = c(0.25, 0.75), na.rm = na.rm, drop = FALSE, ...)
   ans <- Q[, 2L, drop = TRUE] - Q[, 1L, drop = TRUE]
 
   # Remove attributes
@@ -44,7 +45,8 @@ rowIQRs <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ...) {
 #' @rdname rowIQRs
 #' @export
 colIQRs <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ...) {
-  Q <- colQuantiles(x, rows = rows, cols = cols, probs = c(0.25, 0.75), na.rm = na.rm, drop = FALSE, ...)
+  Q <- colQuantiles(x, rows = rows, cols = cols,
+                    probs = c(0.25, 0.75), na.rm = na.rm, drop = FALSE, ...)
   ans <- Q[, 2L, drop = TRUE] - Q[, 1L, drop = TRUE]
 
   # Remove attributes

diff --git a/R/rowLogSumExps.R b/R/rowLogSumExps.R
@@ -35,7 +35,8 @@
 #'
 #' @keywords array
 #' @export
-rowLogSumExps <- function(lx, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(lx), ...) {
+rowLogSumExps <- function(lx, rows = NULL, cols = NULL, na.rm = FALSE,
+                          dim. = dim(lx), ...) {
   dim. <- as.integer(dim.)
   hasNA <- TRUE
   res <- .Call(C_rowLogSumExps,
@@ -54,7 +55,8 @@ rowLogSumExps <- function(lx, rows = NULL, cols = NULL, na.rm = FALSE, dim. = di
 
 #' @rdname rowLogSumExps
 #' @export
-colLogSumExps <- function(lx, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(lx), ...) {
+colLogSumExps <- function(lx, rows = NULL, cols = NULL, na.rm = FALSE,
+                          dim. = dim(lx), ...) {
   dim. <- as.integer(dim.)
   hasNA <- TRUE
   res <- .Call(C_rowLogSumExps,

diff --git a/R/rowMads.R b/R/rowMads.R
@@ -1,12 +1,14 @@
 #' @rdname rowSds
 #' @export
-rowMads <- function(x, rows = NULL, cols = NULL, center = NULL, constant = 1.4826, na.rm = FALSE, dim. = dim(x), centers = NULL, ...) {
+rowMads <- function(x, rows = NULL, cols = NULL, center = NULL,
+                    constant = 1.4826, na.rm = FALSE,
+                    dim. = dim(x), centers = NULL, ...) {
   ## BACKWARD COMPATIBILITY:
   ## - Added to matrixStats 0.14.0.
   ## - Defunct in matrixStats (>= 0.15.0)
   if (!is.null(centers)) {
     center <- centers
-    .Defunct(msg = "Argument 'centers' for matrixStats::rowMads() has been renamed to 'center'. Please update code accordingly.")
+    .Defunct(msg = "Argument 'centers' for matrixStats::rowMads() has been renamed to 'center'. Please update code accordingly.")  #nolint
   }
 
   if (is.null(center)) {
@@ -30,21 +32,23 @@ rowMads <- function(x, rows = NULL, cols = NULL, center = NULL, constant = 1.482
     if (is.null(dim(x))) dim(x) <- dim. # prevent from dim dropping
     x <- abs(x)
     x <- rowMedians(x, na.rm = na.rm, ...)
-    x <- constant*x
+    x <- constant * x
   }
   x
 }
 
 
 #' @rdname rowSds
 #' @export
-colMads <- function(x, rows = NULL, cols = NULL, center = NULL, constant = 1.4826, na.rm = FALSE, dim. = dim(x), centers = NULL, ...) {
+colMads <- function(x, rows = NULL, cols = NULL, center = NULL,
+                    constant = 1.4826, na.rm = FALSE,
+                    dim. = dim(x), centers = NULL, ...) {
   ## BACKWARD COMPATIBILITY:
   ## - Added to matrixStats 0.14.0.
   ## - Defunct in matrixStats (>= 0.15.0)
   if (!is.null(centers)) {
     center <- centers
-    .Defunct(msg = "Argument 'centers' for matrixStats::colMads() has been renamed to 'center'. Please update code accordingly.")
+    .Defunct(msg = "Argument 'centers' for matrixStats::colMads() has been renamed to 'center'. Please update code accordingly.")  #nolint
   }
 
   if (is.null(center)) {
@@ -72,7 +76,7 @@ colMads <- function(x, rows = NULL, cols = NULL, center = NULL, constant = 1.482
     x <- t_tx_OP_y(x, center, OP = "-", na.rm = FALSE)
     x <- abs(x)
     x <- colMedians(x, na.rm = na.rm, ...)
-    x <- constant*x
+    x <- constant * x
   }
   x
 }
diff --git a/R/rowMedians.R b/R/rowMedians.R
@@ -37,7 +37,8 @@
 #'
 #' @keywords array iteration robust univar
 #' @export
-rowMedians <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x), ...) {
+rowMedians <- function(x, rows = NULL, cols = NULL, na.rm = FALSE,
+                       dim. = dim(x), ...) {
   dim. <- as.integer(dim.)
   na.rm <- as.logical(na.rm)
   hasNAs <- TRUE  # Add as an argument? /2007-08-24
@@ -46,7 +47,8 @@ rowMedians <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x)
 
 #' @rdname rowMedians
 #' @export
-colMedians <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x), ...) {
+colMedians <- function(x, rows = NULL, cols = NULL, na.rm = FALSE,
+                       dim. = dim(x), ...) {
   dim. <- as.integer(dim.)
   na.rm <- as.logical(na.rm)
   hasNAs <- TRUE  # Add as an argument? /2007-08-24

diff --git a/R/rowOrderStats.R b/R/rowOrderStats.R
@@ -37,7 +37,8 @@
 #'
 #' @keywords array iteration robust univar
 #' @export
-rowOrderStats <- function(x, rows = NULL, cols = NULL, which, dim. = dim(x), ...) {
+rowOrderStats <- function(x, rows = NULL, cols = NULL, which,
+                          dim. = dim(x), ...) {
   dim. <- as.integer(dim.)
 
   # Check missing values
@@ -52,7 +53,8 @@ rowOrderStats <- function(x, rows = NULL, cols = NULL, which, dim. = dim(x), ...
 
 #' @rdname rowOrderStats
 #' @export
-colOrderStats <- function(x, rows = NULL, cols = NULL, which, dim. = dim(x), ...) {
+colOrderStats <- function(x, rows = NULL, cols = NULL, which,
+                          dim. = dim(x), ...) {
   dim. <- as.integer(dim.)
 
   # Check missing values

diff --git a/R/rowProds.R b/R/rowProds.R
@@ -37,7 +37,8 @@
 #'
 #' @keywords array iteration robust univar
 #' @export
-rowProds <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, method = c("direct", "expSumLog"), ...) {
+rowProds <- function(x, rows = NULL, cols = NULL, na.rm = FALSE,
+                     method = c("direct", "expSumLog"), ...) {
   # Apply subset
   if (!is.null(rows) && !is.null(cols)) x <- x[rows, cols, drop = FALSE]
   else if (!is.null(rows)) x <- x[rows, , drop = FALSE]
@@ -71,7 +72,8 @@ rowProds <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, method = c("dir
 
 #' @rdname rowProds
 #' @export
-colProds <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, method = c("direct", "expSumLog"), ...) {
+colProds <- function(x, rows = NULL, cols = NULL, na.rm = FALSE,
+                     method = c("direct", "expSumLog"), ...) {
   # Apply subset
   if (!is.null(rows) && !is.null(cols)) x <- x[rows, cols, drop = FALSE]
   else if (!is.null(rows)) x <- x[rows, , drop = FALSE]