1. sparseMatrixStats
  2. Commit 2a9241155a6356a6ac5bc0b752ea6d48441fb01f
Browse code

Bring documentation in line with MatrixGenerics

const-ae authored on 03/04/2020 10:19:46
Showing 36 changed files
man/colAlls-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -3,7 +3,8 @@
3 3 
 \name{colAlls,dgCMatrix-method}
4 4 
 \alias{colAlls,dgCMatrix-method}
5 5 
 \alias{rowAlls,dgCMatrix-method}
6 
-\title{Check if all elements in a row (column) of a matrix-like object are equal to a value}
6 
+\title{Check if all elements in a row (column) of a matrix-like object are equal to
7 
+a value}
7 8 
 \usage{
8 9 
 \S4method{colAlls}{dgCMatrix}(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE, ...)
9 10
... ... 
@@ -12,13 +13,15 @@
12 13 
 \arguments{
13 14 
 \item{x}{An NxK matrix-like object.}
14 15
15 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
16 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
16 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
17 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
18 
+subsetting is done.}
17 19
18 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
19 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
20 
+\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
21 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
22 
+subsetting is done.}
20 23
21 
-\item{value}{the value to search for.}
24 
+\item{value}{The value to search for.}
22 25
23 26 
 \item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
24 27 
 are excluded first, otherwise not.}
... ... 
@@ -30,11 +33,13 @@ Returns a \code{\link[base]{logical}} \code{\link[base]{vector}} of
30 33 
 length N (K).
31 34 
 }
32 35 
 \description{
33 
-Check if all elements in a row (column) of a matrix-like object are equal to a value
36 
+Check if all elements in a row (column) of a matrix-like object are equal to
37 
+a value.
34 38 
 }
35 39 
 \details{
36 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
37 
-\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowAlls}}
40 
+The S4 methods for \code{x} of type \code{\link[base]{matrix}},
41 
+\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
42 
+\code{matrixStats::\link[matrixStats]{rowAlls}}
38 43 
 / \code{matrixStats::\link[matrixStats]{colAlls}}.
39 44 
 }
40 45 
 \examples{
... ... 
@@ -52,8 +57,10 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
52 57 
 \itemize{
53 58 
 \item \code{matrixStats::\link[matrixStats]{rowAlls}()} and
54 59 
 \code{matrixStats::\link[matrixStats]{colAlls}()} which are used when
55 
-the input is a \code{matrix} or \code{numeric} vector.
56 
-\item For checks if any element is equal to a value, see \code{\link[MatrixGenerics]{rowAnys}()}.
57 
-\item \link[base:all]{base::all}
60 
+the input is a \code{\link[base]{matrix}}, \code{\link[base]{array}}, or
61 
+\code{\link[base]{numeric}} vector.
62 
+\item For checks if \emph{any} element is equal to a value, see
63 
+\code{\link[MatrixGenerics]{rowAnys}()}.
64 
+\item \code{base::\link[base]{all}()}.
58 65 
 }
59 66 
 }
man/colAnyNAs-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -12,14 +12,13 @@
12 12 
 \arguments{
13 13 
 \item{x}{An NxK matrix-like object.}
14 14
15 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
16 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
15 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
16 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
17 
+subsetting is done.}
17 18
18 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
19 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
20 
-
21 
-\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
22 
-are excluded first, otherwise not.}
19 
+\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
20 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
21 
+subsetting is done.}
23 22
24 23 
 \item{...}{Additional arguments passed to specific methods.}
25 24 
 }
... ... 
@@ -28,11 +27,12 @@ Returns a \code{\link[base]{logical}} \code{\link[base]{vector}} of
28 27 
 length N (K).
29 28 
 }
30 29 
 \description{
31 
-Check if any elements in a row (column) of a matrix-like object is missing
30 
+Check if any elements in a row (column) of a matrix-like object is missing.
32 31 
 }
33 32 
 \details{
34 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
35 
-\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowAnyNAs}}
33 
+The S4 methods for \code{x} of type \code{\link[base]{matrix}},
34 
+\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
35 
+\code{matrixStats::\link[matrixStats]{rowAnyNAs}}
36 36 
 / \code{matrixStats::\link[matrixStats]{colAnyNAs}}.
37 37 
 }
38 38 
 \examples{
... ... 
@@ -47,7 +47,8 @@ The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
47 47 
 \item \code{matrixStats::\link[matrixStats]{rowAnyNAs}()} and
48 48 
 \code{matrixStats::\link[matrixStats]{colAnyNAs}()} which are used when
49 49 
 the input is a \code{matrix} or \code{numeric} vector.
50 
-\item For checks if any element is equal to a value, see \code{\link[MatrixGenerics]{rowAnys}()}.
51 
-\item \link{is.na} and \link{any}
50 
+\item For checks if any element is equal to a value, see
51 
+\code{\link[MatrixGenerics]{rowAnys}()}.
52 
+\item \code{base::\link[base]{is.na}()} and \code{base::\link[base]{any}()}.
52 53 
 }
53 54 
 }
man/colAnys-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -3,7 +3,8 @@
3 3 
 \name{colAnys,dgCMatrix-method}
4 4 
 \alias{colAnys,dgCMatrix-method}
5 5 
 \alias{rowAnys,dgCMatrix-method}
6 
-\title{Check if any elements in a row (column) of a matrix-like object is equal to a value}
6 
+\title{Check if any elements in a row (column) of a matrix-like object is equal to
7 
+a value}
7 8 
 \usage{
8 9 
 \S4method{colAnys}{dgCMatrix}(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE, ...)
9 10
... ... 
@@ -12,13 +13,15 @@
12 13 
 \arguments{
13 14 
 \item{x}{An NxK matrix-like object.}
14 15
15 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
16 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
16 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
17 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
18 
+subsetting is done.}
17 19
18 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
19 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
20 
+\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
21 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
22 
+subsetting is done.}
20 23
21 
-\item{value}{the value to search for.}
24 
+\item{value}{The value to search for.}
22 25
23 26 
 \item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
24 27 
 are excluded first, otherwise not.}
... ... 
@@ -30,11 +33,13 @@ Returns a \code{\link[base]{logical}} \code{\link[base]{vector}} of
30 33 
 length N (K).
31 34 
 }
32 35 
 \description{
33 
-Check if any elements in a row (column) of a matrix-like object is equal to a value
36 
+Check if any elements in a row (column) of a matrix-like object is equal to
37 
+a value.
34 38 
 }
35 39 
 \details{
36 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
37 
-\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowAnys}}
40 
+The S4 methods for \code{x} of type \code{\link[base]{matrix}},
41 
+\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
42 
+\code{matrixStats::\link[matrixStats]{rowAnys}}
38 43 
 / \code{matrixStats::\link[matrixStats]{colAnys}}.
39 44 
 }
40 45 
 \examples{
... ... 
@@ -53,7 +58,6 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
53 58 
 \item \code{matrixStats::\link[matrixStats]{rowAnys}()} and
54 59 
 \code{matrixStats::\link[matrixStats]{colAnys}()} which are used when
55 60 
 the input is a \code{matrix} or \code{numeric} vector.
56 
-\item For checks if any element is equal to a value, see \code{\link[MatrixGenerics]{rowAnys}()}.
57 
-\item \link{any}
61 
+\item \code{base::\link[base]{any}()}.
58 62 
 }
59 63 
 }
man/colAvgsPerRowSet-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -32,11 +32,12 @@
32 32 
 \item{W}{An optional numeric \code{NxM} matrix of weights.}
33 33
34 34 
 \item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
35 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
35 
+columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is
36 
+done.}
36 37
37 
-\item{S}{An \link{integer} \code{KxJ} matrix that specifying the \code{J} subsets. Each column
38 
-hold \code{K} column (row) indices for the corresponding subset. The range of values
39 
-is [1, M] ([1,N]).}
38 
+\item{S}{An \link{integer} \code{KxJ} matrix that specifying the \code{J} subsets. Each
39 
+column hold \code{K} column (row) indices for the corresponding subset. The
40 
+range of values is [1, M] ([1,N]).}
40 41
41 42 
 \item{FUN}{A row-by-row (column-by-column) summary statistic function. It is
42 43 
 applied to to each column (row) subset of \code{X} that is specified by \code{S}.}
... ... 
@@ -46,7 +47,8 @@ applied to to each column (row) subset of \code{X} that is specified by \code{S}
46 47 
 \item{tFUN}{If \code{TRUE}, \code{X} is transposed before it is passed to \code{FUN}.}
47 48
48 49 
 \item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
49 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
50 
+columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is
51 
+done.}
50 52 
 }
51 53 
 \value{
52 54 
 Returns a numeric \code{JxN} (\code{MxJ}) matrix.
... ... 
@@ -77,7 +79,7 @@ mat <- matrix(rnorm(20), nrow = 5, ncol = 4)
77 79 
 \seealso{
78 80 
 \itemize{
79 81 
 \item \code{matrixStats::\link[matrixStats]{rowAvgsPerColSet}()} and
80 
-\code{matrixStats::\link[matrixStats]{colAvgsPerRowSet}()} which are used when
81 
-the input is a \code{matrix} or \code{numeric} vector.
82 
+\code{matrixStats::\link[matrixStats]{colAvgsPerRowSet}()} which are used
83 
+when the input is a \code{matrix} or \code{numeric} vector.
82 84 
 }
83 85 
 }
man/colCollapse-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -15,24 +15,27 @@
15 15 
 \item{idxs}{An index \code{\link[base]{vector}} with the position to extract.
16 16 
 It is recycled to match the number of rows (column)}
17 17
18 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
19 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
18 
+\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
19 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
20 
+subsetting is done.}
20 21
21 22 
 \item{...}{Additional arguments passed to specific methods.}
22 23
23 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
24 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
24 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
25 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
26 
+subsetting is done.}
25 27 
 }
26 28 
 \value{
27 29 
 Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of
28 30 
 length N (K).
29 31 
 }
30 32 
 \description{
31 
-Extract one cell from each row (column) of a matrix-like object
33 
+Extract one cell from each row (column) of a matrix-like object.
32 34 
 }
33 35 
 \details{
34 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
35 
-\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowCollapse}}
36 
+The S4 methods for \code{x} of type \code{\link[base]{matrix}},
37 
+\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
38 
+\code{matrixStats::\link[matrixStats]{rowCollapse}}
36 39 
 / \code{matrixStats::\link[matrixStats]{colCollapse}}.
37 40 
 }
38 41 
 \examples{
man/colCounts-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -3,7 +3,8 @@
3 3 
 \name{colCounts,dgCMatrix-method}
4 4 
 \alias{colCounts,dgCMatrix-method}
5 5 
 \alias{rowCounts,dgCMatrix-method}
6 
-\title{Count how often an element in a row (column) of a matrix-like object is equal to a value}
6 
+\title{Count how often an element in a row (column) of a matrix-like object is
7 
+equal to a value}
7 8 
 \usage{
8 9 
 \S4method{colCounts}{dgCMatrix}(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE, ...)
9 10
... ... 
@@ -12,13 +13,15 @@
12 13 
 \arguments{
13 14 
 \item{x}{An NxK matrix-like object.}
14 15
15 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
16 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
16 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
17 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
18 
+subsetting is done.}
17 19
18 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
19 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
20 
+\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
21 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
22 
+subsetting is done.}
20 23
21 
-\item{value}{the value to search for.}
24 
+\item{value}{The value to search for.}
22 25
23 26 
 \item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
24 27 
 are excluded first, otherwise not.}
... ... 
@@ -30,11 +33,13 @@ Returns a \code{\link[base]{integer}} \code{\link[base]{vector}} of
30 33 
 length N (K).
31 34 
 }
32 35 
 \description{
33 
-Count how often an element in a row (column) of a matrix-like object is equal to a value
36 
+Count how often an element in a row (column) of a matrix-like object is
37 
+equal to a value.
34 38 
 }
35 39 
 \details{
36 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
37 
-\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowCounts}}
40 
+The S4 methods for \code{x} of type \code{\link[base]{matrix}},
41 
+\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
42 
+\code{matrixStats::\link[matrixStats]{rowCounts}}
38 43 
 / \code{matrixStats::\link[matrixStats]{colCounts}}.
39 44 
 }
40 45 
 \examples{
... ... 
@@ -56,7 +61,8 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
56 61 
 \item \code{matrixStats::\link[matrixStats]{rowCounts}()} and
57 62 
 \code{matrixStats::\link[matrixStats]{colCounts}()} which are used when
58 63 
 the input is a \code{matrix} or \code{numeric} vector.
59 
-\item For checks if any element is equal to a value, see \code{\link[MatrixGenerics]{rowAnys}()}. To
60 
-check if all elements are equal, see \code{\link[MatrixGenerics]{rowAlls}()}.
64 
+\item For checks if any element is equal to a value, see
65 
+\code{\link[MatrixGenerics]{rowAnys}()}. To check if all elements are equal, see
66 
+\code{\link[MatrixGenerics]{rowAlls}()}.
61 67 
 }
62 68 
 }
man/colCummaxs-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -3,7 +3,8 @@
3 3 
 \name{colCummaxs,dgCMatrix-method}
4 4 
 \alias{colCummaxs,dgCMatrix-method}
5 5 
 \alias{rowCummaxs,dgCMatrix-method}
6 
-\title{Calculates the cumulative maxima for each row (column) of a matrix-like object}
6 
+\title{Calculates the cumulative maxima for each row (column) of a matrix-like
7 
+object}
7 8 
 \usage{
8 9 
 \S4method{colCummaxs}{dgCMatrix}(x, rows = NULL, cols = NULL, ...)
9 10
... ... 
@@ -12,24 +13,28 @@
12 13 
 \arguments{
13 14 
 \item{x}{An NxK matrix-like object.}
14 15
15 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
16 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
16 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
17 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
18 
+subsetting is done.}
17 19
18 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
19 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
20 
+\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
21 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
22 
+subsetting is done.}
20 23
21 24 
 \item{...}{Additional arguments passed to specific methods.}
22 25 
 }
23 26 
 \value{
24 
-Returns a \code{\link[base]{numeric}} \code{\link[base]{matrix}} with the
25 
-same dimensions as \code{x}.
27 
+Returns a \code{\link[base]{numeric}} \code{\link[base]{matrix}}
28 
+with the same dimensions as \code{x}.
26 29 
 }
27 30 
 \description{
28 
-Calculates the cumulative maxima for each row (column) of a matrix-like object
31 
+Calculates the cumulative maxima for each row (column) of a matrix-like
32 
+object.
29 33 
 }
30 34 
 \details{
31 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
32 
-\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowCummaxs}}
35 
+The S4 methods for \code{x} of type \code{\link[base]{matrix}},
36 
+\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
37 
+\code{matrixStats::\link[matrixStats]{rowCummaxs}}
33 38 
 / \code{matrixStats::\link[matrixStats]{colCummaxs}}.
34 39 
 }
35 40 
 \examples{
... ... 
@@ -49,6 +54,6 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
49 54 
 \code{matrixStats::\link[matrixStats]{colCummaxs}()} which are used when
50 55 
 the input is a \code{matrix} or \code{numeric} vector.
51 56 
 \item For single maximum estimates, see \code{\link[MatrixGenerics]{rowMaxs}()}.
52 
-\item \link{cummax}
57 
+\item \code{base::\link[base]{cummax}()}.
53 58 
 }
54 59 
 }
man/colCummins-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -3,7 +3,8 @@
3 3 
 \name{colCummins,dgCMatrix-method}
4 4 
 \alias{colCummins,dgCMatrix-method}
5 5 
 \alias{rowCummins,dgCMatrix-method}
6 
-\title{Calculates the cumulative minima for each row (column) of a matrix-like object}
6 
+\title{Calculates the cumulative minima for each row (column) of a matrix-like
7 
+object}
7 8 
 \usage{
8 9 
 \S4method{colCummins}{dgCMatrix}(x, rows = NULL, cols = NULL, ...)
9 10
... ... 
@@ -12,24 +13,28 @@
12 13 
 \arguments{
13 14 
 \item{x}{An NxK matrix-like object.}
14 15
15 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
16 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
16 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
17 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
18 
+subsetting is done.}
17 19
18 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
19 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
20 
+\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
21 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
22 
+subsetting is done.}
20 23
21 24 
 \item{...}{Additional arguments passed to specific methods.}
22 25 
 }
23 26 
 \value{
24 
-Returns a \code{\link[base]{numeric}} \code{\link[base]{matrix}} with the
25 
-same dimensions as \code{x}.
27 
+Returns a \code{\link[base]{numeric}} \code{\link[base]{matrix}}
28 
+with the same dimensions as \code{x}.
26 29 
 }
27 30 
 \description{
28 
-Calculates the cumulative minima for each row (column) of a matrix-like object
31 
+Calculates the cumulative minima for each row (column) of a matrix-like
32 
+object.
29 33 
 }
30 34 
 \details{
31 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
32 
-\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowCummins}}
35 
+The S4 methods for \code{x} of type \code{\link[base]{matrix}},
36 
+\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
37 
+\code{matrixStats::\link[matrixStats]{rowCummins}}
33 38 
 / \code{matrixStats::\link[matrixStats]{colCummins}}.
34 39 
 }
35 40 
 \examples{
... ... 
@@ -49,6 +54,6 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
49 54 
 \code{matrixStats::\link[matrixStats]{colCummins}()} which are used when
50 55 
 the input is a \code{matrix} or \code{numeric} vector.
51 56 
 \item For single minimum estimates, see \code{\link[MatrixGenerics]{rowMins}()}.
52 
-\item \link{cummin}
57 
+\item \code{base::\link[base]{cummin}()}.
53 58 
 }
54 59 
 }
man/colCumprods-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -3,7 +3,8 @@
3 3 
 \name{colCumprods,dgCMatrix-method}
4 4 
 \alias{colCumprods,dgCMatrix-method}
5 5 
 \alias{rowCumprods,dgCMatrix-method}
6 
-\title{Calculates the cumulative product for each row (column) of a matrix-like object}
6 
+\title{Calculates the cumulative product for each row (column) of a matrix-like
7 
+object}
7 8 
 \usage{
8 9 
 \S4method{colCumprods}{dgCMatrix}(x, rows = NULL, cols = NULL, ...)
9 10
... ... 
@@ -12,24 +13,28 @@
12 13 
 \arguments{
13 14 
 \item{x}{An NxK matrix-like object.}
14 15
15 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
16 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
16 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
17 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
18 
+subsetting is done.}
17 19
18 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
19 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
20 
+\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
21 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
22 
+subsetting is done.}
20 23
21 24 
 \item{...}{Additional arguments passed to specific methods.}
22 25 
 }
23 26 
 \value{
24 
-Returns a \code{\link[base]{numeric}} \code{\link[base]{matrix}} with the
25 
-same dimensions as \code{x}.
27 
+Returns a \code{\link[base]{numeric}} \code{\link[base]{matrix}}
28 
+with the same dimensions as \code{x}.
26 29 
 }
27 30 
 \description{
28 
-Calculates the cumulative product for each row (column) of a matrix-like object
31 
+Calculates the cumulative product for each row (column) of a matrix-like
32 
+object.
29 33 
 }
30 34 
 \details{
31 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
32 
-\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowCumprods}}
35 
+The S4 methods for \code{x} of type \code{\link[base]{matrix}},
36 
+\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
37 
+\code{matrixStats::\link[matrixStats]{rowCumprods}}
33 38 
 / \code{matrixStats::\link[matrixStats]{colCumprods}}.
34 39 
 }
35 40 
 \examples{
... ... 
@@ -48,6 +53,6 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
48 53 
 \item \code{matrixStats::\link[matrixStats]{rowCumprods}()} and
49 54 
 \code{matrixStats::\link[matrixStats]{colCumprods}()} which are used when
50 55 
 the input is a \code{matrix} or \code{numeric} vector.
51 
-\item \link{cumprod}
56 
+\item \code{base::\link[base]{cumprod}()}.
52 57 
 }
53 58 
 }
man/colCumsums-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -12,24 +12,27 @@
12 12 
 \arguments{
13 13 
 \item{x}{An NxK matrix-like object.}
14 14
15 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
16 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
15 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
16 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
17 
+subsetting is done.}
17 18
18 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
19 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
19 
+\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
20 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
21 
+subsetting is done.}
20 22
21 23 
 \item{...}{Additional arguments passed to specific methods.}
22 24 
 }
23 25 
 \value{
24 
-Returns a \code{\link[base]{numeric}} \code{\link[base]{matrix}} with the
25 
-same dimensions as \code{x}.
26 
+Returns a \code{\link[base]{numeric}} \code{\link[base]{matrix}}
27 
+with the same dimensions as \code{x}.
26 28 
 }
27 29 
 \description{
28 
-Calculates the cumulative sum for each row (column) of a matrix-like object
30 
+Calculates the cumulative sum for each row (column) of a matrix-like object.
29 31 
 }
30 32 
 \details{
31 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
32 
-\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowCumsums}}
33 
+The S4 methods for \code{x} of type \code{\link[base]{matrix}},
34 
+\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
35 
+\code{matrixStats::\link[matrixStats]{rowCumsums}}
33 36 
 / \code{matrixStats::\link[matrixStats]{colCumsums}}.
34 37 
 }
35 38 
 \examples{
... ... 
@@ -48,6 +51,6 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
48 51 
 \item \code{matrixStats::\link[matrixStats]{rowCumsums}()} and
49 52 
 \code{matrixStats::\link[matrixStats]{colCumsums}()} which are used when
50 53 
 the input is a \code{matrix} or \code{numeric} vector.
51 
-\item \link{cumsum}
54 
+\item \code{base::\link[base]{cumsum}()}.
52 55 
 }
53 56 
 }
man/colDiffs-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -3,7 +3,8 @@
3 3 
 \name{colDiffs,dgCMatrix-method}
4 4 
 \alias{colDiffs,dgCMatrix-method}
5 5 
 \alias{rowDiffs,dgCMatrix-method}
6 
-\title{Calculates the difference between each element of a row (column) of a matrix-like object}
6 
+\title{Calculates the difference between each element of a row (column) of a
7 
+matrix-like object}
7 8 
 \usage{
8 9 
 \S4method{colDiffs}{dgCMatrix}(x, rows = NULL, cols = NULL, lag = 1L, differences = 1L, ...)
9 10
... ... 
@@ -12,11 +13,13 @@
12 13 
 \arguments{
13 14 
 \item{x}{An NxK matrix-like object.}
14 15
15 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
16 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
16 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
17 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
18 
+subsetting is done.}
17 19
18 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
19 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
20 
+\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
21 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
22 
+subsetting is done.}
20 23
21 24 
 \item{lag}{An integer specifying the lag.}
22 25
... ... 
@@ -25,15 +28,17 @@ columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
25 28 
 \item{...}{Additional arguments passed to specific methods.}
26 29 
 }
27 30 
 \value{
28 
-Returns a \code{\link[base]{numeric}} \code{\link[base]{matrix}} with one
29 
-column (row) less than x: \eqn{Nx(K-1)} or \eqn{(N-1)xK}.
31 
+Returns a \code{\link[base]{numeric}} \code{\link[base]{matrix}}
32 
+with one column (row) less than x: \eqn{Nx(K-1)} or \eqn{(N-1)xK}.
30 33 
 }
31 34 
 \description{
32 
-Calculates the difference between each element of a row (column) of a matrix-like object
35 
+Calculates the difference between each element of a row (column) of a
36 
+matrix-like object.
33 37 
 }
34 38 
 \details{
35 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
36 
-\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowDiffs}}
39 
+The S4 methods for \code{x} of type \code{\link[base]{matrix}},
40 
+\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
41 
+\code{matrixStats::\link[matrixStats]{rowDiffs}}
37 42 
 / \code{matrixStats::\link[matrixStats]{colDiffs}}.
38 43 
 }
39 44 
 \examples{
... ... 
@@ -52,6 +57,6 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
52 57 
 \item \code{matrixStats::\link[matrixStats]{rowDiffs}()} and
53 58 
 \code{matrixStats::\link[matrixStats]{colDiffs}()} which are used when
54 59 
 the input is a \code{matrix} or \code{numeric} vector.
55 
-\item \link{diff}
60 
+\item \code{base::\link[base]{diff}()}.
56 61 
 }
57 62 
 }
man/colIQRDiffs-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -3,7 +3,8 @@
3 3 
 \name{colIQRDiffs,dgCMatrix-method}
4 4 
 \alias{colIQRDiffs,dgCMatrix-method}
5 5 
 \alias{rowIQRDiffs,dgCMatrix-method}
6 
-\title{Calculates the interquartile range of the difference between each element of a row (column) of a matrix-like object}
6 
+\title{Calculates the interquartile range of the difference between each element of
7 
+a row (column) of a matrix-like object}
7 8 
 \usage{
8 9 
 \S4method{colIQRDiffs}{dgCMatrix}(
9 10 
   x,
... ... 
@@ -28,19 +29,21 @@
28 29 
 \arguments{
29 30 
 \item{x}{An NxK matrix-like object.}
30 31
31 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
32 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
32 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
33 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
34 
+subsetting is done.}
33 35
34 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
35 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
36 
+\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
37 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
38 
+subsetting is done.}
36 39
37 40 
 \item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
38 41 
 are excluded first, otherwise not.}
39 42
40 43 
 \item{diff}{An integer specifying the order of difference.}
41 44
42 
-\item{trim}{A double in [0,1/2] specifying the fraction of observations to be trimmed from
43 
-each end of (sorted) x before estimation.}
45 
+\item{trim}{A double in [0,1/2] specifying the fraction of observations to
46 
+be trimmed from each end of (sorted) x before estimation.}
44 47
45 48 
 \item{...}{Additional arguments passed to specific methods.}
46 49 
 }
... ... 
@@ -49,11 +52,13 @@ Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of
49 52 
 length N (K).
50 53 
 }
51 54 
 \description{
52 
-Calculates the interquartile range of the difference between each element of a row (column) of a matrix-like object
55 
+Calculates the interquartile range of the difference between each element of
56 
+a row (column) of a matrix-like object.
53 57 
 }
54 58 
 \details{
55 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
56 
-\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowIQRDiffs}}
59 
+The S4 methods for \code{x} of type \code{\link[base]{matrix}},
60 
+\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
61 
+\code{matrixStats::\link[matrixStats]{rowIQRDiffs}}
57 62 
 / \code{matrixStats::\link[matrixStats]{colIQRDiffs}}.
58 63 
 }
59 64 
 \examples{
man/colIQRs-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -3,7 +3,8 @@
3 3 
 \name{colIQRs,dgCMatrix-method}
4 4 
 \alias{colIQRs,dgCMatrix-method}
5 5 
 \alias{rowIQRs,dgCMatrix-method}
6 
-\title{Calculates the interquartile range for each row (column) of a matrix-like object}
6 
+\title{Calculates the interquartile range for each row (column) of a matrix-like
7 
+object}
7 8 
 \usage{
8 9 
 \S4method{colIQRs}{dgCMatrix}(x, rows = NULL, cols = NULL, na.rm = FALSE, ...)
9 10
... ... 
@@ -12,11 +13,13 @@
12 13 
 \arguments{
13 14 
 \item{x}{An NxK matrix-like object.}
14 15
15 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
16 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
16 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
17 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
18 
+subsetting is done.}
17 19
18 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
19 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
20 
+\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
21 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
22 
+subsetting is done.}
20 23
21 24 
 \item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
22 25 
 are excluded first, otherwise not.}
... ... 
@@ -28,11 +31,13 @@ Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of
28 31 
 length N (K).
29 32 
 }
30 33 
 \description{
31 
-Calculates the interquartile range for each row (column) of a matrix-like object.
34 
+Calculates the interquartile range for each row (column) of a matrix-like
35 
+object.
32 36 
 }
33 37 
 \details{
34 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
35 
-\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowIQRs}}
38 
+The S4 methods for \code{x} of type \code{\link[base]{matrix}},
39 
+\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
40 
+\code{matrixStats::\link[matrixStats]{rowIQRs}}
36 41 
 / \code{matrixStats::\link[matrixStats]{colIQRs}}.
37 42 
 }
38 43 
 \examples{
... ... 
@@ -53,6 +58,6 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
53 58 
 the input is a \code{matrix} or \code{numeric} vector.
54 59 
 \item For a non-robust analog, see \code{\link[MatrixGenerics]{rowSds}()}. For a more
55 60 
 robust version see \code{\link[MatrixGenerics:rowMads]{rowMads()}}
56 
-\item \link[stats:IQR]{stats::IQR}
61 
+\item \code{stats::\link[stats]{IQR}()}.
57 62 
 }
58 63 
 }
man/colLogSumExps-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -3,7 +3,8 @@
3 3 
 \name{colLogSumExps,dgCMatrix-method}
4 4 
 \alias{colLogSumExps,dgCMatrix-method}
5 5 
 \alias{rowLogSumExps,dgCMatrix-method}
6 
-\title{Accurately calculates the logarithm of the sum of exponentials for each row (column) of a matrix-like object}
6 
+\title{Accurately calculates the logarithm of the sum of exponentials for each row
7 
+(column) of a matrix-like object}
7 8 
 \usage{
8 9 
 \S4method{colLogSumExps}{dgCMatrix}(lx, rows = NULL, cols = NULL, na.rm = FALSE, ...)
9 10
... ... 
@@ -13,10 +14,12 @@
13 14 
 \item{lx}{An NxK matrix-like object. Typically \code{lx} are \code{log(x)} values.}
14 15
15 16 
 \item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
16 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
17 
+columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is
18 
+done.}
17 19
18 20 
 \item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
19 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
21 
+columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is
22 
+done.}
20 23
21 24 
 \item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
22 25 
 are excluded first, otherwise not.}
... ... 
@@ -28,11 +31,13 @@ Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of
28 31 
 length N (K).
29 32 
 }
30 33 
 \description{
31 
-Accurately calculates the logarithm of the sum of exponentials for each row (column) of a matrix-like object
34 
+Accurately calculates the logarithm of the sum of exponentials for each row
35 
+(column) of a matrix-like object.
32 36 
 }
33 37 
 \details{
34 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
35 
-\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowLogSumExps}}
38 
+The S4 methods for \code{x} of type \code{\link[base]{matrix}},
39 
+\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
40 
+\code{matrixStats::\link[matrixStats]{rowLogSumExps}}
36 41 
 / \code{matrixStats::\link[matrixStats]{colLogSumExps}}.
37 42 
 }
38 43 
 \examples{
... ... 
@@ -49,8 +54,8 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
49 54 
 \seealso{
50 55 
 \itemize{
51 56 
 \item \code{matrixStats::\link[matrixStats]{rowLogSumExps}()} and
52 
-\code{matrixStats::\link[matrixStats]{colLogSumExps}()} which are used when
53 
-the input is a \code{matrix} or \code{numeric} vector.
57 
+\code{matrixStats::\link[matrixStats]{colLogSumExps}()} which are used
58 
+when the input is a \code{matrix} or \code{numeric} vector.
54 59 
 \item \code{\link[MatrixGenerics:rowSums2]{rowSums2()}}
55 60 
 }
56 61 
 }
man/colMadDiffs-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -3,7 +3,8 @@
3 3 
 \name{colMadDiffs,dgCMatrix-method}
4 4 
 \alias{colMadDiffs,dgCMatrix-method}
5 5 
 \alias{rowMadDiffs,dgCMatrix-method}
6 
-\title{Calculates the mean absolute deviation of the difference between each element of a row (column) of a matrix-like object}
6 
+\title{Calculates the mean absolute deviation of the difference between each
7 
+element of a row (column) of a matrix-like object}
7 8 
 \usage{
8 9 
 \S4method{colMadDiffs}{dgCMatrix}(
9 10 
   x,
... ... 
@@ -30,19 +31,21 @@
30 31 
 \arguments{
31 32 
 \item{x}{An NxK matrix-like object.}
32 33
33 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
34 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
34 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
35 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
36 
+subsetting is done.}
35 37
36 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
37 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
38 
+\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
39 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
40 
+subsetting is done.}
38 41
39 42 
 \item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
40 43 
 are excluded first, otherwise not.}
41 44
42 45 
 \item{diff}{An integer specifying the order of difference.}
43 46
44 
-\item{trim}{A double in [0,1/2] specifying the fraction of observations to be trimmed from
45 
-each end of (sorted) x before estimation.}
47 
+\item{trim}{A double in [0,1/2] specifying the fraction of observations to
48 
+be trimmed from each end of (sorted) x before estimation.}
46 49
47 50 
 \item{constant}{A scale factor. See \code{\link{mad}} for details.}
48 51
... ... 
@@ -53,11 +56,13 @@ Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of
53 56 
 length N (K).
54 57 
 }
55 58 
 \description{
56 
-Calculates the mean absolute deviation of the difference between each element of a row (column) of a matrix-like object
59 
+Calculates the mean absolute deviation of the difference between each
60 
+element of a row (column) of a matrix-like object.
57 61 
 }
58 62 
 \details{
59 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
60 
-\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowMadDiffs}}
63 
+The S4 methods for \code{x} of type \code{\link[base]{matrix}},
64 
+\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
65 
+\code{matrixStats::\link[matrixStats]{rowMadDiffs}}
61 66 
 / \code{matrixStats::\link[matrixStats]{colMadDiffs}}.
62 67 
 }
63 68 
 \examples{
man/colMads-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -3,7 +3,8 @@
3 3 
 \name{colMads,dgCMatrix-method}
4 4 
 \alias{colMads,dgCMatrix-method}
5 5 
 \alias{rowMads,dgCMatrix-method}
6 
-\title{Calculates the median absolute deviation for each row (column) of a matrix-like object}
6 
+\title{Calculates the median absolute deviation for each row (column) of a
7 
+matrix-like object}
7 8 
 \usage{
8 9 
 \S4method{colMads}{dgCMatrix}(
9 10 
   x,
... ... 
@@ -28,15 +29,18 @@
28 29 
 \arguments{
29 30 
 \item{x}{An NxK matrix-like object.}
30 31
31 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
32 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
32 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
33 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
34 
+subsetting is done.}
33 35
34 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
35 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
36 
+\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
37 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
38 
+subsetting is done.}
36 39
37 40 
 \item{center}{(optional) the center, defaults to the row means}
38 41
39 
-\item{constant}{A scale factor. See \link[stats:mad]{stats::mad} for details.}
42 
+\item{constant}{A scale factor. See \code{stats::\link[stats]{mad}()} for
43 
+details.}
40 44
41 45 
 \item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
42 46 
 are excluded first, otherwise not.}
... ... 
@@ -48,11 +52,13 @@ Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of
48 52 
 length N (K).
49 53 
 }
50 54 
 \description{
51 
-Calculates the median absolute deviation for each row (column) of a matrix-like object.
55 
+Calculates the median absolute deviation for each row (column) of a
56 
+matrix-like object.
52 57 
 }
53 58 
 \details{
54 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
55 
-\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowMads}}
59 
+The S4 methods for \code{x} of type \code{\link[base]{matrix}},
60 
+\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
61 
+\code{matrixStats::\link[matrixStats]{rowMads}}
56 62 
 / \code{matrixStats::\link[matrixStats]{colMads}}.
57 63 
 }
58 64 
 \examples{
... ... 
@@ -73,6 +79,7 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
73 79 
 the input is a \code{matrix} or \code{numeric} vector.
74 80 
 \item For mean estimates, see \code{\link[MatrixGenerics]{rowMeans2}()} and
75 81 
 \code{\link[base:colSums]{rowMeans}()}.
76 
-\item For non-robust standard deviation estimates, see \code{\link[MatrixGenerics]{rowSds}()}.
82 
+\item For non-robust standard deviation estimates, see
83 
+\code{\link[MatrixGenerics]{rowSds}()}.
77 84 
 }
78 85 
 }
man/colMaxs-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -12,11 +12,13 @@
12 12 
 \arguments{
13 13 
 \item{x}{An NxK matrix-like object.}
14 14
15 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
16 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
15 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
16 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
17 
+subsetting is done.}
17 18
18 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
19 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
19 
+\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
20 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
21 
+subsetting is done.}
20 22
21 23 
 \item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
22 24 
 are excluded first, otherwise not.}
... ... 
@@ -31,8 +33,9 @@ length N (K).
31 33 
 Calculates the maximum for each row (column) of a matrix-like object.
32 34 
 }
33 35 
 \details{
34 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
35 
-\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowMaxs}}
36 
+The S4 methods for \code{x} of type \code{\link[base]{matrix}},
37 
+\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
38 
+\code{matrixStats::\link[matrixStats]{rowMaxs}}
36 39 
 / \code{matrixStats::\link[matrixStats]{colMaxs}}.
37 40 
 }
38 41 
 \examples{
man/colMeans2-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -12,11 +12,13 @@
12 12 
 \arguments{
13 13 
 \item{x}{An NxK matrix-like object.}
14 14
15 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
16 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
15 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
16 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
17 
+subsetting is done.}
17 18
18 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
19 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
19 
+\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
20 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
21 
+subsetting is done.}
20 22
21 23 
 \item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
22 24 
 are excluded first, otherwise not.}
... ... 
@@ -31,8 +33,9 @@ length N (K).
31 33 
 Calculates the mean for each row (column) of a matrix-like object.
32 34 
 }
33 35 
 \details{
34 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
35 
-\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowMeans2}}
36 
+The S4 methods for \code{x} of type \code{\link[base]{matrix}},
37 
+\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
38 
+\code{matrixStats::\link[matrixStats]{rowMeans2}}
36 39 
 / \code{matrixStats::\link[matrixStats]{colMeans2}}.
37 40 
 }
38 41 
 \examples{
... ... 
@@ -54,6 +57,6 @@ the input is a \code{matrix} or \code{numeric} vector.
54 57 
 \item See also \code{\link[base:colSums]{rowMeans}()} for the
55 58 
 corresponding function in base R.
56 59 
 \item For variance estimates, see \code{\link[MatrixGenerics]{rowVars}()}.
57 
-\item See also the base R version \link{rowMeans}.
60 
+\item See also the base R version \code{base::\link[base]{rowMeans}()}.
58 61 
 }
59 62 
 }
man/colMedians-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -12,11 +12,13 @@
12 12 
 \arguments{
13 13 
 \item{x}{An NxK matrix-like object.}
14 14
15 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
16 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
15 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
16 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
17 
+subsetting is done.}
17 18
18 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
19 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
19 
+\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
20 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
21 
+subsetting is done.}
20 22
21 23 
 \item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
22 24 
 are excluded first, otherwise not.}
... ... 
@@ -31,8 +33,9 @@ length N (K).
31 33 
 Calculates the median for each row (column) of a matrix-like object.
32 34 
 }
33 35 
 \details{
34 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
35 
-\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowMedians}}
36 
+The S4 methods for \code{x} of type \code{\link[base]{matrix}},
37 
+\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
38 
+\code{matrixStats::\link[matrixStats]{rowMedians}}
36 39 
 / \code{matrixStats::\link[matrixStats]{colMedians}}.
37 40 
 }
38 41 
 \examples{
man/colMins-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -12,11 +12,13 @@
12 12 
 \arguments{
13 13 
 \item{x}{An NxK matrix-like object.}
14 14
15 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
16 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
15 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
16 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
17 
+subsetting is done.}
17 18
18 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
19 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
19 
+\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
20 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
21 
+subsetting is done.}
20 22
21 23 
 \item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
22 24 
 are excluded first, otherwise not.}
... ... 
@@ -31,8 +33,9 @@ length N (K).
31 33 
 Calculates the minimum for each row (column) of a matrix-like object.
32 34 
 }
33 35 
 \details{
34 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
35 
-\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowMins}}
36 
+The S4 methods for \code{x} of type \code{\link[base]{matrix}},
37 
+\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
38 
+\code{matrixStats::\link[matrixStats]{rowMins}}
36 39 
 / \code{matrixStats::\link[matrixStats]{colMins}}.
37 40 
 }
38 41 
 \examples{
man/colOrderStats-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -12,13 +12,16 @@
12 12 
 \arguments{
13 13 
 \item{x}{An NxK matrix-like object.}
14 14
15 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
16 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
15 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
16 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
17 
+subsetting is done.}
17 18
18 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
19 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
19 
+\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
20 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
21 
+subsetting is done.}
20 22
21 
-\item{which}{An integer index in [1,K] ([1,N]) indicating which order statistic to be returned}
23 
+\item{which}{An integer index in [1,K] ([1,N]) indicating which order
24 
+statistic to be returned}
22 25
23 26 
 \item{na.rm}{If TRUE, NAs are excluded first, otherwise not.}
24 27
... ... 
@@ -29,11 +32,12 @@ Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of
29 32 
 length N (K).
30 33 
 }
31 34 
 \description{
32 
-Calculates an order statistic for each row (column) of a matrix-like object
35 
+Calculates an order statistic for each row (column) of a matrix-like object.
33 36 
 }
34 37 
 \details{
35 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
36 
-\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowOrderStats}}
38 
+The S4 methods for \code{x} of type \code{\link[base]{matrix}},
39 
+\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
40 
+\code{matrixStats::\link[matrixStats]{rowOrderStats}}
37 41 
 / \code{matrixStats::\link[matrixStats]{colOrderStats}}.
38 42 
 }
39 43 
 \examples{
man/colProds-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -12,11 +12,13 @@
12 12 
 \arguments{
13 13 
 \item{x}{An NxK matrix-like object.}
14 14
15 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
16 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
15 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
16 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
17 
+subsetting is done.}
17 18
18 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
19 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
19 
+\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
20 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
21 
+subsetting is done.}
20 22
21 23 
 \item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
22 24 
 are excluded first, otherwise not.}
... ... 
@@ -53,7 +55,8 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
53 55 
 \item \code{matrixStats::\link[matrixStats]{rowProds}()} and
54 56 
 \code{matrixStats::\link[matrixStats]{colProds}()} which are used when
55 57 
 the input is a \code{matrix} or \code{numeric} vector.
56 
-\item For sums across rows (columns), see \code{\link[MatrixGenerics]{rowSums2}()} (\code{\link[MatrixGenerics:colSums2]{colSums2()}})
57 
-\item \code{\link[=prod]{prod()}}
58 
+\item For sums across rows (columns), see
59 
+\code{\link[MatrixGenerics]{rowSums2}()} (\code{\link[MatrixGenerics:colSums2]{colSums2()}})
60 
+\item \code{base::\link[base]{prod}()}.
58 61 
 }
59 62 
 }
man/colQuantiles-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -26,11 +26,13 @@
26 26 
 \arguments{
27 27 
 \item{x}{An NxK matrix-like object.}
28 28
29 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
30 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
29 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
30 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
31 
+subsetting is done.}
31 32
32 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
33 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
33 
+\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
34 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
35 
+subsetting is done.}
34 36
35 37 
 \item{probs}{A numeric vector of J probabilities in [0, 1].}
36 38
... ... 
@@ -38,19 +40,21 @@ columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
38 40 
 are excluded first, otherwise not.}
39 41
40 42 
 \item{drop}{If \code{TRUE} a vector is returned if \code{J == 1}.
41 
-Note, that this is not a generic argument and not all implementation of this function
42 
-have to provide it.}
43 
+Note, that this is not a generic argument and not all implementation of
44 
+this function have to provide it.}
43 45 
 }
44 46 
 \value{
45 
-a \code{\link[base]{numeric}} \code{NxJ} (\code{KxJ}) \code{\link{matrix}}, where
46 
-N (K) is the number of rows (columns) for which the J values are calculated.
47 
+a \code{\link[base]{numeric}} \code{NxJ} (\code{KxJ})
48 
+\code{\link{matrix}}, where N (K) is the number of rows (columns) for
49 
+which the J values are calculated.
47 50 
 }
48 51 
 \description{
49 52 
 Calculates quantiles for each row (column) of a matrix-like object.
50 53 
 }
51 54 
 \details{
52 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
53 
-\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowQuantiles}}
55 
+The S4 methods for \code{x} of type \code{\link[base]{matrix}},
56 
+\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
57 
+\code{matrixStats::\link[matrixStats]{rowQuantiles}}
54 58 
 / \code{matrixStats::\link[matrixStats]{colQuantiles}}.
55 59 
 }
56 60 
 \examples{
man/colRanges-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -3,7 +3,8 @@
3 3 
 \name{colRanges,dgCMatrix-method}
4 4 
 \alias{colRanges,dgCMatrix-method}
5 5 
 \alias{rowRanges,dgCMatrix-method}
6 
-\title{Calculates the minimum and maximum for each row (column) of a matrix-like object}
6 
+\title{Calculates the minimum and maximum for each row (column) of a matrix-like
7 
+object}
7 8 
 \usage{
8 9 
 \S4method{colRanges}{dgCMatrix}(x, rows = NULL, cols = NULL, na.rm = FALSE, ...)
9 10
... ... 
@@ -12,11 +13,13 @@
12 13 
 \arguments{
13 14 
 \item{x}{An NxK matrix-like object.}
14 15
15 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
16 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
16 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
17 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
18 
+subsetting is done.}
17 19
18 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
19 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
20 
+\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
21 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
22 
+subsetting is done.}
20 23
21 24 
 \item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
22 25 
 are excluded first, otherwise not.}
... ... 
@@ -24,15 +27,18 @@ are excluded first, otherwise not.}
24 27 
 \item{...}{Additional arguments passed to specific methods.}
25 28 
 }
26 29 
 \value{
27 
-a \code{\link[base]{numeric}} \code{Nx2} (\code{Kx2}) \code{\link{matrix}}, where
28 
-N (K) is the number of rows (columns) for which the ranges are calculated.
30 
+a \code{\link[base]{numeric}} \code{Nx2} (\code{Kx2})
31 
+\code{\link{matrix}}, where N (K) is the number of rows (columns) for
32 
+which the ranges are calculated.
29 33 
 }
30 34 
 \description{
31 
-Calculates the minimum and maximum for each row (column) of a matrix-like object.
35 
+Calculates the minimum and maximum for each row (column) of a matrix-like
36 
+object.
32 37 
 }
33 38 
 \details{
34 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
35 
-\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowRanges}}
39 
+The S4 methods for \code{x} of type \code{\link[base]{matrix}},
40 
+\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
41 
+\code{matrixStats::\link[matrixStats]{rowRanges}}
36 42 
 / \code{matrixStats::\link[matrixStats]{colRanges}}.
37 43 
 }
38 44 
 \examples{
... ... 
@@ -53,6 +59,6 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
53 59 
 the input is a \code{matrix} or \code{numeric} vector.
54 60 
 \item For max estimates, see \code{\link[MatrixGenerics]{rowMaxs}()}.
55 61 
 \item For min estimates, see \code{\link[MatrixGenerics]{rowMins}()}.
56 
-\item \link{range}
62 
+\item \code{base::\link[base]{range}()}.
57 63 
 }
58 64 
 }
man/colRanks-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -3,7 +3,8 @@
3 3 
 \name{colRanks,dgCMatrix-method}
4 4 
 \alias{colRanks,dgCMatrix-method}
5 5 
 \alias{rowRanks,dgCMatrix-method}
6 
-\title{Calculates the rank of the elements for each row (column) of a matrix-like object}
6 
+\title{Calculates the rank of the elements for each row (column) of a matrix-like
7 
+object}
7 8 
 \usage{
8 9 
 \S4method{colRanks}{dgCMatrix}(
9 10 
   x,
... ... 
@@ -28,14 +29,17 @@
28 29 
 \arguments{
29 30 
 \item{x}{An NxK matrix-like object.}
30 31
31 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
32 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
32 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
33 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
34 
+subsetting is done.}
33 35
34 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
35 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
36 
+\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
37 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
38 
+subsetting is done.}
36 39
37 
-\item{ties.method}{A character string specifying how ties are treated. Note that the default specifies
38 
-fewer options than the original matrixStats package.}
40 
+\item{ties.method}{A character string specifying how ties are treated. Note
41 
+that the default specifies fewer options than the original matrixStats
42 
+package.}
39 43
40 44 
 \item{preserve.shape}{a boolean that specifies if the returned matrix has the same
41 45 
 dimensions as the input matrix. By default this is true for `rowRanks()`, but false for
... ... 
@@ -47,12 +51,14 @@ dimensions as the input matrix. By default this is true for `rowRanks()`, but fa
47 51 
 \item{...}{Additional arguments passed to specific methods.}
48 52 
 }
49 53 
 \value{
50 
-a matrix of type \code{\link[base]{integer}} is returned unless \code{ties.method = "average"}. It
51 
-has dimensions` \code{NxJ} (\code{KxJ}) \code{\link{matrix}}, where
52 
-N (K) is the number of rows (columns) of the input x.
54 
+a matrix of type \code{\link[base]{integer}} is returned unless
55 
+\code{ties.method = "average"}. Ithas dimensions` \code{NxJ} (\code{KxJ})
56 
+\code{\link{matrix}}, where N (K) is the number of rows (columns) of the
57 
+input x.
53 58 
 }
54 59 
 \description{
55 
-Calculates the rank of the elements for each row (column) of a matrix-like object
60 
+Calculates the rank of the elements for each row (column) of a matrix-like
61 
+object.
56 62 
 }
57 63 
 \details{
58 64 
 There are three different methods available for handling ties:
man/colSdDiffs-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -3,7 +3,8 @@
3 3 
 \name{colSdDiffs,dgCMatrix-method}
4 4 
 \alias{colSdDiffs,dgCMatrix-method}
5 5 
 \alias{rowSdDiffs,dgCMatrix-method}
6 
-\title{Calculates the standard deviation of the difference between each element of a row (column) of a matrix-like object}
6 
+\title{Calculates the standard deviation of the difference between each element of
7 
+a row (column) of a matrix-like object}
7 8 
 \usage{
8 9 
 \S4method{colSdDiffs}{dgCMatrix}(
9 10 
   x,
... ... 
@@ -28,19 +29,21 @@
28 29 
 \arguments{
29 30 
 \item{x}{An NxK matrix-like object.}
30 31
31 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
32 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
32 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
33 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
34 
+subsetting is done.}
33 35
34 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
35 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
36 
+\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
37 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
38 
+subsetting is done.}
36 39
37 40 
 \item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
38 41 
 are excluded first, otherwise not.}
39 42
40 43 
 \item{diff}{An integer specifying the order of difference.}
41 44
42 
-\item{trim}{A double in [0,1/2] specifying the fraction of observations to be trimmed from
43 
-each end of (sorted) x before estimation.}
45 
+\item{trim}{A double in [0,1/2] specifying the fraction of observations to
46 
+be trimmed from each end of (sorted) x before estimation.}
44 47
45 48 
 \item{...}{Additional arguments passed to specific methods.}
46 49 
 }
... ... 
@@ -49,11 +52,13 @@ Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of
49 52 
 length N (K).
50 53 
 }
51 54 
 \description{
52 
-Calculates the standard deviation of the difference between each element of a row (column) of a matrix-like object
55 
+Calculates the standard deviation of the difference between each element of
56 
+a row (column) of a matrix-like object.
53 57 
 }
54 58 
 \details{
55 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
56 
-\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowSdDiffs}}
59 
+The S4 methods for \code{x} of type \code{\link[base]{matrix}},
60 
+\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
61 
+\code{matrixStats::\link[matrixStats]{rowSdDiffs}}
57 62 
 / \code{matrixStats::\link[matrixStats]{colSdDiffs}}.
58 63 
 }
59 64 
 \examples{
man/colSds-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -3,7 +3,8 @@
3 3 
 \name{colSds,dgCMatrix-method}
4 4 
 \alias{colSds,dgCMatrix-method}
5 5 
 \alias{rowSds,dgCMatrix-method}
6 
-\title{Calculates the standard deviation for each row (column) of a matrix-like object}
6 
+\title{Calculates the standard deviation for each row (column) of a matrix-like
7 
+object}
7 8 
 \usage{
8 9 
 \S4method{colSds}{dgCMatrix}(x, rows = NULL, cols = NULL, na.rm = FALSE, center = NULL, ...)
9 10
... ... 
@@ -12,11 +13,13 @@
12 13 
 \arguments{
13 14 
 \item{x}{An NxK matrix-like object.}
14 15
15 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
16 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
16 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
17 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
18 
+subsetting is done.}
17 19
18 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
19 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
20 
+\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
21 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
22 
+subsetting is done.}
20 23
21 24 
 \item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
22 25 
 are excluded first, otherwise not.}
... ... 
@@ -30,11 +33,13 @@ Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of
30 33 
 length N (K).
31 34 
 }
32 35 
 \description{
33 
-Calculates the standard deviation for each row (column) of a matrix-like object.
36 
+Calculates the standard deviation for each row (column) of a matrix-like
37 
+object.
34 38 
 }
35 39 
 \details{
36 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
37 
-\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowSds}}
40 
+The S4 methods for \code{x} of type \code{\link[base]{matrix}},
41 
+\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
42 
+\code{matrixStats::\link[matrixStats]{rowSds}}
38 43 
 / \code{matrixStats::\link[matrixStats]{colSds}}.
39 44 
 }
40 45 
 \examples{
man/colSums2-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -12,11 +12,13 @@
12 12 
 \arguments{
13 13 
 \item{x}{An NxK matrix-like object.}
14 14
15 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
16 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
15 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
16 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
17 
+subsetting is done.}
17 18
18 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
19 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
19 
+\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
20 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
21 
+subsetting is done.}
20 22
21 23 
 \item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
22 24 
 are excluded first, otherwise not.}
... ... 
@@ -31,8 +33,9 @@ length N (K).
31 33 
 Calculates the sum for each row (column) of a matrix-like object.
32 34 
 }
33 35 
 \details{
34 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
35 
-\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowSums2}}
36 
+The S4 methods for \code{x} of type \code{\link[base]{matrix}},
37 
+\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
38 
+\code{matrixStats::\link[matrixStats]{rowSums2}}
36 39 
 / \code{matrixStats::\link[matrixStats]{colSums2}}.
37 40 
 }
38 41 
 \examples{
... ... 
@@ -53,7 +56,6 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
53 56 
 the input is a \code{matrix} or \code{numeric} vector.
54 57 
 \item For mean estimates, see \code{\link[MatrixGenerics]{rowMeans2}()} and
55 58 
 \code{\link[base:colSums]{rowMeans}()}.
56 
-
57 
-\item \link{sum}
59 
+\item \code{base::\link[base]{sum}()}.
58 60 
 }
59 61 
 }
man/colTabulates-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -12,26 +12,30 @@
12 12 
 \arguments{
13 13 
 \item{x}{An NxK matrix-like object.}
14 14
15 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
16 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
15 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
16 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
17 
+subsetting is done.}
17 18
18 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
19 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
19 
+\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
20 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
21 
+subsetting is done.}
20 22
21 23 
 \item{values}{the values to search for.}
22 24
23 25 
 \item{...}{Additional arguments passed to specific methods.}
24 26 
 }
25 27 
 \value{
26 
-a \code{\link[base]{numeric}} \code{NxJ} (\code{KxJ}) \code{\link{matrix}}, where
27 
-N (K) is the number of rows (columns) for which the J values are calculated.
28 
+a \code{\link[base]{numeric}} \code{NxJ} (\code{KxJ})
29 
+\code{\link{matrix}}, where N (K) is the number of rows (columns) for
30 
+which the J values are calculated.
28 31 
 }
29 32 
 \description{
30 
-Tabulates the values in a matrix-like object by row (column)
33 
+Tabulates the values in a matrix-like object by row (column).
31 34 
 }
32 35 
 \details{
33 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
34 
-\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowTabulates}}
36 
+The S4 methods for \code{x} of type \code{\link[base]{matrix}},
37 
+\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
38 
+\code{matrixStats::\link[matrixStats]{rowTabulates}}
35 39 
 / \code{matrixStats::\link[matrixStats]{colTabulates}}.
36 40 
 }
37 41 
 \examples{
man/colVarDiffs-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -3,7 +3,8 @@
3 3 
 \name{colVarDiffs,dgCMatrix-method}
4 4 
 \alias{colVarDiffs,dgCMatrix-method}
5 5 
 \alias{rowVarDiffs,dgCMatrix-method}
6 
-\title{Calculates the variance of the difference between each element of a row (column) of a matrix-like object}
6 
+\title{Calculates the variance of the difference between each element of a row
7 
+(column) of a matrix-like object}
7 8 
 \usage{
8 9 
 \S4method{colVarDiffs}{dgCMatrix}(
9 10 
   x,
... ... 
@@ -28,19 +29,21 @@
28 29 
 \arguments{
29 30 
 \item{x}{An NxK matrix-like object.}
30 31
31 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
32 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
32 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
33 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
34 
+subsetting is done.}
33 35
34 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
35 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}