1. sparseMatrixStats
  2. Commit 7f055a6a495fecadc68c84ec91fd31838396c864
Browse code

Bring documentation in line with updates from MatrixGenerics

See https://github.com/Bioconductor/MatrixGenerics/issues/11
for more information

const-ae authored on 24/04/2020 07:36:21
Showing 36 changed files
man/colAlls-dgCMatrix-method.Rd
History View file @ 7f055a6
... ... 
@@ -13,32 +13,31 @@ a value}
13 13 
 \arguments{
14 14 
 \item{x}{An NxK matrix-like object.}
15 15
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.}
16 
+\item{rows}{A \code{\link{vector}} indicating the subset of rows
17 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
18 
+done.}
19 19
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 
+\item{cols}{A \code{\link{vector}} indicating the subset of rows
21 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
22 
+done.}
23 23
24 24 
 \item{value}{The value to search for.}
25 25
26 
-\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
26 
+\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link{NA}}s
27 27 
 are excluded first, otherwise not.}
28 28 
 }
29 29 
 \value{
30 
-Returns a \code{\link[base]{logical}} \code{\link[base]{vector}} of
31 
-length N (K).
30 
+Returns a \code{\link{logical}} \code{\link{vector}} of length N (K).
32 31 
 }
33 32 
 \description{
34 33 
 Check if all elements in a row (column) of a matrix-like object are equal to
35 34 
 a value.
36 35 
 }
37 36 
 \details{
38 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}},
39 
-\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
37 
+The S4 methods for \code{x} of type \code{\link{matrix}},
38 
+\code{\link{array}}, or \code{\link{numeric}} call
40 39 
 \code{matrixStats::\link[matrixStats]{rowAlls}}
41 
-/ \code{matrixStats::\link[matrixStats]{colAlls}}.
40 
+/ \code{matrixStats::\link[matrixStats:rowAlls]{colAlls}}.
42 41 
 }
43 42 
 \examples{
44 43 
 mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
... ... 
@@ -54,11 +53,11 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
54 53 
 \seealso{
55 54 
 \itemize{
56 55 
 \item \code{matrixStats::\link[matrixStats]{rowAlls}()} and
57 
-\code{matrixStats::\link[matrixStats]{colAlls}()} which are used when
58 
-the input is a \code{\link[base]{matrix}}, \code{\link[base]{array}}, or
59 
-\code{\link[base]{numeric}} vector.
56 
+\code{matrixStats::\link[matrixStats:rowAlls]{colAlls}()} which are used
57 
+when the input is a \code{\link{matrix}}, \code{\link{array}},
58 
+or \code{\link{numeric}} vector.
60 59 
 \item For checks if \emph{any} element is equal to a value, see
61 60 
 \code{\link[MatrixGenerics]{rowAnys}()}.
62 
-\item \code{base::\link[base]{all}()}.
61 
+\item \code{base::\link{all}()}.
63 62 
 }
64 63 
 }
man/colAnyNAs-dgCMatrix-method.Rd
History View file @ 7f055a6
... ... 
@@ -12,26 +12,25 @@
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 of rows
16 
-(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
17 
-subsetting is done.}
15 
+\item{rows}{A \code{\link{vector}} indicating the subset of rows
16 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
17 
+done.}
18 18
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.}
19 
+\item{cols}{A \code{\link{vector}} indicating the subset of rows
20 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
21 
+done.}
22 22 
 }
23 23 
 \value{
24 
-Returns a \code{\link[base]{logical}} \code{\link[base]{vector}} of
25 
-length N (K).
24 
+Returns a \code{\link{logical}} \code{\link{vector}} of length N (K).
26 25 
 }
27 26 
 \description{
28 27 
 Check if any elements in a row (column) of a matrix-like object is missing.
29 28 
 }
30 29 
 \details{
31 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}},
32 
-\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
30 
+The S4 methods for \code{x} of type \code{\link{matrix}},
31 
+\code{\link{array}}, or \code{\link{numeric}} call
33 32 
 \code{matrixStats::\link[matrixStats]{rowAnyNAs}}
34 
-/ \code{matrixStats::\link[matrixStats]{colAnyNAs}}.
33 
+/ \code{matrixStats::\link[matrixStats:rowAnyNAs]{colAnyNAs}}.
35 34 
 }
36 35 
 \examples{
37 36 
   mat <- matrix(0, nrow=10, ncol=5)
... ... 
@@ -43,10 +42,10 @@ The S4 methods for \code{x} of type \code{\link[base]{matrix}},
43 42 
 \seealso{
44 43 
 \itemize{
45 44 
 \item \code{matrixStats::\link[matrixStats]{rowAnyNAs}()} and
46 
-\code{matrixStats::\link[matrixStats]{colAnyNAs}()} which are used when
47 
-the input is a \code{matrix} or \code{numeric} vector.
45 
+\code{matrixStats::\link[matrixStats:rowAnyNAs]{colAnyNAs}()} which are
46 
+used when the input is a \code{matrix} or \code{numeric} vector.
48 47 
 \item For checks if any element is equal to a value, see
49 48 
 \code{\link[MatrixGenerics]{rowAnys}()}.
50 
-\item \code{base::\link[base]{is.na}()} and \code{base::\link[base]{any}()}.
49 
+\item \code{base::\link{is.na}()} and \code{base::\link{any}()}.
51 50 
 }
52 51 
 }
man/colAnys-dgCMatrix-method.Rd
History View file @ 7f055a6
... ... 
@@ -13,32 +13,31 @@ a value}
13 13 
 \arguments{
14 14 
 \item{x}{An NxK matrix-like object.}
15 15
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.}
16 
+\item{rows}{A \code{\link{vector}} indicating the subset of rows
17 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
18 
+done.}
19 19
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 
+\item{cols}{A \code{\link{vector}} indicating the subset of rows
21 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
22 
+done.}
23 23
24 24 
 \item{value}{The value to search for.}
25 25
26 
-\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
26 
+\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link{NA}}s
27 27 
 are excluded first, otherwise not.}
28 28 
 }
29 29 
 \value{
30 
-Returns a \code{\link[base]{logical}} \code{\link[base]{vector}} of
31 
-length N (K).
30 
+Returns a \code{\link{logical}} \code{\link{vector}} of length N (K).
32 31 
 }
33 32 
 \description{
34 33 
 Check if any elements in a row (column) of a matrix-like object is equal to
35 34 
 a value.
36 35 
 }
37 36 
 \details{
38 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}},
39 
-\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
37 
+The S4 methods for \code{x} of type \code{\link{matrix}},
38 
+\code{\link{array}}, or \code{\link{numeric}} call
40 39 
 \code{matrixStats::\link[matrixStats]{rowAnys}}
41 
-/ \code{matrixStats::\link[matrixStats]{colAnys}}.
40 
+/ \code{matrixStats::\link[matrixStats:rowAnys]{colAnys}}.
42 41 
 }
43 42 
 \examples{
44 43 
 mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
... ... 
@@ -54,8 +53,8 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
54 53 
 \seealso{
55 54 
 \itemize{
56 55 
 \item \code{matrixStats::\link[matrixStats]{rowAnys}()} and
57 
-\code{matrixStats::\link[matrixStats]{colAnys}()} which are used when
58 
-the input is a \code{matrix} or \code{numeric} vector.
59 
-\item \code{base::\link[base]{any}()}.
56 
+\code{matrixStats::\link[matrixStats:rowAnys]{colAnys}()} which are used
57 
+when the input is a \code{matrix} or \code{numeric} vector.
58 
+\item \code{base::\link{any}()}.
60 59 
 }
61 60 
 }
man/colAvgsPerRowSet-dgCMatrix-method.Rd
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... ... 
@@ -31,8 +31,8 @@
31 31
32 32 
 \item{W}{An optional numeric \code{NxM} matrix of weights.}
33 33
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
34 
+\item{cols}{A \code{\link{vector}} indicating the subset (and/or
35 
+columns) to operate over. If \code{\link{NULL}}, no subsetting is
36 36 
 done.}
37 37
38 38 
 \item{S}{An \link{integer} \code{KxJ} matrix that specifying the \code{J} subsets. Each
... ... 
@@ -46,8 +46,8 @@ applied to to each column (row) subset of \code{X} that is specified by \code{S}
46 46
47 47 
 \item{tFUN}{If \code{TRUE}, \code{X} is transposed before it is passed to \code{FUN}.}
48 48
49 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
50 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is
49 
+\item{rows}{A \code{\link{vector}} indicating the subset (and/or
50 
+columns) to operate over. If \code{\link{NULL}}, no subsetting is
51 51 
 done.}
52 52 
 }
53 53 
 \value{
... ... 
@@ -79,7 +79,7 @@ mat <- matrix(rnorm(20), nrow = 5, ncol = 4)
79 79 
 \seealso{
80 80 
 \itemize{
81 81 
 \item \code{matrixStats::\link[matrixStats]{rowAvgsPerColSet}()} and
82 
-\code{matrixStats::\link[matrixStats]{colAvgsPerRowSet}()} which are used
83 
-when the input is a \code{matrix} or \code{numeric} vector.
82 
+\code{matrixStats::\link[matrixStats:rowAvgsPerColSet]{colAvgsPerRowSet}()}
83 
+which are used when the input is a \code{matrix} or \code{numeric} vector.
84 84 
 }
85 85 
 }
man/colCollapse-dgCMatrix-method.Rd
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... ... 
@@ -12,29 +12,28 @@
12 12 
 \arguments{
13 13 
 \item{x}{An NxK matrix-like object.}
14 14
15 
-\item{idxs}{An index \code{\link[base]{vector}} with the position to extract.
15 
+\item{idxs}{An index \code{\link{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 of rows
19 
-(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
20 
-subsetting is done.}
18 
+\item{cols}{A \code{\link{vector}} indicating the subset of rows
19 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
20 
+done.}
21 21
22 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
23 
-(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
24 
-subsetting is done.}
22 
+\item{rows}{A \code{\link{vector}} indicating the subset of rows
23 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
24 
+done.}
25 25 
 }
26 26 
 \value{
27 
-Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of
28 
-length N (K).
27 
+Returns a \code{\link{numeric}} \code{\link{vector}} of length N (K).
29 28 
 }
30 29 
 \description{
31 30 
 Extract one cell from each row (column) of a matrix-like object.
32 31 
 }
33 32 
 \details{
34 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}},
35 
-\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
33 
+The S4 methods for \code{x} of type \code{\link{matrix}},
34 
+\code{\link{array}}, or \code{\link{numeric}} call
36 35 
 \code{matrixStats::\link[matrixStats]{rowCollapse}}
37 
-/ \code{matrixStats::\link[matrixStats]{colCollapse}}.
36 
+/ \code{matrixStats::\link[matrixStats:rowCollapse]{colCollapse}}.
38 37 
 }
39 38 
 \examples{
40 39 
 mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
... ... 
@@ -52,7 +51,7 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
52 51 
 \seealso{
53 52 
 \itemize{
54 53 
 \item \code{matrixStats::\link[matrixStats]{rowCollapse}()} and
55 
-\code{matrixStats::\link[matrixStats]{colCollapse}()} which are used when
56 
-the input is a \code{matrix} or \code{numeric} vector.
54 
+\code{matrixStats::\link[matrixStats:rowCollapse]{colCollapse}()}
55 
+which are used when the input is a \code{matrix} or \code{numeric} vector.
57 56 
 }
58 57 
 }
man/colCounts-dgCMatrix-method.Rd
History View file @ 7f055a6
... ... 
@@ -13,32 +13,31 @@ equal to a value}
13 13 
 \arguments{
14 14 
 \item{x}{An NxK matrix-like object.}
15 15
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.}
16 
+\item{rows}{A \code{\link{vector}} indicating the subset of rows
17 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
18 
+done.}
19 19
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 
+\item{cols}{A \code{\link{vector}} indicating the subset of rows
21 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
22 
+done.}
23 23
24 24 
 \item{value}{The value to search for.}
25 25
26 
-\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
26 
+\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link{NA}}s
27 27 
 are excluded first, otherwise not.}
28 28 
 }
29 29 
 \value{
30 
-Returns a \code{\link[base]{integer}} \code{\link[base]{vector}} of
31 
-length N (K).
30 
+Returns a \code{\link{integer}} \code{\link{vector}} of length N (K).
32 31 
 }
33 32 
 \description{
34 33 
 Count how often an element in a row (column) of a matrix-like object is
35 34 
 equal to a value.
36 35 
 }
37 36 
 \details{
38 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}},
39 
-\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
37 
+The S4 methods for \code{x} of type \code{\link{matrix}},
38 
+\code{\link{array}}, or \code{\link{numeric}} call
40 39 
 \code{matrixStats::\link[matrixStats]{rowCounts}}
41 
-/ \code{matrixStats::\link[matrixStats]{colCounts}}.
40 
+/ \code{matrixStats::\link[matrixStats:rowCounts]{colCounts}}.
42 41 
 }
43 42 
 \examples{
44 43 
 mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
... ... 
@@ -57,8 +56,8 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
57 56 
 \seealso{
58 57 
 \itemize{
59 58 
 \item \code{matrixStats::\link[matrixStats]{rowCounts}()} and
60 
-\code{matrixStats::\link[matrixStats]{colCounts}()} which are used when
61 
-the input is a \code{matrix} or \code{numeric} vector.
59 
+\code{matrixStats::\link[matrixStats:rowCounts]{colCounts}()} which are
60 
+used when the input is a \code{matrix} or \code{numeric} vector.
62 61 
 \item For checks if any element is equal to a value, see
63 62 
 \code{\link[MatrixGenerics]{rowAnys}()}. To check if all elements are equal, see
64 63 
 \code{\link[MatrixGenerics]{rowAlls}()}.
man/colCummaxs-dgCMatrix-method.Rd
History View file @ 7f055a6
... ... 
@@ -13,27 +13,27 @@ object}
13 13 
 \arguments{
14 14 
 \item{x}{An NxK matrix-like object.}
15 15
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.}
16 
+\item{rows}{A \code{\link{vector}} indicating the subset of rows
17 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
18 
+done.}
19 19
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 
+\item{cols}{A \code{\link{vector}} indicating the subset of rows
21 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
22 
+done.}
23 23 
 }
24 24 
 \value{
25 
-Returns a \code{\link[base]{numeric}} \code{\link[base]{matrix}}
26 
-with the same dimensions as \code{x}.
25 
+Returns a \code{\link{numeric}} \code{\link{matrix}}with the same
26 
+dimensions as \code{x}.
27 27 
 }
28 28 
 \description{
29 29 
 Calculates the cumulative maxima for each row (column) of a matrix-like
30 30 
 object.
31 31 
 }
32 32 
 \details{
33 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}},
34 
-\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
33 
+The S4 methods for \code{x} of type \code{\link{matrix}},
34 
+\code{\link{array}}, or \code{\link{numeric}} call
35 35 
 \code{matrixStats::\link[matrixStats]{rowCummaxs}}
36 
-/ \code{matrixStats::\link[matrixStats]{colCummaxs}}.
36 
+/ \code{matrixStats::\link[matrixStats:rowCummaxs]{colCummaxs}}.
37 37 
 }
38 38 
 \examples{
39 39 
 mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
... ... 
@@ -49,9 +49,9 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
49 49 
 \seealso{
50 50 
 \itemize{
51 51 
 \item \code{matrixStats::\link[matrixStats]{rowCummaxs}()} and
52 
-\code{matrixStats::\link[matrixStats]{colCummaxs}()} which are used when
53 
-the input is a \code{matrix} or \code{numeric} vector.
52 
+\code{matrixStats::\link[matrixStats:rowCummaxs]{colCummaxs}()} which are
53 
+used when the input is a \code{matrix} or \code{numeric} vector.
54 54 
 \item For single maximum estimates, see \code{\link[MatrixGenerics]{rowMaxs}()}.
55 
-\item \code{base::\link[base]{cummax}()}.
55 
+\item \code{base::\link{cummax}()}.
56 56 
 }
57 57 
 }
man/colCummins-dgCMatrix-method.Rd
History View file @ 7f055a6
... ... 
@@ -13,27 +13,27 @@ object}
13 13 
 \arguments{
14 14 
 \item{x}{An NxK matrix-like object.}
15 15
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.}
16 
+\item{rows}{A \code{\link{vector}} indicating the subset of rows
17 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
18 
+done.}
19 19
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 
+\item{cols}{A \code{\link{vector}} indicating the subset of rows
21 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
22 
+done.}
23 23 
 }
24 24 
 \value{
25 
-Returns a \code{\link[base]{numeric}} \code{\link[base]{matrix}}
26 
-with the same dimensions as \code{x}.
25 
+Returns a \code{\link{numeric}} \code{\link{matrix}}with the same
26 
+dimensions as \code{x}.
27 27 
 }
28 28 
 \description{
29 29 
 Calculates the cumulative minima for each row (column) of a matrix-like
30 30 
 object.
31 31 
 }
32 32 
 \details{
33 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}},
34 
-\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
33 
+The S4 methods for \code{x} of type \code{\link{matrix}},
34 
+\code{\link{array}}, or \code{\link{numeric}} call
35 35 
 \code{matrixStats::\link[matrixStats]{rowCummins}}
36 
-/ \code{matrixStats::\link[matrixStats]{colCummins}}.
36 
+/ \code{matrixStats::\link[matrixStats:rowCummins]{colCummins}}.
37 37 
 }
38 38 
 \examples{
39 39 
 mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
... ... 
@@ -49,9 +49,9 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
49 49 
 \seealso{
50 50 
 \itemize{
51 51 
 \item \code{matrixStats::\link[matrixStats]{rowCummins}()} and
52 
-\code{matrixStats::\link[matrixStats]{colCummins}()} which are used when
53 
-the input is a \code{matrix} or \code{numeric} vector.
52 
+\code{matrixStats::\link[matrixStats:rowCummins]{colCummins}()} which are
53 
+used when the input is a \code{matrix} or \code{numeric} vector.
54 54 
 \item For single minimum estimates, see \code{\link[MatrixGenerics]{rowMins}()}.
55 
-\item \code{base::\link[base]{cummin}()}.
55 
+\item \code{base::\link{cummin}()}.
56 56 
 }
57 57 
 }
man/colCumprods-dgCMatrix-method.Rd
History View file @ 7f055a6
... ... 
@@ -13,27 +13,27 @@ object}
13 13 
 \arguments{
14 14 
 \item{x}{An NxK matrix-like object.}
15 15
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.}
16 
+\item{rows}{A \code{\link{vector}} indicating the subset of rows
17 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
18 
+done.}
19 19
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 
+\item{cols}{A \code{\link{vector}} indicating the subset of rows
21 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
22 
+done.}
23 23 
 }
24 24 
 \value{
25 
-Returns a \code{\link[base]{numeric}} \code{\link[base]{matrix}}
26 
-with the same dimensions as \code{x}.
25 
+Returns a \code{\link{numeric}} \code{\link{matrix}}with the same
26 
+dimensions as \code{x}.
27 27 
 }
28 28 
 \description{
29 29 
 Calculates the cumulative product for each row (column) of a matrix-like
30 30 
 object.
31 31 
 }
32 32 
 \details{
33 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}},
34 
-\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
33 
+The S4 methods for \code{x} of type \code{\link{matrix}},
34 
+\code{\link{array}}, or \code{\link{numeric}} call
35 35 
 \code{matrixStats::\link[matrixStats]{rowCumprods}}
36 
-/ \code{matrixStats::\link[matrixStats]{colCumprods}}.
36 
+/ \code{matrixStats::\link[matrixStats:rowCumprods]{colCumprods}}.
37 37 
 }
38 38 
 \examples{
39 39 
 mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
... ... 
@@ -49,8 +49,8 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
49 49 
 \seealso{
50 50 
 \itemize{
51 51 
 \item \code{matrixStats::\link[matrixStats]{rowCumprods}()} and
52 
-\code{matrixStats::\link[matrixStats]{colCumprods}()} which are used when
53 
-the input is a \code{matrix} or \code{numeric} vector.
54 
-\item \code{base::\link[base]{cumprod}()}.
52 
+\code{matrixStats::\link[matrixStats:rowCumprods]{colCumprods}()} which
53 
+are used when the input is a \code{matrix} or \code{numeric} vector.
54 
+\item \code{base::\link{cumprod}()}.
55 55 
 }
56 56 
 }
man/colCumsums-dgCMatrix-method.Rd
History View file @ 7f055a6
... ... 
@@ -12,26 +12,26 @@
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 of rows
16 
-(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
17 
-subsetting is done.}
15 
+\item{rows}{A \code{\link{vector}} indicating the subset of rows
16 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
17 
+done.}
18 18
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.}
19 
+\item{cols}{A \code{\link{vector}} indicating the subset of rows
20 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
21 
+done.}
22 22 
 }
23 23 
 \value{
24 
-Returns a \code{\link[base]{numeric}} \code{\link[base]{matrix}}
25 
-with the same dimensions as \code{x}.
24 
+Returns a \code{\link{numeric}} \code{\link{matrix}}with the same
25 
+dimensions as \code{x}.
26 26 
 }
27 27 
 \description{
28 28 
 Calculates the cumulative sum for each row (column) of a matrix-like object.
29 29 
 }
30 30 
 \details{
31 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}},
32 
-\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
31 
+The S4 methods for \code{x} of type \code{\link{matrix}},
32 
+\code{\link{array}}, or \code{\link{numeric}} call
33 33 
 \code{matrixStats::\link[matrixStats]{rowCumsums}}
34 
-/ \code{matrixStats::\link[matrixStats]{colCumsums}}.
34 
+/ \code{matrixStats::\link[matrixStats:rowCumsums]{colCumsums}}.
35 35 
 }
36 36 
 \examples{
37 37 
 mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
... ... 
@@ -47,8 +47,8 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
47 47 
 \seealso{
48 48 
 \itemize{
49 49 
 \item \code{matrixStats::\link[matrixStats]{rowCumsums}()} and
50 
-\code{matrixStats::\link[matrixStats]{colCumsums}()} which are used when
51 
-the input is a \code{matrix} or \code{numeric} vector.
52 
-\item \code{base::\link[base]{cumsum}()}.
50 
+\code{matrixStats::\link[matrixStats:rowCumsums]{colCumsums}()} which are
51 
+used when the input is a \code{matrix} or \code{numeric} vector.
52 
+\item \code{base::\link{cumsum}()}.
53 53 
 }
54 54 
 }
man/colDiffs-dgCMatrix-method.Rd
History View file @ 7f055a6
... ... 
@@ -13,31 +13,31 @@ matrix-like object}
13 13 
 \arguments{
14 14 
 \item{x}{An NxK matrix-like object.}
15 15
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.}
16 
+\item{rows}{A \code{\link{vector}} indicating the subset of rows
17 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
18 
+done.}
19 19
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 
+\item{cols}{A \code{\link{vector}} indicating the subset of rows
21 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
22 
+done.}
23 23
24 24 
 \item{lag}{An integer specifying the lag.}
25 25
26 26 
 \item{differences}{An integer specifying the order of difference.}
27 27 
 }
28 28 
 \value{
29 
-Returns a \code{\link[base]{numeric}} \code{\link[base]{matrix}}
30 
-with one column (row) less than x: \eqn{Nx(K-1)} or \eqn{(N-1)xK}.
29 
+Returns a \code{\link{numeric}} \code{\link{matrix}} with one column
30 
+(row) less than x: \eqn{Nx(K-1)} or \eqn{(N-1)xK}.
31 31 
 }
32 32 
 \description{
33 33 
 Calculates the difference between each element of a row (column) of a
34 34 
 matrix-like object.
35 35 
 }
36 36 
 \details{
37 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}},
38 
-\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
37 
+The S4 methods for \code{x} of type \code{\link{matrix}},
38 
+\code{\link{array}}, or \code{\link{numeric}} call
39 39 
 \code{matrixStats::\link[matrixStats]{rowDiffs}}
40 
-/ \code{matrixStats::\link[matrixStats]{colDiffs}}.
40 
+/ \code{matrixStats::\link[matrixStats:rowDiffs]{colDiffs}}.
41 41 
 }
42 42 
 \examples{
43 43 
 mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
... ... 
@@ -53,8 +53,8 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
53 53 
 \seealso{
54 54 
 \itemize{
55 55 
 \item \code{matrixStats::\link[matrixStats]{rowDiffs}()} and
56 
-\code{matrixStats::\link[matrixStats]{colDiffs}()} which are used when
57 
-the input is a \code{matrix} or \code{numeric} vector.
58 
-\item \code{base::\link[base]{diff}()}.
56 
+\code{matrixStats::\link[matrixStats:rowDiffs]{colDiffs}()} which are used
57 
+when the input is a \code{matrix} or \code{numeric} vector.
58 
+\item \code{base::\link{diff}()}.
59 59 
 }
60 60 
 }
man/colIQRDiffs-dgCMatrix-method.Rd
History View file @ 7f055a6
... ... 
@@ -13,15 +13,15 @@ a row (column) of a matrix-like object}
13 13 
 \arguments{
14 14 
 \item{x}{An NxK matrix-like object.}
15 15
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.}
16 
+\item{rows}{A \code{\link{vector}} indicating the subset of rows
17 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
18 
+done.}
19 19
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 
+\item{cols}{A \code{\link{vector}} indicating the subset of rows
21 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
22 
+done.}
23 23
24 
-\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
24 
+\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link{NA}}s
25 25 
 are excluded first, otherwise not.}
26 26
27 27 
 \item{diff}{An integer specifying the order of difference.}
... ... 
@@ -30,18 +30,17 @@ are excluded first, otherwise not.}
30 30 
 be trimmed from each end of (sorted) x before estimation.}
31 31 
 }
32 32 
 \value{
33 
-Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of
34 
-length N (K).
33 
+Returns a \code{\link{numeric}} \code{\link{vector}} of length N (K).
35 34 
 }
36 35 
 \description{
37 36 
 Calculates the interquartile range of the difference between each element of
38 37 
 a row (column) of a matrix-like object.
39 38 
 }
40 39 
 \details{
41 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}},
42 
-\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
40 
+The S4 methods for \code{x} of type \code{\link{matrix}},
41 
+\code{\link{array}}, or \code{\link{numeric}} call
43 42 
 \code{matrixStats::\link[matrixStats]{rowIQRDiffs}}
44 
-/ \code{matrixStats::\link[matrixStats]{colIQRDiffs}}.
43 
+/ \code{matrixStats::\link[matrixStats:rowIQRDiffs]{colIQRDiffs}}.
45 44 
 }
46 45 
 \examples{
47 46 
 mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
... ... 
@@ -57,8 +56,8 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
57 56 
 \seealso{
58 57 
 \itemize{
59 58 
 \item \code{matrixStats::\link[matrixStats]{rowIQRDiffs}()} and
60 
-\code{matrixStats::\link[matrixStats]{colIQRDiffs}()} which are used when
61 
-the input is a \code{matrix} or \code{numeric} vector.
59 
+\code{matrixStats::\link[matrixStats:rowIQRDiffs]{colIQRDiffs}()} which
60 
+are used when the input is a \code{matrix} or \code{numeric} vector.
62 61 
 \item For the direct interquartile range see also \link[MatrixGenerics]{rowIQRs}.
63 62 
 }
64 63 
 }
man/colIQRs-dgCMatrix-method.Rd
History View file @ 7f055a6
... ... 
@@ -13,30 +13,29 @@ object}
13 13 
 \arguments{
14 14 
 \item{x}{An NxK matrix-like object.}
15 15
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.}
16 
+\item{rows}{A \code{\link{vector}} indicating the subset of rows
17 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
18 
+done.}
19 19
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 
+\item{cols}{A \code{\link{vector}} indicating the subset of rows
21 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
22 
+done.}
23 23
24 
-\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
24 
+\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link{NA}}s
25 25 
 are excluded first, otherwise not.}
26 26 
 }
27 27 
 \value{
28 
-Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of
29 
-length N (K).
28 
+Returns a \code{\link{numeric}} \code{\link{vector}} of length N (K).
30 29 
 }
31 30 
 \description{
32 31 
 Calculates the interquartile range for each row (column) of a matrix-like
33 32 
 object.
34 33 
 }
35 34 
 \details{
36 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}},
37 
-\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
35 
+The S4 methods for \code{x} of type \code{\link{matrix}},
36 
+\code{\link{array}}, or \code{\link{numeric}} call
38 37 
 \code{matrixStats::\link[matrixStats]{rowIQRs}}
39 
-/ \code{matrixStats::\link[matrixStats]{colIQRs}}.
38 
+/ \code{matrixStats::\link[matrixStats:rowIQRs]{colIQRs}}.
40 39 
 }
41 40 
 \examples{
42 41 
 mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
... ... 
@@ -52,8 +51,8 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
52 51 
 \seealso{
53 52 
 \itemize{
54 53 
 \item \code{matrixStats::\link[matrixStats]{rowIQRs}()} and
55 
-\code{matrixStats::\link[matrixStats]{colIQRs}()} which are used when
56 
-the input is a \code{matrix} or \code{numeric} vector.
54 
+\code{matrixStats::\link[matrixStats:rowIQRs]{colIQRs}()} which are used
55 
+when the input is a \code{matrix} or \code{numeric} vector.
57 56 
 \item For a non-robust analog, see \code{\link[MatrixGenerics]{rowSds}()}. For a more
58 57 
 robust version see \code{\link[MatrixGenerics:rowMads]{rowMads()}}
59 58 
 \item \code{stats::\link[stats]{IQR}()}.
man/colLogSumExps-dgCMatrix-method.Rd
History View file @ 7f055a6
... ... 
@@ -13,30 +13,27 @@
13 13 
 \arguments{
14 14 
 \item{lx}{An NxK matrix-like object. Typically \code{lx} are \code{log(x)} values.}
15 15
16 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
17 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is
18 
-done.}
16 
+\item{rows}{A \code{\link{vector}} indicating the subset (and/or
17 
+columns) to operate over. If \code{\link{NULL}}, no subsetting is done.}
19 18
20 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
21 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is
22 
-done.}
19 
+\item{cols}{A \code{\link{vector}} indicating the subset (and/or
20 
+columns) to operate over. If \code{\link{NULL}}, no subsetting is done.}
23 21
24 
-\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
22 
+\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link{NA}}s
25 23 
 are excluded first, otherwise not.}
26 24 
 }
27 25 
 \value{
28 
-Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of
29 
-length N (K).
26 
+Returns a \code{\link{numeric}} \code{\link{vector}} of length N (K).
30 27 
 }
31 28 
 \description{
32 29 
 Accurately calculates the logarithm of the sum of exponentials for each row
33 30 
 (column) of a matrix-like object.
34 31 
 }
35 32 
 \details{
36 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}},
37 
-\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
33 
+The S4 methods for \code{x} of type \code{\link{matrix}},
34 
+\code{\link{array}}, or \code{\link{numeric}} call
38 35 
 \code{matrixStats::\link[matrixStats]{rowLogSumExps}}
39 
-/ \code{matrixStats::\link[matrixStats]{colLogSumExps}}.
36 
+/ \code{matrixStats::\link[matrixStats:rowLogSumExps]{colLogSumExps}}.
40 37 
 }
41 38 
 \examples{
42 39 
 mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
... ... 
@@ -52,8 +49,8 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
52 49 
 \seealso{
53 50 
 \itemize{
54 51 
 \item \code{matrixStats::\link[matrixStats]{rowLogSumExps}()} and
55 
-\code{matrixStats::\link[matrixStats]{colLogSumExps}()} which are used
56 
-when the input is a \code{matrix} or \code{numeric} vector.
52 
+\code{matrixStats::\link[matrixStats:rowLogSumExps]{colLogSumExps}()}
53 
+which are used when the input is a \code{matrix} or \code{numeric} vector.
57 54 
 \item \code{\link[MatrixGenerics:rowSums2]{rowSums2()}}
58 55 
 }
59 56 
 }
man/colMadDiffs-dgCMatrix-method.Rd
History View file @ 7f055a6
... ... 
@@ -29,15 +29,15 @@ element of a row (column) of a matrix-like object}
29 29 
 \arguments{
30 30 
 \item{x}{An NxK matrix-like object.}
31 31
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.}
32 
+\item{rows}{A \code{\link{vector}} indicating the subset of rows
33 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
34 
+done.}
35 35
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 
+\item{cols}{A \code{\link{vector}} indicating the subset of rows
37 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
38 
+done.}
39 39
40 
-\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
40 
+\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link{NA}}s
41 41 
 are excluded first, otherwise not.}
42 42
43 43 
 \item{diff}{An integer specifying the order of difference.}
... ... 
@@ -48,18 +48,17 @@ be trimmed from each end of (sorted) x before estimation.}
48 48 
 \item{constant}{A scale factor. See \code{\link{mad}} for details.}
49 49 
 }
50 50 
 \value{
51 
-Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of
52 
-length N (K).
51 
+Returns a \code{\link{numeric}} \code{\link{vector}} of length N (K).
53 52 
 }
54 53 
 \description{
55 54 
 Calculates the mean absolute deviation of the difference between each
56 55 
 element of a row (column) of a matrix-like object.
57 56 
 }
58 57 
 \details{
59 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}},
60 
-\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
58 
+The S4 methods for \code{x} of type \code{\link{matrix}},
59 
+\code{\link{array}}, or \code{\link{numeric}} call
61 60 
 \code{matrixStats::\link[matrixStats]{rowMadDiffs}}
62 
-/ \code{matrixStats::\link[matrixStats]{colMadDiffs}}.
61 
+/ \code{matrixStats::\link[matrixStats:rowMadDiffs]{colMadDiffs}}.
63 62 
 }
64 63 
 \examples{
65 64 
 mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
... ... 
@@ -75,7 +74,7 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
75 74 
 \seealso{
76 75 
 \itemize{
77 76 
 \item \code{matrixStats::\link[matrixStats]{rowMadDiffs}()} and
78 
-\code{matrixStats::\link[matrixStats]{colMadDiffs}()} which are used when
79 
-the input is a \code{matrix} or \code{numeric} vector.
77 
+\code{matrixStats::\link[matrixStats:rowMadDiffs]{colMadDiffs}()} which
78 
+are used when the input is a \code{matrix} or \code{numeric} vector.
80 79 
 }
81 80 
 }
man/colMads-dgCMatrix-method.Rd
History View file @ 7f055a6
... ... 
@@ -13,33 +13,32 @@ matrix-like object}
13 13 
 \arguments{
14 14 
 \item{x}{An NxK matrix-like object.}
15 15
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.}
16 
+\item{rows}{A \code{\link{vector}} indicating the subset of rows
17 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
18 
+done.}
19 19
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 
+\item{cols}{A \code{\link{vector}} indicating the subset of rows
21 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
22 
+done.}
23 23
24 24 
 \item{constant}{A scale factor. See \code{stats::\link[stats]{mad}()} for
25 25 
 details.}
26 26
27 
-\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
27 
+\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link{NA}}s
28 28 
 are excluded first, otherwise not.}
29 29 
 }
30 30 
 \value{
31 
-Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of
32 
-length N (K).
31 
+Returns a \code{\link{numeric}} \code{\link{vector}} of length N (K).
33 32 
 }
34 33 
 \description{
35 34 
 Calculates the median absolute deviation for each row (column) of a
36 35 
 matrix-like object.
37 36 
 }
38 37 
 \details{
39 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}},
40 
-\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
38 
+The S4 methods for \code{x} of type \code{\link{matrix}},
39 
+\code{\link{array}}, or \code{\link{numeric}} call
41 40 
 \code{matrixStats::\link[matrixStats]{rowMads}}
42 
-/ \code{matrixStats::\link[matrixStats]{colMads}}.
41 
+/ \code{matrixStats::\link[matrixStats:rowMads]{colMads}}.
43 42 
 }
44 43 
 \examples{
45 44 
 mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
... ... 
@@ -55,8 +54,8 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
55 54 
 \seealso{
56 55 
 \itemize{
57 56 
 \item \code{matrixStats::\link[matrixStats]{rowMads}()} and
58 
-\code{matrixStats::\link[matrixStats]{colMads}()} which are used when
59 
-the input is a \code{matrix} or \code{numeric} vector.
57 
+\code{matrixStats::\link[matrixStats:rowMads]{colMads}()} which are used
58 
+when  the input is a \code{matrix} or \code{numeric} vector.
60 59 
 \item For mean estimates, see \code{\link[MatrixGenerics]{rowMeans2}()} and
61 60 
 \code{\link[base:colSums]{rowMeans}()}.
62 61 
 \item For non-robust standard deviation estimates, see
man/colMaxs-dgCMatrix-method.Rd
History View file @ 7f055a6
... ... 
@@ -12,29 +12,28 @@
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 of rows
16 
-(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
17 
-subsetting is done.}
15 
+\item{rows}{A \code{\link{vector}} indicating the subset of rows
16 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
17 
+done.}
18 18
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.}
19 
+\item{cols}{A \code{\link{vector}} indicating the subset of rows
20 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
21 
+done.}
22 22
23 
-\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
23 
+\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link{NA}}s
24 24 
 are excluded first, otherwise not.}
25 25 
 }
26 26 
 \value{
27 
-Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of
28 
-length N (K).
27 
+Returns a \code{\link{numeric}} \code{\link{vector}} of length N (K).
29 28 
 }
30 29 
 \description{
31 30 
 Calculates the maximum for each row (column) of a matrix-like object.
32 31 
 }
33 32 
 \details{
34 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}},
35 
-\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
33 
+The S4 methods for \code{x} of type \code{\link{matrix}},
34 
+\code{\link{array}}, or \code{\link{numeric}} call
36 35 
 \code{matrixStats::\link[matrixStats]{rowMaxs}}
37 
-/ \code{matrixStats::\link[matrixStats]{colMaxs}}.
36 
+/ \code{matrixStats::\link[matrixStats:rowMaxs]{colMaxs}}.
38 37 
 }
39 38 
 \examples{
40 39 
 mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
... ... 
@@ -50,8 +49,8 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
50 49 
 \seealso{
51 50 
 \itemize{
52 51 
 \item \code{matrixStats::\link[matrixStats]{rowMaxs}()} and
53 
-\code{matrixStats::\link[matrixStats]{colMaxs}()} which are used when
54 
-the input is a \code{matrix} or \code{numeric} vector.
52 
+\code{matrixStats::\link[matrixStats:rowMaxs]{colMaxs}()} which are used
53 
+when the input is a \code{matrix} or \code{numeric} vector.
55 54 
 \item For min estimates, see \code{\link[MatrixGenerics]{rowMins}()}.
56 55 
 }
57 56 
 }
man/colMeans2-dgCMatrix-method.Rd
History View file @ 7f055a6
... ... 
@@ -12,29 +12,28 @@
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 of rows
16 
-(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
17 
-subsetting is done.}
15 
+\item{rows}{A \code{\link{vector}} indicating the subset of rows
16 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
17 
+done.}
18 18
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.}
19 
+\item{cols}{A \code{\link{vector}} indicating the subset of rows
20 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
21 
+done.}
22 22
23 
-\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
23 
+\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link{NA}}s
24 24 
 are excluded first, otherwise not.}
25 25 
 }
26 26 
 \value{
27 
-Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of
28 
-length N (K).
27 
+Returns a \code{\link{numeric}} \code{\link{vector}} of length N (K).
29 28 
 }
30 29 
 \description{
31 30 
 Calculates the mean for each row (column) of a matrix-like object.
32 31 
 }
33 32 
 \details{
34 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}},
35 
-\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
33 
+The S4 methods for \code{x} of type \code{\link{matrix}},
34 
+\code{\link{array}}, or \code{\link{numeric}} call
36 35 
 \code{matrixStats::\link[matrixStats]{rowMeans2}}
37 
-/ \code{matrixStats::\link[matrixStats]{colMeans2}}.
36 
+/ \code{matrixStats::\link[matrixStats:rowMeans2]{colMeans2}}.
38 37 
 }
39 38 
 \examples{
40 39 
 mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
... ... 
@@ -50,11 +49,11 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
50 49 
 \seealso{
51 50 
 \itemize{
52 51 
 \item \code{matrixStats::\link[matrixStats]{rowMeans2}()} and
53 
-\code{matrixStats::\link[matrixStats]{colMeans2}()} which are used when
54 
-the input is a \code{matrix} or \code{numeric} vector.
52 
+\code{matrixStats::\link[matrixStats:rowMeans2]{colMeans2}()} which are
53 
+used when the input is a \code{matrix} or \code{numeric} vector.
55 54 
 \item See also \code{\link[base:colSums]{rowMeans}()} for the
56 55 
 corresponding function in base R.
57 56 
 \item For variance estimates, see \code{\link[MatrixGenerics]{rowVars}()}.
58 
-\item See also the base R version \code{base::\link[base]{rowMeans}()}.
57 
+\item See also the base R version \code{base::\link{rowMeans}()}.
59 58 
 }
60 59 
 }
man/colMedians-dgCMatrix-method.Rd
History View file @ 7f055a6
... ... 
@@ -12,29 +12,28 @@
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 of rows
16 
-(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
17 
-subsetting is done.}
15 
+\item{rows}{A \code{\link{vector}} indicating the subset of rows
16 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
17 
+done.}
18 18
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.}
19 
+\item{cols}{A \code{\link{vector}} indicating the subset of rows
20 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
21 
+done.}
22 22
23 
-\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
23 
+\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link{NA}}s
24 24 
 are excluded first, otherwise not.}
25 25 
 }
26 26 
 \value{
27 
-Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of
28 
-length N (K).
27 
+Returns a \code{\link{numeric}} \code{\link{vector}} of length N (K).
29 28 
 }
30 29 
 \description{
31 30 
 Calculates the median for each row (column) of a matrix-like object.
32 31 
 }
33 32 
 \details{
34 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}},
35 
-\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
33 
+The S4 methods for \code{x} of type \code{\link{matrix}},
34 
+\code{\link{array}}, or \code{\link{numeric}} call
36 35 
 \code{matrixStats::\link[matrixStats]{rowMedians}}
37 
-/ \code{matrixStats::\link[matrixStats]{colMedians}}.
36 
+/ \code{matrixStats::\link[matrixStats:rowMedians]{colMedians}}.
38 37 
 }
39 38 
 \examples{
40 39 
 mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
... ... 
@@ -50,8 +49,8 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
50 49 
 \seealso{
51 50 
 \itemize{
52 51 
 \item \code{matrixStats::\link[matrixStats]{rowMedians}()} and
53 
-\code{matrixStats::\link[matrixStats]{colMedians}()} which are used when
54 
-the input is a \code{matrix} or \code{numeric} vector.
52 
+\code{matrixStats::\link[matrixStats:rowMedians]{colMedians}()} which are
53 
+used when the input is a \code{matrix} or \code{numeric} vector.
55 54 
 \item For mean estimates, see \code{\link[MatrixGenerics]{rowMeans2}()} and
56 55 
 \code{\link[base:colSums]{rowMeans}()}.
57 56 
 }
man/colMins-dgCMatrix-method.Rd
History View file @ 7f055a6
... ... 
@@ -12,29 +12,28 @@
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 of rows
16 
-(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
17 
-subsetting is done.}
15 
+\item{rows}{A \code{\link{vector}} indicating the subset of rows
16 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
17 
+done.}
18 18
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.}
19 
+\item{cols}{A \code{\link{vector}} indicating the subset of rows
20 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
21 
+done.}
22 22
23 
-\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
23 
+\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link{NA}}s
24 24 
 are excluded first, otherwise not.}
25 25 
 }
26 26 
 \value{
27 
-Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of
28 
-length N (K).
27 
+Returns a \code{\link{numeric}} \code{\link{vector}} of length N (K).
29 28 
 }
30 29 
 \description{
31 30 
 Calculates the minimum for each row (column) of a matrix-like object.
32 31 
 }
33 32 
 \details{
34 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}},
35 
-\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
33 
+The S4 methods for \code{x} of type \code{\link{matrix}},
34 
+\code{\link{array}}, or \code{\link{numeric}} call
36 35 
 \code{matrixStats::\link[matrixStats]{rowMins}}
37 
-/ \code{matrixStats::\link[matrixStats]{colMins}}.
36 
+/ \code{matrixStats::\link[matrixStats:rowMins]{colMins}}.
38 37 
 }
39 38 
 \examples{
40 39 
 mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
... ... 
@@ -50,8 +49,8 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
50 49 
 \seealso{
51 50 
 \itemize{
52 51 
 \item \code{matrixStats::\link[matrixStats]{rowMins}()} and
53 
-\code{matrixStats::\link[matrixStats]{colMins}()} which are used when
54 
-the input is a \code{matrix} or \code{numeric} vector.
52 
+\code{matrixStats::\link[matrixStats:rowMins]{colMins}()} which are used
53 
+when the input is a \code{matrix} or \code{numeric} vector.
55 54 
 \item For max estimates, see \code{\link[MatrixGenerics]{rowMaxs}()}.
56 55 
 }
57 56 
 }
man/colOrderStats-dgCMatrix-method.Rd
History View file @ 7f055a6
... ... 
@@ -12,13 +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 of rows
16 
-(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
17 
-subsetting is done.}
15 
+\item{rows}{A \code{\link{vector}} indicating the subset of rows
16 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
17 
+done.}
18 18
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.}
19 
+\item{cols}{A \code{\link{vector}} indicating the subset of rows
20 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
21 
+done.}
22 22
23 23 
 \item{which}{An integer index in [1,K] ([1,N]) indicating which order
24 24 
 statistic to be returned}
... ... 
@@ -26,17 +26,16 @@ statistic to be returned}
26 26 
 \item{na.rm}{If TRUE, NAs are excluded first, otherwise not.}
27 27 
 }
28 28 
 \value{
29 
-Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of
30 
-length N (K).
29 
+Returns a \code{\link{numeric}} \code{\link{vector}} of length N (K).
31 30 
 }
32 31 
 \description{
33 32 
 Calculates an order statistic for each row (column) of a matrix-like object.
34 33 
 }
35 34 
 \details{
36 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}},
37 
-\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
35 
+The S4 methods for \code{x} of type \code{\link{matrix}},
36 
+\code{\link{array}}, or \code{\link{numeric}} call
38 37 
 \code{matrixStats::\link[matrixStats]{rowOrderStats}}
39 
-/ \code{matrixStats::\link[matrixStats]{colOrderStats}}.
38 
+/ \code{matrixStats::\link[matrixStats:rowOrderStats]{colOrderStats}}.
40 39 
 }
41 40 
 \examples{
42 41 
 mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
... ... 
@@ -52,7 +51,7 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
52 51 
 \seealso{
53 52 
 \itemize{
54 53 
 \item \code{matrixStats::\link[matrixStats]{rowOrderStats}()} and
55 
-\code{matrixStats::\link[matrixStats]{colOrderStats}()} which are used when
56 
-the input is a \code{matrix} or \code{numeric} vector.
54 
+\code{matrixStats::\link[matrixStats:rowOrderStats]{colOrderStats}()}
55 
+which are used when the input is a \code{matrix} or \code{numeric} vector.
57 56 
 }
58 57 
 }
man/colProds-dgCMatrix-method.Rd
History View file @ 7f055a6
... ... 
@@ -12,20 +12,19 @@
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 of rows
16 
-(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
17 
-subsetting is done.}
15 
+\item{rows}{A \code{\link{vector}} indicating the subset of rows
16 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
17 
+done.}
18 18
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.}
19 
+\item{cols}{A \code{\link{vector}} indicating the subset of rows
20 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
21 
+done.}
22 22
23 
-\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
23 
+\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link{NA}}s
24 24 
 are excluded first, otherwise not.}
25 25 
 }
26 26 
 \value{
27 
-Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of
28 
-length N (K).
27 
+Returns a \code{\link{numeric}} \code{\link{vector}} of length N (K).
29 28 
 }
30 29 
 \description{
31 30 
 Calculates the product for each row (column) in a matrix
... ... 
@@ -51,10 +50,10 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
51 50 
 \seealso{
52 51 
 \itemize{
53 52 
 \item \code{matrixStats::\link[matrixStats]{rowProds}()} and
54 
-\code{matrixStats::\link[matrixStats]{colProds}()} which are used when
55 
-the input is a \code{matrix} or \code{numeric} vector.
53 
+\code{matrixStats::\link[matrixStats:rowProds]{colProds}()} which are used
54 
+when the input is a \code{matrix} or \code{numeric} vector.
56 55 
 \item For sums across rows (columns), see
57 56 
 \code{\link[MatrixGenerics]{rowSums2}()} (\code{\link[MatrixGenerics:colSums2]{colSums2()}})
58 
-\item \code{base::\link[base]{prod}()}.
57 
+\item \code{base::\link{prod}()}.
59 58 
 }
60 59 
 }
man/colQuantiles-dgCMatrix-method.Rd
History View file @ 7f055a6
... ... 
@@ -26,17 +26,17 @@
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 of rows
30 
-(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
31 
-subsetting is done.}
29 
+\item{rows}{A \code{\link{vector}} indicating the subset of rows
30 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
31 
+done.}
32 32
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.}
33 
+\item{cols}{A \code{\link{vector}} indicating the subset of rows
34 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
35 
+done.}
36 36
37 37 
 \item{probs}{A numeric vector of J probabilities in [0, 1].}
38 38
39 
-\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
39 
+\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link{NA}}s
40 40 
 are excluded first, otherwise not.}
41 41
42 42 
 \item{drop}{If \code{TRUE} a vector is returned if \code{J == 1}.
... ... 
@@ -44,7 +44,7 @@ Note, that this is not a generic argument and not all implementation of
44 44 
 this function have to provide it.}
45 45 
 }
46 46 
 \value{
47 
-a \code{\link[base]{numeric}} \code{NxJ} (\code{KxJ})
47 
+a \code{\link{numeric}} \code{NxJ} (\code{KxJ})
48 48 
 \code{\link{matrix}}, where N (K) is the number of rows (columns) for
49 49 
 which the J values are calculated.
50 50 
 }
... ... 
@@ -52,10 +52,10 @@ which the J values are calculated.
52 52 
 Calculates quantiles for each row (column) of a matrix-like object.
53 53 
 }
54 54 
 \details{
55 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}},
56 
-\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
55 
+The S4 methods for \code{x} of type \code{\link{matrix}},
56 
+\code{\link{array}}, or \code{\link{numeric}} call
57 57 
 \code{matrixStats::\link[matrixStats]{rowQuantiles}}
58 
-/ \code{matrixStats::\link[matrixStats]{colQuantiles}}.
58 
+/ \code{matrixStats::\link[matrixStats:rowQuantiles]{colQuantiles}}.
59 59 
 }
60 60 
 \examples{
61 61 
 mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
... ... 
@@ -71,8 +71,8 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
71 71 
 \seealso{
72 72 
 \itemize{
73 73 
 \item \code{matrixStats::\link[matrixStats]{rowQuantiles}()} and
74 
-\code{matrixStats::\link[matrixStats]{colQuantiles}()} which are used when
75 
-the input is a \code{matrix} or \code{numeric} vector.
74 
+\code{matrixStats::\link[matrixStats:rowQuantiles]{colQuantiles}()} which
75 
+are used when the input is a \code{matrix} or \code{numeric} vector.
76 76 
 \item \link[stats:quantile]{stats::quantile}
77 77 
 }
78 78 
 }
man/colRanges-dgCMatrix-method.Rd
History View file @ 7f055a6
... ... 
@@ -13,19 +13,19 @@ object}
13 13 
 \arguments{
14 14 
 \item{x}{An NxK matrix-like object.}
15 15
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.}
16 
+\item{rows}{A \code{\link{vector}} indicating the subset of rows
17 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
18 
+done.}
19 19
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 
+\item{cols}{A \code{\link{vector}} indicating the subset of rows
21 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
22 
+done.}
23 23
24 
-\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
24 
+\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link{NA}}s
25 25 
 are excluded first, otherwise not.}
26 26 
 }
27 27 
 \value{
28 
-a \code{\link[base]{numeric}} \code{Nx2} (\code{Kx2})
28 
+a \code{\link{numeric}} \code{Nx2} (\code{Kx2})
29 29 
 \code{\link{matrix}}, where N (K) is the number of rows (columns) for
30 30 
 which the ranges are calculated.
31 31 
 }
... ... 
@@ -34,10 +34,10 @@ Calculates the minimum and maximum for each row (column) of a matrix-like
34 34 
 object.
35 35 
 }
36 36 
 \details{
37 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}},
38 
-\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
37 
+The S4 methods for \code{x} of type \code{\link{matrix}},
38 
+\code{\link{array}}, or \code{\link{numeric}} call
39 39 
 \code{matrixStats::\link[matrixStats]{rowRanges}}
40 
-/ \code{matrixStats::\link[matrixStats]{colRanges}}.
40 
+/ \code{matrixStats::\link[matrixStats:rowRanges]{colRanges}}.
41 41 
 }
42 42 
 \examples{
43 43 
 mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
... ... 
@@ -53,10 +53,10 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
53 53 
 \seealso{
54 54 
 \itemize{
55 55 
 \item \code{matrixStats::\link[matrixStats]{rowRanges}()} and
56 
-\code{matrixStats::\link[matrixStats]{colRanges}()} which are used when
57 
-the input is a \code{matrix} or \code{numeric} vector.
56 
+\code{matrixStats::\link[matrixStats:rowRanges]{colRanges}()} which are
57 
+used when the input is a \code{matrix} or \code{numeric} vector.
58 58 
 \item For max estimates, see \code{\link[MatrixGenerics]{rowMaxs}()}.
59 59 
 \item For min estimates, see \code{\link[MatrixGenerics]{rowMins}()}.
60 
-\item \code{base::\link[base]{range}()}.
60 
+\item \code{base::\link{range}()}.
61 61 
 }
62 62 
 }
man/colRanks-dgCMatrix-method.Rd
History View file @ 7f055a6
... ... 
@@ -27,13 +27,13 @@ object}
27 27 
 \arguments{
28 28 
 \item{x}{An NxK matrix-like object.}
29 29
30 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
31 
-(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
32 
-subsetting is done.}
30 
+\item{rows}{A \code{\link{vector}} indicating the subset of rows
31 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
32 
+done.}
33 33
34 
-\item{cols}{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.}
34 
+\item{cols}{A \code{\link{vector}} indicating the subset of rows
35 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
36 
+done.}
37 37
38 38 
 \item{ties.method}{A character string specifying how ties are treated. Note
39 39 
 that the default specifies fewer options than the original matrixStats
... ... 
@@ -47,7 +47,7 @@ dimensions as the input matrix. By default this is true for `rowRanks()`, but fa
47 47 
 ('keep') or sorted in at the end ('last'). Default is 'keep' derived from the behavior of the equivalent}
48 48 
 }
49 49 
 \value{
50 
-a matrix of type \code{\link[base]{integer}} is returned unless
50 
+a matrix of type \code{\link{integer}} is returned unless
51 51 
 \code{ties.method = "average"}. Ithas dimensions` \code{NxJ} (\code{KxJ})
52 52 
 \code{\link{matrix}}, where N (K) is the number of rows (columns) of the
53 53 
 input x.
... ... 
@@ -79,8 +79,8 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
79 79 
 \seealso{
80 80 
 \itemize{
81 81 
 \item \code{matrixStats::\link[matrixStats]{rowRanks}()} and
82 
-\code{matrixStats::\link[matrixStats]{colRanks}()} which are used when
83 
-the input is a \code{matrix} or \code{numeric} vector.
82 
+\code{matrixStats::\link[matrixStats:rowRanks]{colRanks}()} which are used
83 
+when the input is a \code{matrix} or \code{numeric} vector.
84 84 
 \item \link[base:rank]{base::rank}
85 85 
 }
86 86 
 }
man/colSdDiffs-dgCMatrix-method.Rd
History View file @ 7f055a6
... ... 
@@ -13,15 +13,15 @@ a row (column) of a matrix-like object}
13 13 
 \arguments{
14 14 
 \item{x}{An NxK matrix-like object.}
15 15
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.}
16 
+\item{rows}{A \code{\link{vector}} indicating the subset of rows
17 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
18 
+done.}
19 19
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 
+\item{cols}{A \code{\link{vector}} indicating the subset of rows
21 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
22 
+done.}
23 23
24 
-\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
24 
+\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link{NA}}s
25 25 
 are excluded first, otherwise not.}
26 26
27 27 
 \item{diff}{An integer specifying the order of difference.}
... ... 
@@ -30,18 +30,17 @@ are excluded first, otherwise not.}
30 30 
 be trimmed from each end of (sorted) x before estimation.}
31 31 
 }
32 32 
 \value{
33 
-Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of
34 
-length N (K).
33 
+Returns a \code{\link{numeric}} \code{\link{vector}} of length N (K).
35 34 
 }
36 35 
 \description{
37 36 
 Calculates the standard deviation of the difference between each element of
38 37 
 a row (column) of a matrix-like object.
39 38 
 }
40 39 
 \details{
41 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}},
42 
-\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
40 
+The S4 methods for \code{x} of type \code{\link{matrix}},
41 
+\code{\link{array}}, or \code{\link{numeric}} call
43 42 
 \code{matrixStats::\link[matrixStats]{rowSdDiffs}}
44 
-/ \code{matrixStats::\link[matrixStats]{colSdDiffs}}.
43 
+/ \code{matrixStats::\link[matrixStats:rowSdDiffs]{colSdDiffs}}.
45 44 
 }
46 45 
 \examples{
47 46 
 mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
... ... 
@@ -57,8 +56,8 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
57 56 
 \seealso{
58 57 
 \itemize{
59 58 
 \item \code{matrixStats::\link[matrixStats]{rowSdDiffs}()} and
60 
-\code{matrixStats::\link[matrixStats]{colSdDiffs}()} which are used when
61 
-the input is a \code{matrix} or \code{numeric} vector.
59 
+\code{matrixStats::\link[matrixStats:rowSdDiffs]{colSdDiffs}()} which are
60 
+used when the input is a \code{matrix} or \code{numeric} vector.
62 61 
 \item for the direct standard deviation see \code{\link[MatrixGenerics:rowSds]{rowSds()}}.
63 62 
 }
64 63 
 }
man/colSds-dgCMatrix-method.Rd
History View file @ 7f055a6
... ... 
@@ -13,30 +13,29 @@ object}
13 13 
 \arguments{
14 14 
 \item{x}{An NxK matrix-like object.}
15 15
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.}
16 
+\item{rows}{A \code{\link{vector}} indicating the subset of rows
17 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
18 
+done.}
19 19
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 
+\item{cols}{A \code{\link{vector}} indicating the subset of rows
21 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
22 
+done.}
23 23
24 
-\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
24 
+\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link{NA}}s
25 25 
 are excluded first, otherwise not.}
26 26 
 }
27 27 
 \value{
28 
-Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of
29 
-length N (K).
28 
+Returns a \code{\link{numeric}} \code{\link{vector}} of length N (K).
30 29 
 }
31 30 
 \description{
32 31 
 Calculates the standard deviation for each row (column) of a matrix-like
33 32 
 object.
34 33 
 }
35 34 
 \details{
36 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}},
37 
-\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
35 
+The S4 methods for \code{x} of type \code{\link{matrix}},
36 
+\code{\link{array}}, or \code{\link{numeric}} call
38 37 
 \code{matrixStats::\link[matrixStats]{rowSds}}
39 
-/ \code{matrixStats::\link[matrixStats]{colSds}}.
38 
+/ \code{matrixStats::\link[matrixStats:rowSds]{colSds}}.
40 39 
 }
41 40