#### Bring documentation in line with MatrixGenerics

const-ae authored on 03/04/2020 10:19:46
Showing 36 changed files

 ... ... @@ -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  }
 ... ... @@ -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  }
 ... ... @@ -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  }
 ... ... @@ -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  }
 ... ... @@ -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{
 ... ... @@ -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  }
 ... ... @@ -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  }
 ... ... @@ -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  }
 ... ... @@ -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  }
 ... ... @@ -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  }
 ... ... @@ -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  }
 ... ... @@ -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{
 ... ... @@ -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  }
 ... ... @@ -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  }
 ... ... @@ -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{
 ... ... @@ -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  }
 ... ... @@ -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{
 ... ... @@ -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  }
 ... ... @@ -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{
 ... ... @@ -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{
 ... ... @@ -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{
 ... ... @@ -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  }
 ... ... @@ -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{
 ... ... @@ -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  }
 ... ... @@ -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:
 ... ... @@ -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{
 ... ... @@ -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{
 ... ... @@ -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  }
 ... ... @@ -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{
 ... ... @@ -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.}