1. sparseMatrixStats
  2. man
  3. colSdDiffs-dgCMatrix-method.Rd
Browse code

Add useNames argument

This makes sparseMatrixStats compatible with v0.60 of matrixStats

In this commit
* I introduce a set of function called `set_result_names()`
that take the internally computed result and add correct names if needed
* Add colnames to the matrices of the unit tests
* Update the documentation to reflect the changed method signatures

const-ae authored on 05/08/2021 13:05:38
Showing 1 changed files
man/colSdDiffs-dgCMatrix-method.Rd
History View file @ eaab674
... ... 
@@ -6,9 +6,25 @@
6 6 
 \title{Calculates the standard deviation of the difference between each element of
7 7 
 a row (column) of a matrix-like object}
8 8 
 \usage{
9 
-\S4method{colSdDiffs}{dgCMatrix}(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L, trim = 0)
9 
+\S4method{colSdDiffs}{dgCMatrix}(
10 
+  x,
11 
+  rows = NULL,
12 
+  cols = NULL,
13 
+  na.rm = FALSE,
14 
+  diff = 1L,
15 
+  trim = 0,
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+  useNames = NA
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+)
10 18
11 
-\S4method{rowSdDiffs}{dgCMatrix}(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L, trim = 0)
19 
+\S4method{rowSdDiffs}{dgCMatrix}(
20 
+  x,
21 
+  rows = NULL,
22 
+  cols = NULL,
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+  na.rm = FALSE,
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+  diff = 1L,
25 
+  trim = 0,
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+  useNames = NA
27 
+)
12 28 
 }
13 29 
 \arguments{
14 30 
 \item{x}{An NxK matrix-like object.}
... ... 
@@ -28,6 +44,8 @@ are excluded first, otherwise not.}
28 44
29 45 
 \item{trim}{A double in [0,1/2] specifying the fraction of observations to
30 46 
 be trimmed from each end of (sorted) x before estimation.}
47 
+
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+\item{useNames}{If \code{\link{NA}}, the default behavior of the function about naming support is remained. If \code{\link{FALSE}}, no naming support is done. Else if \code{\link{TRUE}}, names attributes of result are set.}
31 49 
 }
32 50 
 \value{
33 51 
 Returns a \code{\link{numeric}} \code{\link{vector}} of length N (K).
Browse code

Update documentation to latest version of MatrixGenerics

const-ae authored on 21/05/2020 11:07:40
Showing 1 changed files
man/colSdDiffs-dgCMatrix-method.Rd
History View file @ fd0ef25
... ... 
@@ -39,8 +39,8 @@ a row (column) of a matrix-like object.
39 39 
 \details{
40 40 
 The S4 methods for \code{x} of type \code{\link{matrix}},
41 41 
 \code{\link{array}}, or \code{\link{numeric}} call
42 
-\code{matrixStats::\link[matrixStats]{rowSdDiffs}}
43 
-/ \code{matrixStats::\link[matrixStats:rowSdDiffs]{colSdDiffs}}.
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+\code{matrixStats::rowSdDiffs}
43 
+/ \code{matrixStats::colSdDiffs}.
44 44 
 }
45 45 
 \examples{
46 46 
 mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
... ... 
@@ -55,8 +55,8 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
55 55 
 }
56 56 
 \seealso{
57 57 
 \itemize{
58 
-\item \code{matrixStats::\link[matrixStats]{rowSdDiffs}()} and
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-\code{matrixStats::\link[matrixStats:rowSdDiffs]{colSdDiffs}()} which are
58 
+\item \code{matrixStats::\link[matrixStats:varDiff]{rowSdDiffs}()} and
59 
+\code{matrixStats::\link[matrixStats:varDiff]{colSdDiffs}()} which are
60 60 
 used when the input is a \code{matrix} or \code{numeric} vector.
61 61 
 \item for the direct standard deviation see \code{\link[MatrixGenerics:rowSds]{rowSds()}}.
62 62 
 }
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 1 changed files
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.}
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+\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 
 }
Browse code

Remove superfluous ... from method signatures

const-ae authored on 03/04/2020 10:39:05
Showing 1 changed files
man/colSdDiffs-dgCMatrix-method.Rd
History View file @ 8ee76bd
... ... 
@@ -6,25 +6,9 @@
6 6 
 \title{Calculates the standard deviation of the difference between each element of
7 7 
 a row (column) of a matrix-like object}
8 8 
 \usage{
9 
-\S4method{colSdDiffs}{dgCMatrix}(
10 
-  x,
11 
-  rows = NULL,
12 
-  cols = NULL,
13 
-  na.rm = FALSE,
14 
-  diff = 1L,
15 
-  trim = 0,
16 
-  ...
17 
-)
9 
+\S4method{colSdDiffs}{dgCMatrix}(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L, trim = 0)
18 10
19 
-\S4method{rowSdDiffs}{dgCMatrix}(
20 
-  x,
21 
-  rows = NULL,
22 
-  cols = NULL,
23 
-  na.rm = FALSE,
24 
-  diff = 1L,
25 
-  trim = 0,
26 
-  ...
27 
-)
11 
+\S4method{rowSdDiffs}{dgCMatrix}(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L, trim = 0)
28 12 
 }
29 13 
 \arguments{
30 14 
 \item{x}{An NxK matrix-like object.}
... ... 
@@ -44,8 +28,6 @@ are excluded first, otherwise not.}
44 28
45 29 
 \item{trim}{A double in [0,1/2] specifying the fraction of observations to
46 30 
 be trimmed from each end of (sorted) x before estimation.}
47 
-
48 
-\item{...}{Additional arguments passed to specific methods.}
49 31 
 }
50 32 
 \value{
51 33 
 Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of
Browse code

Bring documentation in line with MatrixGenerics

const-ae authored on 03/04/2020 10:19:46
Showing 1 changed files
man/colSdDiffs-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -3,7 +3,8 @@
3 3 
 \name{colSdDiffs,dgCMatrix-method}
4 4 
 \alias{colSdDiffs,dgCMatrix-method}
5 5 
 \alias{rowSdDiffs,dgCMatrix-method}
6 
-\title{Calculates the standard deviation of the difference between each element of a row (column) of a matrix-like object}
6 
+\title{Calculates the standard deviation of the difference between each element of
7 
+a row (column) of a matrix-like object}
7 8 
 \usage{
8 9 
 \S4method{colSdDiffs}{dgCMatrix}(
9 10 
   x,
... ... 
@@ -28,19 +29,21 @@
28 29 
 \arguments{
29 30 
 \item{x}{An NxK matrix-like object.}
30 31
31 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
32 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
32 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
33 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
34 
+subsetting is done.}
33 35
34 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
35 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
36 
+\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
37 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
38 
+subsetting is done.}
36 39
37 40 
 \item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
38 41 
 are excluded first, otherwise not.}
39 42
40 43 
 \item{diff}{An integer specifying the order of difference.}
41 44
42 
-\item{trim}{A double in [0,1/2] specifying the fraction of observations to be trimmed from
43 
-each end of (sorted) x before estimation.}
45 
+\item{trim}{A double in [0,1/2] specifying the fraction of observations to
46 
+be trimmed from each end of (sorted) x before estimation.}
44 47
45 48 
 \item{...}{Additional arguments passed to specific methods.}
46 49 
 }
... ... 
@@ -49,11 +52,13 @@ Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of
49 52 
 length N (K).
50 53 
 }
51 54 
 \description{
52 
-Calculates the standard deviation of the difference between each element of a row (column) of a matrix-like object
55 
+Calculates the standard deviation of the difference between each element of
56 
+a row (column) of a matrix-like object.
53 57 
 }
54 58 
 \details{
55 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
56 
-\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowSdDiffs}}
59 
+The S4 methods for \code{x} of type \code{\link[base]{matrix}},
60 
+\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
61 
+\code{matrixStats::\link[matrixStats]{rowSdDiffs}}
57 62 
 / \code{matrixStats::\link[matrixStats]{colSdDiffs}}.
58 63 
 }
59 64 
 \examples{
Browse code

Use MatrixGenerics for all rowXXX functions

const-ae authored on 16/03/2020 20:22:08
Showing 1 changed files
man/colSdDiffs-dgCMatrix-method.Rd
History View file @ 17c056e
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,77 @@
1 
+% Generated by roxygen2: do not edit by hand
2 
+% Please edit documentation in R/methods.R, R/methods_row.R
3 
+\name{colSdDiffs,dgCMatrix-method}
4 
+\alias{colSdDiffs,dgCMatrix-method}
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}
7 
+\usage{
8 
+\S4method{colSdDiffs}{dgCMatrix}(
9 
+  x,
10 
+  rows = NULL,
11 
+  cols = NULL,
12 
+  na.rm = FALSE,
13 
+  diff = 1L,
14 
+  trim = 0,
15 
+  ...
16 
+)
17 
+
18 
+\S4method{rowSdDiffs}{dgCMatrix}(
19 
+  x,
20 
+  rows = NULL,
21 
+  cols = NULL,
22 
+  na.rm = FALSE,
23 
+  diff = 1L,
24 
+  trim = 0,
25 
+  ...
26 
+)
27 
+}
28 
+\arguments{
29 
+\item{x}{An NxK matrix-like object.}
30 
+
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.}
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 done.}
36 
+
37 
+\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
38 
+are excluded first, otherwise not.}
39 
+
40 
+\item{diff}{An integer specifying the order of difference.}
41 
+
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.}
44 
+
45 
+\item{...}{Additional arguments passed to specific methods.}
46 
+}
47 
+\value{
48 
+Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of
49 
+length N (K).
50 
+}
51 
+\description{
52 
+Calculates the standard deviation of the difference between each element of a row (column) of a matrix-like object
53 
+}
54 
+\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}}
57 
+/ \code{matrixStats::\link[matrixStats]{colSdDiffs}}.
58 
+}
59 
+\examples{
60 
+mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
61 
+  mat[2, 1] <- NA
62 
+  mat[3, 3] <- Inf
63 
+  mat[4, 1] <- 0
64 
+
65 
+  print(mat)
66 
+
67 
+  rowSdDiffs(mat)
68 
+  colSdDiffs(mat)
69 
+}
70 
+\seealso{
71 
+\itemize{
72 
+\item \code{matrixStats::\link[matrixStats]{rowSdDiffs}()} and
73 
+\code{matrixStats::\link[matrixStats]{colSdDiffs}()} which are used when
74 
+the input is a \code{matrix} or \code{numeric} vector.
75 
+\item for the direct standard deviation see \code{\link[MatrixGenerics:rowSds]{rowSds()}}.
76 
+}
77 
+}