Package 'matrixStats' reference manual

Title:	Functions that Apply to Rows and Columns of Matrices (and to Vectors)
Description:	High-performing functions operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized. There are also optimized vector-based methods, e.g. binMeans(), madDiff() and weightedMedian().
Authors:	Henrik Bengtsson [aut, cre, cph], Constantin Ahlmann-Eltze [ctb], Hector Corrada Bravo [ctb], Robert Gentleman [ctb], Jan Gleixner [ctb], Peter Hickey [ctb], Ola Hossjer [ctb], Harris Jaffee [ctb], Dongcan Jiang [ctb], Peter Langfelder [ctb], Brian Montgomery [ctb], Angelina Panagopoulou [ctb], Hugh Parsonage [ctb], Jakob Peder Pettersen [ctb]
Maintainer:	Henrik Bengtsson <[email protected]>
License:	Artistic-2.0
Version:	1.4.1-9002
Built:	2024-11-14 08:18:57 UTC
Source:	https://github.com/HenrikBengtsson/matrixStats

Package matrixStats

Description

High-performing functions operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized. There are also optimized vector-based methods, e.g. binMeans(), madDiff() and weightedMedian().

How to cite this package

Henrik Bengtsson (2017). matrixStats: Functions that Apply to Rows and Columns of Matrices (and to Vectors). R package version 0.52.2. https://github.com/HenrikBengtsson/matrixStats

Author(s)

Henrik Bengtsson, Hector Corrada Bravo, Robert Gentleman, Ola Hossjer, Harris Jaffee, Dongcan Jiang, Peter Langfelder

Checks if there are any missing values in an object or not

Description

Checks if there are any missing values in an object or not. Please use base::anyNA() instead of anyMissing(), colAnyNAs() instead of colAnyMissings(), and rowAnyNAs() instead of rowAnyMissings().

Usage

anyMissing(x, idxs = NULL, ...)

colAnyMissings(x, rows = NULL, cols = NULL, ..., useNames = TRUE)

rowAnyMissings(x, rows = NULL, cols = NULL, ..., useNames = TRUE)

colAnyNAs(x, rows = NULL, cols = NULL, ..., useNames = TRUE)

rowAnyNAs(x, rows = NULL, cols = NULL, ..., useNames = TRUE)
anyMissing(x, idxs = NULL, ...)

colAnyMissings(x, rows = NULL, cols = NULL, ..., useNames = TRUE)

rowAnyMissings(x, rows = NULL, cols = NULL, ..., useNames = TRUE)

colAnyNAs(x, rows = NULL, cols = NULL, ..., useNames = TRUE)

rowAnyNAs(x, rows = NULL, cols = NULL, ..., useNames = TRUE)

Arguments

`x`	A `vector`, a `list`, a `matrix`, a `data.frame`, or `NULL`.
`idxs`	A `vector` indicating subset of elements to operate over. If `NULL`, no subsetting is done.
`...`	Not used.
`rows`	A `vector` indicating subset of rows to operate over. If `NULL`, no subsetting is done.
`cols`	A `vector` indicating subset of columns to operate over. If `NULL`, no subsetting is done.
`useNames`	If `TRUE` (default), names attributes of the result are set, otherwise not.

Details

The implementation of this method is optimized for both speed and memory. The method will return TRUE as soon as a missing value is detected.

Value

Returns TRUE if a missing value was detected, otherwise FALSE.

Author(s)

Henrik Bengtsson

Examples

 x <- rnorm(n = 1000)
 x[seq(300, length(x), by = 100)] <- NA
 stopifnot(anyMissing(x) == any(is.na(x)))

x <- rnorm(n = 1000)
 x[seq(300, length(x), by = 100)] <- NA
 stopifnot(anyMissing(x) == any(is.na(x)))

Fast element counting in non-overlapping bins

Description

Counts the number of elements in non-overlapping bins

Usage

binCounts(x, idxs = NULL, bx, right = FALSE, ...)
binCounts(x, idxs = NULL, bx, right = FALSE, ...)

Arguments

`x`	A `numeric` `vector` of K positions for to be binned and counted.
`idxs`	A `vector` indicating subset of elements to operate over. If `NULL`, no subsetting is done.
`bx`	A `numeric` `vector` of B + 1 ordered positions specifying the B > 0 bins `[bx[1], bx[2])`, `[bx[2], bx[3])`, ..., `[bx[B], bx[B + 1])`.
`right`	If `TRUE`, the bins are right-closed (left open), otherwise left-closed (right open).
`...`	Not used.

Details

binCounts(x, bx, right = TRUE) gives equivalent results as rev(binCounts(-x, bx = rev(-bx), right = FALSE)), but is faster and more memory efficient.

Value

Returns an integer vector of length B with non-negative integers.

Missing and non-finite values

Missing values in x are ignored/dropped. Missing values in bx are not allowed and gives an error.

Author(s)

Henrik Bengtsson

Fast mean calculations in non-overlapping bins

Description

Computes the sample means in non-overlapping bins

Usage

binMeans(y, x, idxs = NULL, bx, na.rm = TRUE, count = TRUE,
  right = FALSE, ...)
binMeans(y, x, idxs = NULL, bx, na.rm = TRUE, count = TRUE,
  right = FALSE, ...)

Arguments

`y`	A `numeric` or `logical` `vector` of K values to calculate means on.
`x`	A `numeric` `vector` of K positions for to be binned.
`idxs`	A `vector` indicating subset of elements to operate over. If `NULL`, no subsetting is done.
`bx`	A `numeric` `vector` of B + 1 ordered positions specifying the B > 0 bins `[bx[1], bx[2])`, `[bx[2], bx[3])`, ..., `[bx[B], bx[B + 1])`.
`na.rm`	If `TRUE`, missing values in `y` are dropped before calculating the mean, otherwise not.
`count`	If `TRUE`, the number of data points in each bins is returned as attribute `count`, which is an `integer` `vector` of length B.
`right`	If `TRUE`, the bins are right-closed (left open), otherwise left-closed (right open).
`...`	Not used.

Details

binMeans(x, bx, right = TRUE) gives equivalent results as rev(binMeans(-x, bx = sort(-bx), right = FALSE)), but is faster.

Value

Returns a numeric vector of length B.

Missing and non-finite values

Data points where either of y and x is missing are dropped (and therefore are also not counted). Non-finite values in y are not allowed and gives an error. Missing values in bx are not allowed and gives an error.

Author(s)

Henrik Bengtsson with initial code contributions by Martin Morgan [1].

References

[1] R-devel thread Fastest non-overlapping binning mean function out there? on Oct 3, 2012

Examples

x <- 1:200
mu <- double(length(x))
mu[1:50] <- 5
mu[101:150] <- -5
y <- mu + rnorm(length(x))

# Binning
bx <- c(0, 50, 100, 150, 200) + 0.5
y_s <- binMeans(y, x = x, bx = bx)

plot(x, y)
for (kk in seq_along(y_s)) {
  lines(bx[c(kk, kk + 1)], y_s[c(kk, kk)], col = "blue", lwd = 2)
}
x <- 1:200
mu <- double(length(x))
mu[1:50] <- 5
mu[101:150] <- -5
y <- mu + rnorm(length(x))

# Binning
bx <- c(0, 50, 100, 150, 200) + 0.5
y_s <- binMeans(y, x = x, bx = bx)

plot(x, y)
for (kk in seq_along(y_s)) {
  lines(bx[c(kk, kk + 1)], y_s[c(kk, kk)], col = "blue", lwd = 2)
}

Translates matrix indices by rows into indices by columns

Description

Translates matrix indices by rows into indices by columns.

Usage

indexByRow(dim, idxs = NULL, ...)
indexByRow(dim, idxs = NULL, ...)

Arguments

`dim`	A `numeric` `vector` of length two specifying the length of the "template" matrix.
`idxs`	A `vector` indicating subset of elements to operate over. If `NULL`, no subsetting is done.
`...`	Not used.

Value

Returns an integer vector of indices.

Known limitations

The current implementation does not support long-vector indices, because both input and output indices are of type integers. This means that the indices in argument idxs can only be in range [1,2^31-1]. Using a greater value will be coerced to NA_integer_. Moreover, returned indices can only be in the same range [1,2^31-1].

Author(s)

Henrik Bengtsson

Examples

dim <- c(5, 4)
X <- matrix(NA_integer_, nrow = dim[1], ncol = dim[2])
Y <- t(X)
idxs <- seq_along(X)

# Assign by columns
X[idxs] <- idxs
print(X)

# Assign by rows
Y[indexByRow(dim(Y), idxs)] <- idxs
print(Y)

stopifnot(X == t(Y))
dim <- c(5, 4)
X <- matrix(NA_integer_, nrow = dim[1], ncol = dim[2])
Y <- t(X)
idxs <- seq_along(X)

# Assign by columns
X[idxs] <- idxs
print(X)

# Assign by rows
Y[indexByRow(dim(Y), idxs)] <- idxs
print(Y)

stopifnot(X == t(Y))

Accurately computes the logarithm of the sum of exponentials

Description

Accurately computes the logarithm of the sum of exponentials, that is, $log(sum(exp(lx)))$ . If $lx = log(x)$ , then this is equivalently to calculating $log(sum(x))$ .

Usage

logSumExp(lx, idxs = NULL, na.rm = FALSE, ...)
logSumExp(lx, idxs = NULL, na.rm = FALSE, ...)

Arguments

`lx`	A `numeric` `vector`. Typically `lx` are $log(x)$ values.
`idxs`	A `vector` indicating subset of elements to operate over. If `NULL`, no subsetting is done.
`na.rm`	If `TRUE`, missing values are excluded.
`...`	Not used.

Details

This function, which avoid numerical underflow, is often used when computing the logarithm of the sum of small numbers ( $|x| << 1$ ) such as probabilities.

This is function is more accurate than log(sum(exp(lx))) when the values of $x = exp(lx)$ are $|x| << 1$ . The implementation of this function is based on the observation that

$log(a + b) = [ la = log(a), lb = log(b) ] = log( exp(la) + exp(lb) ) = la + log ( 1 + exp(lb - la) )$

Assuming $la > lb$ , then $|lb - la| < |lb|$ , and it is less likely that the computation of $1 + exp(lb - la)$ will not underflow/overflow numerically. Because of this, the overall result from this function should be more accurate. Analogously to this, the implementation of this function finds the maximum value of lx and subtracts it from the remaining values in lx.

Value

Returns a numeric scalar.

Benchmarking

This method is optimized for correctness, that avoiding underflowing. It is implemented in native code that is optimized for speed and memory.

Author(s)

Henrik Bengtsson

References

[1] R Core Team, Writing R Extensions, v3.0.0, April 2013.
[2] Laurent El Ghaoui, Hyper-Textbook: Optimization Models and Applications, University of California at Berkeley, August 2012. (Chapter 'Log-Sum-Exp (LSE) Function and Properties')
[3] R-help thread logsumexp function in R, 2011-02-17. https://stat.ethz.ch/pipermail/r-help/2011-February/269205.html

Examples

## EXAMPLE #1
lx <- c(1000.01, 1000.02)
y0 <- log(sum(exp(lx)))
print(y0) ## Inf

y1 <- logSumExp(lx)
print(y1) ## 1000.708


## EXAMPLE #2
lx <- c(-1000.01, -1000.02)
y0 <- log(sum(exp(lx)))
print(y0) ## -Inf

y1 <- logSumExp(lx)
print(y1) ## -999.3218


## EXAMPLE #3
## R-help thread 'Beyond double-precision?' on May 9, 2009.

set.seed(1)
x <- runif(50)

## The logarithm of the harmonic mean
y0 <- log(1 / mean(1 / x))
print(y0)  ## -1.600885

lx <- log(x)
y1 <- log(length(x)) - logSumExp(-lx)
print(y1)  ## [1] -1.600885

# Sanity check
stopifnot(all.equal(y1, y0))
## EXAMPLE #1
lx <- c(1000.01, 1000.02)
y0 <- log(sum(exp(lx)))
print(y0) ## Inf

y1 <- logSumExp(lx)
print(y1) ## 1000.708


## EXAMPLE #2
lx <- c(-1000.01, -1000.02)
y0 <- log(sum(exp(lx)))
print(y0) ## -Inf

y1 <- logSumExp(lx)
print(y1) ## -999.3218


## EXAMPLE #3
## R-help thread 'Beyond double-precision?' on May 9, 2009.

set.seed(1)
x <- runif(50)

## The logarithm of the harmonic mean
y0 <- log(1 / mean(1 / x))
print(y0)  ## -1.600885

lx <- log(x)
y1 <- log(length(x)) - logSumExp(-lx)
print(y1)  ## [1] -1.600885

# Sanity check
stopifnot(all.equal(y1, y0))

Calculates the product for each row (column) in a matrix

Description

Calculates the product for each row (column) in a matrix.

Usage

product(x, idxs = NULL, na.rm = FALSE, ...)

rowProds(x, rows = NULL, cols = NULL, na.rm = FALSE,
  method = c("direct", "expSumLog"), ..., useNames = TRUE)

colProds(x, rows = NULL, cols = NULL, na.rm = FALSE,
  method = c("direct", "expSumLog"), ..., useNames = TRUE)
product(x, idxs = NULL, na.rm = FALSE, ...)

rowProds(x, rows = NULL, cols = NULL, na.rm = FALSE,
  method = c("direct", "expSumLog"), ..., useNames = TRUE)

colProds(x, rows = NULL, cols = NULL, na.rm = FALSE,
  method = c("direct", "expSumLog"), ..., useNames = TRUE)

Arguments

`x`	An NxK `matrix` or, if `dim.` is specified, an N * K `vector`.
`idxs`	A `vector` indicating subset of elements to operate over. If `NULL`, no subsetting is done.
`na.rm`	If `TRUE`, missing values are excluded.
`...`	Not used.
`rows`	A `vector` indicating subset of rows to operate over. If `NULL`, no subsetting is done.
`cols`	A `vector` indicating subset of columns to operate over. If `NULL`, no subsetting is done.
`method`	A `character` string specifying how each product is calculated.
`useNames`	If `TRUE` (default), names attributes of the result are set, otherwise not.

Details

If method = "expSumLog", then then product() function is used, which calculates the product via the logarithmic transform (treating negative values specially). This improves the precision and lowers the risk for numeric overflow. If method = "direct", the direct product is calculated via the prod() function.

Value

Returns a numeric vector of length N (K).

Missing values

Note, if method = "expSumLog", na.rm = FALSE, and x contains missing values (NA or NaN), then the calculated value is also missing value. Note that it depends on platform whether NaN or NA is returned when an NaN exists, cf. is.nan().

Author(s)

Henrik Bengtsson

Checks if a value exists / does not exist in each row (column) of a matrix

Description

Checks if a value exists / does not exist in each row (column) of a matrix.

Usage

rowAlls(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE,
  dim. = dim(x), ..., useNames = TRUE)

colAlls(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE,
  dim. = dim(x), ..., useNames = TRUE)

allValue(x, idxs = NULL, value = TRUE, na.rm = FALSE, ...)

rowAnys(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE,
  dim. = dim(x), ..., useNames = TRUE)

colAnys(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE,
  dim. = dim(x), ..., useNames = TRUE)

anyValue(x, idxs = NULL, value = TRUE, na.rm = FALSE, ...)
rowAlls(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE,
  dim. = dim(x), ..., useNames = TRUE)

colAlls(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE,
  dim. = dim(x), ..., useNames = TRUE)

allValue(x, idxs = NULL, value = TRUE, na.rm = FALSE, ...)

rowAnys(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE,
  dim. = dim(x), ..., useNames = TRUE)

colAnys(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE,
  dim. = dim(x), ..., useNames = TRUE)

anyValue(x, idxs = NULL, value = TRUE, na.rm = FALSE, ...)

Arguments

`x`	An NxK `matrix` or, if `dim.` is specified, an N * K `vector`.
`rows`	A `vector` indicating subset of rows to operate over. If `NULL`, no subsetting is done.
`cols`	A `vector` indicating subset of columns to operate over. If `NULL`, no subsetting is done.
`value`	A value to search for.
`na.rm`	If `TRUE`, missing values are excluded.
`dim.`	An `integer` `vector` of length two specifying the dimension of `x`, also when not a `matrix`. Comment: The reason for this argument being named with a period at the end is purely technical (we get a run-time error if we try to name it `dim`).
`...`	Not used.
`useNames`	If `TRUE` (default), names attributes of the result are set, otherwise not.
`idxs`	A `vector` indicating subset of elements to operate over. If `NULL`, no subsetting is done.

Details

These functions takes either a matrix or a vector as input. If a vector, then argument dim. must be specified and fulfill prod(dim.) == length(x). The result will be identical to the results obtained when passing matrix(x, nrow = dim.[1L], ncol = dim.[2L]), but avoids having to temporarily create/allocate a matrix, if only such is needed only for these calculations.

Value

rowAlls() (colAlls()) returns an logical vector of length N (K). Analogously for rowAnys() (rowAlls()).

Logical `value`

When value is logical, the result is as if the function is applied on as.logical(x). More specifically, if x is numeric, then all zeros are treated as FALSE, non-zero values as TRUE, and all missing values as NA.

Author(s)

Henrik Bengtsson

Examples

x <- matrix(FALSE, nrow = 10, ncol = 5)
x[3:7, c(2, 4)] <- TRUE
x[2:4, ] <- TRUE
x[, 1] <- TRUE
x[5, ] <- FALSE
x[, 5] <- FALSE
print(x)

print(rowCounts(x))       # 1 4 4 4 0 3 3 1 1 1
print(colCounts(x))       # 9 5 3 5 0

print(rowAnys(x))
print(which(rowAnys(x)))  # 1  2  3  4  6  7  8  9 10
print(colAnys(x))
print(which(colAnys(x)))  # 1 2 3 4
x <- matrix(FALSE, nrow = 10, ncol = 5)
x[3:7, c(2, 4)] <- TRUE
x[2:4, ] <- TRUE
x[, 1] <- TRUE
x[5, ] <- FALSE
x[, 5] <- FALSE
print(x)

print(rowCounts(x))       # 1 4 4 4 0 3 3 1 1 1
print(colCounts(x))       # 9 5 3 5 0

print(rowAnys(x))
print(which(rowAnys(x)))  # 1  2  3  4  6  7  8  9 10
print(colAnys(x))
print(which(colAnys(x)))  # 1 2 3 4

Extracts one cell per row (column) from a matrix

Description

Extracts one cell per row (column) from a matrix. The implementation is optimized for memory and speed.

Usage

rowCollapse(x, idxs, rows = NULL, dim. = dim(x), ..., useNames = TRUE)

colCollapse(x, idxs, cols = NULL, dim. = dim(x), ..., useNames = TRUE)
rowCollapse(x, idxs, rows = NULL, dim. = dim(x), ..., useNames = TRUE)

colCollapse(x, idxs, cols = NULL, dim. = dim(x), ..., useNames = TRUE)

Arguments

`x`	An NxK `matrix` or, if `dim.` is specified, an N * K `vector`.
`idxs`	An index `vector` of (maximum) length N (K) specifying the columns (rows) to be extracted.
`rows`	A `vector` indicating subset of rows to operate over. If `NULL`, no subsetting is done.
`dim.`	An `integer` `vector` of length two specifying the dimension of `x`, also when not a `matrix`. Comment: The reason for this argument being named with a period at the end is purely technical (we get a run-time error if we try to name it `dim`).
`...`	Not used.
`useNames`	If `TRUE` (default), names attributes of the result are set, otherwise not.
`cols`	A `vector` indicating subset of columns to operate over. If `NULL`, no subsetting is done.

Value

Returns a vector of length N (K).

Author(s)

Henrik Bengtsson

Examples

x <- matrix(1:27, ncol = 3)

y <- rowCollapse(x, 1)
stopifnot(identical(y, x[, 1]))

y <- rowCollapse(x, 2)
stopifnot(identical(y, x[, 2]))

y <- rowCollapse(x, c(1, 1, 1, 1, 1, 3, 3, 3, 3))
stopifnot(identical(y, c(x[1:5, 1], x[6:9, 3])))

y <- rowCollapse(x, 1:3)
print(y)
y_truth <- c(x[1, 1], x[2, 2], x[3, 3], x[4, 1], x[5, 2],
             x[6, 3], x[7, 1], x[8, 2], x[9, 3])
stopifnot(identical(y, y_truth))
x <- matrix(1:27, ncol = 3)

y <- rowCollapse(x, 1)
stopifnot(identical(y, x[, 1]))

y <- rowCollapse(x, 2)
stopifnot(identical(y, x[, 2]))

y <- rowCollapse(x, c(1, 1, 1, 1, 1, 3, 3, 3, 3))
stopifnot(identical(y, c(x[1:5, 1], x[6:9, 3])))

y <- rowCollapse(x, 1:3)
print(y)
y_truth <- c(x[1, 1], x[2, 2], x[3, 3], x[4, 1], x[5, 2],
             x[6, 3], x[7, 1], x[8, 2], x[9, 3])
stopifnot(identical(y, y_truth))

Counts the number of occurrences of a specific value

Description

The row- and column-wise functions take either a matrix or a vector as input. If a vector, then argument dim. must be specified and fulfill prod(dim.) == length(x). The result will be identical to the results obtained when passing matrix(x, nrow = dim.[1L], ncol = dim.[2L]), but avoids having to temporarily create/allocate a matrix, if only such is needed only for these calculations.

Usage

rowCounts(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE,
  dim. = dim(x), ..., useNames = TRUE)

colCounts(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE,
  dim. = dim(x), ..., useNames = TRUE)

count(x, idxs = NULL, value = TRUE, na.rm = FALSE, ...)
rowCounts(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE,
  dim. = dim(x), ..., useNames = TRUE)

colCounts(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE,
  dim. = dim(x), ..., useNames = TRUE)

count(x, idxs = NULL, value = TRUE, na.rm = FALSE, ...)

Arguments

`x`	An NxK `matrix` or, if `dim.` is specified, an N * K `vector`.
`rows`	A `vector` indicating subset of rows to operate over. If `NULL`, no subsetting is done.
`cols`	A `vector` indicating subset of columns to operate over. If `NULL`, no subsetting is done.
`value`	A value to search for.
`na.rm`	If `TRUE`, missing values are excluded.
`dim.`	An `integer` `vector` of length two specifying the dimension of `x`, also when not a `matrix`. Comment: The reason for this argument being named with a period at the end is purely technical (we get a run-time error if we try to name it `dim`).
`...`	Not used.
`useNames`	If `TRUE` (default), names attributes of the result are set, otherwise not.
`idxs`	A `vector` indicating subset of elements to operate over. If `NULL`, no subsetting is done.

Value

rowCounts() (colCounts()) returns an integer vector of length N (K). count() returns a scalar of type integer if the count is less than 2^31-1 (= .Machine$integer.max) otherwise a scalar of type double.

Author(s)

Henrik Bengtsson

Examples

x <- matrix(0:11, nrow = 4, ncol = 3)
x[2:3, 2:3] <- 2:5
x[3, 3] <- NA_integer_
print(x)

print(rowCounts(x, value = 2))
## [1]  0  1 NA  0
print(colCounts(x, value = 2))
## [1]  1  1 NA
print(colCounts(x, value = NA_integer_))
## [1] 0 0 1

print(rowCounts(x, value = 2, na.rm = TRUE))
## [1] 0 1 1 0
print(colCounts(x, value = 2, na.rm = TRUE))
## [1] 1 1 0

print(rowAnys(x, value = 2))
## [1] FALSE  TRUE  TRUE FALSE
print(rowAnys(x, value = NA_integer_))
## [1] FALSE FALSE  TRUE FALSE

print(colAnys(x, value = 2))
## [1] TRUE TRUE   NA
print(colAnys(x, value = 2, na.rm = TRUE))
## [1]  TRUE  TRUE FALSE

print(colAlls(x, value = 2))
## [1] FALSE FALSE FALSE
x <- matrix(0:11, nrow = 4, ncol = 3)
x[2:3, 2:3] <- 2:5
x[3, 3] <- NA_integer_
print(x)

print(rowCounts(x, value = 2))
## [1]  0  1 NA  0
print(colCounts(x, value = 2))
## [1]  1  1 NA
print(colCounts(x, value = NA_integer_))
## [1] 0 0 1

print(rowCounts(x, value = 2, na.rm = TRUE))
## [1] 0 1 1 0
print(colCounts(x, value = 2, na.rm = TRUE))
## [1] 1 1 0

print(rowAnys(x, value = 2))
## [1] FALSE  TRUE  TRUE FALSE
print(rowAnys(x, value = NA_integer_))
## [1] FALSE FALSE  TRUE FALSE

print(colAnys(x, value = 2))
## [1] TRUE TRUE   NA
print(colAnys(x, value = 2, na.rm = TRUE))
## [1]  TRUE  TRUE FALSE

print(colAlls(x, value = 2))
## [1] FALSE FALSE FALSE

Cumulative sums, products, minima and maxima for each row (column) in a matrix

Description

Cumulative sums, products, minima and maxima for each row (column) in a matrix.

Usage

rowCumsums(x, rows = NULL, cols = NULL, dim. = dim(x), ...,
  useNames = TRUE)

colCumsums(x, rows = NULL, cols = NULL, dim. = dim(x), ...,
  useNames = TRUE)

rowCumprods(x, rows = NULL, cols = NULL, dim. = dim(x), ...,
  useNames = TRUE)

colCumprods(x, rows = NULL, cols = NULL, dim. = dim(x), ...,
  useNames = TRUE)

rowCummins(x, rows = NULL, cols = NULL, dim. = dim(x), ...,
  useNames = TRUE)

colCummins(x, rows = NULL, cols = NULL, dim. = dim(x), ...,
  useNames = TRUE)

rowCummaxs(x, rows = NULL, cols = NULL, dim. = dim(x), ...,
  useNames = TRUE)

colCummaxs(x, rows = NULL, cols = NULL, dim. = dim(x), ...,
  useNames = TRUE)
rowCumsums(x, rows = NULL, cols = NULL, dim. = dim(x), ...,
  useNames = TRUE)

colCumsums(x, rows = NULL, cols = NULL, dim. = dim(x), ...,
  useNames = TRUE)

rowCumprods(x, rows = NULL, cols = NULL, dim. = dim(x), ...,
  useNames = TRUE)

colCumprods(x, rows = NULL, cols = NULL, dim. = dim(x), ...,
  useNames = TRUE)

rowCummins(x, rows = NULL, cols = NULL, dim. = dim(x), ...,
  useNames = TRUE)

colCummins(x, rows = NULL, cols = NULL, dim. = dim(x), ...,
  useNames = TRUE)

rowCummaxs(x, rows = NULL, cols = NULL, dim. = dim(x), ...,
  useNames = TRUE)

colCummaxs(x, rows = NULL, cols = NULL, dim. = dim(x), ...,
  useNames = TRUE)

Arguments

`x`	An NxK `matrix` or, if `dim.` is specified, an N * K `vector`.
`rows`	A `vector` indicating subset of rows to operate over. If `NULL`, no subsetting is done.
`cols`	A `vector` indicating subset of columns to operate over. If `NULL`, no subsetting is done.
`dim.`	An `integer` `vector` of length two specifying the dimension of `x`, also when not a `matrix`. Comment: The reason for this argument being named with a period at the end is purely technical (we get a run-time error if we try to name it `dim`).
`...`	Not used.
`useNames`	If `TRUE` (default), names attributes of the result are set, otherwise not.

Value

Returns a numeric NxK matrix of the same mode as x, except when x is of mode logical, then the return type is integer.

Author(s)

Henrik Bengtsson

Examples

x <- matrix(1:12, nrow = 4, ncol = 3)
print(x)

yr <- rowCumsums(x)
print(yr)

yc <- colCumsums(x)
print(yc)

yr <- rowCumprods(x)
print(yr)

yc <- colCumprods(x)
print(yc)

yr <- rowCummaxs(x)
print(yr)

yc <- colCummaxs(x)
print(yc)

yr <- rowCummins(x)
print(yr)

yc <- colCummins(x)
print(yc)
x <- matrix(1:12, nrow = 4, ncol = 3)
print(x)

yr <- rowCumsums(x)
print(yr)

yc <- colCumsums(x)
print(yc)

yr <- rowCumprods(x)
print(yr)

yc <- colCumprods(x)
print(yc)

yr <- rowCummaxs(x)
print(yr)

yc <- colCummaxs(x)
print(yc)

yr <- rowCummins(x)
print(yr)

yc <- colCummins(x)
print(yc)

Calculates difference for each row (column) in a matrix

Description

Calculates difference for each row (column) in a matrix.

Usage

rowDiffs(x, rows = NULL, cols = NULL, lag = 1L, differences = 1L,
  dim. = dim(x), ..., useNames = TRUE)

colDiffs(x, rows = NULL, cols = NULL, lag = 1L, differences = 1L,
  dim. = dim(x), ..., useNames = TRUE)
rowDiffs(x, rows = NULL, cols = NULL, lag = 1L, differences = 1L,
  dim. = dim(x), ..., useNames = TRUE)

colDiffs(x, rows = NULL, cols = NULL, lag = 1L, differences = 1L,
  dim. = dim(x), ..., useNames = TRUE)

Arguments

`x`	An NxK `matrix` or, if `dim.` is specified, an N * K `vector`.
`rows`	A `vector` indicating subset of rows to operate over. If `NULL`, no subsetting is done.
`cols`	A `vector` indicating subset of columns to operate over. If `NULL`, no subsetting is done.
`lag`	An `integer` specifying the lag.
`differences`	An `integer` specifying the order of difference.
`dim.`	An `integer` `vector` of length two specifying the dimension of `x`, also when not a `matrix`. Comment: The reason for this argument being named with a period at the end is purely technical (we get a run-time error if we try to name it `dim`).
`...`	Not used.
`useNames`	If `TRUE` (default), names attributes of the result are set, otherwise not.

Value

Returns a numeric Nx(K-1) or (N-1)xK matrix.

Author(s)

Henrik Bengtsson

Examples

x <- matrix(1:27, ncol = 3)

d1 <- rowDiffs(x)
print(d1)

d2 <- t(colDiffs(t(x)))
stopifnot(all.equal(d2, d1))
x <- matrix(1:27, ncol = 3)

d1 <- rowDiffs(x)
print(d1)

d2 <- t(colDiffs(t(x)))
stopifnot(all.equal(d2, d1))

Estimates of the interquartile range for each row (column) in a matrix

Description

Estimates of the interquartile range for each row (column) in a matrix.

Usage

rowIQRs(x, rows = NULL, cols = NULL, na.rm = FALSE, ...,
  useNames = TRUE)

colIQRs(x, rows = NULL, cols = NULL, na.rm = FALSE, ...,
  useNames = TRUE)

iqr(x, idxs = NULL, na.rm = FALSE, ...)
rowIQRs(x, rows = NULL, cols = NULL, na.rm = FALSE, ...,
  useNames = TRUE)

colIQRs(x, rows = NULL, cols = NULL, na.rm = FALSE, ...,
  useNames = TRUE)

iqr(x, idxs = NULL, na.rm = FALSE, ...)

Arguments

`x`	An NxK `matrix` or, if `dim.` is specified, an N * K `vector`.
`rows`	A `vector` indicating subset of rows to operate over. If `NULL`, no subsetting is done.
`cols`	A `vector` indicating subset of columns to operate over. If `NULL`, no subsetting is done.
`na.rm`	If `TRUE`, missing values are excluded.
`...`	Additional arguments passed to `rowQuantiles`() (`colQuantiles()`).
`useNames`	If `TRUE` (default), names attributes of the result are set, otherwise not.
`idxs`	A `vector` indicating subset of elements to operate over. If `NULL`, no subsetting is done.

Value

Returns a numeric vector of length N (K).

Missing values

Contrary to IQR, which gives an error if there are missing values and na.rm = FALSE, iqr() and its corresponding row and column-specific functions return NA_real_.

Author(s)

Henrik Bengtsson

Examples

set.seed(1)

x <- matrix(rnorm(50 * 40), nrow = 50, ncol = 40)
str(x)

# Row IQRs
q <- rowIQRs(x)
print(q)
q0 <- apply(x, MARGIN = 1, FUN = IQR)
stopifnot(all.equal(q0, q))

# Column IQRs
q <- colIQRs(x)
print(q)
q0 <- apply(x, MARGIN = 2, FUN = IQR)
stopifnot(all.equal(q0, q))
set.seed(1)

x <- matrix(rnorm(50 * 40), nrow = 50, ncol = 40)
str(x)

# Row IQRs
q <- rowIQRs(x)
print(q)
q0 <- apply(x, MARGIN = 1, FUN = IQR)
stopifnot(all.equal(q0, q))

# Column IQRs
q <- colIQRs(x)
print(q)
q0 <- apply(x, MARGIN = 2, FUN = IQR)
stopifnot(all.equal(q0, q))

Accurately computes the logarithm of the sum of exponentials across rows or columns

Description

Accurately computes the logarithm of the sum of exponentials across rows or columns.

Usage

rowLogSumExps(lx, rows = NULL, cols = NULL, na.rm = FALSE,
  dim. = dim(lx), ..., useNames = TRUE)

colLogSumExps(lx, rows = NULL, cols = NULL, na.rm = FALSE,
  dim. = dim(lx), ..., useNames = TRUE)
rowLogSumExps(lx, rows = NULL, cols = NULL, na.rm = FALSE,
  dim. = dim(lx), ..., useNames = TRUE)

colLogSumExps(lx, rows = NULL, cols = NULL, na.rm = FALSE,
  dim. = dim(lx), ..., useNames = TRUE)

Arguments

`lx`	A `numeric` NxK `matrix`. Typically `lx` are $log(x)$ values.
`rows`, `cols`	A `vector` indicating subset of rows (and/or columns) to operate over. If `NULL`, no subsetting is done.
`na.rm`	If `TRUE`, any missing values are ignored, otherwise not.
`dim.`	An `integer` `vector` of length two specifying the dimension of `x`, also when not a `matrix`.
`...`	Not used.
`useNames`	If `TRUE` (default), names attributes of the result are set, otherwise not.

Value

A numeric vector of length N (K).

Benchmarking

These methods are implemented in native code and have been optimized for speed and memory.

Author(s)

Native implementation by Henrik Bengtsson. Original R code by Nakayama ??? (Japan).

Standard deviation estimates for each row (column) in a matrix

Description

Standard deviation estimates for each row (column) in a matrix.

Usage

rowMads(x, rows = NULL, cols = NULL, center = NULL, constant = 1.4826,
  na.rm = FALSE, dim. = dim(x), ..., useNames = TRUE)

colMads(x, rows = NULL, cols = NULL, center = NULL, constant = 1.4826,
  na.rm = FALSE, dim. = dim(x), ..., useNames = TRUE)

rowSds(x, rows = NULL, cols = NULL, na.rm = FALSE, refine = TRUE,
  center = NULL, dim. = dim(x), ..., useNames = TRUE)

colSds(x, rows = NULL, cols = NULL, na.rm = FALSE, refine = TRUE,
  center = NULL, dim. = dim(x), ..., useNames = TRUE)
rowMads(x, rows = NULL, cols = NULL, center = NULL, constant = 1.4826,
  na.rm = FALSE, dim. = dim(x), ..., useNames = TRUE)

colMads(x, rows = NULL, cols = NULL, center = NULL, constant = 1.4826,
  na.rm = FALSE, dim. = dim(x), ..., useNames = TRUE)

rowSds(x, rows = NULL, cols = NULL, na.rm = FALSE, refine = TRUE,
  center = NULL, dim. = dim(x), ..., useNames = TRUE)

colSds(x, rows = NULL, cols = NULL, na.rm = FALSE, refine = TRUE,
  center = NULL, dim. = dim(x), ..., useNames = TRUE)

Arguments

`x`	An NxK `matrix` or, if `dim.` is specified, an N * K `vector`.
`rows`	A `vector` indicating subset of rows to operate over. If `NULL`, no subsetting is done.
`cols`	A `vector` indicating subset of columns to operate over. If `NULL`, no subsetting is done.
`center`	(optional) The center, defaults to the row means for the SD estimators and row medians for the MAD estimators.
`constant`	A scale factor. See `mad` for details.
`na.rm`	If `TRUE`, missing values are excluded.
`dim.`	An `integer` `vector` of length two specifying the dimension of `x`, also when not a `matrix`. Comment: The reason for this argument being named with a period at the end is purely technical (we get a run-time error if we try to name it `dim`).
`...`	Additional arguments passed to `rowMeans()` and `rowSums()`.
`useNames`	If `TRUE` (default), names attributes of the result are set, otherwise not.
`refine`	If `TRUE`, 'center' is NULL, and `x` is `numeric`, then extra effort is used to calculate the average with greater numerical precision, otherwise not.

Value

Returns a numeric vector of length N (K).

Author(s)

Henrik Bengtsson

Calculates the mean for each row (column) in a matrix

Description

Calculates the mean for each row (column) in a matrix.

Usage

rowMeans2(x, rows = NULL, cols = NULL, na.rm = FALSE, refine = TRUE,
  dim. = dim(x), ..., useNames = TRUE)

colMeans2(x, rows = NULL, cols = NULL, na.rm = FALSE, refine = TRUE,
  dim. = dim(x), ..., useNames = TRUE)
rowMeans2(x, rows = NULL, cols = NULL, na.rm = FALSE, refine = TRUE,
  dim. = dim(x), ..., useNames = TRUE)

colMeans2(x, rows = NULL, cols = NULL, na.rm = FALSE, refine = TRUE,
  dim. = dim(x), ..., useNames = TRUE)

Arguments

`x`	An NxK `matrix` or, if `dim.` is specified, an N * K `vector`.
`rows`	A `vector` indicating subset of rows to operate over. If `NULL`, no subsetting is done.
`cols`	A `vector` indicating subset of columns to operate over. If `NULL`, no subsetting is done.
`na.rm`	If `TRUE`, missing values are excluded.
`refine`	If `TRUE` and `x` is `numeric`, then extra effort is used to calculate the average with greater numerical precision, otherwise not.
`dim.`	An `integer` `vector` of length two specifying the dimension of `x`, also when not a `matrix`. Comment: The reason for this argument being named with a period at the end is purely technical (we get a run-time error if we try to name it `dim`).
`...`	Not used.
`useNames`	If `TRUE` (default), names attributes of the result are set, otherwise not.

Details

The implementation of rowMeans2() and colMeans2() is optimized for both speed and memory.

Value

Returns a numeric vector of length N (K).

Author(s)

Henrik Bengtsson

Calculates the median for each row (column) in a matrix

Description

Calculates the median for each row (column) in a matrix.

Usage

rowMedians(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x),
  ..., useNames = TRUE)

colMedians(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x),
  ..., useNames = TRUE)
rowMedians(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x),
  ..., useNames = TRUE)

colMedians(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x),
  ..., useNames = TRUE)

Arguments

`x`	An NxK `matrix` or, if `dim.` is specified, an N * K `vector`.
`rows`, `cols`	A `vector` indicating subset of rows (and/or columns) to operate over. If `NULL`, no subsetting is done.
`na.rm`	If `TRUE`, `NA`s are excluded first, otherwise not.
`dim.`	An `integer` `vector` of length two specifying the dimension of `x`, also when not a `matrix`.
`...`	Not used.
`useNames`	If `TRUE` (default), names attributes of the result are set, otherwise not.

Details

The implementation of rowMedians() and colMedians() is optimized for both speed and memory. To avoid coercing to doubles (and hence memory allocation), there is a special implementation for integer matrices. That is, if x is an integer matrix, then rowMedians(as.double(x)) (rowMedians(as.double(x))) would require three times the memory of rowMedians(x) (colMedians(x)), but all this is avoided.

Value

Returns a numeric vector of length N (K).

Author(s)

Henrik Bengtsson, Harris Jaffee

Gets an order statistic for each row (column) in a matrix

Description

Gets an order statistic for each row (column) in a matrix.

Usage

rowOrderStats(x, rows = NULL, cols = NULL, which, dim. = dim(x), ...,
  useNames = TRUE)

colOrderStats(x, rows = NULL, cols = NULL, which, dim. = dim(x), ...,
  useNames = TRUE)
rowOrderStats(x, rows = NULL, cols = NULL, which, dim. = dim(x), ...,
  useNames = TRUE)

colOrderStats(x, rows = NULL, cols = NULL, which, dim. = dim(x), ...,
  useNames = TRUE)

Arguments

`x`	An NxK `matrix` or, if `dim.` is specified, an N * K `vector`.
`rows`	A `vector` indicating subset of rows to operate over. If `NULL`, no subsetting is done.
`cols`	A `vector` indicating subset of columns to operate over. If `NULL`, no subsetting is done.
`which`	An `integer` index in [1,K] ([1,N]) indicating which order statistic to be returned.
`dim.`	An `integer` `vector` of length two specifying the dimension of `x`, also when not a `matrix`. Comment: The reason for this argument being named with a period at the end is purely technical (we get a run-time error if we try to name it `dim`).
`...`	Not used.
`useNames`	If `TRUE` (default), names attributes of the result are set, otherwise not.

Details

The implementation of rowOrderStats() is optimized for both speed and memory. To avoid coercing to doubles (and hence memory allocation), there is a unique implementation for integer matrices.

Value

Returns a numeric vector of length N (K).

Missing values

This method does not handle missing values, that is, the result corresponds to having na.rm = FALSE (if such an argument would be available).

Author(s)

The native implementation of rowOrderStats() was adopted by Henrik Bengtsson from Robert Gentleman's rowQ() in the Biobase package.

Estimates quantiles for each row (column) in a matrix

Description

Estimates quantiles for each row (column) in a matrix.

Usage

rowQuantiles(x, rows = NULL, cols = NULL, probs = seq(from = 0, to = 1,
  by = 0.25), na.rm = FALSE, type = 7L, digits = 7L, ...,
  useNames = TRUE, drop = TRUE)

colQuantiles(x, rows = NULL, cols = NULL, probs = seq(from = 0, to = 1,
  by = 0.25), na.rm = FALSE, type = 7L, digits = 7L, ...,
  useNames = TRUE, drop = TRUE)
rowQuantiles(x, rows = NULL, cols = NULL, probs = seq(from = 0, to = 1,
  by = 0.25), na.rm = FALSE, type = 7L, digits = 7L, ...,
  useNames = TRUE, drop = TRUE)

colQuantiles(x, rows = NULL, cols = NULL, probs = seq(from = 0, to = 1,
  by = 0.25), na.rm = FALSE, type = 7L, digits = 7L, ...,
  useNames = TRUE, drop = TRUE)

Arguments

`x`	An `integer`, `numeric` or `logical` NxK `matrix` with N >= 0.
`rows`	A `vector` indicating subset of rows to operate over. If `NULL`, no subsetting is done.
`cols`	A `vector` indicating subset of columns to operate over. If `NULL`, no subsetting is done.
`probs`	A `numeric` `vector` of J probabilities in [0, 1].
`na.rm`	If `TRUE`, missing values are excluded.
`type`	An `integer` specifying the type of estimator. See `quantile` for more details.
`digits`	An `integer` specifying the precision of the formatted percentages. Not used when 'useNames = FALSE'. In matrixStats (< 0.63.0), the default used to be 'max(2L, getOption("digits"))' inline with R (< 4.1.0).
`...`	Additional arguments passed to `quantile`.
`useNames`	If `TRUE` (default), names attributes of the result are set, otherwise not.
`drop`	If TRUE, singleton dimensions in the result are dropped, otherwise not.

Value

Returns a NxJ (KxJ) matrix, where N (K) is the number of rows (columns) for which the J quantiles are calculated. The return type is either integer or numeric depending on type.

Author(s)

Henrik Bengtsson

Examples

set.seed(1)

x <- matrix(rnorm(50 * 40), nrow = 50, ncol = 40)
str(x)

probs <- c(0.25, 0.5, 0.75)

# Row quantiles
q <- rowQuantiles(x, probs = probs)
print(q)
q_0 <- apply(x, MARGIN = 1, FUN = quantile, probs = probs)
stopifnot(all.equal(q_0, t(q)))

# Column IQRs
q <- colQuantiles(x, probs = probs)
print(q)
q_0 <- apply(x, MARGIN = 2, FUN = quantile, probs = probs)
stopifnot(all.equal(q_0, t(q)))
set.seed(1)

x <- matrix(rnorm(50 * 40), nrow = 50, ncol = 40)
str(x)

probs <- c(0.25, 0.5, 0.75)

# Row quantiles
q <- rowQuantiles(x, probs = probs)
print(q)
q_0 <- apply(x, MARGIN = 1, FUN = quantile, probs = probs)
stopifnot(all.equal(q_0, t(q)))

# Column IQRs
q <- colQuantiles(x, probs = probs)
print(q)
q_0 <- apply(x, MARGIN = 2, FUN = quantile, probs = probs)
stopifnot(all.equal(q_0, t(q)))

Gets the range of values in each row (column) of a matrix

Description

Gets the range of values in each row (column) of a matrix.

Usage

rowRanges(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x),
  ..., useNames = TRUE)

rowMins(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x), ...,
  useNames = TRUE)

rowMaxs(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x), ...,
  useNames = TRUE)

colRanges(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x),
  ..., useNames = TRUE)

colMins(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x), ...,
  useNames = TRUE)

colMaxs(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x), ...,
  useNames = TRUE)
rowRanges(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x),
  ..., useNames = TRUE)

rowMins(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x), ...,
  useNames = TRUE)

rowMaxs(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x), ...,
  useNames = TRUE)

colRanges(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x),
  ..., useNames = TRUE)

colMins(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x), ...,
  useNames = TRUE)

colMaxs(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x), ...,
  useNames = TRUE)

Arguments

`x`	An NxK `matrix` or, if `dim.` is specified, an N * K `vector`.
`rows`	A `vector` indicating subset of rows to operate over. If `NULL`, no subsetting is done.
`cols`	A `vector` indicating subset of columns to operate over. If `NULL`, no subsetting is done.
`na.rm`	If `TRUE`, missing values are excluded.
`dim.`	An `integer` `vector` of length two specifying the dimension of `x`, also when not a `matrix`. Comment: The reason for this argument being named with a period at the end is purely technical (we get a run-time error if we try to name it `dim`).
`...`	Not used.
`useNames`	If `TRUE` (default), names attributes of the result are set, otherwise not.

Value

rowRanges() (colRanges()) returns a numeric Nx2 (Kx2) matrix, where N (K) is the number of rows (columns) for which the ranges are calculated.

rowMins()/rowMaxs() (colMins()/colMaxs()) returns a numeric vector of length N (K).

Author(s)

Henrik Bengtsson

Gets the rank of the elements in each row (column) of a matrix

Description

Gets the rank of the elements in each row (column) of a matrix.

Usage

rowRanks(x, rows = NULL, cols = NULL, ties.method = c("max", "average",
  "first", "last", "random", "max", "min", "dense"), dim. = dim(x), ...,
  useNames = TRUE)

colRanks(x, rows = NULL, cols = NULL, ties.method = c("max", "average",
  "first", "last", "random", "max", "min", "dense"), dim. = dim(x),
  preserveShape = FALSE, ..., useNames = TRUE)
rowRanks(x, rows = NULL, cols = NULL, ties.method = c("max", "average",
  "first", "last", "random", "max", "min", "dense"), dim. = dim(x), ...,
  useNames = TRUE)

colRanks(x, rows = NULL, cols = NULL, ties.method = c("max", "average",
  "first", "last", "random", "max", "min", "dense"), dim. = dim(x),
  preserveShape = FALSE, ..., useNames = TRUE)

Arguments

`x`	An NxK `matrix` or, if `dim.` is specified, an N * K `vector`.
`rows`	A `vector` indicating subset of rows to operate over. If `NULL`, no subsetting is done.
`cols`	A `vector` indicating subset of columns to operate over. If `NULL`, no subsetting is done.
`ties.method`	A `character` string specifying how ties are treated. For details, see below.
`dim.`	An `integer` `vector` of length two specifying the dimension of `x`, also when not a `matrix`. Comment: The reason for this argument being named with a period at the end is purely technical (we get a run-time error if we try to name it `dim`).
`...`	Not used.
`useNames`	If `TRUE` (default), names attributes of the result are set, otherwise not.
`preserveShape`	A `logical` specifying whether the `matrix` returned should preserve the input shape of `x`, or not.

Details

These functions rank values and treats missing values the same way as rank(). For equal values ("ties"), argument ties.method determines how these are ranked among each other. More precisely, for the following values of ties.method, each index set of ties consists of:

"first" - increasing values that are all unique
"last" - decreasing values that are all unique
"min" - identical values equaling the minimum of their original ranks
"max" - identical values equaling the maximum of their original ranks
"average" - identical values that equal the sample mean of their original ranks. Because the average is calculated, the returned ranks may be non-integer values
"random" - randomly shuffled values of their original ranks.
"dense" - increasing values that are all unique and, contrary to "first", never contain any gaps

For more information on ties.method = "dense", see frank() of the data.table package. For more information on the other alternatives, see rank().

Note that, due to different randomization strategies, the shuffling order produced by these functions when using ties.method = "random" does not reproduce that of rank().

WARNING: For backward-compatibility reasons, the default is ties.method = "max", which differs from rank() which uses ties.method = "average" by default. Since we plan to change the default behavior in a future version, we recommend to explicitly specify the intended value of argument ties.method.

Value

A matrix of type integer is returned, unless ties.method = "average" when it is of type numeric.

The rowRanks() function always returns an NxK matrix, where N (K) is the number of rows (columns) whose ranks are calculated.

The colRanks() function returns an NxK matrix, if preserveShape = TRUE, otherwise a KxN matrix.

Any names of x are ignored and absent in the result.

Missing values

Missing values are ranked as NA_integer_, as with na.last = "keep" in the rank() function.

Performance

The implementation is optimized for both speed and memory. To avoid coercing to doubles (and hence memory allocation), there is a unique implementation for integer matrices. Furthermore, it is more memory efficient to do colRanks(x, preserveShape = TRUE) than t(colRanks(x, preserveShape = FALSE)).

Author(s)

Hector Corrada Bravo and Harris Jaffee. Peter Langfelder for adding 'ties.method' support. Brian Montgomery for adding more 'ties.method's. Henrik Bengtsson adapted the original native implementation of rowRanks() from Robert Gentleman's rowQ() in the Biobase package.

Calculates the sum for each row (column) in a matrix

Description

Calculates the sum for each row (column) in a matrix.

Usage

rowSums2(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x),
  ..., useNames = TRUE)

colSums2(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x),
  ..., useNames = TRUE)
rowSums2(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x),
  ..., useNames = TRUE)

colSums2(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x),
  ..., useNames = TRUE)

Arguments

`x`	An NxK `matrix` or, if `dim.` is specified, an N * K `vector`.
`rows`	A `vector` indicating subset of rows to operate over. If `NULL`, no subsetting is done.
`cols`	A `vector` indicating subset of columns to operate over. If `NULL`, no subsetting is done.
`na.rm`	If `TRUE`, missing values are excluded.
`dim.`	An `integer` `vector` of length two specifying the dimension of `x`, also when not a `matrix`. Comment: The reason for this argument being named with a period at the end is purely technical (we get a run-time error if we try to name it `dim`).
`...`	Not used.
`useNames`	If `TRUE` (default), names attributes of the result are set, otherwise not.

Details

The implementation of rowSums2() and colSums2() is optimized for both speed and memory.

Value

Returns a numeric vector of length N (K).

Author(s)

Henrik Bengtsson

Tabulates the values in a matrix by row (column).

Description

Tabulates the values in a matrix by row (column).

Usage

rowTabulates(x, rows = NULL, cols = NULL, values = NULL, ...,
  useNames = TRUE)

colTabulates(x, rows = NULL, cols = NULL, values = NULL, ...,
  useNames = TRUE)
rowTabulates(x, rows = NULL, cols = NULL, values = NULL, ...,
  useNames = TRUE)

colTabulates(x, rows = NULL, cols = NULL, values = NULL, ...,
  useNames = TRUE)

Arguments

`x`	An `integer`, a `logical`, or a `raw` NxK `matrix`.
`rows`	A `vector` indicating subset of rows to operate over. If `NULL`, no subsetting is done.
`cols`	A `vector` indicating subset of columns to operate over. If `NULL`, no subsetting is done.
`values`	An `vector` of J values of count. If `NULL`, all (unique) values are counted.
`...`	Not used.
`useNames`	If `TRUE` (default), names attributes of the result are set, otherwise not.

Details

An alternative to these functions, is to use table(x, row(x)) and table(x, col(x)), with the exception that the latter do not support the raw data type. When there are no missing values in x, we have that all(rowTabulates(x) == t(table(x, row(x)))) and all(colTabulates(x) == t(table(x, col(x)))). When there are missing values, we have that all(rowTabulates(x) == t(table(x, row(x), useNA = "always")[, seq_len(nrow(x))])) and all(colTabulates(x) == t(table(x, col(x), useNA = "always")[, seq_len(ncol(x))])).

Value

Returns a NxJ (KxJ) matrix where N (K) is the number of row (column) vectors tabulated and J is the number of values counted.

Author(s)

Henrik Bengtsson

Examples

x <- matrix(1:5, nrow = 10, ncol = 5)
print(x)
print(rowTabulates(x))
print(colTabulates(x))
# Count only certain values
print(rowTabulates(x, values = 1:3))


y <- as.raw(x)
dim(y) <- dim(x)
print(y)
print(rowTabulates(y))
print(colTabulates(y))
x <- matrix(1:5, nrow = 10, ncol = 5)
print(x)
print(rowTabulates(x))
print(colTabulates(x))
# Count only certain values
print(rowTabulates(x, values = 1:3))


y <- as.raw(x)
dim(y) <- dim(x)
print(y)
print(rowTabulates(y))
print(colTabulates(y))

Variance estimates for each row (column) in a matrix

Description

Variance estimates for each row (column) in a matrix.

Usage

rowVars(x, rows = NULL, cols = NULL, na.rm = FALSE, refine = TRUE,
  center = NULL, dim. = dim(x), ..., useNames = TRUE)

colVars(x, rows = NULL, cols = NULL, na.rm = FALSE, refine = TRUE,
  center = NULL, dim. = dim(x), ..., useNames = TRUE)
rowVars(x, rows = NULL, cols = NULL, na.rm = FALSE, refine = TRUE,
  center = NULL, dim. = dim(x), ..., useNames = TRUE)

colVars(x, rows = NULL, cols = NULL, na.rm = FALSE, refine = TRUE,
  center = NULL, dim. = dim(x), ..., useNames = TRUE)

Arguments

`x`	An NxK `matrix` or, if `dim.` is specified, an N * K `vector`.
`rows`	A `vector` indicating subset of rows to operate over. If `NULL`, no subsetting is done.
`cols`	A `vector` indicating subset of columns to operate over. If `NULL`, no subsetting is done.
`na.rm`	If `TRUE`, missing values are excluded.
`refine`	If `TRUE`, 'center' is NULL, and `x` is `numeric`, then extra effort is used to calculate the average with greater numerical precision, otherwise not.
`center`	(optional; a vector or length N (K)) If the row (column) means are already estimated, they can be pre-specified using this argument. This avoid re-estimating them again. _Warning: It is important that a non-biased sample mean estimate is passed. If not, then the variance estimate of the spread will also be biased._ If NULL (default), the row/column means are estimated internally.
`dim.`	An `integer` `vector` of length two specifying the dimension of `x`, also when not a `matrix`. Comment: The reason for this argument being named with a period at the end is purely technical (we get a run-time error if we try to name it `dim`).
`...`	Additional arguments passed to `rowMeans()` and `rowSums()`.
`useNames`	If `TRUE` (default), names attributes of the result are set, otherwise not.

Value

Returns a numeric vector of length N (K).

Providing center estimates

The sample variance is estimated as

$n/(n-1) * mean((x - center)^2)$ ,

where $center$ is estimated as the sample mean, by default. In matrixStats (< 0.58.0),

$n/(n-1) * (mean(x^2) - center^2)$

was used. Both formulas give the same result _when_ 'center' is the sample mean estimate.

Argument 'center' can be used to provide an already existing estimate. It is important that the sample mean estimate is passed. If not, then the variance estimate of the spread will be biased.

For the time being, in order to lower the risk for such mistakes, argument 'center' is occasionally validated against the sample-mean estimate. If a discrepancy is detected, an informative error is provided to prevent incorrect variance estimates from being used. For performance reasons, this check is only performed once every 50 times. The frequency can be controlled by R option 'matrixStats.vars.formula.freq', whose default can be set by environment variable 'R_MATRIXSTATS_VARS_FORMULA_FREQ'.

Author(s)

Henrik Bengtsson

Examples

set.seed(1)

x <- matrix(rnorm(20), nrow = 5, ncol = 4)
print(x)

# Row averages
print(rowMeans(x))
print(rowMedians(x))

# Column averages
print(colMeans(x))
print(colMedians(x))


# Row variabilities
print(rowVars(x))
print(rowSds(x))
print(rowMads(x))
print(rowIQRs(x))

# Column variabilities
print(rowVars(x))
print(colSds(x))
print(colMads(x))
print(colIQRs(x))

# Row ranges
print(rowRanges(x))
print(cbind(rowMins(x), rowMaxs(x)))
print(cbind(rowOrderStats(x, which = 1), rowOrderStats(x, which = ncol(x))))

# Column ranges
print(colRanges(x))
print(cbind(colMins(x), colMaxs(x)))
print(cbind(colOrderStats(x, which = 1), colOrderStats(x, which = nrow(x))))


x <- matrix(rnorm(2000), nrow = 50, ncol = 40)

# Row standard deviations
d <- rowDiffs(x)
s1 <- rowSds(d) / sqrt(2)
s2 <- rowSds(x)
print(summary(s1 - s2))

# Column standard deviations
d <- colDiffs(x)
s1 <- colSds(d) / sqrt(2)
s2 <- colSds(x)
print(summary(s1 - s2))
set.seed(1)

x <- matrix(rnorm(20), nrow = 5, ncol = 4)
print(x)

# Row averages
print(rowMeans(x))
print(rowMedians(x))

# Column averages
print(colMeans(x))
print(colMedians(x))


# Row variabilities
print(rowVars(x))
print(rowSds(x))
print(rowMads(x))
print(rowIQRs(x))

# Column variabilities
print(rowVars(x))
print(colSds(x))
print(colMads(x))
print(colIQRs(x))

# Row ranges
print(rowRanges(x))
print(cbind(rowMins(x), rowMaxs(x)))
print(cbind(rowOrderStats(x, which = 1), rowOrderStats(x, which = ncol(x))))

# Column ranges
print(colRanges(x))
print(cbind(colMins(x), colMaxs(x)))
print(cbind(colOrderStats(x, which = 1), colOrderStats(x, which = nrow(x))))


x <- matrix(rnorm(2000), nrow = 50, ncol = 40)

# Row standard deviations
d <- rowDiffs(x)
s1 <- rowSds(d) / sqrt(2)
s2 <- rowSds(x)
print(summary(s1 - s2))

# Column standard deviations
d <- colDiffs(x)
s1 <- colSds(d) / sqrt(2)
s2 <- colSds(x)
print(summary(s1 - s2))

Calculates the weighted means for each row (column) in a matrix

Description

Calculates the weighted means for each row (column) in a matrix.

Usage

rowWeightedMeans(x, w = NULL, rows = NULL, cols = NULL, na.rm = FALSE,
  ..., useNames = TRUE)

colWeightedMeans(x, w = NULL, rows = NULL, cols = NULL, na.rm = FALSE,
  ..., useNames = TRUE)
rowWeightedMeans(x, w = NULL, rows = NULL, cols = NULL, na.rm = FALSE,
  ..., useNames = TRUE)

colWeightedMeans(x, w = NULL, rows = NULL, cols = NULL, na.rm = FALSE,
  ..., useNames = TRUE)

Arguments

`x`	An NxK `matrix` or, if `dim.` is specified, an N * K `vector`.
`w`	A `numeric` `vector` of length K (N).
`rows`	A `vector` indicating subset of rows to operate over. If `NULL`, no subsetting is done.
`cols`	A `vector` indicating subset of columns to operate over. If `NULL`, no subsetting is done.
`na.rm`	If `TRUE`, missing values are excluded.
`...`	Not used.
`useNames`	If `TRUE` (default), names attributes of the result are set, otherwise not.

Details

The implementations of these methods are optimized for both speed and memory. If no weights are given, the corresponding rowMeans()/colMeans() is used.

Value

Returns a numeric vector of length N (K).

Author(s)

Henrik Bengtsson

Examples

x <- matrix(rnorm(20), nrow = 5, ncol = 4)
print(x)

# Non-weighted row averages
mu_0 <- rowMeans(x)
mu <- rowWeightedMeans(x)
stopifnot(all.equal(mu, mu_0))

# Weighted row averages (uniform weights)
w <- rep(2.5, times = ncol(x))
mu <- rowWeightedMeans(x, w = w)
stopifnot(all.equal(mu, mu_0))

# Weighted row averages (excluding some columns)
w <- c(1, 1, 0, 1)
mu_0 <- rowMeans(x[, (w == 1), drop = FALSE])
mu <- rowWeightedMeans(x, w = w)
stopifnot(all.equal(mu, mu_0))

# Weighted row averages (excluding some columns)
w <- c(0, 1, 0, 0)
mu_0 <- rowMeans(x[, (w == 1), drop = FALSE])
mu <- rowWeightedMeans(x, w = w)
stopifnot(all.equal(mu, mu_0))

# Weighted averages by rows and columns
w <- 1:4
mu_1 <- rowWeightedMeans(x, w = w)
mu_2 <- colWeightedMeans(t(x), w = w)
stopifnot(all.equal(mu_2, mu_1))
x <- matrix(rnorm(20), nrow = 5, ncol = 4)
print(x)

# Non-weighted row averages
mu_0 <- rowMeans(x)
mu <- rowWeightedMeans(x)
stopifnot(all.equal(mu, mu_0))

# Weighted row averages (uniform weights)
w <- rep(2.5, times = ncol(x))
mu <- rowWeightedMeans(x, w = w)
stopifnot(all.equal(mu, mu_0))

# Weighted row averages (excluding some columns)
w <- c(1, 1, 0, 1)
mu_0 <- rowMeans(x[, (w == 1), drop = FALSE])
mu <- rowWeightedMeans(x, w = w)
stopifnot(all.equal(mu, mu_0))

# Weighted row averages (excluding some columns)
w <- c(0, 1, 0, 0)
mu_0 <- rowMeans(x[, (w == 1), drop = FALSE])
mu <- rowWeightedMeans(x, w = w)
stopifnot(all.equal(mu, mu_0))

# Weighted averages by rows and columns
w <- 1:4
mu_1 <- rowWeightedMeans(x, w = w)
mu_2 <- colWeightedMeans(t(x), w = w)
stopifnot(all.equal(mu_2, mu_1))

Calculates the weighted medians for each row (column) in a matrix

Description

Calculates the weighted medians for each row (column) in a matrix.

Usage

rowWeightedMedians(x, w = NULL, rows = NULL, cols = NULL,
  na.rm = FALSE, ..., useNames = TRUE)

colWeightedMedians(x, w = NULL, rows = NULL, cols = NULL,
  na.rm = FALSE, ..., useNames = TRUE)
rowWeightedMedians(x, w = NULL, rows = NULL, cols = NULL,
  na.rm = FALSE, ..., useNames = TRUE)

colWeightedMedians(x, w = NULL, rows = NULL, cols = NULL,
  na.rm = FALSE, ..., useNames = TRUE)

Arguments

`x`	An NxK `matrix` or, if `dim.` is specified, an N * K `vector`.
`w`	A `numeric` `vector` of length K (N).
`rows`	A `vector` indicating subset of rows to operate over. If `NULL`, no subsetting is done.
`cols`	A `vector` indicating subset of columns to operate over. If `NULL`, no subsetting is done.
`na.rm`	If `TRUE`, missing values are excluded.
`...`	Additional arguments passed to `weightedMedian`().
`useNames`	If `TRUE` (default), names attributes of the result are set, otherwise not.

Details

The implementations of these methods are optimized for both speed and memory. If no weights are given, the corresponding rowMedians()/colMedians() is used.

Value

Returns a numeric vector of length N (K).

Author(s)

Henrik Bengtsson

Examples

x <- matrix(rnorm(20), nrow = 5, ncol = 4)
print(x)

# Non-weighted row averages
mu_0 <- rowMedians(x)
mu <- rowWeightedMedians(x)
stopifnot(all.equal(mu, mu_0))

# Weighted row averages (uniform weights)
w <- rep(2.5, times = ncol(x))
mu <- rowWeightedMedians(x, w = w)
stopifnot(all.equal(mu, mu_0))

# Weighted row averages (excluding some columns)
w <- c(1, 1, 0, 1)
mu_0 <- rowMedians(x[, (w == 1), drop = FALSE])
mu <- rowWeightedMedians(x, w = w)
stopifnot(all.equal(mu, mu_0))

# Weighted row averages (excluding some columns)
w <- c(0, 1, 0, 0)
mu_0 <- rowMedians(x[, (w == 1), drop = FALSE])
mu <- rowWeightedMedians(x, w = w)
stopifnot(all.equal(mu, mu_0))

# Weighted averages by rows and columns
w <- 1:4
mu_1 <- rowWeightedMedians(x, w = w)
mu_2 <- colWeightedMedians(t(x), w = w)
stopifnot(all.equal(mu_2, mu_1))
x <- matrix(rnorm(20), nrow = 5, ncol = 4)
print(x)

# Non-weighted row averages
mu_0 <- rowMedians(x)
mu <- rowWeightedMedians(x)
stopifnot(all.equal(mu, mu_0))

# Weighted row averages (uniform weights)
w <- rep(2.5, times = ncol(x))
mu <- rowWeightedMedians(x, w = w)
stopifnot(all.equal(mu, mu_0))

# Weighted row averages (excluding some columns)
w <- c(1, 1, 0, 1)
mu_0 <- rowMedians(x[, (w == 1), drop = FALSE])
mu <- rowWeightedMedians(x, w = w)
stopifnot(all.equal(mu, mu_0))

# Weighted row averages (excluding some columns)
w <- c(0, 1, 0, 0)
mu_0 <- rowMedians(x[, (w == 1), drop = FALSE])
mu <- rowWeightedMedians(x, w = w)
stopifnot(all.equal(mu, mu_0))

# Weighted averages by rows and columns
w <- 1:4
mu_1 <- rowWeightedMedians(x, w = w)
mu_2 <- colWeightedMedians(t(x), w = w)
stopifnot(all.equal(mu_2, mu_1))

Estimation of scale based on sequential-order differences

Description

Estimation of scale based on sequential-order differences, corresponding to the scale estimates provided by var, sd, mad and IQR.

Usage

varDiff(x, idxs = NULL, na.rm = FALSE, diff = 1L, trim = 0, ...)

sdDiff(x, idxs = NULL, na.rm = FALSE, diff = 1L, trim = 0, ...)

madDiff(x, idxs = NULL, na.rm = FALSE, diff = 1L, trim = 0,
  constant = 1.4826, ...)

iqrDiff(x, idxs = NULL, na.rm = FALSE, diff = 1L, trim = 0, ...)

rowVarDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L,
  trim = 0, ..., useNames = TRUE)

colVarDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L,
  trim = 0, ..., useNames = TRUE)

rowSdDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L,
  trim = 0, ..., useNames = TRUE)

colSdDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L,
  trim = 0, ..., useNames = TRUE)

rowMadDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L,
  trim = 0, ..., useNames = TRUE)

colMadDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L,
  trim = 0, ..., useNames = TRUE)

rowIQRDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L,
  trim = 0, ..., useNames = TRUE)

colIQRDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L,
  trim = 0, ..., useNames = TRUE)
varDiff(x, idxs = NULL, na.rm = FALSE, diff = 1L, trim = 0, ...)

sdDiff(x, idxs = NULL, na.rm = FALSE, diff = 1L, trim = 0, ...)

madDiff(x, idxs = NULL, na.rm = FALSE, diff = 1L, trim = 0,
  constant = 1.4826, ...)

iqrDiff(x, idxs = NULL, na.rm = FALSE, diff = 1L, trim = 0, ...)

rowVarDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L,
  trim = 0, ..., useNames = TRUE)

colVarDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L,
  trim = 0, ..., useNames = TRUE)

rowSdDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L,
  trim = 0, ..., useNames = TRUE)

colSdDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L,
  trim = 0, ..., useNames = TRUE)

rowMadDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L,
  trim = 0, ..., useNames = TRUE)

colMadDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L,
  trim = 0, ..., useNames = TRUE)

rowIQRDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L,
  trim = 0, ..., useNames = TRUE)

colIQRDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L,
  trim = 0, ..., useNames = TRUE)

Arguments

`x`	A `numeric` `vector` of length N or a `numeric` NxK `matrix`.
`idxs`	A `vector` indicating subset of elements to operate over. If `NULL`, no subsetting is done.
`na.rm`	If `TRUE`, missing values are excluded.
`diff`	The positional distance of elements for which the difference should be calculated.
`trim`	A `double` in [0,1/2] specifying the fraction of observations to be trimmed from each end of (sorted) `x` before estimation.
`...`	Not used.
`constant`	A scale factor adjusting for asymptotically normal consistency.
`rows`	A `vector` indicating subset of rows to operate over. If `NULL`, no subsetting is done.
`cols`	A `vector` indicating subset of columns to operate over. If `NULL`, no subsetting is done.
`useNames`	If `TRUE` (default), names attributes of the result are set, otherwise not.

Details

Note that n-order difference MAD estimates, just like the ordinary MAD estimate by mad, apply a correction factor such that the estimates are consistent with the standard deviation under Gaussian distributions.

The interquartile range (IQR) estimates does not apply such a correction factor. If asymptotically normal consistency is wanted, the correction factor for IQR estimate is 1 / (2 * qnorm(3/4)), which is half of that used for MAD estimates, which is 1 / qnorm(3/4). This correction factor needs to be applied manually, i.e. there is no constant argument for the IQR functions.

Value

Returns a numeric vector of length 1, length N, or length K.

Author(s)

Henrik Bengtsson

References

[1] J. von Neumann et al., The mean square successive difference. Annals of Mathematical Statistics, 1941, 12, 153-162.

Weighted Median Absolute Deviation (MAD)

Description

Computes a weighted MAD of a numeric vector.

Usage

weightedMad(x, w = NULL, idxs = NULL, na.rm = FALSE, constant = 1.4826,
  center = NULL, ...)

rowWeightedMads(x, w = NULL, rows = NULL, cols = NULL, na.rm = FALSE,
  constant = 1.4826, center = NULL, ..., useNames = TRUE)

colWeightedMads(x, w = NULL, rows = NULL, cols = NULL, na.rm = FALSE,
  constant = 1.4826, center = NULL, ..., useNames = TRUE)
weightedMad(x, w = NULL, idxs = NULL, na.rm = FALSE, constant = 1.4826,
  center = NULL, ...)

rowWeightedMads(x, w = NULL, rows = NULL, cols = NULL, na.rm = FALSE,
  constant = 1.4826, center = NULL, ..., useNames = TRUE)

colWeightedMads(x, w = NULL, rows = NULL, cols = NULL, na.rm = FALSE,
  constant = 1.4826, center = NULL, ..., useNames = TRUE)

Arguments

`x`	`vector` of type `integer`, `numeric`, or `logical`.
`w`	a vector of weights the same length as `x` giving the weights to use for each element of `x`. Negative weights are treated as zero weights. Default value is equal weight to all values.
`idxs`	A `vector` indicating subset of elements to operate over. If `NULL`, no subsetting is done.
`na.rm`	If `TRUE`, missing values are excluded.
`constant`	A `numeric` scale factor, cf. `mad`.
`center`	Optional `numeric` scalar specifying the center location of the data. If `NULL`, it is estimated from data.
`...`	Not used.
`rows`	A `vector` indicating subset of rows to operate over. If `NULL`, no subsetting is done.
`cols`	A `vector` indicating subset of columns to operate over. If `NULL`, no subsetting is done.
`useNames`	If `TRUE` (default), names attributes of the result are set, otherwise not.

Value

Returns a numeric scalar.

Missing values

Missing values are dropped at the very beginning, if argument na.rm is TRUE, otherwise not.

Author(s)

Henrik Bengtsson

Examples

x <- 1:10
n <- length(x)

m1 <- mad(x)
m2 <- weightedMad(x)
stopifnot(identical(m1, m2))

w <- rep(1, times = n)
m1 <- weightedMad(x, w)
stopifnot(identical(m1, m2))

# All weight on the first value
w[1] <- Inf
m <- weightedMad(x, w)
stopifnot(m  == 0)

# All weight on the first two values
w[1:2] <- Inf
m1 <- mad(x[1:2])
m2 <- weightedMad(x, w)
stopifnot(identical(m1, m2))

# All weights set to zero
w <- rep(0, times = n)
m <- weightedMad(x, w)
stopifnot(is.na(m))
x <- 1:10
n <- length(x)

m1 <- mad(x)
m2 <- weightedMad(x)
stopifnot(identical(m1, m2))

w <- rep(1, times = n)
m1 <- weightedMad(x, w)
stopifnot(identical(m1, m2))

# All weight on the first value
w[1] <- Inf
m <- weightedMad(x, w)
stopifnot(m  == 0)

# All weight on the first two values
w[1:2] <- Inf
m1 <- mad(x[1:2])
m2 <- weightedMad(x, w)
stopifnot(identical(m1, m2))

# All weights set to zero
w <- rep(0, times = n)
m <- weightedMad(x, w)
stopifnot(is.na(m))

Weighted Arithmetic Mean

Description

Computes the weighted sample mean of a numeric vector.

Usage

weightedMean(x, w = NULL, idxs = NULL, na.rm = FALSE, refine = FALSE,
  ...)
weightedMean(x, w = NULL, idxs = NULL, na.rm = FALSE, refine = FALSE,
  ...)

Arguments

`x`	An NxK `matrix` or, if `dim.` is specified, an N * K `vector`.
`w`	a vector of weights the same length as `x` giving the weights to use for each element of `x`. Negative weights are treated as zero weights. Default value is equal weight to all values. If a missing-value weight exists, the result is always a missing value.
`idxs`	A `vector` indicating subset of elements to operate over. If `NULL`, no subsetting is done.
`na.rm`	If `TRUE`, missing values are excluded.
`refine`	If `TRUE` and `x` is `numeric`, then extra effort is used to calculate the average with greater numerical precision, otherwise not.
`...`	Not used.

Value

Returns a numeric scalar. If x is of zero length, then NaN is returned, which is consistent with mean().

Missing values

This function handles missing values consistently with weighted.mean. More precisely, if na.rm = FALSE, then any missing values in either x or w will give result NA_real_. If na.rm = TRUE, then all (x, w) data points for which x is missing are skipped. Note that if both x and w are missing for a data points, then it is also skipped (by the same rule). However, if only w is missing, then the final results will always be NA_real_ regardless of na.rm.

Author(s)

Henrik Bengtsson

Examples

x <- 1:10
n <- length(x)

w <- rep(1, times = n)
m0 <- weighted.mean(x, w)
m1 <- weightedMean(x, w)
stopifnot(identical(m1, m0))

# Pull the mean towards zero
w[1] <- 5
m0 <- weighted.mean(x, w)
m1 <- weightedMean(x, w)
stopifnot(identical(m1, m0))

# Put even more weight on the zero
w[1] <- 8.5
m0 <- weighted.mean(x, w)
m1 <- weightedMean(x, w)
stopifnot(identical(m1, m0))

# All weight on the first value
w[1] <- Inf
m0 <- weighted.mean(x, w)
m1 <- weightedMean(x, w)
stopifnot(identical(m1, m0))

# All weight on the last value
w[1] <- 1
w[n] <- Inf
m0 <- weighted.mean(x, w)
m1 <- weightedMean(x, w)
stopifnot(identical(m1, m0))

# All weights set to zero
w <- rep(0, times = n)
m0 <- weighted.mean(x, w)
m1 <- weightedMean(x, w)
stopifnot(identical(m1, m0))
x <- 1:10
n <- length(x)

w <- rep(1, times = n)
m0 <- weighted.mean(x, w)
m1 <- weightedMean(x, w)
stopifnot(identical(m1, m0))

# Pull the mean towards zero
w[1] <- 5
m0 <- weighted.mean(x, w)
m1 <- weightedMean(x, w)
stopifnot(identical(m1, m0))

# Put even more weight on the zero
w[1] <- 8.5
m0 <- weighted.mean(x, w)
m1 <- weightedMean(x, w)
stopifnot(identical(m1, m0))

# All weight on the first value
w[1] <- Inf
m0 <- weighted.mean(x, w)
m1 <- weightedMean(x, w)
stopifnot(identical(m1, m0))

# All weight on the last value
w[1] <- 1
w[n] <- Inf
m0 <- weighted.mean(x, w)
m1 <- weightedMean(x, w)
stopifnot(identical(m1, m0))

# All weights set to zero
w <- rep(0, times = n)
m0 <- weighted.mean(x, w)
m1 <- weightedMean(x, w)
stopifnot(identical(m1, m0))

Weighted Median Value

Description

Computes a weighted median of a numeric vector.

Usage

weightedMedian(x, w = NULL, idxs = NULL, na.rm = FALSE,
  interpolate = is.null(ties), ties = NULL, ...)
weightedMedian(x, w = NULL, idxs = NULL, na.rm = FALSE,
  interpolate = is.null(ties), ties = NULL, ...)

Arguments

`x`	`vector` of type `integer`, `numeric`, or `logical`.
`w`	a vector of weights the same length as `x` giving the weights to use for each element of `x`. Negative weights are treated as zero weights. Default value is equal weight to all values.
`idxs`	A `vector` indicating subset of elements to operate over. If `NULL`, no subsetting is done.
`na.rm`	a logical value indicating whether `NA` values in `x` should be stripped before the computation proceeds, or not. If `NA`, no check at all for `NA`s is done.
`interpolate`	If `TRUE`, linear interpolation is used to get a consistent estimate of the weighted median.
`ties`	If `interpolate == FALSE`, a character string specifying how to solve ties between two `x`'s that are satisfying the weighted median criteria. Note that at most two values can satisfy the criteria. When `ties` is `"min"` ("lower weighted median"), the smaller value of the two is returned and when it is `"max"` ("upper weighted median"), the larger value is returned. If `ties` is `"mean"`, the mean of the two values is returned. Finally, if `ties` is `"weighted"` (or `NULL`) a weighted average of the two are returned, where the weights are weights of all values `x[i] <= x[k]` and `x[i] >= x[k]`, respectively.
`...`	Not used.

Value

Returns a numeric scalar.

For the n elements x = c(x[1], x[2], ..., x[n]) with positive weights w = c(w[1], w[2], ..., w[n]) such that sum(w) = S, the weighted median is defined as the element x[k] for which the total weight of all elements x[i] < x[k] is less or equal to S/2 and for which the total weight of all elements x[i] > x[k] is less or equal to S/2 (c.f. [1]).

When using linear interpolation, the weighted mean of x[k-1] and x[k] with weights S[k-1] and S[k] corresponding to the cumulative weights of those two elements is used as an estimate.

If w is missing then all elements of x are given the same positive weight. If all weights are zero, NA_real_ is returned.

If one or more weights are Inf, it is the same as these weights have the same weight and the others have zero. This makes things easier for cases where the weights are result of a division with zero.

If there are missing values in w that are part of the calculation (after subsetting and dropping missing values in x), then the final result is always NA of the same type as x.

The weighted median solves the following optimization problem:

$\alpha^* = \arg_\alpha \min \sum_{i = 1}^{n} w_i |x_i-\alpha|$

where $x = (x_1, x_2, \ldots, x_n)$ are scalars and $w = (w_1, w_2, \ldots, w_n)$ are the corresponding "weights" for each individual $x$ value.

Author(s)

Henrik Bengtsson and Ola Hossjer, Centre for Mathematical Sciences, Lund University. Thanks to Roger Koenker, Econometrics, University of Illinois, for the initial ideas.

References

[1] T.H. Cormen, C.E. Leiserson, R.L. Rivest, Introduction to Algorithms, The MIT Press, Massachusetts Institute of Technology, 1989.

Examples

x <- 1:10
n <- length(x)

m1 <- median(x)                             # 5.5
m2 <- weightedMedian(x)                     # 5.5
stopifnot(identical(m1, m2))

w <- rep(1, times = n)
m1 <- weightedMedian(x, w)                  # 5.5 (default)
m2 <- weightedMedian(x, ties = "weighted")  # 5.5 (default)
m3 <- weightedMedian(x, ties = "min")       # 5
m4 <- weightedMedian(x, ties = "max")       # 6
stopifnot(identical(m1, m2))

# Pull the median towards zero
w[1] <- 5
m1 <- weightedMedian(x, w)                  # 3.5
y <- c(rep(0, times = w[1]), x[-1])         # Only possible for integer weights
m2 <- median(y)                             # 3.5
stopifnot(identical(m1, m2))

# Put even more weight on the zero
w[1] <- 8.5
weightedMedian(x, w)                # 2

# All weight on the first value
w[1] <- Inf
weightedMedian(x, w)                # 1

# All weight on the last value
w[1] <- 1
w[n] <- Inf
weightedMedian(x, w)                # 10

# All weights set to zero
w <- rep(0, times = n)
weightedMedian(x, w)                # NA

# Simple benchmarking
bench <- function(N = 1e5, K = 10) {
  x <- rnorm(N)
  gc()
  t <- c()
  t[1] <- system.time(for (k in 1:K) median(x))[3]
  t[2] <- system.time(for (k in 1:K) weightedMedian(x))[3]
  t <- t / t[1]
  names(t) <- c("median", "weightedMedian")
  t
}

print(bench(N =     5, K = 100))
print(bench(N =    50, K = 100))
print(bench(N =   200, K = 100))
print(bench(N =  1000, K = 100))
print(bench(N =  10e3, K =  20))
print(bench(N = 100e3, K =  20))
x <- 1:10
n <- length(x)

m1 <- median(x)                             # 5.5
m2 <- weightedMedian(x)                     # 5.5
stopifnot(identical(m1, m2))

w <- rep(1, times = n)
m1 <- weightedMedian(x, w)                  # 5.5 (default)
m2 <- weightedMedian(x, ties = "weighted")  # 5.5 (default)
m3 <- weightedMedian(x, ties = "min")       # 5
m4 <- weightedMedian(x, ties = "max")       # 6
stopifnot(identical(m1, m2))

# Pull the median towards zero
w[1] <- 5
m1 <- weightedMedian(x, w)                  # 3.5
y <- c(rep(0, times = w[1]), x[-1])         # Only possible for integer weights
m2 <- median(y)                             # 3.5
stopifnot(identical(m1, m2))

# Put even more weight on the zero
w[1] <- 8.5
weightedMedian(x, w)                # 2

# All weight on the first value
w[1] <- Inf
weightedMedian(x, w)                # 1

# All weight on the last value
w[1] <- 1
w[n] <- Inf
weightedMedian(x, w)                # 10

# All weights set to zero
w <- rep(0, times = n)
weightedMedian(x, w)                # NA

# Simple benchmarking
bench <- function(N = 1e5, K = 10) {
  x <- rnorm(N)
  gc()
  t <- c()
  t[1] <- system.time(for (k in 1:K) median(x))[3]
  t[2] <- system.time(for (k in 1:K) weightedMedian(x))[3]
  t <- t / t[1]
  names(t) <- c("median", "weightedMedian")
  t
}

print(bench(N =     5, K = 100))
print(bench(N =    50, K = 100))
print(bench(N =   200, K = 100))
print(bench(N =  1000, K = 100))
print(bench(N =  10e3, K =  20))
print(bench(N = 100e3, K =  20))

Weighted variance and weighted standard deviation

Description

Computes a weighted variance / standard deviation of a numeric vector or across rows or columns of a matrix.

Usage

weightedVar(x, w = NULL, idxs = NULL, na.rm = FALSE, center = NULL,
  ...)

weightedSd(...)

rowWeightedVars(x, w = NULL, rows = NULL, cols = NULL, na.rm = FALSE,
  ..., useNames = TRUE)

colWeightedVars(x, w = NULL, rows = NULL, cols = NULL, na.rm = FALSE,
  ..., useNames = TRUE)

rowWeightedSds(x, w = NULL, rows = NULL, cols = NULL, na.rm = FALSE,
  ..., useNames = TRUE)

colWeightedSds(x, w = NULL, rows = NULL, cols = NULL, na.rm = FALSE,
  ..., useNames = TRUE)
weightedVar(x, w = NULL, idxs = NULL, na.rm = FALSE, center = NULL,
  ...)

weightedSd(...)

rowWeightedVars(x, w = NULL, rows = NULL, cols = NULL, na.rm = FALSE,
  ..., useNames = TRUE)

colWeightedVars(x, w = NULL, rows = NULL, cols = NULL, na.rm = FALSE,
  ..., useNames = TRUE)

rowWeightedSds(x, w = NULL, rows = NULL, cols = NULL, na.rm = FALSE,
  ..., useNames = TRUE)

colWeightedSds(x, w = NULL, rows = NULL, cols = NULL, na.rm = FALSE,
  ..., useNames = TRUE)

Arguments

`x`	`vector` of type `integer`, `numeric`, or `logical`.
`w`	a vector of weights the same length as `x` giving the weights to use for each element of `x`. Negative weights are treated as zero weights. Default value is equal weight to all values.
`idxs`	A `vector` indicating subset of elements to operate over. If `NULL`, no subsetting is done.
`na.rm`	If `TRUE`, missing values are excluded.
`center`	Optional `numeric` scalar specifying the center location of the data. If `NULL`, it is estimated from data.
`...`	Not used.
`rows`	A `vector` indicating subset of rows to operate over. If `NULL`, no subsetting is done.
`cols`	A `vector` indicating subset of columns to operate over. If `NULL`, no subsetting is done.
`useNames`	If `TRUE` (default), names attributes of the result are set, otherwise not.

Details

The estimator used here is the same as the one used by the "unbiased" estimator of the Hmisc package. More specifically, weightedVar(x, w = w) == Hmisc::wtd.var(x, weights = w),

Value

Returns a numeric scalar.

Missing values

This function handles missing values consistently with weightedMean(). More precisely, if na.rm = FALSE, then any missing values in either x or w will give result NA_real_. If na.rm = TRUE, then all (x, w) data points for which x is missing are skipped. Note that if both x and w are missing for a data points, then it is also skipped (by the same rule). However, if only w is missing, then the final results will always be NA_real_ regardless of na.rm.

Author(s)

Henrik Bengtsson

Package 'matrixStats'

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