sacvf - 1 month ago 23
R Question

# Is there such "colsd" in R?

I am using in my code

`colSums`
but I also need the standard deviation beside the sum.
I searched in the internet and found this page which contain only:

``````colSums
colMeans
``````

http://stat.ethz.ch/R-manual/R-devel/library/base/html/colSums.html

I tried this:

``````colSd
``````

but I got this error:

``````Error: could not find function "colSd"
``````

How I can do the same thing but for standard deviation:

``````colSd
``````

Here is the code:

``````results <- colSums(x,na.rm=TRUE)#### here I want colsd
``````

I want to provide a fourth (very similar to @Thomas) approach and some benchmarking:

``````library("microbenchmark")
library("matrixStats")

colSdApply <- function(x, ...)apply(X=x, MARGIN=2, FUN=sd, ...)
colSdMatrixStats <- colSds

colSdColMeans <- function(x, na.rm=TRUE) {
if (na.rm) {
n <- colSums(!is.na(x)) # thanks @flodel
} else {
n <- nrow(x)
}
colVar <- colMeans(x*x, na.rm=na.rm) - (colMeans(x, na.rm=na.rm))^2
return(sqrt(colVar * n/(n-1)))
}

colSdThomas <- function(x)sqrt(rowMeans((t(x)-colMeans(x))^2)*((dim(x)[1])/(dim(x)[1]-1)))

m <- matrix(runif(1e7), nrow=1e3)

microbenchmark(colSdApply(m), colSdMatrixStats(m), colSdColMeans(m), colSdThomas(m))

# Unit: milliseconds
#                 expr      min       lq   median       uq      max neval
#        colSdApply(m) 435.7346 448.8673 456.6176 476.8373 512.9783   100
#  colSdMatrixStats(m) 344.6416 357.5439 383.8736 389.0258 465.5715   100
#     colSdColMeans(m) 124.2028 128.9016 132.9446 137.6254 172.6407   100
#       colSdThomas(m) 231.5567 240.3824 245.4072 274.6611 307.3806   100

all.equal(colSdApply(m), colSdMatrixStats(m))
# [1] TRUE
all.equal(colSdApply(m), colSdColMeans(m))
# [1] TRUE
all.equal(colSdApply(m), colSdThomas(m))
# [1] TRUE
``````
Source (Stackoverflow)