How to remove attributes from scale() in a matrix?
Hi Mike,
If you check ?scale
For ?scale.default?, the centered, scaled matrix.? The numeric
???? centering and scalings used (if any) are returned as attributes
???? ?"scaled:center"? and ?"scaled:scale"?
By checking the source code:
methods(scale)
getAnywhere('scale.default')
function (x, center = TRUE, scale = TRUE)
{
??? x <- as.matrix(x)
??? nc <- ncol(x)
??? if (is.logical(center)) {
??????? if (center) {
??????????? center <- colMeans(x, na.rm = TRUE)
??????????? x <- sweep(x, 2L, center, check.margin = FALSE)
??????? }
??? }
??? else if (is.numeric(center) && (length(center) == nc))
??????? x <- sweep(x, 2L, center, check.margin = FALSE)
??? else stop("length of 'center' must equal the number of columns of 'x'")
??? if (is.logical(scale)) {
??????? if (scale) {
??????????? f <- function(v) {
??????????????? v <- v[!is.na(v)]
??????????????? sqrt(sum(v^2)/max(1, length(v) - 1L))
??????????? }
??????????? scale <- apply(x, 2L, f)
??????????? x <- sweep(x, 2L, scale, "/", check.margin = FALSE)
??????? }
??? }
??? else if (is.numeric(scale) && length(scale) == nc)
??????? x <- sweep(x, 2L, scale, "/", check.margin = FALSE)
??? else stop("length of 'scale' must equal the number of columns of 'x'")
??? if (is.numeric(center))
??????? attr(x, "scaled:center") <- center
??? if (is.numeric(scale))
??????? attr(x, "scaled:scale") <- scale
??? x
}
#You can comment out the last few lines:
scale1<- function (x, center = TRUE, scale = TRUE)
{
??? x <- as.matrix(x)
??? nc <- ncol(x)
??? if (is.logical(center)) {
??????? if (center) {
??????????? center <- colMeans(x, na.rm = TRUE)
??????????? x <- sweep(x, 2L, center, check.margin = FALSE)
??????? }
??? }
??? else if (is.numeric(center) && (length(center) == nc))
??????? x <- sweep(x, 2L, center, check.margin = FALSE)
??? else stop("length of 'center' must equal the number of columns of 'x'")
??? if (is.logical(scale)) {
??????? if (scale) {
??????????? f <- function(v) {
??????????????? v <- v[!is.na(v)]
??????????????? sqrt(sum(v^2)/max(1, length(v) - 1L))
??????????? }
??????????? scale <- apply(x, 2L, f)
??????????? x <- sweep(x, 2L, scale, "/", check.margin = FALSE)
??????? }
??? }
??? else if (is.numeric(scale) && length(scale) == nc)
??????? x <- sweep(x, 2L, scale, "/", check.margin = FALSE)
??? else stop("length of 'scale' must equal the number of columns of 'x'")
??? #if (is.numeric(center))
??? #??? attr(x, "scaled:center") <- center
??? #if (is.numeric(scale))
??? #??? attr(x, "scaled:scale") <- scale
??? x
}
?x2<-scale1(x,center=TRUE,scale=TRUE)
?str(x2)
# num [1:15, 1:10] -0.2371 -0.5606 -0.8242 1.5985 -0.0164 ...
identical(x1,x2)
#[1] TRUE
A.K.
----- Original Message -----
From: C W <tmrsg11 at gmail.com>
To: arun <smartpink111 at yahoo.com>
Cc: R help <r-help at r-project.org>
Sent: Tuesday, July 16, 2013 6:58 PM
Subject: Re: [R] How to remove attributes from scale() in a matrix?
Arun, thanks for the quick response.? That helps.
Why does scale() give attributes?? What's the point of that?? I don't
see apply() or any similar functions do it.? Just for my curiosity.
Mike
On Tue, Jul 16, 2013 at 4:07 PM, arun <smartpink111 at yahoo.com> wrote:
HI, Try: x1<-scale(x,center=TRUE,scale=TRUE) str(x1) # num [1:15, 1:10] -0.2371 -0.5606 -0.8242 1.5985 -0.0164 ... # - attr(*, "scaled:center")= num [1:10] 50.2 50 49.8 49.8 50.3 ... ? #- attr(*, "scaled:scale")= num [1:10] 1.109 0.956 0.817 0.746 1.019 ... ? attr(x1,"scaled:center")<-NULL ? attr(x1,"scaled:scale")<-NULL str(x1) ? #num [1:15, 1:10] -0.2371 -0.5606 -0.8242 1.5985 -0.0164 ... A.K. ----- Original Message ----- From: C W <tmrsg11 at gmail.com> To: r-help <r-help at r-project.org> Cc: Sent: Tuesday, July 16, 2013 3:59 PM Subject: [R] How to remove attributes from scale() in a matrix? Hi list, I am using scale() to standardize a distribution?? But why does it give me attributes attached to the data?? I just want a standardized matrix, that is all. library(mvtnorm)
x <- rmvnorm(15, mean=rep(50, 10)) x
? ? ? ? ? [,1]? ? [,2]? ? [,3]? ? [,4]? ? [,5]? ? [,6]? ? [,7] ? [,8]? ? [,9] [1,] 51.17519 52.34341 49.63084 47.99234 51.63113 50.91391 49.36819 49.23901 51.17377 [2,] 50.57039 49.17210 48.64395 49.03940 49.65761 49.93840 49.94883 50.69044 49.57632 [3,] 50.64811 50.21503 50.13786 49.15879 48.51550 50.19444 50.23710 50.98040 51.37032 [4,] 49.22797 49.66445 49.93287 48.63681 50.49457 50.33302 52.29552 49.98424 51.04724 [5,] 49.72099 50.84510 50.60976 49.60883 53.59509 49.14728 50.23134 49.09141 49.23780 [6,] 49.49126 50.90938 49.67140 50.08951 49.79854 49.03711 50.26037 50.24975 48.26958 [7,] 51.12384 47.92778 50.60112 49.01554 49.47515 50.12756 51.65216 49.21998 49.63808 [8,] 51.45123 50.44037 50.01039 50.27511 49.97658 51.63002 50.37156 50.02685 48.95423 [9,] 51.16989 50.16200 51.17724 50.71678 50.79565 50.27128 51.05608 49.61165 47.81732 [10,] 49.54263 49.93501 49.71762 49.33378 51.44935 51.53775 50.54346 49.98333 49.59422 [11,] 51.16497 49.82914 49.08821 51.02918 49.67663 49.53498 50.26647 49.48569 50.94504 [12,] 51.16827 50.50244 49.13003 49.00155 50.26457 48.85465 49.11593 50.58031 51.14926 [13,] 48.26216 49.94866 48.62526 49.11995 50.40082 49.25359 48.57677 50.66760 49.44108 [14,] 49.82530 49.17352 50.05588 50.51265 51.04926 50.32474 49.78180 50.48349 49.92431 [15,] 50.55772 49.84691 47.95021 50.24911 49.85335 50.73062 51.48718 51.36693 50.18307 ? ? ? ? ? [,10] [1,] 50.13859 [2,] 51.54920 [3,] 49.23230 [4,] 50.92683 [5,] 50.97708 [6,] 50.78799 [7,] 50.53913 [8,] 49.30832 [9,] 49.43606 [10,] 49.42060 [11,] 50.21002 [12,] 51.94848 [13,] 49.41352 [14,] 52.24064 [15,] 51.19474
scale(x, center=TRUE, scale=TRUE)
? ? ? ? ? ? [,1]? ? ? [,2]? ? ? ? [,3]? ? ? ? [,4]? ? ? ? [,5] [,6]? ? ? ? [,7] [1,]? 0.8890317? 2.3390090 -0.040395734 -1.86089754? 1.00159470 0.92533476 -0.99715965 [2,]? 0.2452502 -0.9109703 -1.190404546 -0.63771097 -0.66104313 -0.21446975 -0.40514793 [3,]? 0.3279747? 0.1578297? 0.550427419 -0.49823662 -1.62323564 0.08468695 -0.11121941 [4,] -1.1837031 -0.4064112? 0.311551281 -1.10802250? 0.04407804 0.24660932? 1.98754311 [5,] -0.6589074? 0.8035298? 1.100314901? 0.02749734? 2.65618150 -1.13883336 -0.11709623 [6,] -0.9034419? 0.8694088? 0.006865424? 0.58904255 -0.54231158 -1.26755243 -0.08749646 [7,]? 0.8343705 -2.1861602? 1.090250934 -0.66558751 -0.81476108 0.00655050? 1.33157578 [8,]? 1.1828615? 0.3887665? 0.401888014? 0.80585326 -0.39231482 1.76205433? 0.02587038 [9,]? 0.8833860? 0.1034854? 1.761589113? 1.32181395? 0.29773018 0.17447101? 0.72381232 [10,] -0.8487569 -0.1291363? 0.060728488 -0.29381647? 0.84844800 1.65423826? 0.20113824 [11,]? 0.8781560 -0.2376361 -0.672712386? 1.68676651 -0.64501776 -0.68583461 -0.08127647 [12,]? 0.8816611? 0.4523675 -0.623990804 -0.68193230 -0.14968994 -1.48074503 -1.25436403 [13,] -2.2117715 -0.1151423 -1.212190165 -0.54361597 -0.03490809 -1.01461386 -1.80409304 [14,] -0.5478718 -0.9095198? 0.454889973? 1.08335795? 0.51138447 0.23693367 -0.57544865 [15,]? 0.2317608 -0.2194204 -1.998811911? 0.77548830 -0.49613484 0.71117025? 1.16336204 ? ? ? ? ? ? [,8]? ? ? ? [,9]? ? ? [,10] [1,] -1.2666791? 1.17934107 -0.35061189 [2,]? 0.8423439 -0.28600703? 1.06389274 [3,]? 1.2636749? 1.35963155 -1.25940610 [4,] -0.1838111? 1.06327078? 0.43980595 [5,] -1.4811512 -0.59653247? 0.49019839 [6,]? 0.2019965 -1.48467432? 0.30058779 [7,] -1.2943281 -0.22935616? 0.05103467 [8,] -0.1218950 -0.85664924 -1.18316969 [9,] -0.7252082 -1.89953387 -1.05507780 [10,] -0.1851315 -0.26958168 -1.07058564 [11,] -0.9082374? 0.96952049 -0.27897948 [12,]? 0.6823136? 1.15685832? 1.46428187 [13,]? 0.8091562 -0.41005981 -1.07768018 [14,]? 0.5416286? 0.03320871? 1.75724879 [15,]? 1.8253278? 0.27056365? 0.70846058 attr(,"scaled:center") [1] 50.33999 50.06102 49.66551 49.58529 50.44225 50.12196 50.34618 50.11074 49.88811 [10] 50.48823 attr(,"scaled:scale") [1] 0.9394453 0.9757930 0.8581604 0.8560117 1.1869812 0.8558562 0.9807762 0.6882016 [9] 1.0901550 0.9972455 Also,
attributes(x) <- NULL
will not work since this is matrix not vector. Thanks, Mike
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