How to remove attributes from scale() in a matrix?
Thanks, very clear!
On Tue, Jul 16, 2013 at 7:08 PM, arun <smartpink111 at yahoo.com> wrote:
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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