[R] permutation/randomization test assumption on observations
Hi, I have two groups of data of different size: group A: x1, x2, , x_n; group B: y1, y2, , y_m; (m is not equal to n) The two groups are independent but observations within each group are not independent, i.e., x1, x2, ..., x_n are not independent; but x's are independent from y's I wonder if randomization test is still applicable to this case; if so, anything I have to pay attention? Thank you very much, Wenjin __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] permutation/randomization
Hello,
I have what I suspect might be an easy problem but I am new to R and
stumped. I have a data set that looks something like this
b-c(2,3,4,5,6,7,8,9)
x-c(2,3,4,5,6,7,8,9)
y-c(9,8,7,6,5,4,3,2)
z-c(9,8,7,6,1,2,3,4)
data-cbind(x,y,z)
row.names(data)-c('a','b','c','d','e','f','g','h')
which gives:
x y z
a 2 9 9
b 3 8 8
c 4 7 7
d 5 6 6
e 6 5 1
f 7 4 2
g 8 3 3
h 9 2 4
I would like to randomize data within columns. The closest I have been able
to come permutes data within the columns but keeps rows together along with
row names(example below). For some context, eventually I would like use
this to generate many data sets and perform calculations on these random
data sets (I think I know how to do this but we'll see). So ideally I would
like row names to remain the same (in order a through h) and column data to
randomize within columns but independently of the other columns. Just
shuffle the data deck I guess
data[permute(1:length(data[,1])),]
x y z
b 3 8 8
c 4 7 7
h 9 2 4
e 6 5 1
f 7 4 2
a 2 9 9
g 8 3 3
d 5 6 6
Thanks in advance for the help and also for the good advice earlier this
week.
Cheers
[[alternative HTML version deleted]]
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Re: [R] permutation/randomization
Grant Gillis wrote:
Hello,
I have what I suspect might be an easy problem but I am new to R and
stumped. I have a data set that looks something like this
b-c(2,3,4,5,6,7,8,9)
x-c(2,3,4,5,6,7,8,9)
y-c(9,8,7,6,5,4,3,2)
z-c(9,8,7,6,1,2,3,4)
data-cbind(x,y,z)
row.names(data)-c('a','b','c','d','e','f','g','h')
which gives:
x y z
a 2 9 9
b 3 8 8
c 4 7 7
d 5 6 6
e 6 5 1
f 7 4 2
g 8 3 3
h 9 2 4
I would like to randomize data within columns. The closest I have been able
to come permutes data within the columns but keeps rows together along with
row names(example below). For some context, eventually I would like use
this to generate many data sets and perform calculations on these random
data sets (I think I know how to do this but we'll see). So ideally I would
like row names to remain the same (in order a through h) and column data to
randomize within columns but independently of the other columns. Just
shuffle the data deck I guess
data[permute(1:length(data[,1])),]
x y z
b 3 8 8
c 4 7 7
h 9 2 4
e 6 5 1
f 7 4 2
a 2 9 9
g 8 3 3
d 5 6 6
I changed 'data' to 'mymat' as 'data' is a function in R (see ?data)
and added the row names after permuting:
someMatrix - cbind(x, y, z)
permutedMat - apply(someMatrix, 2, sample)
row.names(permutedMat)-c('a','b','c','d','e','f','g','h')
permutedMat
HTH,
Tobias
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Re: [R] permutation/randomization
On Wed, Apr 09, 2008 at 11:08:28AM -0700, Grant Gillis wrote: I would like to randomize data within columns. I think the following line does what you want (minus preserving the row labels): apply(data, 2, sample) Maybe someone smarter than me knows how to preserve the row names. I would probably just steal them from the original data frame: nam = row.names(data) apply(data, 2, sample) row.names(foo) = nam cu Philipp -- Dr. Philipp Pagel Tel. +49-8161-71 2131 Lehrstuhl für Genomorientierte Bioinformatik Fax. +49-8161-71 2186 Technische Universität München Wissenschaftszentrum Weihenstephan 85350 Freising, Germany http://mips.gsf.de/staff/pagel __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] permutation/randomization
You can randomize the order (permute) of a single column with something
like:
x - cbind( x=1:10, y=101:110, z=201:210 )
rownames(x) - letters[1:10]
new.x - x
new.x[,1] - sample(new.x[,1])
new.x
x y z
a 8 101 201
b 10 102 202
c 5 103 203
d 9 104 204
e 3 105 205
f 1 106 206
g 7 107 207
h 4 108 208
i 2 109 209
j 6 110 210
You could do that for each of the columns that you want randomized. A
quick way to do a separate randomization on each column is:
new.x - apply(x, 2, sample)
rownames(new.x) - letters[1:10]
new.x
x y z
a 2 101 203
b 3 107 204
c 6 102 205
d 1 104 207
e 4 105 208
f 7 108 201
g 10 110 206
h 8 106 209
i 5 103 210
j 9 109 202
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
(801) 408-8111
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Grant Gillis
Sent: Wednesday, April 09, 2008 12:08 PM
To: r-help@r-project.org
Subject: [R] permutation/randomization
Hello,
I have what I suspect might be an easy problem but I am new
to R and stumped. I have a data set that looks something like this
b-c(2,3,4,5,6,7,8,9)
x-c(2,3,4,5,6,7,8,9)
y-c(9,8,7,6,5,4,3,2)
z-c(9,8,7,6,1,2,3,4)
data-cbind(x,y,z)
row.names(data)-c('a','b','c','d','e','f','g','h')
which gives:
x y z
a 2 9 9
b 3 8 8
c 4 7 7
d 5 6 6
e 6 5 1
f 7 4 2
g 8 3 3
h 9 2 4
I would like to randomize data within columns. The closest I
have been able to come permutes data within the columns but
keeps rows together along with row names(example below). For
some context, eventually I would like use this to generate
many data sets and perform calculations on these random data
sets (I think I know how to do this but we'll see). So
ideally I would like row names to remain the same (in order a
through h) and column data to randomize within columns but
independently of the other columns. Just shuffle the data
deck I guess
data[permute(1:length(data[,1])),]
x y z
b 3 8 8
c 4 7 7
h 9 2 4
e 6 5 1
f 7 4 2
a 2 9 9
g 8 3 3
d 5 6 6
Thanks in advance for the help and also for the good advice
earlier this week.
Cheers
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
