# [R] Permutations

Jordi Altirriba Gutiérrez altirriba at hotmail.com
Wed Jul 14 18:16:34 CEST 2004

```  Dear R users,
First of all, thanks to Rolf, Brad, Robin, Erich, Fernando and Adaikalavan
for your time and suggestions.
I’ve been testing some algorithms (sorry for the delay, I’m very slow, and
I’m a completely beginner in R’s world).
First, the Robin algorithm.
I think that there is a problem because I’ve done 200 permutations and
I’ve found that these permutations are the same:
52 and 91, 99 and 110, 121 and 122, 51 and 141, 130 and 134.
Thanks again,

Jordi Altirriba
Hospital Clinic - Barcelona - Spain

>x <- c(1,2,3,4,5,6,7,8,9,10,11,12)
>dim(x) <- c(3,4) a<-matrix(1,200,12)
>for (i in 1:200)
+ {
+  jj <- t(apply(x,1,sample))
+ a[i,]<-as.vector(jj)
+ }
>a
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
[1,]    7    2    3    1   11    6    4    8    9    10     5    12
[2,]    1    2    9    7   11    6    4    8   12    10     5     3
[3,]    7    2    9    1   11    3    4    5    6    10     8    12
[4,]   10    8    6    4    5   12    7    2    9     1    11     3
[5,]   10    2   12    1   11    9    7    8    6     4     5     3
[6,]    7    8    6    1    5    9    4   11   12    10     2     3
[7,]    1    5   12    7    2    6    4    8    9    10    11     3
[8,]    1    5    9   10    8    6    4    2    3     7    11    12
[9,]    1   11    6    7    2   12    4    5    9    10     8     3
[10,]    4    5   12   10   11    9    1    8    6     7     2     3
[11,]    1   11    9    7    5    6    4    8   12    10     2     3
[12,]    1    8    3    4    2   12   10    5    9     7    11     6
[13,]    1    2    3    7   11    6   10    5   12     4     8     9
[14,]    4    8    3   10    5   12    7    2    9     1    11     6
[15,]   10    2    3    4    8    6    7   11    9     1     5    12
[16,]    4    8    9   10    2   12    7    5    6     1    11     3
[17,]    1    2    6   10    5    3    7    8   12     4    11     9
[18,]   10    2    9    4   11   12    1    5    6     7     8     3
[19,]    4    8    6    7   11   12    1    2    9    10     5     3
[20,]    1    8   12    7    2    3   10   11    6     4     5     9
[21,]   10    2   12    1    5    9    7   11    6     4     8     3
[22,]    4   11   12    1    2    3   10    8    6     7     5     9
[23,]    1   11    3    7    2    6   10    5    9     4     8    12
[24,]    7    2    9   10    5   12    1   11    3     4     8     6
[25,]    7    8    9    1    2    6    4    5    3    10    11    12
[26,]    4    5   12   10    2    3    7   11    6     1     8     9
[27,]    4    5    9    1   11    3    7    8   12    10     2     6
[28,]    1    5    6    4   11    3    7    8    9    10     2    12
[29,]    4    5    6    1   11    9   10    2   12     7     8     3
[30,]    4   11    3    7    8   12   10    5    6     1     2     9
[31,]   10    2    3    1   11    6    7    8    9     4     5    12
[32,]   10    2    3    7    8    9    1   11    6     4     5    12
[33,]    7   11    6    1    8    9    4    5   12    10     2     3
[34,]    7    5   12    1    8    6    4   11    3    10     2     9
[35,]    1    2    3    4    8    6    7    5    9    10    11    12
[36,]    7    8    3    1   11    9   10    2   12     4     5     6
[37,]   10    2    6    1   11   12    7    5    3     4     8     9
[38,]    1    5    9    4   11   12    7    8    3    10     2     6
[39,]    1    2   12    7    5    9   10    8    3     4    11     6
[40,]    1    8    3   10    2   12    7   11    6     4     5     9
[41,]    1    2    9    4    8    3   10   11   12     7     5     6
[42,]    4    5    6    1    2    9   10    8    3     7    11    12
[43,]    1    2    6    7   11   12   10    5    9     4     8     3
[44,]    1    2    9   10   11   12    4    8    6     7     5     3
[45,]   10    5    9    7   11    6    4    2    3     1     8    12
[46,]    1    2    3    4   11    6    7    5    9    10     8    12
[47,]    4    2    6    1    8    3   10    5   12     7    11     9
[48,]    4    8    9    7    2    3    1    5   12    10    11     6
[49,]   10    8   12    1    2    9    4   11    3     7     5     6
[50,]   10    8    6    1    2    3    7    5   12     4    11     9
[51,]    7    2   12   10   11    6    4    8    3     1     5     9
[52,]    4    5    6    1    2   12   10   11    9     7     8     3
[53,]    1    2    3    7    5    6    4    8    9    10    11    12
[54,]   10    5    3    7   11    9    1    8    6     4     2    12
[55,]    7   11   12    4    2    3   10    8    6     1     5     9
[56,]    1    5    9    4   11   12   10    8    3     7     2     6
[57,]    4    5    9    7   11    3   10    2    6     1     8    12
[58,]   10   11    3    4    5    6    1    8   12     7     2     9
[59,]    4    8    9   10    5    6    7    2    3     1    11    12
[60,]    4    2   12    1    8    6   10    5    9     7    11     3
[61,]    4    8    6    7   11    9   10    5   12     1     2     3
[62,]    7    8    3   10    5    6    1   11   12     4     2     9
[63,]   10    5    3    7    8    6    1    2    9     4    11    12
[64,]   10    2    9    4   11   12    1    5    3     7     8     6
[65,]    1   11    6    4    8   12    7    2    3    10     5     9
[66,]    1    5    3    7   11    9    4    2   12    10     8     6
[67,]    4    2    6    7    5   12   10    8    9     1    11     3
[68,]    4   11   12   10    2    3    7    8    6     1     5     9
[69,]    4    5    6   10    2    3    7    8    9     1    11    12
[70,]    1   11   12   10    2    6    4    5    3     7     8     9
[71,]   10    5    6    7    8   12    4    2    9     1    11     3
[72,]   10    8   12    1   11    9    7    5    3     4     2     6
[73,]   10    8    3    7   11    9    4    5   12     1     2     6
[74,]    7    2   12    1    5    6    4    8    9    10    11     3
[75,]    7    2   12   10    8    9    1   11    6     4     5     3
[76,]    7    2    3    1    5    9    4    8   12    10    11     6
[77,]    1   11    3   10    5    6    7    2    9     4     8    12
[78,]    7    2    6   10   11   12    4    8    9     1     5     3
[79,]   10    8    6    7    5    3    1    2    9     4    11    12
[80,]   10   11    3    7    2   12    4    8    6     1     5     9
[81,]   10    5    6    1    8    3    4   11    9     7     2    12
[82,]    1   11    3    7    5   12   10    2    6     4     8     9
[83,]    4   11    9   10    5   12    7    2    6     1     8     3
[84,]    1   11   12    7    8    3    4    2    6    10     5     9
[85,]   10    2    9    7    5    6    1   11   12     4     8     3
[86,]    7   11    9    4    5    6   10    2   12     1     8     3
[87,]    4    5   12    7    2    3   10   11    6     1     8     9
[88,]    1    2   12    7    5    3   10    8    6     4    11     9
[89,]    1    8   12    7   11    9   10    2    6     4     5     3
[90,]    4    5    3   10   11    9    7    2    6     1     8    12
[91,]    4    5    6    1    2   12   10   11    9     7     8     3
[92,]   10   11    9    7    5   12    1    2    6     4     8     3
[93,]    4    2    3    7    8    6    1   11   12    10     5     9
[94,]    4    5    3   10    2   12    7    8    9     1    11     6
[95,]    4    8    3   10   11    9    1    2    6     7     5    12
[96,]    7    5   12   10   11    3    1    8    9     4     2     6
[97,]    4    2    3    1    8    6    7   11    9    10     5    12
[98,]    4   11    9    7    5   12   10    8    6     1     2     3
[99,]    1   11   12    4    5    6    7    8    3    10     2     9
[100,]    1    8    3    7    5    6   10    2   12     4    11     9
[101,]    7   11    6    4    8    3    1    2   12    10     5     9
[102,]    7   11   12    1    2    3   10    8    6     4     5     9
[103,]    4    5   12    1    2    9    7    8    3    10    11     6
[104,]   10   11   12    4    8    3    7    5    9     1     2     6
[105,]   10    5    9    1    2    3    4    8    6     7    11    12
[106,]   10   11    9    1    2   12    7    8    3     4     5     6
[107,]   10   11    3    4    8    9    7    5   12     1     2     6
[108,]    7    2    6    1   11    9    4    5   12    10     8     3
[109,]    1    8    6    7    2   12   10    5    3     4    11     9
[110,]    1   11   12    4    5    6    7    8    3    10     2     9
[111,]    7    8    6    1    5    3   10    2   12     4    11     9
[112,]    4    8    3    7    5    6    1    2    9    10    11    12
[113,]    1    2    9    4   11    6    7    5    3    10     8    12
[114,]    4   11    9    1    8    6    7    2    3    10     5    12
[115,]   10    8    3    4   11   12    7    2    9     1     5     6
[116,]    7   11   12    1    2    3    4    8    9    10     5     6
[117,]    1    5    3   10   11   12    7    8    9     4     2     6
[118,]    1   11    6    4    2    9   10    5   12     7     8     3
[119,]   10    2    3    1    5    9    4    8   12     7    11     6
[120,]    1    2    3    4   11   12    7    8    9    10     5     6
[121,]    7    8    3    4    5   12   10    2    6     1    11     9
[122,]    7    8    3    4    5   12   10    2    6     1    11     9
[123,]    4    5    3   10   11    9    7    8    6     1     2    12
[124,]    4    5    6    7   11    9    1    8   12    10     2     3
[125,]   10    8    6    1   11    9    4    2   12     7     5     3
[126,]   10    8   12    4   11    9    7    2    6     1     5     3
[127,]    7    8   12    1   11    6   10    5    9     4     2     3
[128,]    1    8   12   10   11    3    7    5    9     4     2     6
[129,]    7    8    3   10    2    6    1   11    9     4     5    12
[130,]    7   11    9    1    2    6   10    8    3     4     5    12
[131,]   10    2    3    4   11    9    1    5    6     7     8    12
[132,]    4   11    3    1    5    9   10    2    6     7     8    12
[133,]   10    2   12    7    8    3    4    5    6     1    11     9
[134,]    7   11    9    1    2    6   10    8    3     4     5    12
[135,]    7    8    3    4   11    6   10    2    9     1     5    12
[136,]   10    8    9    7   11   12    1    2    6     4     5     3
[137,]   10    8   12    4    5    3    1    2    9     7    11     6
[138,]    1    2    6   10    8   12    7   11    9     4     5     3
[139,]    4    5    3    7   11    9    1    2   12    10     8     6
[140,]    4    5   12    7    8    6   10   11    3     1     2     9
[141,]    7    2   12   10   11    6    4    8    3     1     5     9
[142,]   10   11   12    7    2    6    1    5    3     4     8     9
[143,]    7    2    3   10   11    6    1    8    9     4     5    12
[144,]    1    2    9   10    5   12    4    8    3     7    11     6
[145,]    1   11    6    4    8    9    7    5   12    10     2     3
[146,]    4    5    3   10    2    6    1   11    9     7     8    12
[147,]    7   11    9    1    2    3   10    8   12     4     5     6
[148,]    4    2    3    1    5   12    7    8    6    10    11     9
[149,]   10   11   12    4    8    3    1    2    9     7     5     6
[150,]    4    8    3   10    5    6    1   11    9     7     2    12
[151,]    1    8    6   10    5    9    4   11    3     7     2    12
[152,]    4    8    6    7   11   12   10    5    3     1     2     9
[153,]    7    2    3   10    5    6    4   11    9     1     8    12
[154,]   10    5   12    1    8    9    7    2    3     4    11     6
[155,]    1    8    6    4    2    9   10    5    3     7    11    12
[156,]   10    2    3    7    5    9    4   11   12     1     8     6
[157,]   10    5    3    1    2    6    7    8    9     4    11    12
[158,]    7   11   12    4    5    9   10    8    3     1     2     6
[159,]    7    5    3    1    8   12   10    2    6     4    11     9
[160,]    7    2    6    4   11    3    1    5   12    10     8     9
[161,]    7    5    3    1    2   12    4    8    9    10    11     6
[162,]    7    8   12    1    5    6   10   11    9     4     2     3
[163,]   10   11    9    4    8    6    1    2    3     7     5    12
[164,]    7   11    6    1    5    9    4    2   12    10     8     3
[165,]    4   11    9   10    8    3    7    2   12     1     5     6
[166,]    4    2    6   10    8    9    7   11   12     1     5     3
[167,]    7    5    3   10    2   12    4    8    6     1    11     9
[168,]    1    8   12    7    2    3    4    5    9    10    11     6
[169,]    7    8   12    1    5    6    4    2    3    10    11     9
[170,]    4    5    3    7    8    9    1    2   12    10    11     6
[171,]    7   11    9    1    8    6    4    2   12    10     5     3
[172,]   10    8    3    1    2    9    4   11   12     7     5     6
[173,]   10    5   12    7    8    9    4   11    3     1     2     6
[174,]   10   11    6    7    5    3    4    8   12     1     2     9
[175,]    7   11   12    1    2    3   10    8    9     4     5     6
[176,]    1   11   12    7    2    3    4    8    9    10     5     6
[177,]   10   11   12    4    5    3    7    8    6     1     2     9
[178,]   10    5    3    7    2    6    4    8   12     1    11     9
[179,]    1    5    6    7    2    9   10   11    3     4     8    12
[180,]    1   11   12   10    5    6    4    2    3     7     8     9
[181,]    7    2   12    4   11    9    1    5    6    10     8     3
[182,]   10   11   12    1    5    3    7    8    9     4     2     6
[183,]    4    8    3    1   11    9    7    2    6    10     5    12
[184,]    4    8    9    7    2    3   10    5    6     1    11    12
[185,]   10   11    9    1    5    6    7    2   12     4     8     3
[186,]   10    5   12    4    8    9    7    2    6     1    11     3
[187,]    4    2    3    1    8    6    7    5   12    10    11     9
[188,]   10    2    9    4   11   12    1    8    3     7     5     6
[189,]   10    2   12    7   11    3    4    5    9     1     8     6
[190,]    4    5    6    7    8    3   10   11    9     1     2    12
[191,]   10    5    9    1    2    3    7   11   12     4     8     6
[192,]    4   11    9    7    2    6   10    5    3     1     8    12
[193,]   10   11   12    1    2    6    4    5    9     7     8     3
[194,]   10    2    3    4   11   12    7    5    6     1     8     9
[195,]    4    2    6    7    8    9    1   11    3    10     5    12
[196,]   10    2   12    4    8    6    7    5    3     1    11     9
[197,]    7    5   12    4   11    9    1    2    3    10     8     6
[198,]   10    5    6    1   11    3    7    2    9     4     8    12
[199,]    1    2    9    7   11    3    4    8    6    10     5    12
[200,]    4    8    3    7   11   12    1    2    6    10     5     9

>From: Robin Hankin <rksh at soc.soton.ac.uk>
>To: Jordi Altirriba Gutiérrez  	<altirriba at hotmail.com>
>CC: r-help at stat.math.ethz.ch
>Subject: Re: [R] (no subject) (was: Permutations)
>Date: Wed, 14 Jul 2004 09:11:48 +0100
>
>Jordi
>
>try this
>
>
>R> x <- c(1,2,3,  10,11,12,  41,42,43,  81,82,83)
>R> dim(x) <- c(3,4)
>R> x
>      [,1] [,2] [,3] [,4]
>[1,]    1   10   41   81
>[2,]    2   11   42   82
>[3,]    3   12   43   83
>R>  jj <- t(apply(x,1,sample))
>R> jj
>      [,1] [,2] [,3] [,4]
>[1,]    1   41   10   81
>[2,]    2   11   82   42
>[3,]   12    3   43   83
>R> as.vector(jj)
>R>
>    [1]  1 2 12 41 11 3 10 82 43 81 42 83
>
>
>
>
>and I think that does what you want...
>
>We take the vector, rearrange it into a matrix with three rows, then sample
>*within* the rows,
>then rearrange into a vector again.
>
>There will be one forbidden permutation, namely the identity (which may or
>may not be
>desirable).
>
>This method doesn't allow "intra block" permutations.
>
>best
>
>rksh
>
>
>
>>  Dear R users,
>>  First of all, thanks for the incredibly fast answers and help of Rolf,
>>Marc and Robert.
>>  Yes, I noticed that it was a lot of permutacions, but my intention was
>>to make this process automatic and take only 5.000 - 10.000 permutations.
>>Therefore, I wanted only to take that "interesting permutations" with
>>"some information" [inter-block permutations].
>>  The reason why I'm interested in these permutations is because I'm using
>>some packages of Bioconductor to analyse my data from some microarrays and
>>I thought that perhaps could be interesting to see what happens when I
>>permute my data and I compare it against the not permuted data.
>>  Thanks again for your time and suggestions.
>>
>>Jordi Altirriba
>>Ph. D. Student
>>
>>Hospital Clinic-Barcelona-Spain
>>
>>______________________________________________
>>R-help at stat.math.ethz.ch mailing list
>>https://www.stat.math.ethz.ch/mailman/listinfo/r-help
>>http://www.R-project.org/posting-guide.html
>
>
>--
>Robin Hankin
>Uncertainty Analyst
>Southampton Oceanography Centre
>SO14 3ZH
>tel +44(0)23-8059-7743
>initialDOTsurname at soc.soton.ac.uk (edit in obvious way; spam precaution)

```