[R] subsetting to exclude different values for each subject in study

arun smartpink111 at yahoo.com
Sat May 24 03:41:26 CEST 2014


Hi,
Sorry, there is a mistake. XO[2,] should be:
XO[2,] <-  sapply(seq_along(col.tri.nb), function(i){ind1 <- as.character(ind[i]); ind2 <- as.character(ind[col.tri.nb[[i]]]); mean(abs(XO[1,ind1]-XO[1,ind2]))} )
A.K.






On Friday, May 23, 2014 12:56 PM, arun <smartpink111 at yahoo.com> wrote:

Hi Monaly,
May be this helps:
b<- 77:99
ao1 <- ao[-b,]
##Your code:

XO<- matrix( 0,6, 76, byrow=TRUE);XO
abo<-ao$NestkastNummer[-b];abo  #removed values that were NA
rownames(XO) = c("EB_score","avg","pop_size","pop_avg_score",
"adj_pop_avg", "ind_pop_dif")
colnames(XO) = abo
t <- ao$COR_LOC;t
i <- c(77:99)
ti <- t[-i];ti
XO[1,] = c(ti);XO
  

library(deldir)
library(spdep)
mat <- cbind(lat=ao1$lat_xm, long=ao1$long_ym)
library(spdep)
 coords <- coordinates(mat)
ind <- ao1$NestkastNummer

col.tri.nb <- tri2nb(coords, row.names=ind)
 lapply(col.tri.nb,function(x) ind[x])[1:5] ###
[[1]]
[1] 713 715 162 148 140 117

[[2]]
[1] 130 128 172  64 113 117

[[3]]
[1] 54 19 16 73 74

[[4]]
[1]   2  31 704  34 707

[[5]]
[1] 51 94 57 73 62

XO[2,] <- sapply(seq_along(col.tri.nb),function(i) mean(abs(ind[i]-ind[col.tri.nb[[i]]])))

A.K.



On Friday, May 23, 2014 7:17 AM, Monaly Mistry <monaly.mistry at gmail.com> wrote:



Hi Arun and Frede,

So the dput() is below (it's the same data file as before), but below that is the code I used to make the tessellation.  Thanks for your help.

> dput(ao)
structure(list(num = 1:99, FORM_CHK = c(20870L, 22018L, 30737L, 
22010L, 22028L, 36059L, 36063L, 36066L, 30587L, 30612L, 36056L, 
30376L, 35153L, 30435L, 30536L, 30486L, 30475L, 36053L, 36048L, 
36076L, 36045L, 36065L, 35772L, 36949L, 35702L, 36894L, 36080L, 
35542L, 35457L, 35533L, 36042L, 36925L, 36827L, 36008L, 35817L, 
36350L, 35985L, 35973L, 35801L, 36639L, 35810L, 35812L, 35807L, 
36351L, 35967L, 35944L, 37006L, 36345L, 36062L, 36077L, 35802L, 
35984L, 36043L, 35769L, 36360L, 36082L, 36071L, 36354L, 35771L, 
35754L, 36295L, 35746L, 36064L, 35779L, 35751L, 35752L, 35785L, 
35792L, 37011L, 36003L, 36040L, 36831L, 36031L, 36652L, 36992L, 
36965L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 
NA, NA, NA, NA, NA, NA, NA, NA, NA), RingNummerMan = structure(c(1L, 
2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 
16L, 17L, 19L, 22L, 23L, 24L, 25L, 26L, 27L, 29L, 30L, 31L, 34L, 
35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 46L, 47L, 48L, 
49L, 50L, 51L, 52L, 54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 63L, 
65L, 67L, 69L, 70L, 73L, 74L, 75L, 76L, 78L, 79L, 80L, 81L, 82L, 
83L, 85L, 86L, 87L, 88L, 89L, 93L, 96L, 97L, 18L, 20L, 21L, 28L, 
32L, 33L, 45L, 53L, 62L, 64L, 66L, 68L, 71L, 72L, 77L, 84L, 90L, 
91L, 92L, 94L, 95L, 98L, 99L), .Label = c("AJ...75425", "AL...62371", 
"AR...11060", "AR...29297", "AR...29307", "AR...29502", "AR...29504", 
"AR...29507", "AR...30039", "AR...30085", "AR...30165", "AR...30491", 
"AR...30563", "AR...30616", "AR...30652", "AR...30687", "AR...30701", 
"AR...30927", "AR...30959", "AR...30963", "AR...30964", "AR...30965", 
"AR...30966", "AR...30985", "AR...30988", "AR...40917", "AR...40996", 
"AR...45735", "AR...45904", "AR...45928", "AR...47609", "AR...65387", 
"AR...65479", "AR...65550", "AR...65629", "AR...65948", "AR...86074", 
"AR...86521", "AR...86527", "AR...90061", "AR...90064", "AR...90067", 
"AR...90077", "AR...90081", "AR...90098", "AR...90101", "AR...90106", 
"AR...90112", "AR...90133", "AR...90155", "AR...90176", "AR...90178", 
"AR...90180", "AR...90187", "AR...90212", "AR...90247", "AR...90252", 
"AR...90256", "AR...90258", "AR...90269", "AR...90272", "AR...90275", 
"AR...90294", "AR...90298", "AR...90300", "AR...90337", "AR...90338", 
"AR...90367", "AR...90397", "AR...90410", "AR...90463", "AR...90520", 
"AR...90544", "AR...90556", "AR...90678", "AR...90712", "AR...90737", 
"AR...90744", "AR...90829", "AR...90862", "AR...90863", "AR...90873", 
"AR...90880", "AR...90892", "AR...90898", "AR...90945", "AR...90951", 
"AR...90965", "AR...90970", "AR...90972", "AU...15008", "AU...15009", 
"AU...15027", "AU...15032", "AU...15036", "AU...15038", "AU...15046", 
"AU...15049", "AU...15505"), class = "factor"), year_score_taken = c(2006L, 
2008L, 2009L, 2008L, 2008L, 2011L, 2011L, 2011L, 2009L, 2009L, 
2011L, 2009L, 2010L, 2009L, 2009L, 2009L, 2009L, 2011L, 2011L, 
2011L, 2011L, 2011L, 2011L, 2012L, 2011L, 2012L, 2011L, 2010L, 
2010L, 2010L, 2011L, 2012L, 2012L, 2011L, 2011L, 2012L, 2011L, 
2011L, 2011L, 2012L, 2011L, 2011L, 2011L, 2012L, 2011L, 2011L, 
2013L, 2012L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2012L, 
2012L, 2011L, 2012L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 
2011L, 2011L, 2011L, 2011L, 2013L, 2011L, 2011L, 2012L, 2011L, 
2012L, 2012L, 2012L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA), COR_LOC = c(15.13404, 
13.88054, 30.0969, 19.09152, 16.88054, 14.15718, 39.15718, 16.15718, 
16.13566, 23.07538, 39.15718, 24.56838, 12.13942, 21.4123, 19.06945, 
12.33264, 32.48872, 30.15718, 37.15718, 37.15718, 49.15718, 22.15718, 
18.50272, 23.69432, 24.9322, 47.29712, 41.15718, 21.47903, 38.6588, 
34.99572, 28.15718, 13.08614, 16.71908, 22.68894, 19.2616, 15.96234, 
22.83964, 13.89992, 14.2616, 18.17118, 24.2616, 22.2616, 13.2616, 
23.96234, 24.89992, 24.05062, 10.20884, 6.96234, 13.15718, 17.15718, 
40.2616, 21.83964, 20.15718, 39.50272, 26.81164, 20.3843, 14.15718, 
7.96234, 19.50272, 40.74384, 5.7675, 42.95482, 29.15718, 18.32188, 
28.74384, 37.74384, 22.32188, 25.32188, 18.20884, 14.68894, 22.15718, 
39.71908, 18.2067, 15.1109, 15.61466, 47.4532, NA, NA, NA, NA, 
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 
NA, NA, NA), IndividuID = c(11394L, 15676L, 342518L, 344902L, 
344909L, 377497L, 377499L, 377504L, 352003L, 351986L, 352260L, 
352392L, 353800L, 353892L, 353949L, 354060L, 354074L, 377487L, 
377490L, 377511L, 377513L, 377495L, 377297L, 357796L, 366326L, 
378446L, 377518L, 358157L, 358730L, 366215L, 377519L, 378407L, 
378453L, 377443L, 377358L, 377726L, 377422L, 377402L, 377341L, 
378354L, 377350L, 377352L, 377347L, 378408L, 377396L, 377374L, 
377774L, 377743L, 377500L, 377510L, 377342L, 377421L, 377786L, 
377294L, 377836L, 378291L, 377508L, 378199L, 377296L, 377280L, 
373000L, 373020L, 377496L, 377306L, 373025L, 377278L, 377310L, 
377317L, 377337L, 377439L, 377450L, 377464L, 377478L, 400290L, 
400361L, 400260L, 357889L, 377477L, 377298L, 400370L, 356930L, 
356939L, 378115L, 377562L, 378018L, 377834L, 378290L, 378228L, 
378268L, 378052L, 378103L, 377332L, 377514L, 400356L, 400357L, 
400372L, 400259L, 400256L, 400354L), BroedJaar = c(2012L, 2012L, 
2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 
2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 
2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 
2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 
2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 
2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 
2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 
2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 
2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 
2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 
2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L), ManipulatieOuders = c(0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L), LegBeginDag = c(11L, 15L, 15L, 13L, 8L, 26L, 15L, 16L, 
1L, 3L, 4L, 9L, 13L, 20L, 11L, 2L, 9L, 13L, 31L, 1L, 12L, 8L, 
13L, 7L, 10L, 11L, 17L, 10L, 11L, 19L, 20L, 13L, 14L, 24L, 17L, 
10L, 8L, 29L, 7L, 26L, 10L, 15L, 2L, 6L, 8L, 13L, 1L, 5L, 12L, 
12L, 15L, 19L, 10L, 1L, 5L, 13L, 6L, 5L, 16L, 2L, 2L, 30L, 10L, 
21L, 8L, 19L, 8L, 27L, 3L, 8L, 14L, 18L, 17L, 7L, 4L, 10L, 13L, 
11L, 31L, 25L, 23L, 7L, 7L, 7L, 8L, 3L, 14L, 14L, 15L, 5L, 10L, 
11L, 18L, 1L, 31L, 3L, 8L, 20L, 14L), LegBeginMaand = c(4L, 4L, 
5L, 4L, 5L, 4L, 4L, 4L, 4L, 5L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 
3L, 4L, 4L, 4L, 5L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 4L, 4L, 
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 4L, 4L, 4L, 
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 3L, 4L, 4L, 4L, 4L, 
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 3L, 4L, 4L, 4L, 
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 3L, 4L, 4L, 4L, 
4L), broodinfo = c(55334L, 55325L, 55317L, 55349L, 55366L, 55303L, 
55461L, 55528L, 55296L, 55297L, 55630L, 55567L, 55345L, 55444L, 
55526L, 55571L, 55462L, 55346L, 55576L, 55577L, 55601L, 55300L, 
55607L, 55634L, 55558L, 55633L, 55590L, 55594L, 55537L, 55466L, 
55327L, 55603L, 55600L, 55302L, 55319L, 55609L, 55574L, 55310L, 
55554L, 55582L, 55561L, 55320L, 55555L, 55578L, 55343L, 55331L, 
55314L, 55560L, 55460L, 55551L, 55322L, 55306L, 55348L, 55589L, 
55572L, 55565L, 55595L, 55606L, 55323L, 55635L, 55568L, 55614L, 
55447L, 55312L, 55344L, 55321L, 55569L, 55309L, 55570L, 55562L, 
55550L, 55605L, 55465L, 55445L, 55587L, 55332L, 55629L, 55613L, 
55448L, 55632L, 55636L, 55531L, 55329L, 55597L, 55298L, 55596L, 
55318L, 55608L, 55463L, 55532L, 55557L, 55536L, 55333L, 55533L, 
55538L, 55637L, 55330L, 55326L, 55525L), BroedselID = c(55334L, 
55325L, 55317L, 55349L, 55366L, 55303L, 55461L, 55528L, 55296L, 
55297L, 55630L, 55567L, 55345L, 55444L, 55526L, 55571L, 55462L, 
55346L, 55576L, 55577L, 55601L, 55300L, 55607L, 55634L, 55558L, 
55633L, 55590L, 55594L, 55537L, 55466L, 55327L, 55603L, 55600L, 
55302L, 55319L, 55609L, 55574L, 55310L, 55554L, 55582L, 55561L, 
55320L, 55555L, 55578L, 55343L, 55331L, 55314L, 55560L, 55460L, 
55551L, 55322L, 55306L, 55348L, 55589L, 55572L, 55565L, 55595L, 
55606L, 55323L, 55635L, 55568L, 55614L, 55447L, 55312L, 55344L, 
55321L, 55569L, 55309L, 55570L, 55562L, 55550L, 55605L, 55465L, 
55445L, 55587L, 55332L, 55629L, 55613L, 55448L, 55632L, 55636L, 
55531L, 55329L, 55597L, 55298L, 55596L, 55318L, 55608L, 55463L, 
55532L, 55557L, 55536L, 55333L, 55533L, 55538L, 55637L, 55330L, 
55326L, 55525L), NestkastNummer = c(176L, 124L, 51L, 717L, 54L, 
19L, 11L, 42L, 90L, 9L, 713L, 82L, 709L, 2L, 39L, 86L, 16L, 710L, 
93L, 94L, 163L, 14L, 170L, 718L, 79L, 715L, 130L, 133L, 57L, 
25L, 128L, 164L, 162L, 15L, 60L, 172L, 91L, 31L, 73L, 97L, 111L, 
64L, 74L, 95L, 704L, 148L, 36L, 80L, 8L, 68L, 105L, 22L, 716L, 
127L, 88L, 81L, 140L, 169L, 109L, 719L, 35L, 185L, 6L, 34L, 707L, 
101L, 38L, 28L, 84L, 113L, 62L, 168L, 23L, 3L, 117L, 150L, 705L, 
183L, 7L, 714L, 720L, 49L, 144L, 153L, 12L, 143L, 56L, 171L, 
17L, 50L, 77L, 55L, 175L, 52L, 58L, 722L, 145L, 125L, 32L), lat_xm = c(729.2669944, 
1001.809576, 501.4865527, 105.2662516, 622.0842564, 313.4718688, 
198.828763, 248.3819471, 466.4434076, 155.709257, 433.2482345, 
388.4860969, 306.5590574, 14.98895776, 191.9843836, 309.4336924, 
308.6123573, 351.526526, 606.8213156, 601.8249333, 912.0799656, 
267.5461811, 1084.557939, 264.26089, 359.6713191, 488.4822672, 
1018.578266, 915.707476, 773.276261, 171.4513083, 1084.831712, 
952.5985963, 878.4741353, 288.3530553, 913.9963847, 1071.827424, 
456.313756, 51.12730755, 582.6607182, 592.1059359, 740.3548678, 
1042.875765, 476.8468377, 654.0474325, 276.375404, 877.6528113, 
135.7921596, 300.9466765, 145.6480126, 829.1262723, 601.4827177, 
237.6363065, 500.3230173, 1129.730741, 398.06821, 340.8493193, 
770.4016222, 1051.63655, 571.7097287, 314.4300781, 117.5861334, 
437.9708453, 95.41039954, 105.7453938, 235.5829892, 627.9704095, 
177.0636713, 99.17481232, 396.6993402, 973.4739067, 1034.662528, 
1046.77705, 221.278275, 27.24031031, 724.0652756, 942.6742674, 
325.9970589, 261.933799, 116.7648206, 464.0478832, 532.6968545, 
423.9399058, 656.8536222, 979.9076146, 221.2098377, 701.5473216, 
709.8290013, 1120.559295, 345.5719307, 463.4318862, 429.6207308, 
659.112262, 717.7684649, 533.3812884, 819.3388243, 600.9351721, 
722.4910753, 1126.719223, 26.8297633), long_ym = c(385.4016022, 
744.3388344, 1278.519267, 582.1054392, 1183.781188, 1313.545671, 
1155.204087, 1008.093201, 812.6125238, 1045.899477, 474.135164, 
887.4467064, 626.9169985, 700.9728169, 849.3068501, 799.1579293, 
1418.180093, 598.1175046, 928.3664402, 1111.83807, 367.2768291, 
1318.32705, 501.4891137, 542.5200518, 1095.7148, 552.6387801, 
636.2573659, 479.9172936, 1057.018971, 980.7392501, 739.0014835, 
485.8106446, 371.9470232, 1365.91848, 942.3769994, 664.2784869, 
887.335514, 669.5046549, 1156.983212, 893.8960158, 933.9261864, 
783.4794517, 1191.342439, 975.8466709, 453.8976828, 55.70866057, 
731.2178331, 973.6227733, 1002.199869, 920.5827929, 678.1778549, 
1141.415921, 578.9919757, 710.2019861, 738.8902861, 936.706063, 
480.8068625, 454.8984371, 771.1368166, 510.940689, 680.7353401, 
1087.041598, 895.6751282, 641.8171157, 573.7658194, 651.9358502, 
816.2819528, 819.6178023, 828.7357905, 801.8266126, 856.9792948, 
415.0906484, 1086.374437, 737.4447458, 559.866446, 0, 423.6526577, 
1166.990753, 957.8330951, 562.8687158, 564.7590286, 1339.676479, 
197.5933584, 132.099559, 1205.686591, 246.6303384, 1106.500715, 
597.3391415, 1389.380609, 1312.878499, 1155.760068, 1152.090634, 
433.6602223, 1252.833235, 1028.88666, 522.3937678, 151.7810272, 
796.3780665, 631.3647851), avg_pop_eb = c(23.57103359, 23.57103359, 
23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
23.57103359, 23.57103359, 23.57103359, 23.57103359, 23.57103359, 
23.57103359, 23.57103359)), .Names = c("num", "FORM_CHK", "RingNummerMan", 
"year_score_taken", "COR_LOC", "IndividuID", "BroedJaar", "ManipulatieOuders", 
"LegBeginDag", "LegBeginMaand", "broodinfo", "BroedselID", "NestkastNummer", 
"lat_xm", "long_ym", "avg_pop_eb"), class = "data.frame", row.names = c(NA, 
-99L))


#Code for  tessellation
library(deldir)

ao= read.table("C:/Users/Monaly/Desktop/2012_malenest.txt", header=TRUE)

a29= deldir(ao$lat_xm, ao$long_ym)

a30=tile.list(a29)

plot(a30, close=TRUE, main="2012 Male Nest", xlab="latitude (m)", ylab="longitude (m)", wpoints="real", verbose=FALSE,num=TRUE, rw=c(0, 1200, 0, 2000))

text(ao$lat_xm, ao$long_ym,col=c(2,1,4),labels=round(ao$NestkastNummer, 3), pos=2, offset=0.2, cex=0.7)  #this was to identify the points



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