[BioC] [devteam-bioc] Converting \"data.frame\" to appropriate format for tau.dist() in bioDist library
Paul Shannon
paul.thurmond.shannon at gmail.com
Mon Aug 19 16:10:38 CEST 2013
Hi Nicole,
If you could send me (off-list) a copy of your demonstration data file, "Social sample test.csv", I'll be glad to explore and try to help with the difficulty you report.
Once we figure it out, I will summarize back to the list.
- Paul
On Aug 15, 2013, at 3:24 AM, Maintainer wrote:
>
> Hello,
>
> I am a graduate student in evolutionary primatology at Columbia University and a guest to the Bioconductor help mailing list.
>
> I am trying to test how long a subject (female monkey) must be observed in order to capture an accurate representation of her sociality over a year. I decided to compare the similarity of 5 pair-wise matrices of social behavior using a matrix correlation test. These matrices describe dyadic social relationships between monkeys after 1, 2, 3, 4, and 12 months of observation. The different interaction types are rates of proximity while resting, test$Beep == "R-grm", and rates of grooming or test$Beep == "Grm".
>
> Due to the nature of our data collection, R-grm matrices are ASYMMETRIC, therefore I am unable to use the mantel() function within the vegan library or any other matrix correlation test whose arguments are "dist" objects, which only show the bottom half of a distance matrix.
>
> In order to deal with the asymmetry of my matrices, I am trying to perform a row-wise matrix correlation test (or Kr test) using the output of the tau.dist() function in the bioDist package, but I am having a difficult time formatting my data appropriately. The only literature on the tau.dist function that I have found is in the bioDist pdf. From what I understand, tau.dist() calculates Kendall's tau for each row of the matrix compared with another. As such, I have tried to construct a numeric matrix where each row represents the relationships of a single subject (e.g. "Arte", in example) as observed after 1 month (row 1), 2 months (row 2), etc.
>
> I have truncated the number of partners (columns) for the example below. Forgive the lengthiness if altogether unnecessary.
>
> I greatly appreciate anyone's insight or instruction on the matter.
>
> Many thanks,
>
> Nicole A. Thompson
> Department of Ecology, Evolution, and Environmental Biology, Columbia University
>
> -- output of sessionInfo():
>
>> sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] vegan_2.0-7 permute_0.7-0 bioDist_1.30.0 KernSmooth_2.23-10 Biobase_2.18.0
> [6] BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
> [1] grid_2.15.1 lattice_0.20-15 tools_2.15.1
>
>
>
>> library(bioDist)
>> test<- read.csv("Social sample test.csv", header=T)
>
>
>> str(test)
> 'data.frame': 255 obs. of 20 variables:
> $ Beep : Factor w/ 3 levels "Grm","R-grm",..: 2 2 2 2 2 2 2 2 2 2 ...
> $ Months : int 1 1 1 1 1 1 1 1 1 1 ...
> $ Subject: Factor w/ 17 levels "Arte","Bif","Bill",..: 1 2 3 4 5 6 7 8 9 10 ...
> $ Arte : Factor w/ 69 levels "*","0","0.011090163",..: 1 2 2 68 2 2 2 2 2 2 ...
> $ Bif : Factor w/ 52 levels "*","0","0.011137098",..: 2 1 2 2 2 2 2 2 2 2 ...
> $ Bill : Factor w/ 37 levels "*","0","0.010856585",..: 2 2 1 2 2 2 2 2 2 2 ...
> $ Blaz : Factor w/ 60 levels "*","0","0.010856585",..: 2 2 2 1 2 2 2 2 2 2 ...
> $ Bonn : Factor w/ 58 levels "*","0","0.010877842",..: 2 2 2 2 1 53 2 2 2 2 ...
> $ Bow : Factor w/ 76 levels "*","0","0.011030223",..: 2 2 2 2 66 1 2 2 43 2 ...
> $ Dixi : Factor w/ 51 levels "*","0","0.011041184",..: 2 2 2 2 2 2 1 2 30 2 ...
> $ Elle : Factor w/ 42 levels "*","0","0.011048503",..: 2 2 2 2 2 2 2 1 2 2 ...
> $ Flet : Factor w/ 60 levels "*","0","0.011058277",..: 2 2 2 2 2 2 2 2 1 2 ...
> $ Gaun : Factor w/ 47 levels "*","0","0.011086475",..: 2 2 2 2 2 2 2 2 2 1 ...
> $ Kami : Factor w/ 54 levels "*","0","0.011185682",..: 2 47 2 2 2 33 2 2 2 2 ...
> $ KK : Factor w/ 60 levels "*","0","0.011096316",..: 2 2 2 2 2 2 2 2 2 51 ...
> $ Pans : Factor w/ 52 levels "*","0","0.010873111",..: 2 2 28 2 2 2 2 2 2 2 ...
> $ Quan : Factor w/ 51 levels "*","0","0.010873111",..: 2 2 2 2 2 2 2 2 2 2 ...
> $ Sauc : Factor w/ 53 levels "*","0","0.013294337",..: 2 2 30 2 2 2 2 2 2 2 ...
> $ Trim : Factor w/ 77 levels "*","0","0.011069294",..: 2 2 2 2 2 2 2 2 2 2 ...
> $ Twin : Factor w/ 65 levels "*","0","0.011090163",..: 2 2 2 2 2 2 35 2 2 2 ...
>
>> test
> Beep Months Subject Arte Bif Bill Blaz Bonn Bow
> 1 R-grm 1 Arte * 0 0 0 0 0
> 2 R-grm 1 Bif 0 * 0 0 0 0
> 3 R-grm 1 Bill 0 0 * 0 0 0
> 4 R-grm 1 Blaz 1.940755873 0 0 * 0 0
> 5 R-grm 1 Bonn 0 0 0 0 * 0.3125
> 6 R-grm 1 Bow 0 0 0 0 0.3125 *
> 7 R-grm 1 Dixi 0 0 0 0 0 0
> 8 R-grm 1 Elle 0 0 0 0 0 0
> 9 R-grm 1 Flet 0 0 0 0 0 0.107526882
> 10 R-grm 1 Gaun 0 0 0 0 0 0
> 11 R-grm 1 Kami 0 0 0 0 0 0
> 12 R-grm 1 KK 0 0 0 0 0 0
> 13 R-grm 1 Pans 0 0 0 0 0 0
> 14 R-grm 1 Quan 0 0 0 0 0 0.208333333
> 15 R-grm 1 Sauc 0 0 0 0 0 0.114942529
> 16 R-grm 1 Trim 0 0 0 0 0 0.114942529
> 17 R-grm 1 Twin 0 0 0 0 0 0
> 18 R-grm 2 Arte * 0.169779287 0 0 0 0.333889816
> 19 R-grm 2 Bif 0 * 0 0 0.114942529 0
> 20 R-grm 2 Bill 0 0 * 0 0 0
> 21 R-grm 2 Blaz 2.459474567 0 0 * 0 0
> 22 R-grm 2 Bonn 0 0 0 0 * 0.338983051
> 23 R-grm 2 Bow 0 0 0 0 0.169491525 *
> 24 R-grm 2 Dixi 0 0 0 0 0 0
> 25 R-grm 2 Elle 0 0 0 0 0 0
> 26 R-grm 2 Flet 0.278241514 0.11299435 0 0 0 0.055555556
> 27 R-grm 2 Gaun 0 0 0 0 0 0
> 28 R-grm 2 Kami 0 0 0 0 0 0
> 29 R-grm 2 KK 0 0 0 0 0 0
> 30 R-grm 2 Pans 0 0 0 0 0 0
> 31 R-grm 2 Quan 0 0.111111111 0 0 0 0.109289617
> 32 R-grm 2 Sauc 0 0 0 0 0 0.109289617
> 33 R-grm 2 Trim 0 0 0 0.56753689 0 0.056497175
> 34 R-grm 2 Twin 0 0 0 0 0 0
> 35 R-grm 3 Arte * 0.077609624 0 0.036778227 0 0.151687524
> 36 R-grm 3 Bif 0 * 0 0.3756574 0.037878788 0
> 37 R-grm 3 Bill 0 0 * 0 0 0
> 38 R-grm 3 Blaz 1.728576683 0 0 * 0 0
> 39 R-grm 3 Bonn 0 0 0 0 * 0.185185185
> 40 R-grm 3 Bow 0 0 0 0 0.111111111 *
> 41 R-grm 3 Dixi 0 0 0 0 0 0
> 42 R-grm 3 Elle 0.037078235 0 0 0 0 0
> 43 R-grm 3 Flet 0.151687524 0.07751938 0 0 0 0.037878788
> 44 R-grm 3 Gaun 0 0 0 0 0 0
> 45 R-grm 3 Kami 0 0 0 0 0 0
> 46 R-grm 3 KK 0 0 0 0 0 0
> 47 R-grm 3 Pans 0 0 0 0 0 0
> 48 R-grm 3 Quan 0.037495313 0.076628352 0 0.072674419 0 0.074906367
> 49 R-grm 3 Sauc 0 0 0 0 0 0.036643459
> 50 R-grm 3 Trim 0.038819876 0 0 0.338218715 0 0.038774719
> 51 R-grm 3 Twin 0 0 0 0 0 0
> 52 R-grm 4 Arte * 0.057126535 0 0.027181299 0 0.113090189
> 53 R-grm 4 Bif 0 * 0 0.278862242 0.028058361 0
> 54 R-grm 4 Bill 0 0 * 0 0 0
> 55 R-grm 4 Blaz 1.277521066 0 0 * 0 0.248481502
> 56 R-grm 4 Bonn 0 0 0 0 * 0.138888889
> 57 R-grm 4 Bow 0 0 0 0 0.083333333 *
> 58 R-grm 4 Dixi 0 0 0 0 0 0.115174201
> 59 R-grm 4 Elle 0.027800945 0 0 0 0 0
> 60 R-grm 4 Flet 0.112139052 0.057570524 0 0 0 0.028490028
> 61 R-grm 4 Gaun 0 0 0 0 0 0
> 62 R-grm 4 Kami 0 0 0 0 0 0
> 63 R-grm 4 KK 0 0 0 0 0 0
> 64 R-grm 4 Pans 0 0 0 0 0 0.166805671
> 65 R-grm 4 Quan 0.027800945 0.057077626 0 0.054318305 0 0.056497175
> 66 R-grm 4 Sauc 0 0 0 0 0 0.027785496
> 67 R-grm 4 Trim 0.028522533 0 0 0.250626566 0 0.028993911
> 68 R-grm 4 Twin 0 0 0.163043478 0 0 0
> 69 R-grm 12 Arte * 0.044179368 0.110448421 0.066269052 0.198807157 0.463883366
> 70 R-grm 12 Bif 0 * 0.402594498 0.22366361 0.044732722 0.089465444
> 71 R-grm 12 Bill 0.021263024 0.191367212 * 0.063789071 0 0.021263024
> 72 R-grm 12 Blaz 1.220053239 0 0 * 0.110913931 0.199645075
> 73 R-grm 12 Bonn 0.43449924 0.021724962 0 0 * 0.21724962
> 74 R-grm 12 Bow 0 0 0 0 0.067219359 *
> 75 R-grm 12 Dixi 0 0.022451729 0.112258644 0.022451729 0.067355186 0.269420745
> 76 R-grm 12 Elle 0.198106978 0 0.022011886 0.066035659 0.352190183 0.022011886
> 77 R-grm 12 Flet 0.088888889 0.044444444 0 0 0.288888889 0.955555556
> 78 R-grm 12 Gaun 0.022123894 0 0.951327434 0 0 0
> 79 R-grm 12 Kami 0.089166295 0.089166295 0.111457869 1.404369148 0 0.312082033
> 80 R-grm 12 KK 0.021829295 0.349268719 0 0.240122244 0 0.08731718
> 81 R-grm 12 Pans 0.173648795 0.173648795 0.151942696 0.130236596 0.130236596 0.130236596
> 82 R-grm 12 Quan 0.021786492 0.043572985 0 0.261437908 0.196078431 0.043572985
> 83 R-grm 12 Sauc 0 0 0 0 0 0.02625361
> 84 R-grm 12 Trim 0.067704807 0.112841345 0 0.203114421 0.022568269 0.045136538
> 85 R-grm 12 Twin 0.445434298 0 0.13363029 0.08908686 0.244988864 0.556792873
> 86 Grm 1 Arte * 0 0 0.204290092 0 0
> 87 Grm 1 Bif 0 * 0 0 0 0
> 88 Grm 1 Bill 0 0 * 0 0 0
> 89 Grm 1 Blaz 0.204290092 0 0 * 0 0
> 90 Grm 1 Bonn 0 0 0 0 * 0.104166667
> 91 Grm 1 Bow 0 0 0 0 0.104166667 *
> 92 Grm 1 Dixi 0 0 0 0 0 0
> 93 Grm 1 Elle 0 0 0 0 0 0
> 94 Grm 1 Flet 0 0 0 0 0 0
> 95 Grm 1 Gaun 0 0 0 0 0 0
> 96 Grm 1 Kami 0 0 0 0 0 0
> 97 Grm 1 KK 0 0 0 0 0 0
> 98 Grm 1 Pans 0 0 0 0 0 0
> 99 Grm 1 Quan 0 0 0 0 0 0
> 100 Grm 1 Sauc 0 0 0 0 0 0.114942529
> 101 Grm 1 Trim 0 0 0 0 0 0
> 102 Grm 1 Twin 0 0 0 0 0 0
> 103 Grm 2 Arte * 0.056593096 0 0.279485746 0 0.111296605
> 104 Grm 2 Bif 0.056593096 * 0 0 0.057471264 0
> 105 Grm 2 Bill 0 0 * 0 0 0
> 106 Grm 2 Blaz 0.279485746 0 0 * 0 0
> 107 Grm 2 Bonn 0 0.057471264 0 0 * 0.056497175
> 108 Grm 2 Bow 0.111296605 0 0 0 0.056497175 *
> 109 Grm 2 Dixi 0 0 0 0 0 0
> 110 Grm 2 Elle 0 0 0 0 0 0
> 111 Grm 2 Flet 0.111296605 0 0 0 0 0
> 112 Grm 2 Gaun 0 0 0 0 0 0
> 113 Grm 2 Kami 0 0 0 0 0 0
> 114 Grm 2 KK 0 0 0 0 0 0
> 115 Grm 2 Pans 0 0 0 0 0 0
> 116 Grm 2 Quan 0 0 0 0 0 0
> 117 Grm 2 Sauc 0 0 0 0 0 0.054644809
> 118 Grm 2 Trim 0 0 0 0.056753689 0 0
> 119 Grm 2 Twin 0 0 0 0 0 0
> 120 Grm 3 Arte * 0.038804812 0 0.294225818 0 0.075843762
> 121 Grm 3 Bif 0.038804812 * 0 0.03756574 0.037878788 0
> 122 Grm 3 Bill 0 0 * 0 0 0
> 123 Grm 3 Blaz 0.294225818 0.03756574 0 * 0 0
> 124 Grm 3 Bonn 0 0.037878788 0 0 * 0.037037037
> 125 Grm 3 Bow 0.075843762 0 0 0 0.037037037 *
> 126 Grm 3 Dixi 0 0 0 0 0 0.116595414
> 127 Grm 3 Elle 0.111234705 0 0 0 0 0
> 128 Grm 3 Flet 0.075843762 0 0 0 0.037037037 0
> 129 Grm 3 Gaun 0 0 0 0 0 0
> 130 Grm 3 Kami 0 0 0 0 0 0
> 131 Grm 3 KK 0 0 0 0 0 0
> 132 Grm 3 Pans 0 0 0 0 0 0
> 133 Grm 3 Quan 0 0 0 0 0 0
> 134 Grm 3 Sauc 0 0 0 0 0 0.036643459
> 135 Grm 3 Trim 0.038819876 0 0 0.037579857 0 0
> 136 Grm 3 Twin 0 0 0 0 0 0
> 137 Grm 4 Arte * 0.028563268 0 0.217450394 0 0.056545095
> 138 Grm 4 Bif 0.028563268 * 0 0.027886224 0.028058361 0
> 139 Grm 4 Bill 0 0 * 0 0 0
> 140 Grm 4 Blaz 0.217450394 0.027886224 0 * 0 0.027609056
> 141 Grm 4 Bonn 0 0.028058361 0 0 * 0.027777778
> 142 Grm 4 Bow 0.056545095 0 0 0.027609056 0.027777778 *
> 143 Grm 4 Dixi 0 0 0 0 0.027831895 0.143967751
> 144 Grm 4 Elle 0.083402836 0 0 0 0 0
> 145 Grm 4 Flet 0.056069526 0 0 0 0.027548209 0
> 146 Grm 4 Gaun 0 0 0 0 0 0
> 147 Grm 4 Kami 0 0 0 0 0.027654867 0.028604119
> 148 Grm 4 KK 0 0 0 0 0 0
> 149 Grm 4 Pans 0 0 0 0 0 0
> 150 Grm 4 Quan 0 0 0 0 0 0
> 151 Grm 4 Sauc 0 0 0 0 0 0.027785496
> 152 Grm 4 Trim 0.028522533 0 0 0.027847396 0 0
> 153 Grm 4 Twin 0 0 0.027173913 0 0 0
> 154 Grm 12 Arte * 0.022227162 0.021668472 0.121748755 0.120481928 0.022246941
> 155 Grm 12 Bif 0.022227162 * 0.032701112 0.011137098 0.044081993 0.022386389
> 156 Grm 12 Bill 0.021668472 0.032701112 * 0.010856585 0.021491511 0
> 157 Grm 12 Blaz 0.121748755 0.011137098 0.010856585 * 0.021951487 0.011147029
> 158 Grm 12 Bonn 0.120481928 0.044081993 0.021491511 0.021951487 * 0.011030223
> 159 Grm 12 Bow 0.022246941 0.022386389 0 0.011147029 0.011030223 *
> 160 Grm 12 Dixi 0 0 0 0 0.011041184 0.100930806
> 161 Grm 12 Elle 0.033076075 0 0 0.011048503 0.054668708 0
> 162 Grm 12 Flet 0.022155755 0 0 0 0.032956168 0.08925583
> 163 Grm 12 Gaun 0 0 0.097582132 0 0 0
> 164 Grm 12 Kami 0 0.04465781 0.043530308 0.25572604 0.033006931 0.033523299
> 165 Grm 12 KK 0.054896794 0.055236412 0 0.055011552 0 0.055285272
> 166 Grm 12 Pans 0 0 0 0.043883708 0 0
> 167 Grm 12 Quan 0.021937041 0 0.043043151 0 0.010877842 0
> 168 Grm 12 Sauc 0 0.093507881 0 0 0 0.013294337
> 169 Grm 12 Trim 0.011163206 0.134801168 0 0.033560801 0.011069294 0.011243535
> 170 Grm 12 Twin 0.011090163 0 0.054389209 0.044454323 0.043989882 0.055847202
> 171 R-grm2 1 Arte * 0 0 1.940755873 0 0
> 172 R-grm2 1 Bif 0 * 0 0 0 0
> 173 R-grm2 1 Bill 0 0 * 0 0 0
> 174 R-grm2 1 Blaz 0 0 0 * 0 0
> 175 R-grm2 1 Bonn 0 0 0 0 * 0.3125
> 176 R-grm2 1 Bow 0 0 0 0 0.3125 *
> 177 R-grm2 1 Dixi 0 0 0 0 0 0
> 178 R-grm2 1 Elle 0 0 0 0 0 0
> 179 R-grm2 1 Flet 0 0 0 0 0 0
> 180 R-grm2 1 Gaun 0 0 0 0 0 0
> 181 R-grm2 1 Kami 0 0.240096038 0 0 0 0.111982083
> 182 R-grm2 1 KK 0 0 0 0 0 0
> 183 R-grm2 1 Pans 0 0 0.098039216 0 0 0
> 184 R-grm2 1 Quan 0 0 0 0 0 0
> 185 R-grm2 1 Sauc 0 0 0.101010101 0 0 0
> 186 R-grm2 1 Trim 0 0 0 0 0 0
> 187 R-grm2 1 Twin 0 0 0 0 0 0
> 188 R-grm2 2 Arte * 0 0 2.459474567 0 0
> 189 R-grm2 2 Bif 0.169779287 * 0 0 0 0
> 190 R-grm2 2 Bill 0 0 * 0 0 0
> 191 R-grm2 2 Blaz 0 0 0 * 0 0
> 192 R-grm2 2 Bonn 0 0.114942529 0 0 * 0.169491525
> 193 R-grm2 2 Bow 0.333889816 0 0 0 0.338983051 *
> 194 R-grm2 2 Dixi 0 0 0 0 0 0
> 195 R-grm2 2 Elle 0 0 0 0 0 0
> 196 R-grm2 2 Flet 0.389538119 0 0 0 0 0
> 197 R-grm2 2 Gaun 0 0 0 0 0 0
> 198 R-grm2 2 Kami 0 0.113442995 0 0 0 0.055772448
> 199 R-grm2 2 KK 0 0 0 0 0 0
> 200 R-grm2 2 Pans 0 0 0.051282051 0 0 0
> 201 R-grm2 2 Quan 0 0 0 0 0 0
> 202 R-grm2 2 Sauc 0 0 0.051282051 0 0 0
> 203 R-grm2 2 Trim 0 0 0 0 0.114942529 0
> 204 R-grm2 2 Twin 0 0 0 0 0 0
> 205 R-grm2 3 Arte * 0 0 1.728576683 0 0
> 206 R-grm2 3 Bif 0.077609624 * 0 0 0 0
> 207 R-grm2 3 Bill 0 0 * 0 0 0
> 208 R-grm2 3 Blaz 0.036778227 0.3756574 0 * 0 0
> 209 R-grm2 3 Bonn 0 0.037878788 0 0 * 0.111111111
> 210 R-grm2 3 Bow 0.151687524 0 0 0 0.185185185 *
> 211 R-grm2 3 Dixi 0 0 0 0 0 0.505246794
> 212 R-grm2 3 Elle 0 0 0 0 0 0
> 213 R-grm2 3 Flet 0.227531286 0 0 0 0.518518519 0
> 214 R-grm2 3 Gaun 0 0 0 0 0 0
> 215 R-grm2 3 Kami 0 0.078647267 0 0 0 0.038417211
> 216 R-grm2 3 KK 0 0 0 0 0 0
> 217 R-grm2 3 Pans 0 0 0.034399725 0 0 0
> 218 R-grm2 3 Quan 0 0 0 0.181686047 0 0
> 219 R-grm2 3 Sauc 0 0 0.034376074 0 0 0
> 220 R-grm2 3 Trim 0 0 0.036245016 0 0.075786283 0
> 221 R-grm2 3 Twin 0 0 0 0 0 0
> 222 R-grm2 4 Arte * 0 0 1.277521066 0 0
> 223 R-grm2 4 Bif 0.057126535 * 0 0 0 0
> 224 R-grm2 4 Bill 0 0 * 0 0 0
> 225 R-grm2 4 Blaz 0.027181299 0.278862242 0 * 0 0
> 226 R-grm2 4 Bonn 0 0.028058361 0 0 * 0.083333333
> 227 R-grm2 4 Bow 0.113090189 0 0 0.248481502 0.138888889 *
> 228 R-grm2 4 Dixi 0 0 0 0 0.111327581 0.374316153
> 229 R-grm2 4 Elle 0 0 0 0 0 0
> 230 R-grm2 4 Flet 0.168208579 0 0 0 0.385674931 0
> 231 R-grm2 4 Gaun 0 0 0 0 0 0
> 232 R-grm2 4 Kami 0 0.057803468 0 0 0.138274336 0.028604119
> 233 R-grm2 4 KK 0 0 0.052910053 0 0 0
> 234 R-grm2 4 Pans 0 0 0.026267402 0 0 0
> 235 R-grm2 4 Quan 0 0 0 0.135795763 0 0
> 236 R-grm2 4 Sauc 0 0 0.02625361 0 0 0
> 237 R-grm2 4 Trim 0 0 0.027329872 0 0.056038106 0
> 238 R-grm2 4 Twin 0 0 0 0 0 0
> 239 R-grm2 12 Arte * 0 0.021263024 1.220053239 0.43449924 0
> 240 R-grm2 12 Bif 0.044179368 * 0.191367212 0 0.021724962 0
> 241 R-grm2 12 Bill 0.110448421 0.402594498 * 0 0 0
> 242 R-grm2 12 Blaz 0.066269052 0.22366361 0.063789071 * 0 0
> 243 R-grm2 12 Bonn 0.198807157 0.044732722 0 0.110913931 * 0.067219359
> 244 R-grm2 12 Bow 0.463883366 0.089465444 0.021263024 0.199645075 0.21724962 *
> 245 R-grm2 12 Dixi 0 0 0 0.022182786 0.10862481 0.358503249
> 246 R-grm2 12 Elle 0 0 0.063789071 0 0.152074734 0
> 247 R-grm2 12 Flet 0.132538105 0 0 0.110913931 0.304149468 0.470535514
> 248 R-grm2 12 Gaun 0 0.290762693 0.021263024 0.044365572 0 0
> 249 R-grm2 12 Kami 0.441793682 0.089465444 0.148841165 1.708074534 0.238974582 0.112032265
> 250 R-grm2 12 KK 0.198807157 0.044732722 0.042526047 0.310559006 0 0.448129061
> 251 R-grm2 12 Pans 0 0 0.021263024 0.199645075 0 0
> 252 R-grm2 12 Quan 0.088358736 0 0.616627684 0.177462289 0 0.044812906
> 253 R-grm2 12 Sauc 0 1.087843351 0.051374261 0 0 0
> 254 R-grm2 12 Trim 0.022089684 1.274882577 0.042526047 0.155279503 0.043449924 0
> 255 R-grm2 12 Twin 0.044179368 0 0.148841165 0.28837622 0.065174886 0.044812906
>
>
>
>
>
>> R.Arte <- test[test$Beep=="R-grm"&test$Subject=="Arte",4:9]
>
>> R.Arte
> Arte Bif Bill Blaz Bonn Bow
> 1 * 0 0 0 0 0
> 18 * 0.169779287 0 0 0 0.333889816
> 35 * 0.077609624 0 0.036778227 0 0.151687524
> 52 * 0.057126535 0 0.027181299 0 0.113090189
> 69 * 0.044179368 0.110448421 0.066269052 0.198807157 0.463883366
>
>
>
>
>> tau.dist(R.Arte)
> #Error in function (classes, fdef, mtable) :
> unable to find an inherited method for function "tau.dist", for signature "data.frame"
>> traceback()
> 3: stop("unable to find an inherited method for function \"", fdef at generic,
> "\", for signature ", cnames)
> 2: function (classes, fdef, mtable)
> {
> methods <- .findInheritedMethods(classes, fdef, mtable)
> if (length(methods) == 1L)
> return(methods[[1L]])
> else if (length(methods) == 0L) {
> cnames <- paste0("\"", sapply(classes, as.character),
> "\"", collapse = ", ")
> stop("unable to find an inherited method for function \"",
> fdef at generic, "\", for signature ", cnames)
> }
> else stop("Internal error in finding inherited methods; didn't return a unique method")
> }(list("data.frame"), function (x, ...)
> standardGeneric("tau.dist"), <environment>)
> 1: tau.dist(R.Arte)
>
>
>
>> tau.dist(as.matrix(R.Arte))
> Error in cor(t(x), method = "kendall") : 'x' must be numeric
>> traceback()
> 5: stop("'x' must be numeric")
> 4: cor(t(x), method = "kendall")
> 3: .local(x, ...)
> 2: tau.dist(as.matrix(R.Arte))
> 1: tau.dist(as.matrix(R.Arte))
>
>
>
>
>> tau.dist(as.matrix(as.numeric(R.Arte)))
> Error in tau.dist(as.matrix(as.numeric(R.Arte))) :
> error in evaluating the argument 'x' in selecting a method for function 'tau.dist': Error in as.matrix(as.numeric(R.Arte)) :
> (list) object cannot be coerced to type 'double'
>> traceback()
> 1: tau.dist(as.matrix(as.numeric(R.Arte)))
>
>
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