[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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