[BioC] Converting \"data.frame\" to appropriate format for tau.dist() in bioDist library

Nicole A Thompson [guest] guest at bioconductor.org
Thu Aug 15 12:24:49 CEST 2013


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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