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Question: Converting \"data.frame\" to appropriate format for tau.dist() in bioDist library
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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))) -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink modified 4.3 years ago by Paul Shannon360 • written 4.3 years ago by Guest User12k
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4.3 years ago by
Paul Shannon360
Paul Shannon360 wrote:
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))) > > > -- > Sent via the guest posting facility at bioconductor.org. > > ____________________________________________________________________ ____ > devteam-bioc mailing list > To unsubscribe from this mailing list send a blank email to > devteam-bioc-leave at lists.fhcrc.org > You can also unsubscribe or change your personal options at > https://lists.fhcrc.org/mailman/listinfo/devteam-bioc
ADD COMMENTlink written 4.3 years ago by Paul Shannon360
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4.3 years ago by
Paul Shannon360
Paul Shannon360 wrote:
Nicole, Another look at your error message and I see the first thing you should try >> tau.dist(R.Arte) > #Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "tau.dist", for signature "data.frame" You are passing the tau.dist function a data.frame. If you look at tau.dist's man page: ?tau.dist you will see that the first argument should be a matrix. If this distinction (between matrix and data.frame) is unclear -- and there have been times for all of us when that is the case -- a little reading and experimenting with the two data structures will likely pay off nicely. - Paul
ADD COMMENTlink written 4.3 years ago by Paul Shannon360
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