[R] multi-class classification using rpart
WeiWei Shi
helprhelp at gmail.com
Tue Jan 25 20:38:12 CET 2005
Hi,
I am trying to make a multi-class classification tree by using rpart.
I used MASS package'd data: fgl to test and it works well.
However, when I used my small-sampled data as below, the program seems
to take forever. I am not sure if it is due to slowness or there is
something wrong with my codes or data manipulation.
Please be advised !
The data is described as the output from str() function. The call to
rpart is like:
library(rpart)
test_tree<-rpart(x$V142 ~ ., data=x, parms=list(split='gini'), cp =0.01)
the response variable is $V142, with 3 levels.
Thanks for your suggestions!
Ed.
> str(x)
`data.frame': 500 obs. of 142 variables
$ V1 : int 4 4 4 4 4 4 4 4 4 4 ...
$ V2 : Factor w/ 8 levels "1","2","3","4",..: 4 4 4 5 5 7 6 4 5 4 ...
$ V3 : num 0.00803 0.00111 0.00995 0.01032 0.01295 ...
$ V4 : num -0.011034 -0.003711 0.003436 0.000968 -0.006914 ...
$ V5 : num 0.00524 0.00563 0.00973 0.01285 0.02148 ...
$ V6 : num 0.00633 0.00831 0.02750 0.03375 0.01254 ...
$ V7 : num -0.00422 -0.00151 0.00214 -0.00101 0.00299 ...
$ V8 : num 0.02224 0.01761 0.01359 0.01045 0.00592 ...
$ V9 : num -0.00301 -0.00260 0.01338 0.01129 0.00604 ...
$ V10 : num 0.00224 0.00303 0.02312 0.02414 0.02752 ...
$ V11 : num 0.00857 0.01134 0.05062 0.05789 0.04007 ...
$ V12 : num 0.00435 0.00983 0.05276 0.05688 0.04305 ...
$ V13 : num 0.025627 0.000429 0.055087 0.088517 0.068946 ...
$ V14 : num 0.21 0.15 0.34 0.31 0.36 ...
$ V15 : int 157 81 39 40 40 40 38 72 105 31 ...
$ V16 : int 21 238 236 259 253 253 258 258 259 246 ...
$ V17 : int 82 81 39 40 40 40 38 72 105 31 ...
$ V18 : int 21 15 7 129 14 129 129 6 9 110 ...
$ V19 : int 60 45 39 40 40 40 38 59 63 31 ...
$ V20 : int 21 15 7 14 14 12 53 6 9 62 ...
$ V21 : num 0.953 0.893 0.913 0.843 0.872 ...
$ V22 : num 1.19 1.08 1.03 1.04 1.11 ...
$ V23 : num 0.953 0.893 0.913 0.898 0.872 ...
$ V24 : num 0.955 0.893 0.913 0.898 0.872 ...
$ V25 : num 1.013 0.979 0.985 0.998 0.994 ...
$ V26 : num 0.972 0.940 0.913 0.909 0.895 ...
$ V27 : num 0.999 0.979 0.985 0.998 0.994 ...
$ V28 : num 0.979 0.959 0.928 0.940 0.926 ...
$ V29 : num 0.999 0.979 0.985 0.998 0.994 ...
$ V30 : num 0.989 0.969 0.962 0.976 0.951 ...
$ V31 : num 0.992 0.973 0.971 0.980 0.973 ...
$ V32 : num 0.992 0.975 0.977 0.989 0.980 ...
$ V33 : num 0.999 0.979 0.985 0.998 0.994 ...
$ V34 : num 0.585 0.633 0.878 1.355 0.880 ...
$ V35 : num 1.40 1.18 1.55 1.99 1.62 ...
$ V36 : num 0.906 1.156 1.661 1.981 1.372 ...
$ V37 : num 0.375 0.881 1.445 1.603 0.605 ...
$ V38 : num 0.462 1.016 1.448 1.766 0.718 ...
$ V39 : num 0.424 0.509 1.322 1.754 0.566 ...
$ V40 : num 0.341 0.514 1.393 1.786 0.546 ...
$ V41 : num -0.0681 0.8196 1.2009 1.6561 2.7571 ...
$ V42 : num -4.354 -1.388 0.761 -0.145 -3.107 ...
$ V43 : num 0.478 0.341 0.501 0.983 0.511 ...
$ V44 : num 0.341 0.274 0.504 1.108 0.447 ...
$ V45 : num 0.440 0.196 0.631 1.076 0.535 ...
$ V46 : num 0.873 0.326 0.933 1.354 0.977 ...
$ V47 : num -0.383 -0.170 0.686 0.843 0.328 ...
$ V48 : num 0.138 0.384 1.332 1.352 0.217 ...
$ V49 : num -0.105 0.311 0.984 1.201 -0.196 ...
$ V50 : num -0.118 0.215 0.942 1.173 -0.233 ...
$ V51 : num -0.245 0.165 0.890 1.057 -0.354 ...
$ V52 : num -1.568 -0.577 -0.399 -0.748 -1.883 ...
$ V53 : num -1.530 -0.420 -0.264 -0.522 -1.430 ...
$ V54 : num 0.331 0.264 0.324 0.574 0.308 ...
$ V55 : num 0.426 0.497 1.209 1.296 0.901 ...
$ V56 : num 0.149 0.282 1.028 0.888 0.277 ...
$ V57 : num 0.384 0.430 1.039 1.387 0.541 ...
$ V58 : num 0.334 0.420 1.033 1.348 0.524 ...
$ V59 : num 0.780 0.866 0.792 1.296 2.664 ...
$ V60 : num -8.25 -3.22 6.06 3.82 -2.95 ...
$ V61 : Factor w/ 20 levels "1","2","3","4",..: 3 14 8 3 14 10 9 16 17 14 ...
$ V62 : num 0.589 1.062 1.083 0.721 2.764 ...
$ V63 : num 0.830 0.878 1.030 1.218 3.371 ...
$ V64 : num 0.0477 0.0183 0.0195 0.0535 0.0230 ...
$ V65 : num 1.01 1.04 1.04 1.05 1.07 ...
$ V66 : num 1.00 1.00 1.01 1.01 1.01 ...
$ V67 : num 1.01 1.02 1.04 1.05 1.06 ...
$ V68 : num 0.865 1.181 0.797 0.863 1.584 ...
$ V69 : num 0.955 1.105 0.876 0.953 1.434 ...
$ V70 : num 0.769 0.974 1.036 0.935 1.809 ...
$ V71 : num 0.665 1.150 0.826 0.807 2.866 ...
$ V72 : num 1.001 0.999 0.997 0.999 NA ...
$ V73 : num 0.998 0.000 NA 0.992 NA ...
$ V74 : num 1462 1462 1462 1462 1462 ...
$ V75 : num 1 1 1 1 1 ...
$ V76 : num 1.00 1.00 1.00 1.00 1.00 ...
$ V77 : num 1.00 1.00 1.00 1.00 1.00 ...
$ V78 : num 1.00 1.00 1.00 1.00 1.00 ...
$ V79 : num 1.17 4.25 0.37 0.60 NA ...
$ V80 : num 0.4375 0.6296 0.0855 0.0411 4.3333 ...
$ V81 : num 0.500 0.160 NA 0.167 NA ...
$ V82 : num 0.0625 0.0000 0.4444 0.2740 1.0000 ...
$ V83 : num 0.0714 0.0000 NA 1.1111 NA ...
$ V84 : num 3 1 3 NA NA ...
$ V85 : num 0.600 0.667 0.750 0.667 1.000 ...
$ V86 : num 0.200 0.667 0.500 0.667 3.000 ...
$ V87 : num 4.16 4.16 4.16 4.16 4.16 ...
$ V88 : int -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 ...
$ V89 : num 1 1 1 1 1 ...
$ V90 : num 1.01 1.01 1.01 1.01 1.01 ...
$ V91 : num 1.02 1.02 1.02 1.02 1.02 ...
$ V92 : num 1.00 1.00 1.00 1.00 1.00 ...
$ V93 : num 0.998 0.998 0.998 0.998 0.998 ...
$ V94 : num 0.28851 -0.00130 0.16621 0.19513 0.15963 ...
$ V95 : num 0.2804 -0.1910 0.1693 0.2661 0.0609 ...
$ V96 : num 0.290 -0.238 0.233 0.287 0.147 ...
$ V97 : num 0.4559 -0.4030 0.0401 0.0264 -0.0420 ...
$ V98 : num -1.64 -1.58 -1.15 -1.90 -1.48 ...
$ V99 : num -1.47 -1.47 -1.19 -2.30 -1.85 ...
$ V100: num -1.350 -1.517 -0.362 -2.072 -1.323 ...
$ V101: num -1.070 -0.450 -1.064 -1.175 -0.453 ...
$ V102: num -1.038 -0.183 -0.948 -1.094 -0.355 ...
$ V103: num -1.093 -0.215 -1.019 -1.205 -0.399 ...
$ V104: num -0.9914 0.0897 -0.1980 -0.1433 -0.2038 ...
$ V105: num -2.168 -0.535 -0.850 -1.161 -2.329 ...
$ V106: num 1.00 1.00 1.00 1.00 1.00 ...
$ V107: num 0.261 0.119 0.199 0.248 0.214 ...
$ V108: num 0.2236 -0.0521 0.1689 0.2283 0.1619 ...
$ V109: num 0.247 -0.127 0.128 0.198 0.159 ...
$ V110: num 0.22516 -0.25404 -0.10006 -0.00692 0.00511 ...
$ V111: num -0.994 -0.720 -0.796 -1.127 -0.684 ...
$ V112: num -0.707 -0.188 -0.492 -1.176 -0.445 ...
$ V113: num -0.535 0.150 -0.566 -0.864 -0.183 ...
$ V114: num -0.636 -0.296 -0.812 -1.070 -0.365 ...
$ V115: num -0.596 -0.263 -0.755 -0.964 -0.318 ...
$ V116: num -0.6744 -0.0153 -0.0433 -0.0560 -0.2140 ...
$ V117: num -1.195 -0.316 -0.298 -0.489 -1.175 ...
$ V118: num 0.974 0.974 0.974 0.974 0.974 ...
$ V119: num 0.98 0.98 0.98 0.98 0.98 ...
$ V120: num 1.01 1.01 1.01 1.01 1.01 ...
$ V121: num 0.00896 0.02651 -0.04939 0.00899 -0.08663 ...
$ V122: num 0.0738 -0.1606 -0.1370 -0.1215 -0.2073 ...
$ V123: num 0.0198 -0.3605 -0.2717 -0.1872 -0.3372 ...
$ V124: num 0.16734 -0.41323 -0.10217 -0.05534 0.00103 ...
$ V125: num -0.601 -0.845 -0.541 -0.669 -0.304 ...
$ V126: num -0.803 -1.478 -1.113 -1.634 -1.208 ...
$ V127: num -0.201 -1.387 -1.049 -1.007 -0.366 ...
$ V128: num -0.0721 -0.3654 -1.3118 -1.6504 0.2691 ...
$ V129: num -0.0444 -0.3489 -1.2789 -1.5970 0.2938 ...
$ V130: num 2.52 1.28 1.79 2.53 4.80 ...
$ V131: num 3.572 0.769 2.283 2.694 4.399 ...
$ V132: num 0.379 0.295 0.352 0.541 0.373 ...
$ V133: num 0.401 0.264 0.488 0.728 0.554 ...
$ V134: num 0.859 0.214 0.572 0.801 0.683 ...
$ V135: num 0.367 0.149 1.021 1.161 0.480 ...
$ V136: num 0.2451 0.0938 0.7866 1.1074 0.2471 ...
$ V137: num 0.290 0.357 0.933 1.231 0.353 ...
$ V138: num 0.238 0.343 0.922 1.188 0.320 ...
$ V139: num -0.00656 1.05492 0.84693 1.45898 2.93747 ...
$ V140: num -9.64 -2.58 -2.16 -3.73 -9.33 ...
$ V141: Factor w/ 88 levels "1001","1002",..: 59 59 59 59 59 59 55 78 7 73 ...
$ V142: Factor w/ 3 levels "1","2","3": 3 3 3 3 3 3 3 3 3 3 ...
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