[R] multi-class classification using rpart

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 ...