Radar Plots
op <- par(no.readonly = TRUE)
library(fmsb)
par(mfrow = c(1,2),xpd = TRUE,pty = "s",mar = c(1,1,1,1))
mNames <- names(cp$cpuElapsedTimes)
classRanks <- c(pr$minMaxMetrics$BER[1],pr$minMaxMetrics$ACC[2],pr$minMaxMetrics$AUC[2],pr$minMaxMetrics$SEN[2],pr$minMaxMetrics$SPE[2],min(cp$cpuElapsedTimes))
classRanks <- rbind(classRanks,c(pr$minMaxMetrics$BER[2],0,0,0,0,max(cp$cpuElapsedTimes)))
classRanks <- as.data.frame(rbind(classRanks,cbind(t(pr$metrics[c("BER","ACC","AUC","SEN","SPE"),mNames]),cp$cpuElapsedTimes)))
colnames(classRanks) <- c("BER","ACC","AUC","SEN","SPE","CPU")
classRanks$BER <- -classRanks$BER
classRanks$CPU <- -classRanks$CPU
colors_border = c( rgb(1.0,0.0,0.0,1.0), rgb(0.0,1.0,0.0,1.0) , rgb(0.0,0.0,1.0,1.0), rgb(0.2,0.2,0.0,1.0), rgb(0.0,1.0,1.0,1.0), rgb(1.0,0.0,1.0,1.0), rgb(0.0,0.0,0.0,1.0) )
colors_in = c( rgb(1.0,0.0,0.0,0.05), rgb(0.0,1.0,0.0,0.05) , rgb(0.0,0.0,1.0,0.05),rgb(1.0,1.0,0.0,0.05), rgb(0.0,1.0,1.0,0.05) , rgb(1.0,0.0,1.0,0.05), rgb(0.0,0.0,0.0,0.05) )
radarchart(classRanks,axistype = 0,maxmin = T,pcol = colors_border,pfcol = colors_in,plwd = c(6,2,2,2,2,2,2),plty = 1, cglcol = "grey", cglty = 1,axislabcol = "black",cglwd = 0.8, vlcex = 0.5 ,title = "Prediction Model")
legend("topleft",legend = rownames(classRanks[-c(1,2),]),bty = "n",pch = 20,col = colors_in,text.col = colors_border,cex = 0.5,pt.cex = 2)
filnames <- c("BSWiMS","LASSO_MIN","RF","IDI","tStudent","kendall","mRMR.classic")
filterRanks <- c(pr$minMaxMetrics$BER[1],pr$minMaxMetrics$ACC[2],pr$minMaxMetrics$AUC[2],pr$minMaxMetrics$SEN[2],pr$minMaxMetrics$SPE[2],max(cp$jaccard),min(cp$featsize));
filterRanks <- rbind(filterRanks,c(pr$minMaxMetrics$BER[2],0,0,0,0,min(cp$jaccard),max(cp$featsize)));
filterRanks <- as.data.frame(rbind(filterRanks,cbind(t(pr$metrics_filter[c("BER","ACC","AUC","SEN","SPE"),filnames]),cp$jaccard[filnames],cp$featsize[filnames])));
colnames(filterRanks) <- c("BER","ACC","AUC","SEN","SPE","Jaccard","SIZE")
filterRanks$BER <- -filterRanks$BER
filterRanks$SIZE <- -filterRanks$SIZE
colors_border = c( rgb(1.0,0.0,0.0,1.0), rgb(0.0,1.0,0.0,1.0) , rgb(0.0,0.0,1.0,1.0), rgb(0.2,0.2,0.0,1.0), rgb(0.0,1.0,1.0,1.0), rgb(1.0,0.0,1.0,1.0), rgb(0.0,0.0,0.0,1.0) )
colors_in = c( rgb(1.0,0.0,0.0,0.05), rgb(0.0,1.0,0.0,0.05) , rgb(0.0,0.0,1.0,0.05),rgb(1.0,1.0,0.0,0.05), rgb(0.0,1.0,1.0,0.05) , rgb(1.0,0.0,1.0,0.05), rgb(0.0,0.0,0.0,0.05) )
radarchart(filterRanks,axistype = 0,maxmin = T,pcol = colors_border,pfcol = colors_in,plwd = c(6,2,2,2,2,2,2),plty = 1, cglcol = "grey", cglty = 1,axislabcol = "black",cglwd = 0.8, vlcex = 0.6,title = "Filter Method" )
legend("topleft",legend = rownames(filterRanks[-c(1,2),]),bty = "n",pch = 20,col = colors_in,text.col = colors_border,cex = 0.5,pt.cex = 2)

detach("package:fmsb", unload=TRUE)
par(mfrow = c(1,1))
par(op)
Feature Analysis
rm <- rowMeans(cp$featureSelectionFrequency)
selFrequency <- cp$featureSelectionFrequency[rm > 0.1,]
gplots::heatmap.2(as.matrix(selFrequency),trace = "none",mar = c(10,10),main = "Features",cexRow = 0.25,cexCol = 0.5)

topFeat <- min(ncol(BSWiMSMODEL$bagging$formulaNetwork),30);
gplots::heatmap.2(BSWiMSMODEL$bagging$formulaNetwork[1:topFeat,1:topFeat],trace="none",mar = c(10,10),main = "B:SWiMS Formula Network",cexRow = 0.5,cexCol = 0.5)

pander::pander(summary(BSWiMSMODEL$bagging$bagged.model,caption="Colon",round = 3))
coefficients:
Table continues below
| V11 |
1.516 |
2.697 |
4.553 |
7.688 |
0.7452 |
0.7187 |
| V45 |
1.658 |
2.841 |
5.249 |
9.696 |
0.6394 |
0.7392 |
| V49 |
4.972 |
19.54 |
144.3 |
1066 |
0.6827 |
0.7281 |
| V37 |
-0.8486 |
0.3023 |
0.428 |
0.606 |
0.6346 |
0.712 |
| V12 |
1.194 |
2.005 |
3.302 |
5.436 |
0.7404 |
0.7132 |
| V36 |
-0.6306 |
0.4067 |
0.5323 |
0.6967 |
0.6587 |
0.73 |
| V47 |
1.634 |
2.511 |
5.123 |
10.45 |
0.6202 |
0.727 |
| V46 |
0.7694 |
1.535 |
2.158 |
3.035 |
0.6106 |
0.7198 |
| V48 |
3.132 |
5.573 |
22.92 |
94.24 |
0.6875 |
0.7269 |
| V10 |
1.178 |
1.824 |
3.249 |
5.786 |
0.6971 |
0.7202 |
| V20 |
0.1839 |
1.099 |
1.202 |
1.315 |
0.6394 |
0.6841 |
| V35 |
-0.5254 |
0.4565 |
0.5913 |
0.7661 |
0.5865 |
0.7127 |
| V44 |
0.5503 |
1.31 |
1.734 |
2.295 |
0.5913 |
0.7078 |
| V4 |
3.65 |
5.812 |
38.49 |
255 |
0.6058 |
0.7385 |
| V9 |
1.068 |
1.675 |
2.909 |
5.053 |
0.6923 |
0.7 |
| V13 |
0.9644 |
1.581 |
2.623 |
4.352 |
0.6683 |
0.704 |
| V21 |
0.4517 |
1.229 |
1.571 |
2.009 |
0.6298 |
0.7104 |
| V22 |
0.3246 |
1.151 |
1.383 |
1.663 |
0.5865 |
0.7101 |
| V43 |
0.1341 |
1.057 |
1.144 |
1.237 |
0.5865 |
0.6747 |
| V1 |
1.933 |
2.204 |
6.91 |
21.67 |
0.601 |
0.7005 |
| V14 |
-0.3944 |
0.5294 |
0.6741 |
0.8582 |
0.5962 |
0.742 |
| V28 |
0.2202 |
1.083 |
1.246 |
1.434 |
0.5144 |
0.7073 |
| V51 |
4.672 |
5.118 |
106.9 |
2234 |
0.6683 |
0.7025 |
| V34 |
-0.06093 |
0.9047 |
0.9409 |
0.9785 |
0.5865 |
0.6811 |
| V52 |
7.683 |
14.06 |
2172 |
335383 |
0.6394 |
0.729 |
Table continues below
| V11 |
0.782 |
0.7418 |
0.7162 |
0.7817 |
0.1263 |
0.7231 |
| V45 |
0.7745 |
0.6446 |
0.7377 |
0.7744 |
0.1219 |
0.7548 |
| V49 |
0.7606 |
0.6832 |
0.7264 |
0.7583 |
0.1079 |
0.8228 |
| V37 |
0.7635 |
0.6258 |
0.7126 |
0.7622 |
0.09691 |
0.616 |
| V12 |
0.7603 |
0.736 |
0.712 |
0.7581 |
0.09952 |
0.8158 |
| V36 |
0.782 |
0.6516 |
0.728 |
0.7817 |
0.08792 |
0.5747 |
| V47 |
0.7511 |
0.6201 |
0.7241 |
0.7492 |
0.08936 |
0.5684 |
| V46 |
0.7456 |
0.6124 |
0.7164 |
0.7435 |
0.08846 |
0.6466 |
| V48 |
0.7632 |
0.6877 |
0.724 |
0.7612 |
0.08286 |
0.6913 |
| V10 |
0.7635 |
0.6961 |
0.7187 |
0.7619 |
0.06302 |
0.7082 |
| V20 |
0.7184 |
0.6362 |
0.6841 |
0.7161 |
0.07619 |
0.646 |
| V35 |
0.7466 |
0.5775 |
0.7139 |
0.7445 |
0.0669 |
0.3521 |
| V44 |
0.7382 |
0.5924 |
0.7056 |
0.7372 |
0.06744 |
0.577 |
| V4 |
0.7649 |
0.6053 |
0.7363 |
0.7637 |
0.0543 |
0.5115 |
| V9 |
0.7454 |
0.6929 |
0.697 |
0.7433 |
0.06077 |
0.5509 |
| V13 |
0.7512 |
0.6658 |
0.7014 |
0.7493 |
0.06036 |
0.5833 |
| V21 |
0.7579 |
0.6239 |
0.708 |
0.7556 |
0.05837 |
0.652 |
| V22 |
0.7574 |
0.5782 |
0.7083 |
0.7553 |
0.05438 |
0.4785 |
| V43 |
0.7131 |
0.5834 |
0.6729 |
0.7117 |
0.0506 |
0.538 |
| V1 |
0.7335 |
0.6027 |
0.6977 |
0.7321 |
0.04787 |
0.329 |
| V14 |
0.7756 |
0.5885 |
0.7388 |
0.7733 |
0.04283 |
0.4263 |
| V28 |
0.7446 |
0.4956 |
0.7053 |
0.7428 |
0.04334 |
0.4918 |
| V51 |
0.7326 |
0.6664 |
0.7014 |
0.7311 |
0.04252 |
0.4976 |
| V34 |
0.7196 |
0.5769 |
0.6808 |
0.7186 |
0.04254 |
0.3909 |
| V52 |
0.7469 |
0.6394 |
0.7266 |
0.7453 |
0.04292 |
0.4801 |
| V11 |
5.625 |
5.628 |
1 |
| V45 |
5.244 |
6.102 |
1 |
| V49 |
4.852 |
6.67 |
1 |
| V37 |
4.76 |
4.682 |
1 |
| V12 |
4.683 |
6.438 |
1 |
| V36 |
4.556 |
4.323 |
1 |
| V47 |
4.475 |
4.477 |
0.9 |
| V46 |
4.39 |
5.049 |
0.55 |
| V48 |
4.249 |
5.367 |
1 |
| V10 |
3.975 |
5.531 |
1 |
| V20 |
3.971 |
4.928 |
0.35 |
| V35 |
3.925 |
2.59 |
1 |
| V44 |
3.804 |
4.441 |
0.45 |
| V4 |
3.766 |
3.914 |
1 |
| V9 |
3.74 |
4.255 |
1 |
| V13 |
3.645 |
4.445 |
0.8 |
| V21 |
3.566 |
4.964 |
0.85 |
| V22 |
3.428 |
3.559 |
0.65 |
| V43 |
3.314 |
4.049 |
0.15 |
| V1 |
3.275 |
2.463 |
0.35 |
| V14 |
3.198 |
3.144 |
0.3 |
| V28 |
3.066 |
3.685 |
0.4 |
| V51 |
3 |
3.746 |
0.4 |
| V34 |
2.986 |
2.891 |
0.15 |
| V52 |
2.952 |
3.636 |
0.55 |
- Accuracy: 0.8077
- tAUC: 0.8062
- sensitivity: 0.8288
- specificity: 0.7835
bootstrap:
hm <- heatMaps(Outcome = theOutcome,data = theData[,c(theOutcome,rownames(selFrequency))],title = "Heat Map",Scale = TRUE,hCluster = "col",cexRow = 0.25,cexCol = 0.5,srtCol = 45)

vlist <- rownames(selFrequency)
vlist <- cbind(vlist,vlist)
univ <- univariateRankVariables(variableList = vlist,formula = paste(theOutcome,"~1"),Outcome = theOutcome,data = theData,type = "LOGIT",rankingTest = "zIDI",uniType = "Binary")[,c("controlMean","controlStd","caseMean","caseStd","ROCAUC","WilcoxRes.p")]
cnames <- colnames(univ);
univ <- cbind(univ,rm[rownames(univ)])
colnames(univ) <- c(cnames,"Frequency")
univ <- univ[order(-univ[,5]),]
pander::pander(univ[1:topFeat,],caption = "Features",round = 4)
Features (continued below)
| V11 |
0.1747 |
0.1134 |
0.2896 |
0.1254 |
0.7811 |
0 |
| V12 |
0.1916 |
0.1347 |
0.3015 |
0.1241 |
0.7429 |
0 |
| V10 |
0.1593 |
0.1132 |
0.251 |
0.1374 |
0.7327 |
0 |
| V49 |
0.0384 |
0.0304 |
0.0637 |
0.0364 |
0.7313 |
0 |
| V9 |
0.1374 |
0.0999 |
0.2135 |
0.1222 |
0.7308 |
0 |
| V48 |
0.0695 |
0.0482 |
0.1106 |
0.0671 |
0.7063 |
0 |
| V13 |
0.2262 |
0.1381 |
0.3144 |
0.1307 |
0.7047 |
0 |
| V51 |
0.0123 |
0.0086 |
0.0194 |
0.0135 |
0.6994 |
0 |
| V47 |
0.0945 |
0.0678 |
0.1469 |
0.0945 |
0.6974 |
0 |
| V52 |
0.0105 |
0.0071 |
0.016 |
0.0108 |
0.688 |
0 |
| V46 |
0.1169 |
0.0938 |
0.1988 |
0.1514 |
0.6871 |
0 |
| V45 |
0.1423 |
0.0957 |
0.2452 |
0.1741 |
0.6727 |
0 |
| V4 |
0.0414 |
0.0312 |
0.0648 |
0.0545 |
0.6652 |
0 |
| V36 |
0.4607 |
0.2623 |
0.3186 |
0.2484 |
0.6652 |
0 |
| V5 |
0.062 |
0.0472 |
0.0867 |
0.0598 |
0.6537 |
2e-04 |
| V1 |
0.0225 |
0.0147 |
0.035 |
0.0271 |
0.6523 |
1e-04 |
| V44 |
0.1751 |
0.1074 |
0.2481 |
0.1444 |
0.6511 |
1e-04 |
| V21 |
0.5423 |
0.2488 |
0.6674 |
0.2524 |
0.6445 |
1e-04 |
| V35 |
0.4555 |
0.2612 |
0.3376 |
0.2455 |
0.6415 |
6e-04 |
| V8 |
0.1176 |
0.0798 |
0.1498 |
0.0872 |
0.641 |
8e-04 |
| V43 |
0.2118 |
0.1303 |
0.2769 |
0.1398 |
0.6409 |
2e-04 |
| V37 |
0.4173 |
0.243 |
0.317 |
0.2281 |
0.6281 |
6e-04 |
| V6 |
0.0962 |
0.065 |
0.1119 |
0.0526 |
0.6246 |
0.0018 |
| V20 |
0.5002 |
0.2594 |
0.6179 |
0.2541 |
0.6236 |
9e-04 |
| V2 |
0.0303 |
0.024 |
0.0455 |
0.0378 |
0.6228 |
0.0015 |
| V50 |
0.0178 |
0.0126 |
0.0227 |
0.0142 |
0.6218 |
0.003 |
| V11 |
0.9975 |
| V12 |
0.9725 |
| V10 |
0.8 |
| V49 |
0.9017 |
| V9 |
0.8258 |
| V48 |
0.7917 |
| V13 |
0.78 |
| V51 |
0.8158 |
| V47 |
0.775 |
| V52 |
0.8467 |
| V46 |
0.7625 |
| V45 |
0.8575 |
| V4 |
0.8608 |
| V36 |
0.9367 |
| V5 |
0.74 |
| V1 |
0.8217 |
| V44 |
0.8058 |
| V21 |
0.85 |
| V35 |
0.7317 |
| V8 |
0.6975 |
| V43 |
0.6908 |
| V37 |
0.7825 |
| V6 |
0.6217 |
| V20 |
0.7292 |
| V2 |
0.6675 |
| V50 |
0.6233 |
Feature Analysis
rm <- rowMeans(cp$featureSelectionFrequency)
selFrequency <- cp$featureSelectionFrequency[rm > 0.1,]
gplots::heatmap.2(as.matrix(selFrequency),trace = "none",mar = c(10,10),main = "Features",cexRow = 0.25,cexCol = 0.5)

topFeat <- min(ncol(BSWiMSMODEL$bagging$formulaNetwork),30);
gplots::heatmap.2(BSWiMSMODEL$bagging$formulaNetwork[1:topFeat,1:topFeat],trace="none",mar = c(10,10),main = "B:SWiMS Formula Network",cexRow = 0.5,cexCol = 0.5)

pander::pander(summary(BSWiMSMODEL$bagging$bagged.model,caption="Colon",round = 3))
coefficients:
Table continues below
| V11 |
1.516 |
2.697 |
4.553 |
7.688 |
0.7452 |
0.7187 |
| V45 |
1.658 |
2.841 |
5.249 |
9.696 |
0.6394 |
0.7392 |
| V49 |
4.972 |
19.54 |
144.3 |
1066 |
0.6827 |
0.7281 |
| V37 |
-0.8486 |
0.3023 |
0.428 |
0.606 |
0.6346 |
0.712 |
| V12 |
1.194 |
2.005 |
3.302 |
5.436 |
0.7404 |
0.7132 |
| V36 |
-0.6306 |
0.4067 |
0.5323 |
0.6967 |
0.6587 |
0.73 |
| V47 |
1.634 |
2.511 |
5.123 |
10.45 |
0.6202 |
0.727 |
| V46 |
0.7694 |
1.535 |
2.158 |
3.035 |
0.6106 |
0.7198 |
| V48 |
3.132 |
5.573 |
22.92 |
94.24 |
0.6875 |
0.7269 |
| V10 |
1.178 |
1.824 |
3.249 |
5.786 |
0.6971 |
0.7202 |
| V20 |
0.1839 |
1.099 |
1.202 |
1.315 |
0.6394 |
0.6841 |
| V35 |
-0.5254 |
0.4565 |
0.5913 |
0.7661 |
0.5865 |
0.7127 |
| V44 |
0.5503 |
1.31 |
1.734 |
2.295 |
0.5913 |
0.7078 |
| V4 |
3.65 |
5.812 |
38.49 |
255 |
0.6058 |
0.7385 |
| V9 |
1.068 |
1.675 |
2.909 |
5.053 |
0.6923 |
0.7 |
| V13 |
0.9644 |
1.581 |
2.623 |
4.352 |
0.6683 |
0.704 |
| V21 |
0.4517 |
1.229 |
1.571 |
2.009 |
0.6298 |
0.7104 |
| V22 |
0.3246 |
1.151 |
1.383 |
1.663 |
0.5865 |
0.7101 |
| V43 |
0.1341 |
1.057 |
1.144 |
1.237 |
0.5865 |
0.6747 |
| V1 |
1.933 |
2.204 |
6.91 |
21.67 |
0.601 |
0.7005 |
| V14 |
-0.3944 |
0.5294 |
0.6741 |
0.8582 |
0.5962 |
0.742 |
| V28 |
0.2202 |
1.083 |
1.246 |
1.434 |
0.5144 |
0.7073 |
| V51 |
4.672 |
5.118 |
106.9 |
2234 |
0.6683 |
0.7025 |
| V34 |
-0.06093 |
0.9047 |
0.9409 |
0.9785 |
0.5865 |
0.6811 |
| V52 |
7.683 |
14.06 |
2172 |
335383 |
0.6394 |
0.729 |
Table continues below
| V11 |
0.782 |
0.7418 |
0.7162 |
0.7817 |
0.1263 |
0.7231 |
| V45 |
0.7745 |
0.6446 |
0.7377 |
0.7744 |
0.1219 |
0.7548 |
| V49 |
0.7606 |
0.6832 |
0.7264 |
0.7583 |
0.1079 |
0.8228 |
| V37 |
0.7635 |
0.6258 |
0.7126 |
0.7622 |
0.09691 |
0.616 |
| V12 |
0.7603 |
0.736 |
0.712 |
0.7581 |
0.09952 |
0.8158 |
| V36 |
0.782 |
0.6516 |
0.728 |
0.7817 |
0.08792 |
0.5747 |
| V47 |
0.7511 |
0.6201 |
0.7241 |
0.7492 |
0.08936 |
0.5684 |
| V46 |
0.7456 |
0.6124 |
0.7164 |
0.7435 |
0.08846 |
0.6466 |
| V48 |
0.7632 |
0.6877 |
0.724 |
0.7612 |
0.08286 |
0.6913 |
| V10 |
0.7635 |
0.6961 |
0.7187 |
0.7619 |
0.06302 |
0.7082 |
| V20 |
0.7184 |
0.6362 |
0.6841 |
0.7161 |
0.07619 |
0.646 |
| V35 |
0.7466 |
0.5775 |
0.7139 |
0.7445 |
0.0669 |
0.3521 |
| V44 |
0.7382 |
0.5924 |
0.7056 |
0.7372 |
0.06744 |
0.577 |
| V4 |
0.7649 |
0.6053 |
0.7363 |
0.7637 |
0.0543 |
0.5115 |
| V9 |
0.7454 |
0.6929 |
0.697 |
0.7433 |
0.06077 |
0.5509 |
| V13 |
0.7512 |
0.6658 |
0.7014 |
0.7493 |
0.06036 |
0.5833 |
| V21 |
0.7579 |
0.6239 |
0.708 |
0.7556 |
0.05837 |
0.652 |
| V22 |
0.7574 |
0.5782 |
0.7083 |
0.7553 |
0.05438 |
0.4785 |
| V43 |
0.7131 |
0.5834 |
0.6729 |
0.7117 |
0.0506 |
0.538 |
| V1 |
0.7335 |
0.6027 |
0.6977 |
0.7321 |
0.04787 |
0.329 |
| V14 |
0.7756 |
0.5885 |
0.7388 |
0.7733 |
0.04283 |
0.4263 |
| V28 |
0.7446 |
0.4956 |
0.7053 |
0.7428 |
0.04334 |
0.4918 |
| V51 |
0.7326 |
0.6664 |
0.7014 |
0.7311 |
0.04252 |
0.4976 |
| V34 |
0.7196 |
0.5769 |
0.6808 |
0.7186 |
0.04254 |
0.3909 |
| V52 |
0.7469 |
0.6394 |
0.7266 |
0.7453 |
0.04292 |
0.4801 |
| V11 |
5.625 |
5.628 |
1 |
| V45 |
5.244 |
6.102 |
1 |
| V49 |
4.852 |
6.67 |
1 |
| V37 |
4.76 |
4.682 |
1 |
| V12 |
4.683 |
6.438 |
1 |
| V36 |
4.556 |
4.323 |
1 |
| V47 |
4.475 |
4.477 |
0.9 |
| V46 |
4.39 |
5.049 |
0.55 |
| V48 |
4.249 |
5.367 |
1 |
| V10 |
3.975 |
5.531 |
1 |
| V20 |
3.971 |
4.928 |
0.35 |
| V35 |
3.925 |
2.59 |
1 |
| V44 |
3.804 |
4.441 |
0.45 |
| V4 |
3.766 |
3.914 |
1 |
| V9 |
3.74 |
4.255 |
1 |
| V13 |
3.645 |
4.445 |
0.8 |
| V21 |
3.566 |
4.964 |
0.85 |
| V22 |
3.428 |
3.559 |
0.65 |
| V43 |
3.314 |
4.049 |
0.15 |
| V1 |
3.275 |
2.463 |
0.35 |
| V14 |
3.198 |
3.144 |
0.3 |
| V28 |
3.066 |
3.685 |
0.4 |
| V51 |
3 |
3.746 |
0.4 |
| V34 |
2.986 |
2.891 |
0.15 |
| V52 |
2.952 |
3.636 |
0.55 |
- Accuracy: 0.8077
- tAUC: 0.8062
- sensitivity: 0.8288
- specificity: 0.7835
bootstrap:
hm <- heatMaps(Outcome = theOutcome,data = theData[,c(theOutcome,rownames(selFrequency))],title = "Heat Map",Scale = TRUE,hCluster = "col",cexRow = 0.25,cexCol = 0.5,srtCol = 45)

vlist <- rownames(selFrequency)
vlist <- cbind(vlist,vlist)
univ <- univariateRankVariables(variableList = vlist,formula = paste(theOutcome,"~1"),Outcome = theOutcome,data = theData,type = "LOGIT",rankingTest = "zIDI",uniType = "Binary")[,c("controlMean","controlStd","caseMean","caseStd","ROCAUC","WilcoxRes.p")]
cnames <- colnames(univ);
univ <- cbind(univ,rm[rownames(univ)])
colnames(univ) <- c(cnames,"Frequency")
univ <- univ[order(-univ[,5]),]
pander::pander(univ[1:topFeat,],caption = "Features",round = 4)
Features (continued below)
| V11 |
0.1747 |
0.1134 |
0.2896 |
0.1254 |
0.7811 |
0 |
| V12 |
0.1916 |
0.1347 |
0.3015 |
0.1241 |
0.7429 |
0 |
| V10 |
0.1593 |
0.1132 |
0.251 |
0.1374 |
0.7327 |
0 |
| V49 |
0.0384 |
0.0304 |
0.0637 |
0.0364 |
0.7313 |
0 |
| V9 |
0.1374 |
0.0999 |
0.2135 |
0.1222 |
0.7308 |
0 |
| V48 |
0.0695 |
0.0482 |
0.1106 |
0.0671 |
0.7063 |
0 |
| V13 |
0.2262 |
0.1381 |
0.3144 |
0.1307 |
0.7047 |
0 |
| V51 |
0.0123 |
0.0086 |
0.0194 |
0.0135 |
0.6994 |
0 |
| V47 |
0.0945 |
0.0678 |
0.1469 |
0.0945 |
0.6974 |
0 |
| V52 |
0.0105 |
0.0071 |
0.016 |
0.0108 |
0.688 |
0 |
| V46 |
0.1169 |
0.0938 |
0.1988 |
0.1514 |
0.6871 |
0 |
| V45 |
0.1423 |
0.0957 |
0.2452 |
0.1741 |
0.6727 |
0 |
| V4 |
0.0414 |
0.0312 |
0.0648 |
0.0545 |
0.6652 |
0 |
| V36 |
0.4607 |
0.2623 |
0.3186 |
0.2484 |
0.6652 |
0 |
| V5 |
0.062 |
0.0472 |
0.0867 |
0.0598 |
0.6537 |
2e-04 |
| V1 |
0.0225 |
0.0147 |
0.035 |
0.0271 |
0.6523 |
1e-04 |
| V44 |
0.1751 |
0.1074 |
0.2481 |
0.1444 |
0.6511 |
1e-04 |
| V21 |
0.5423 |
0.2488 |
0.6674 |
0.2524 |
0.6445 |
1e-04 |
| V35 |
0.4555 |
0.2612 |
0.3376 |
0.2455 |
0.6415 |
6e-04 |
| V8 |
0.1176 |
0.0798 |
0.1498 |
0.0872 |
0.641 |
8e-04 |
| V43 |
0.2118 |
0.1303 |
0.2769 |
0.1398 |
0.6409 |
2e-04 |
| V37 |
0.4173 |
0.243 |
0.317 |
0.2281 |
0.6281 |
6e-04 |
| V6 |
0.0962 |
0.065 |
0.1119 |
0.0526 |
0.6246 |
0.0018 |
| V20 |
0.5002 |
0.2594 |
0.6179 |
0.2541 |
0.6236 |
9e-04 |
| V2 |
0.0303 |
0.024 |
0.0455 |
0.0378 |
0.6228 |
0.0015 |
| V50 |
0.0178 |
0.0126 |
0.0227 |
0.0142 |
0.6218 |
0.003 |
| V11 |
0.9975 |
| V12 |
0.9725 |
| V10 |
0.8 |
| V49 |
0.9017 |
| V9 |
0.8258 |
| V48 |
0.7917 |
| V13 |
0.78 |
| V51 |
0.8158 |
| V47 |
0.775 |
| V52 |
0.8467 |
| V46 |
0.7625 |
| V45 |
0.8575 |
| V4 |
0.8608 |
| V36 |
0.9367 |
| V5 |
0.74 |
| V1 |
0.8217 |
| V44 |
0.8058 |
| V21 |
0.85 |
| V35 |
0.7317 |
| V8 |
0.6975 |
| V43 |
0.6908 |
| V37 |
0.7825 |
| V6 |
0.6217 |
| V20 |
0.7292 |
| V2 |
0.6675 |
| V50 |
0.6233 |