version 1.0.2

DESCRIPTION

@@ -1,15 +1,15 @@
 Package: cpt
 Title: Classification Permutation Test
 Description: Non-parametric test for equality of multivariate distributions.  Trains a classifier to classify (multivariate) observations as coming from one of several distributions.  If the classifier is able to classify the observations better than would be expected by chance (using permutation inference), then the null hypothesis that the distributions are equal is rejected.  
-Version: 1.0
-Date: 2018-2-26
+Version: 1.0.2
+Date: 2018-10-30
 Imports: MASS, nnet, randomForest, glmnet
 Author: Johann Gagnon-Bartsch <johanngb@umich.edu> 
 Maintainer: Johann Gagnon-Bartsch <johanngb@umich.edu>
 License: GPL
 URL: http://dept.stat.lsa.umich.edu/~johanngb
 LazyLoad: yes
 NeedsCompilation: no
-Packaged: 2018-02-27 18:59:14 UTC; johann
+Packaged: 2018-10-30 16:55:38 UTC; johanngb
 Repository: CRAN
-Date/Publication: 2018-02-27 19:20:03 UTC
+Date/Publication: 2018-10-30 17:40:03 UTC

MD5

@@ -1,15 +1,15 @@
-d29d8d81f29e25dca836e4f116ad6aac *DESCRIPTION
+3b29645f6d4d31ff0f92773d3cce84d3 *DESCRIPTION
 de0e7172cef2b50e23d2b4a58f96bd23 *NAMESPACE
 ee246132368348b606def55cff7be0c5 *R/applyclassifiers.R
-3a23a9a8d40ba0ee31b4b306c5126481 *R/cpt.R
+107ca412f6fe9ca198340c3c0992e6ec *R/cpt.R
 e8063fc42ba577005bdd919ead877071 *R/getcombmethod.R
-7235781e1c25370cb4c23208fb885eab *R/getensemble.metric.R
-b9d644400fc9a4ef70ffb1b9f9b21832 *R/getmetric.R
+f589e97909049db0ac6f429ce239c1cd *R/getensemble.metric.R
+a364d83d1d68c31684600da470a3e48b *R/getmetric.R
 7437c39174c27c502cd17294475545a7 *R/gettestmethod.R
 70f2ae6f2a683d5776ab392189bee83a *R/gettestmethods.R
 32b30252abef51dc55ab31c6cfc68f3f *R/getteststat.R
 9cbe378084ceb7abaa5f3d9f56c6d26e *R/gettrainmethod.R
 ef2d130d68e57477a20eb762e0c00b53 *R/gettrainmethods.R
 35014fd243d937533e3d2940766615fd *R/train.R
-c1cf85e07ad2f2ad289c2a741031861d *man/cpt-package.Rd
+59a2c9609ccf5feade2c67b83ff23f54 *man/cpt-package.Rd
 e72967beb125f37eb1b0a6640516f045 *man/cpt.Rd

R/cpt.R

@@ -46,8 +46,8 @@ function (Z, T, leaveout = 0, class.methods = "forest", metric = "probability",
     colnames(nullpvaldist) = names(pvals)
     for (method.i in 1:ncol(nulldist)) {
         pvals[method.i] = sum(nulldist[, method.i] >= teststat[method.i])/perm.N
-        nullpvaldist[, method.i] = rank(nulldist[, method.i], 
-            ties.method = "max")/perm.N
+        nullpvaldist[, method.i] = 1 - (rank(nulldist[, method.i], 
+            ties.method = "min") - 1)/perm.N
     }
     nullcombpvaldist = apply(nullpvaldist[, comb.methods, drop = FALSE], 
         1, comb.method)

R/getensemble.metric.R

@@ -20,6 +20,13 @@ function (ensemble.metric)
             return(mean(meanprob[indexmat]))
         }
     }
+    if (ensemble.metric == "mean.log") {
+        rval = function(class.output, tstT) {
+            meanprob = apply(class.output, c(1, 3), mean)
+            indexmat = cbind(1:nrow(meanprob), tstT)
+            return(mean(log(meanprob[indexmat] + 1e-04)))
+        }
+    }
     if (ensemble.metric == "mean.mse") {
         rval = function(class.output, tstT) {
             meanprob = apply(class.output, c(1, 3), mean)

R/getmetric.R

@@ -7,6 +7,12 @@ function (metric)
             return(mean(prob[indexmat]))
         }
     }
+    if (metric == "logscore") {
+        rval = function(prob, tstT) {
+            indexmat = cbind(1:nrow(prob), tstT)
+            return(mean(log(prob[indexmat] + 1e-04)))
+        }
+    }
     else if (metric == "rate") {
         rval = function(prob, tstT) {
             indexmat = cbind(1:nrow(prob), tstT)

man/cpt-package.Rd

@@ -14,8 +14,8 @@ Description: Non-parametric test for equality of multivariate distributions.  Tr
 \tabular{ll}{
 Package: \tab cpt\cr
 Type: \tab Package\cr
-Version: \tab 1.0\cr
-Date: \tab 2018-2-26\cr
+Version: \tab 1.0.2\cr
+Date: \tab 2018-10-30\cr
 License: \tab GPL\cr
 LazyLoad: \tab yes\cr
 }