Merge pull request #238 from kkholst/master

Moved BradleyTerry2 to Suggested packages.
topepo · Sep 8, 2015 · b5060d4 · b5060d4
2 parents f2cfcca + 966cc40
commit b5060d4
Show file tree

Hide file tree

Showing 3 changed files with 11 additions and 9 deletions.
diff --git a/pkg/caret/DESCRIPTION b/pkg/caret/DESCRIPTION
@@ -17,17 +17,17 @@ URL: https://github.com/topepo/caret/
 BugReports: https://github.com/topepo/caret/issues
 Imports:
     car,
-    reshape2,
     foreach,
     methods,
     plyr,
     nlme,
-    BradleyTerry2,
+    reshape2,
     stats,
     stats4,
     utils,
     grDevices
 Suggests:
+    BradleyTerry2,
     e1071,
     earth (>= 2.2-3),
     fastICA,

diff --git a/pkg/caret/NAMESPACE b/pkg/caret/NAMESPACE
@@ -1,5 +1,5 @@
 useDynLib(caret)
-import(foreach, methods, plyr, reshape2, ggplot2, lattice, nlme, BradleyTerry2)
+import(foreach, methods, plyr, reshape2, ggplot2, lattice, nlme)
 importFrom(car, powerTransform, yjPower)
 importFrom(grDevices, extendrange)
 importFrom(stats, .checkMFClasses, .getXlevels, aggregate, anova, 

diff --git a/pkg/caret/R/adaptive.R b/pkg/caret/R/adaptive.R
@@ -788,6 +788,7 @@ get_id <- function(x, param) {
 }
 
 bt_eval <- function(rs, metric, maximize, alpha = 0.05) {
+  if (!requireNamespace("BradleyTerry2")) stop("BradleyTerry2 package missing")
   se_thresh <- 100
   constant <- qnorm(1 - alpha)
   rs <- rs[order(rs$Resample, rs$model_id),]
@@ -799,12 +800,12 @@ bt_eval <- function(rs, metric, maximize, alpha = 0.05) {
   best_mod <- if(maximize) 
     best_mod$model_id[which.max(best_mod$V1)] else 
       best_mod$model_id[which.min(best_mod$V1)]
-  btModel <- BTm(cbind(win1, win2), player1, player2, data = scores, refcat = best_mod)
-  upperBound <- BTabilities(btModel)[,1] + constant*BTabilities(btModel)[,2]
-  if(any(BTabilities(btModel)[,2] > se_thresh)) {
+  btModel <- BradleyTerry2::BTm(cbind(win1, win2), player1, player2, data = scores, refcat = best_mod)
+  upperBound <- BradleyTerry2::BTabilities(btModel)[,1] + constant*BradleyTerry2::BTabilities(btModel)[,2]
+  if(any(BradleyTerry2::BTabilities(btModel)[,2] > se_thresh)) {
     ## These players either are uniformly dominated (='dom') or dominating
-    dom1 <- BTabilities(btModel)[,2] > se_thresh 
-    dom2 <- if(maximize) BTabilities(btModel)[,1] <= 0 else BTabilities(btModel)[,1] >= 0
+    dom1 <- BradleyTerry2::BTabilities(btModel)[,2] > se_thresh 
+    dom2 <- if(maximize) BradleyTerry2::BTabilities(btModel)[,1] <= 0 else BradleyTerry2::BTabilities(btModel)[,1] >= 0
     dom <- dom1 & dom2    
   } else dom <- rep(FALSE, length(upperBound))
   bound <- upperBound >= 0
@@ -814,14 +815,15 @@ bt_eval <- function(rs, metric, maximize, alpha = 0.05) {
 
 get_scores <- function(x, maximize = NULL, metric = NULL)
 {
+  if (!requireNamespace("BradleyTerry2")) stop("BradleyTerry2 package missing")
   delta <- outer(x[,metric], x[,metric], "-")
   tied <- ifelse(delta == 0, 1, 0)*.5
   diag(tied) <- 0
   binary <- if(maximize) ifelse(delta > 0, 1, 0) else ifelse(delta > 0, 0, 1) 
   binary <- binary + tied
   diag(binary) <- 0  
   rownames(binary) <- colnames(binary) <- x$model_id
-  countsToBinomial(as.table(binary))
+  BradleyTerry2::countsToBinomial(as.table(binary))
 }
 
 skunked <- function(scores, verbose = TRUE) {