8     predicted <- rec_pred(method = object$modelInfo,  functionVar
12     names(predicted) <- NULL
14       predicted <- if (attr(object$levels, "ordered"))
15         ordered(as.character(predicted), levels = object$levels)
17         factor(as.character(predicted), levels = object$levels)
20     predicted <- rec_prob(method = object$modelInfo,
24     predicted <- predicted[, object$levels]
26   predicted
253                 predicted <- try(  functionVar
260                 if(pred_failed(predicted)) {
262                                msg  = predicted,
267                   predicted <- fill_failed_pred(index = holdoutIndex, lev = lev, submod)
274                 predicted <- fill_failed_pred(index = holdoutIndex, lev = lev, submod)
277               if(testing) print(head(predicted))
290               predicted <- trim_values(predicted, ctrl, is.null(lev))
301                 predicted <- lapply(predicted,
309                 if(testing) print(head(predicted))
312                   for(k in seq(along = predicted)) predicted[[k]] <-
313                       cbind(predicted[[k]], probValues[[k]])
315                 predicted <- do.call("rbind", predicted)
317                 rownames(predicted) <- NULL
318                 predicted <- cbind(predicted, allParam)
321                 pred_val <- outcome_conversion(predicted, lv = lev)
322                 predicted <-  ho_data
323                 predicted$pred <- pred_val
324                 if(ctrl$classProbs) predicted <- cbind(predicted, probValues)
325                 predicted <- cbind(predicted, info$loop[parm,,drop = FALSE])
331               predicted
451         predicted <- try(  functionVar
458         if(pred_failed(predicted)) {
460                        msg  = predicted,
465           predicted <- fill_failed_pred(index = holdoutIndex, lev = lev, submod)
473         predicted <- fill_failed_pred(index = holdoutIndex, lev = lev, submod)
476       if(testing) print(head(predicted))
491       predicted <- trim_values(predicted, ctrl, is.null(lev))
505         predicted <- lapply(predicted,
513         if(testing) print(head(predicted))
516         if(ctrl$classProbs) predicted <- mapply(cbind, predicted, probValues, SIMPLIFY = FALSE)
519           tmpPred <- predicted
530         thisResample <- lapply(predicted,
538           cells <- lapply(predicted,
547         pred_val <- outcome_conversion(predicted, lv = lev)
574       thisResampleExtra <- optimism_rec(ctrl, dat, iter, lev, method, mod_rec, predicted,
713                 predicted <- try(  functionVar
720                 if(pred_failed(predicted)) {
722                                msg  = predicted,
727                   predicted <- fill_failed_pred(index = holdoutIndex, lev = lev, submod)
735                 predicted <- fill_failed_pred(index = holdoutIndex, lev = lev, submod)
738               if(testing) print(head(predicted))
753               predicted <- trim_values(predicted, ctrl, is.null(lev))
767                 predicted <- lapply(predicted,
775                 if(testing) print(head(predicted))
779                   for(k in seq(along = predicted))
780                     predicted[[k]] <- cbind(predicted[[k]], probValues[[k]])
784                   tmpPred <- predicted
796                 thisResample <- lapply(predicted,
803                   cells <- lapply(predicted,
811                 pred_val <- outcome_conversion(predicted, lv = lev)
890                     predicted <- try(
897                     if(pred_failed(predicted)) {
899                                    msg  = predicted,
904                       predicted <- fill_failed_pred(index = holdoutIndex, lev = lev, submod)
912                     predicted <- fill_failed_pred(index = holdoutIndex, lev = lev, submod)
915                   if(testing) print(head(predicted))
930                   predicted <- trim_values(predicted, ctrl, is.null(lev))
945                     predicted <- lapply(predicted,
954                     if(testing) print(head(predicted))
958                       for(k in seq(along = predicted))
959                         predicted[[k]] <- cbind(predicted[[k]], probValues[[k]])
963                       tmpPred <- predicted
975                     thisResample <- lapply(predicted,
982                       cells <- lapply(predicted,
991                     pred_val <- outcome_conversion(predicted, lv = lev)
1137                   predicted <- try(
1144                   if(pred_failed(predicted)) {
1146                                  msg  = predicted,
1151                     predicted <- fill_failed_pred(index = holdoutIndex, lev = lev, submod)
1159                   predicted <- fill_failed_pred(index = holdoutIndex, lev = lev, submod)
1162                 if(testing) print(head(predicted))
1176                 predicted <- trim_values(predicted, ctrl, is.null(lev))
1191                   predicted <- lapply(predicted,
1199                   if(testing) print(head(predicted))
1203                     for(k in seq(along = predicted))
1204                       predicted[[k]] <- cbind(predicted[[k]], probValues[[k]])
1208                     tmpPred <- predicted
1220                   thisResample <- lapply(predicted,
1227                     cells <- lapply(predicted,
1236                   pred_val <- outcome_conversion(predicted, lv = lev)