diff --git a/ccn2019.rev2.Rmd b/ccn2019.rev2.Rmd index 119fd43..986ae32 100644 --- a/ccn2019.rev2.Rmd +++ b/ccn2019.rev2.Rmd @@ -23,6 +23,8 @@ library(tidyverse) library(stringi) library(plsRglm) +library(plsdof) +library(caret) ``` ```{r params} @@ -106,10 +108,30 @@ pca <- prcomp(~x_sl+x_ul+x_t+x_l, NB2, center = TRUE,scale. = TRUE, na.action=na.exclude) NB2 <- NB2 %>% mutate(pc1=pca$x[,'PC1'], pc2=pca$x[,'PC2']) -rt <- unlist(NB2[,"rt"]) -dm <- NB2[,c("x_sl","x_ul","x_t","x_l")] -set.seed(250) -plsR(rt,dm,3) +# caret +library(caret) +# Compile cross-validation settings + + +any(is.na(NB2)) +NB2 <- na.omit(NB2) + +set.seed(100) +trainingfold <- createMultiFolds(NB2@correct, k = 5, times = 10) + +# PLS +mod1 <- train(correct ~ ., data = NB2[,c("correct","x_sl","x_ul","x_t","x_l")], + method = "pls", + metric = "Accuracy", + tuneLength = 20, + trControl = trainControl("repeatedcv", index = trainingfold, selectionFunction = "oneSE"), + preProc = c("zv","center","scale")) + +# Check CV +plot(mod1) + + +plsR(correct ~ ., data=NB2[,c("correct","x_sl","x_ul","x_t","x_l")])