[R] maintenance Nov 2017; SHAP plots (#2888)

* [R] fix predict contributions for data with no colnames

* [R] add a render parameter for xgb.plot.multi.trees; fixes #2628

* [R] update Rd's

* [R] remove unnecessary dep-package from R cmake install

* silence type warnings; readability

* [R] silence complaint about incomplete line at the end

* [R] initial version of xgb.plot.shap()

* [R] more work on xgb.plot.shap

* [R] enforce black font in xgb.plot.tree; fixes #2640

* [R] if feature names are available, check in predict that they are the same; fixes #2857

* [R] cran check and lint fixes

* remove tabs

* [R] add references; a test for plot.shap

R-package/man/xgb.train.Rd

@@ -258,6 +258,10 @@ bst <- xgboost(data = agaricus.train$data, label = agaricus.train$label,
                objective = "binary:logistic")
 pred <- predict(bst, agaricus.test$data)
 
+}
+\references{
+Tianqi Chen and Carlos Guestrin, "XGBoost: A Scalable Tree Boosting System",
+22nd SIGKDD Conference on Knowledge Discovery and Data Mining, 2016, \url{https://arxiv.org/abs/1603.02754}
 }
 \seealso{
 \code{\link{callbacks}},