[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/tests/testthat/test_helpers.R

@@ -81,6 +81,11 @@ test_that("predict feature contributions works", {
   expect_equal(colnames(pred_contr), c(colnames(sparse_matrix), "BIAS"))
   pred <- predict(bst.Tree, sparse_matrix, outputmargin = TRUE)
   expect_lt(max(abs(rowSums(pred_contr) - pred)), 1e-5)
+  # must work with data that has no column names
+  X <- sparse_matrix
+  colnames(X) <- NULL
+  expect_error(pred_contr_ <- predict(bst.Tree, X, predcontrib = TRUE), regexp = NA)
+  expect_equal(pred_contr, pred_contr_, check.attributes = FALSE)
 
   # gbtree binary classifier (approximate method)
   expect_error(pred_contr <- predict(bst.Tree, sparse_matrix, predcontrib = TRUE, approxcontrib = TRUE), regexp = NA)
@@ -289,6 +294,13 @@ test_that("xgb.plot.deepness works", {
   xgb.ggplot.deepness(model = bst.Tree)
 })
 
+test_that("xgb.plot.shap works", {
+  sh <- xgb.plot.shap(data = sparse_matrix, model = bst.Tree, top_n = 2, col = 4)
+  expect_equal(names(sh), c("data", "shap_contrib"))
+  expect_equal(NCOL(sh$data), 2)
+  expect_equal(NCOL(sh$shap_contrib), 2)
+})
+
 test_that("check.deprecation works", {
   ttt <- function(a = NNULL, DUMMY=NULL, ...) {
     check.deprecation(...)