Roxygen2 updates, xgboost fixes

DESCRIPTION

@@ -1,20 +1,23 @@
 Package: SuperLearner
 Type: Package
 Title: Super Learner Prediction
-Version: 2.0-30-9000
-Date: 2024-02-06
-Authors@R: c(person("Eric", "Polley", email = "epolley@uchicago.edu", role = c("aut", "cre")), person("Erin", "LeDell", role = c("aut")), person("Chris", "Kennedy", role = c("aut")), person("Sam", "Lendle", role = c("ctb")), person("Mark", "van der Laan", role = c("aut", "ths")))
-Maintainer: Eric Polley <epolley@uchicago.edu>
+Version: 2.0-30-9001
+Authors@R: c(person("Eric", "Polley", email = "epolley@uchicago.edu", role = c("aut", "cre")),
+             person("Erin", "LeDell", role = c("aut")),
+             person("Chris", "Kennedy", role = c("aut")),
+             person("Sam", "Lendle", role = c("ctb")),
+             person("Mark", "van der Laan", role = c("aut", "ths")))
 Description: Implements the super learner prediction method and contains a
     library of prediction algorithms to be used in the super learner.
 License: GPL-3
 URL: https://github.com/ecpolley/SuperLearner
+BugReports: https://github.com/ecpolley/SuperLearner/issues
 Depends:
-    R (>= 2.14.0),
-    nnls
+    R (>= 4.0.0)
 Imports:
     cvAUC,
-    methods
+    nnls,
+    stats
 Suggests:
     arm,
     bartMachine,
@@ -40,6 +43,7 @@ Suggests:
     mlbench,
     nloptr,
     nnet,
+    parallel,
     party,
     polspline,
     prettydoc,
@@ -55,7 +59,9 @@ Suggests:
     spls,
     sva,
     testthat,
-    xgboost (>= 0.6)
+    xgboost (>= 3.1.2.1)
 LazyLoad: yes
-VignetteBuilder: knitr, rmarkdown
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+VignetteBuilder: knitr
+RoxygenNote: 7.3.3
+Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -1,57 +1,120 @@
-import(nnls)
-exportPattern("^[^\\.]")
+# Generated by roxygen2: do not edit by hand
 
-importFrom(stats, coef)
-importFrom(stats, predict)
-importFrom(graphics, plot)
-importFrom(methods, is)
-
-importFrom("stats", "as.formula", "binomial", "cor.test", "dlogis", "formula", "gaussian", "glm", "lm", "loess", "loess.control", "model.matrix", "optim", "plogis", "pnorm", "predict.lm", "qnorm", "reorder", "sd", "step", "var", "weighted.mean")
-importFrom("utils", "capture.output", "RShowDoc", "packageVersion")
-
-S3method(print, SuperLearner)
-S3method(coef, SuperLearner)
-S3method(predict, SuperLearner)
-
-S3method(print, CV.SuperLearner)
-S3method(coef, CV.SuperLearner)
-S3method(plot, CV.SuperLearner)
-S3method(summary, CV.SuperLearner)
-S3method(print, summary.CV.SuperLearner)
-
-S3method(predict, SL.bartMachine)
-S3method(predict, SL.bayesglm)
-S3method(predict, SL.biglasso)
-S3method(predict, SL.caret)
-S3method(predict, SL.cforest)
-S3method(predict, SL.earth)
-S3method(predict, SL.gam)
-S3method(predict, SL.gbm)
-S3method(predict, SL.glm)
-S3method(predict, SL.glmnet)
-S3method(predict, SL.ipredbagg)
-S3method(predict, SL.knn)
-S3method(predict, SL.kernelKnn)
-S3method(predict, SL.ksvm)
-S3method(predict, SL.leekasso)
-S3method(predict, SL.lda)
-S3method(predict, SL.lm)
-S3method(predict, SL.loess)
-S3method(predict, SL.logreg)
-S3method(predict, SL.mean)
-S3method(predict, SL.nnet)
-S3method(predict, SL.nnls)
-S3method(predict, SL.polymars)
-S3method(predict, SL.qda)
-S3method(predict, SL.randomForest)
-S3method(predict, SL.ranger)
-S3method(predict, SL.ridge)
-S3method(predict, SL.rpart)
-S3method(predict, SL.speedglm)
-S3method(predict, SL.speedlm)
-S3method(predict, SL.step)
-S3method(predict, SL.stepAIC)
-S3method(predict, SL.svm)
-S3method(predict, SL.template)
-S3method(predict, SL.xgboost)
-S3method(predict, SuperLearner)
+S3method(plot,CV.SuperLearner)
+S3method(predict,SL.bartMachine)
+S3method(predict,SL.bayesglm)
+S3method(predict,SL.biglasso)
+S3method(predict,SL.caret)
+S3method(predict,SL.cforest)
+S3method(predict,SL.earth)
+S3method(predict,SL.gam)
+S3method(predict,SL.gbm)
+S3method(predict,SL.glm)
+S3method(predict,SL.glmnet)
+S3method(predict,SL.ipredbagg)
+S3method(predict,SL.kernelKnn)
+S3method(predict,SL.knn)
+S3method(predict,SL.ksvm)
+S3method(predict,SL.lda)
+S3method(predict,SL.leekasso)
+S3method(predict,SL.lm)
+S3method(predict,SL.loess)
+S3method(predict,SL.logreg)
+S3method(predict,SL.mean)
+S3method(predict,SL.nnet)
+S3method(predict,SL.nnls)
+S3method(predict,SL.polymars)
+S3method(predict,SL.qda)
+S3method(predict,SL.randomForest)
+S3method(predict,SL.ranger)
+S3method(predict,SL.ridge)
+S3method(predict,SL.rpart)
+S3method(predict,SL.speedglm)
+S3method(predict,SL.speedlm)
+S3method(predict,SL.step)
+S3method(predict,SL.stepAIC)
+S3method(predict,SL.svm)
+S3method(predict,SL.xgboost)
+S3method(predict,SuperLearner)
+S3method(print,CV.SuperLearner)
+S3method(print,SuperLearner)
+S3method(print,summary.CV.SuperLearner)
+S3method(stats::coef,CV.SuperLearner)
+S3method(stats::coef,SuperLearner)
+S3method(summary,CV.SuperLearner)
+export(All)
+export(CVFolds)
+export(SL.bartMachine)
+export(SL.bayesglm)
+export(SL.biglasso)
+export(SL.caret)
+export(SL.caret.rpart)
+export(SL.cforest)
+export(SL.earth)
+export(SL.gam)
+export(SL.gbm)
+export(SL.glm)
+export(SL.glm.interaction)
+export(SL.glmnet)
+export(SL.ipredbagg)
+export(SL.kernelKnn)
+export(SL.knn)
+export(SL.ksvm)
+export(SL.lda)
+export(SL.leekasso)
+export(SL.lm)
+export(SL.loess)
+export(SL.logreg)
+export(SL.mean)
+export(SL.nnet)
+export(SL.nnls)
+export(SL.polymars)
+export(SL.qda)
+export(SL.randomForest)
+export(SL.ranger)
+export(SL.ridge)
+export(SL.rpart)
+export(SL.rpartPrune)
+export(SL.speedglm)
+export(SL.speedlm)
+export(SL.step)
+export(SL.step.forward)
+export(SL.step.interaction)
+export(SL.stepAIC)
+export(SL.svm)
+export(SL.xgboost)
+export(SampleSplitSuperLearner)
+export(SuperLearner)
+export(SuperLearner.control)
+export(SuperLearnerDocs)
+export(SuperLearnerNews)
+export(`CV.SuperLearner`)
+export(`SL.template`)
+export(`SuperLearner.CV.control`)
+export(`create.Learner`)
+export(`predict.SL.template`)
+export(`write.SL.template`)
+export(`write.predict.SL.template`)
+export(`write.screen.template`)
+export(create.SL.xgboost)
+export(listWrappers)
+export(mcSuperLearner)
+export(method.AUC)
+export(method.CC_LS)
+export(method.CC_nloglik)
+export(method.NNLS)
+export(method.NNLS2)
+export(method.NNloglik)
+export(method.template)
+export(recombineCVSL)
+export(screen.SIS)
+export(screen.corP)
+export(screen.corRank)
+export(screen.glmnet)
+export(screen.randomForest)
+export(screen.template)
+export(screen.ttest)
+export(snowSuperLearner)
+export(trimLogit)
+export(write.method.template)
+import(stats)