# 1. packages via checkpoint snapshot

# the following packages will be loaded by checkpoint (all library instances)

library(pec) 

library(glmnet) 

library(prioritylasso) 

library(CoxBoost) 

library(ipflasso)

library(randomForestSRC) 

library(ranger)

library(dplyr)

library(data.table) 

library(survival)

library(GRridge) 

library(batchtools)

library(devtools)

library(SGL)

library(mboost)

library(blockForest)

library(tuneRanger)

library(survAUC)

# 2. packages not covered by checkpoint

# some of the packages could not be snapshoted via checkpoint, so we cloned them

# !!!

# mlr branch with advanced survial methods not included in the CRAN version

# !!!

devtools::install_github("HerrMo/mlr@survival_probabilities_ibrier",

                         dependencies = FALSE) 

devtools::install_github("HerrMo/GRridge") # is not coverd by checkpoint since bioconductor package

install.packages(ipflasso) # version with two-step ipf-lasso was not available on CRAN at the time of experiment

# additional clones

# devtools::install_github("HerrMo/blockForest") 

# devtools::install_github("HerrMo/tuneRanger")

# devtools::install_github("HerrMo/mboost") 

# If problems with devtools occure (under windows)

# library(devtools)             

#

# assignInNamespace("version_info",                                              

#                   c(devtools:::version_info, 

#                     list("3.5" = list(version_min = "3.3.0", 

#                                       version_max = "99.99.99",

#                                       path = "bin"))), 

#                   "devtools")

#                                                                                

# install_github("mlr-org/mlr@survival_probabilities_ibrier",                    

#                dependencies = FALSE)