main_running_v3/00_InstallPackage.R

In yujijun/neoantigenML: Machine Learning Methods for Neoantigen Filtering

# BASIC INFO ---------------------------
##
## Script name: InstallPackage.R
##
## Purpose of script: This is package for package install
##
## Author: JijunYu
##
## Date Created: 2021-11-28
## Update Date:
##
## Copyright (c) Jijun Yu, 2021
## Email: jijunyuedu@outlook.com
##
## Notes:
##
# INSTALL PACKAGES & LOAD LIBRARIES -----------------
cat("INSTALLING PACKAGES & LOADING LIBRARIES... \n\n", sep = "")
packages <- c( "data.table",
               "mlr3",
               "bbotk","mlr3misc","mlr3pipelines","mlr3cluster","mlr3filters","mlr3fselect","mlr3learners","mlr3proba","mlr3tuning","mlr3viz","paradox",
              "tidyverse",
              "stringr",
              "devtools",
              "mlr3verse",
              "praznik",
              "kknn",
              "xgboost",
              "forestmodel",
              "rpart",
              "stats",
              "FSelectorRcpp",
              "care",
              "iml",
              "DALEX",
              "apcluster",
              "mlr3tuningspaces",
              "precrec",
              "janitor",
              "ranger",
              "glmnet",
              "e1071",
              "motifStack",
              "stringdist",
              "plotfunctions",
              "groupdata2",
              "Deducer",
              "BBmisc", "car",
              "cvAUC",
              "DescTools",
              "doParallel",
              "doSNOW",
              "extraTrees",
              "fst",
              "ggpubr",
              "ggsci",
              "mlr",
              "psych",
              "randomForestSRC",
              "rlecuyer",
              "seqinr",
              "stringdist",
              "survminer") # list of packages to load
n_packages <- length(packages) # count how many packages are required
new.pkg <- packages[!(packages %in% installed.packages())] # determine which packages aren't installed
# install missing packages
if(length(new.pkg)){
  install.packages(new.pkg)
}
cat("ALL PACKAGES HAVE BEEN INSTALLED... \n\n", sep = "")
#--------------Main -----------------------