R/loadPackagesForRegistration.R

In snandi/Registration: Contains functions for registration algorithms, simulation and testing

## This function loads all the require packages for functions in this R Package
## Registration. 

## If the package does not exist, it installs them from CRAN Mirror IA ( USA ). 
## It returns a lit of all packages loaded and a list of all packages to be 
## loaded in case of parallel computation

#'@importFrom utils install.packages getCRANmirrors chooseCRANmirror
#'
#'@export 

loadPackagesForRegistration <- function( CRANMirror = 83, tryToInstall = FALSE ){
  
  Packages <- c( 
    'Biostrings',  ## For sequence comparison
    'boot',
    'car',
    'cluster',
    'clusterSim',
    'clValid',
    'doParallel',  ## For parallel execution with foreach
    'doSNOW',
    'fda',
    'fdakma',
    # 'fdasrvf',
    'fda.usc',     ## For functional data depth
    'foreach',
    'gbm',         ## For gradient boosting
    'ggplot2',
    'gridBase',
    'gridExtra',
    'gtools',
    'lattice',
    'MASS',
    'Matrix',
    'matrixStats', ## For weighted row means
    'mclust',
    'Metrics',     ## For estimating model metrics
    'parallel',
    'png',
    'plyr',
    'dplyr',       ## It is recommended that dplyr is loaded after plyr
    'randomForest',
    'refund', 
    'reshape',
    'reshape2',
    'RFunctionsSN', 
    'robustX',     ## For multivariate median
    'rpart',
    'seqinr',
    'tree',        ## For extracting and plotting Random forest trees
    'utils',
    'xtable'
  )

  ## Requiring packages and installing them if something doesnt exist
  for( Package in Packages ){
    if( require( package = Package, character.only = T ) == F ){
      if( tryToInstall ){
        ## Choose USA ( IA ) as the CRAN mirror
        Mirrors <- getCRANmirrors( all = FALSE, local.only = FALSE )
        chooseCRANmirror( graphics = F, ind = which( Mirrors$Name == 'USA (IA)' ) )
        
        print( paste( 'Installing', Package ) )
        try( install.packages( Package, dependencies = TRUE ) )
      } else{
        print( paste( 'Please install', Package ) )
      }
    } else{
      print( paste( 'Loading', Package ) )
      require( package = Package, character.only = T )
    }
  }

  ## For parallel processing, when passing the list of packages to load
  ## in all the cores. Could be different from Packages
  Packages_Par <- Packages
  
  PackageList <- list( Packages = Packages, Packages_Par = Packages_Par )
  return( PackageList )
}