inst/dataprep/Makefile.R

In MiguelRodo/VaccCompData: Data package for novel TBV vaccine comparison paper

# Initial set-up ----------------------------------------------------------

# saving results? clear wd first
currObjVec = ls()

# find library containing raw data
dataprepPath = system.file( "dataprep", package = "VaccCompData" )
dirFunc = function(x) paste0( dataprepPath, "/", x )

# Individual datasets -----------------------------------------------------

# h564Tbl
source( file = dirFunc( "H56-CD4.R") )

# h568Tbl
source( file = dirFunc( "H56-CD8.R") )

# l4Tbl
source( file = dirFunc( "BCG-CD4.R") )

# l8Tbl
source( file = dirFunc( "BCG-CD8.R") )

# lOrigMainTbl
source( file = dirFunc( "Main.R") )

# idri
source( file = dirFunc( "ID93.R") )

# h1
source( file = dirFunc( "H1.R") )

# megapool
source( file = dirFunc( "Megapool.R") )

# aeras402
source( file = dirFunc( "AERAS402.R") )

# Joining and calculating -------------------------------------------------

# join
source( file = dirFunc( "Data_Join.R" ) )

# il17
source( file = dirFunc( "IL_17-Calc_And_Removal.R" ) )

# sub time zero
source( file = dirFunc( "Sub_Baseline.R" ) )

# summary statistics
source( file = dirFunc( "Summ_Stat_Calc.R" ) )

# Saving ------------------------------------------------------------------

#' making availabe in package
if( 1 == 0 ){ # run manually if neeeded
  devtools::use_data( bl17ExcTbl, overwrite = TRUE )
  devtools::use_data( bl17ExcITbl, overwrite = TRUE )
  devtools::use_data( join17ExcTbl, overwrite = TRUE )
  devtools::use_data( join17ExcITbl, overwrite = TRUE )
  devtools::use_data( join17IncITbl, overwrite = TRUE )
  devtools::use_data( megITbl, overwrite = TRUE )
  devtools::use_data( sub17ExcTbl, overwrite = TRUE )
  devtools::use_data( sub17ExcITbl, overwrite = TRUE )
  devtools::use_data( tmax17ExcTbl, overwrite = TRUE )
  devtools::use_data( tmax17ExcITbl, overwrite = TRUE )
  devtools::use_data( tmaxSub17ExcTbl, overwrite = TRUE )
  devtools::use_data( tmaxSub17ExcITbl, overwrite = TRUE )
  devtools::use_data( blSingle17Tbl, overwrite = TRUE )
  devtools::use_data( single17Tbl, overwrite = TRUE )
  devtools::use_data( single17ITbl, overwrite = TRUE )
  devtools::use_data( tmaxSingle17Tbl, overwrite = TRUE )
  devtools::use_data( tmaxSingle17ITbl, overwrite = TRUE )
  devtools::use_data( subSingle17Tbl, overwrite = TRUE )
  devtools::use_data( subSingle17ITbl, overwrite = TRUE )
  devtools::use_data( tmaxSubSingle17Tbl, overwrite = TRUE )
  devtools::use_data( tmaxSubSingle17ITbl, overwrite = TRUE )
}

# write to spreadsheet
if( 1 == 0 ){
  openxlsx::write.xlsx( join17IncITbl %>%
                          spread( key = cytCombo, value = resp ) %>%
                          select( -prid ),
                        file = "C:/Users/migue/Dropbox/Rodo et al Vaccine Immune Response paper/Data/Publicly available/Vaccines.xlsx",
                        overwrite = TRUE )
  openxlsx::write.xlsx( joinMegITbl1 %>%
                          spread( key = cytCombo, value = resp ) %>%
                          select( -c( prid, timePoint, vaccine, stim, infxn ) ),
                        file = "C:/Users/migue/Dropbox/Rodo et al Vaccine Immune Response paper/Data/Publicly available/Megapool.xlsx",
                        overwrite = TRUE )
}