R/compileDatabase.R

In powellcenter-soilcarbon/soilcarbon: Tools to Analyze Soil Carbon Database Created by Powell Center Working Group and Max Planck Institute for Biogeochemistry

#' compileDatabase
#'
#' adds dataset to soilcarbon database
#'
#' @param dataset_directory directory where compeleted and QC passed soilcarbon datasets are stored
#' @export
#' @import devtools
#' @import stringi

compileDatabase <- function(dataset_directory ){

  requireNamespace("stringi")

  data_files<-list.files(dataset_directory, full.names = T)
  data_files<-data_files[grep("xlsx", data_files)]

   # special dataset (Yujie)
   Yujie_file<-system.file("extdata", "Yujie_dataset.csv", package = "soilcarbon")
   Yujie_database<-readYujie(Yujie_file)
   working_database<-Yujie_database
   working_database[] <- lapply(working_database, as.character)

  for(i in 1:length(data_files)){
    soilcarbon_data<-read.soilcarbon(data_files[i])

    qc_file<-basename(gsub("\\.xlsx", "_QCreport.txt", attributes(soilcarbon_data)$file_name))
    qc_file<-paste0(dataset_directory, "dataQC_log/", qc_file)
    qc_out<-dataQC(soilcarbon_data, writeQCreport = T, outfile = qc_file)

    if (qc_out>0){
      print(paste(basename(data_files[i]),"...", qc_out,"errors"))
    } else{
      print(paste(basename(data_files[i]),"...", "passed and added to database"))
      flat_data <- flatten(soilcarbon_data)
      flat_data[] <- lapply(flat_data, as.character)
      working_database<-rbind(working_database, flat_data)

  }
}
   working_database[]<-lapply(working_database, function(x) stri_trans_general(x, "latin-ascii"))
   working_database[]<-lapply(working_database, type.convert)
   soilcarbon_database<-working_database
  return(soilcarbon_database)
}