R/read.soilcarbon.R

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

#' read.soilcarbon
#'
#' This function imports data from xlsx format matching the standard soil carbon data template
#'
#' @param file directory to data file
#' @param template set to TRUE if reading in a template file
#' @param format default is "original." Also accepted, "MPI" which modifies the read function for compatability with the MPI template V9.
#' @import openxlsx
#' @import utils
#' @export

read.soilcarbon<-function(file, format="original", template=F){

  requireNamespace("openxlsx")

  # TEST
  # #####
  # file="~/Dropbox/14Cdatabase/MPI-BGC Completed templates/MPI_v9_templates/Berg_2004.xlsx"
  # format="MPI"
  # template=F
  #
  # #####
  # TEST

  # comprae sheets found in datafile to the necessary sheets in the standard data template
  sheets_found<-getSheetNames(file)
  sheets_needed<-c("metadata","site","profile","layer", "fraction")
  if (format=="MPI") sheets_needed<-c(sheets_needed, "flux","interstitial","incubation")
  if (F %in% (sheets_needed %in% sheets_found)){
    sheets_missing<-setdiff(sheets_needed, sheets_found)
    stop(paste("Sheet(s) '",sheets_missing,"' missing from data file", sep="")) # if sheets are missing, return error message with the missing sheets
  }

  metadata<-read.xlsx(file , sheet="metadata")
  site<-read.xlsx(file , sheet="site")
  profile<-read.xlsx(file , sheet="profile")
  layer<-read.xlsx(file , sheet="layer", check.names=T)
  fraction<-read.xlsx(file , sheet="fraction")
  if (format=="MPI") {
    flux<-read.xlsx(file , sheet="flux")
    interstitial<-read.xlsx(file , sheet="interstitial")
    incubation<-read.xlsx(file , sheet="incubation")
    }


  data_workbook=list(metadata=metadata, site=site, profile=profile, layer=layer, fraction=fraction)
  if (format=="MPI") {
    data_workbook=list(metadata=metadata, site=site, profile=profile, flux=flux, layer=layer, interstitial=interstitial, incubation=incubation, fraction=fraction )
  }
  data_workbook<-lapply(data_workbook, function(x) x<-x[-1:-2,])


  #remove empty rows
  if (template==F){
  for (i in 1:length(data_workbook)){
    data<-data_workbook[[i]]
      for (j in 1:ncol(data)){
     data[,j][grep("^[ ]+$", data[,j])]<-NA
      }
    data_workbook[[i]]<-data
    data_workbook[[i]]<-data_workbook[[i]][rowSums(is.na(data_workbook[[i]])) != ncol(data_workbook[[i]]),]

  }
  }

  data_workbook<-lapply(data_workbook, function(x) lapply(x, as.character))
  data_workbook<-lapply(data_workbook, function(x) lapply(x, type.convert))
  data_workbook<-lapply(data_workbook, as.data.frame)


  attributes(data_workbook)$file_name<-file

  return(data_workbook)
}