R/readYujie.R

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

#' readYujie
#'
#' This function converts data compiled by Yuije (in csv) into a format compatible with the soilcarbon template
#'
#' @param Yujie_file directory to Yuije data file
#' @import utils
#' @import stringi
#'
#' @return a list with data organized in 'tabs'
#'
#' @export

readYujie<- function(Yujie_file){

  requireNamespace("stringi")

  Yujie_dataset<-read.csv(Yujie_file, na.strings = c(""," ", "  "))

  levels(Yujie_dataset$pc_dataset_name)<-c(levels(Yujie_dataset$pc_dataset_name), "no_ref")
  Yujie_dataset$pc_dataset_name[which(is.na(Yujie_dataset$pc_dataset_name))] <- as.factor("no_ref")
  Yujie_dataset<-Yujie_dataset[-which(is.na(Yujie_dataset$Lon)),]

  Yujie_dataset_clean<-data.frame()
  sites<-unique(Yujie_dataset$Site)
  for (i in 1:length(sites)){
    site<-subset(Yujie_dataset, Yujie_dataset$Site==sites[i])
    site$Site<-paste(site$pc_dataset_name, site$Site, sep="_")
    if (length(unique(site$Lon))>1 | length(unique(site$Lat))>1){
      site$Site<-as.character(site$Site)
      latlons<-as.list(as.data.frame(t(cbind(site$Lat, site$Lon))))
      for (j in 1:length(unique(latlons))){
        site$Site[which(as.numeric(site$Lon)==unique(latlons)[[j]][2] & as.numeric(site$Lat)==unique(latlons)[[j]][1])]<-paste(sites[i], j, sep="_")
      }
    }
    Yujie_dataset_clean<-rbind(Yujie_dataset_clean, site)
  }

  clean_sources<-unique(Yujie_dataset_clean$pc_dataset_name)
  Yujie_dataset_sources<-data.frame()
  for (i in 1:length(clean_sources)){
    source<-subset(Yujie_dataset_clean, Yujie_dataset_clean$pc_dataset_name==clean_sources[i])[1,]
    Yujie_dataset_sources<-rbind(Yujie_dataset_sources, source)
  }

  clean_sites<-unique(Yujie_dataset_clean$Site)
  Yujie_dataset_sites<-data.frame()
  for (i in 1:length(clean_sites)){
    site<-subset(Yujie_dataset_clean, Yujie_dataset_clean$Site==clean_sites[i])[1,]
    Yujie_dataset_sites<-rbind(Yujie_dataset_sites, site)
  }

  Yujie_dataset_clean$profile_name<-paste(Yujie_dataset_clean$Site, Yujie_dataset_clean$ProfileID, sep="_")

  clean_profiles<-unique(Yujie_dataset_clean$profile_name)
  Yujie_dataset_profiles<-data.frame()
  for (i in 1:length(clean_profiles)){
    profile<-subset(Yujie_dataset_clean, Yujie_dataset_clean$profile_name==clean_profiles[i])[1,]
    Yujie_dataset_profiles<-rbind(Yujie_dataset_profiles, profile)
  }

  Yujie_dataset_clean$layer_name<-paste(Yujie_dataset_clean$profile_name, Yujie_dataset_clean$Layer_top, Yujie_dataset_clean$Layer_bottom, sep="_")

  Yujie_dataset_clean$Layer_bottom_norm<-Yujie_dataset_clean$Layer_bottom_norm
  Yujie_dataset_clean$Layer_top_norm<-Yujie_dataset_clean$Layer_top_norm

  Yujie_soilcarbon<-list(metadata=data.frame(dataset_name=Yujie_dataset_sources$pc_dataset_name,
                                          doi_number=Yujie_dataset_sources$doi,
                                         curator_name=rep("Yujie He", nrow(Yujie_dataset_sources))),
                         site=data.frame(dataset_name=Yujie_dataset_sites$pc_dataset_name,
                                         site_name=Yujie_dataset_sites$Site,
                                         lat=Yujie_dataset_sites$Lat,
                                         long=Yujie_dataset_sites$Lon,
                                         elevation=Yujie_dataset_sites$Elevation),
                         profile=data.frame(dataset_name=Yujie_dataset_profiles$pc_dataset_name,
                                          site_name=Yujie_dataset_profiles$Site,
                                          profile_name=Yujie_dataset_profiles$profile_name,
                                          observation_date=Yujie_dataset_profiles$SampleYear,
                                          p_MAT=Yujie_dataset_profiles$MAT_original,
                                          p_MAP=Yujie_dataset_profiles$MAP_original,
                                          soil_age=Yujie_dataset_profiles$Soil_Age,
                                          soil_taxon=Yujie_dataset_profiles$SoilOrder_LEN_USDA,
                                          parent_material_notes=Yujie_dataset_profiles$ParentMaterial,
                                          slope=Yujie_dataset_profiles$Slope,
                                          slope_shape=Yujie_dataset_profiles$SlopePosition,
                                          aspect=Yujie_dataset_profiles$Aspect,
                                          veg_note_profile=Yujie_dataset_profiles$VegTypeCodeStr_Local),
                         layer=data.frame(dataset_name=Yujie_dataset_clean$pc_dataset_name,
                                          site_name=Yujie_dataset_clean$Site,
                                          profile_name=Yujie_dataset_clean$profile_name,
                                          layer_name=Yujie_dataset_clean$layer_name,
                                          layer_top=Yujie_dataset_clean$Layer_top_norm,
                                          layer_bot=Yujie_dataset_clean$Layer_bottom_norm,
                                          hzn=Yujie_dataset_clean$HorizonDesignation,
                                          rc_year=Yujie_dataset_clean$Measurement_Year,
                                          X13c=Yujie_dataset_clean$d13C,
                                          X14c=Yujie_dataset_clean$D14C_BulkLayer,
                                          X14c_sigma=Yujie_dataset_clean$D14C_err,
                                          fraction_modern=Yujie_dataset_clean$FractionModern,
                                          fraction_modern_sigma=Yujie_dataset_clean$FractionModern_sigma,
                                          bd_tot=Yujie_dataset_clean$BulkDensity,
                                          bet_surface_area=Yujie_dataset_clean$SpecificSurfaceArea,
                                          ph_h2o=Yujie_dataset_clean$PH_H2O,
                                          c_tot=Yujie_dataset_clean$pct_C,
                                          n_tot=Yujie_dataset_clean$pct_N,
                                          c_to_n=Yujie_dataset_clean$CN,
                                          sand_tot_psa=Yujie_dataset_clean$sand_pct,
                                          silt_tot_psa=Yujie_dataset_clean$silt_pct,
                                          clay_tot_psa=Yujie_dataset_clean$clay_pct,
                                          cat_exch=Yujie_dataset_clean$cation_exch,
                                          fe_dith=Yujie_dataset_clean$Fe_d,
                                          fe_ox=Yujie_dataset_clean$Fe_o,
                                          fe_py=Yujie_dataset_clean$Fep,
                                          al_py=Yujie_dataset_clean$Alp,
                                          al_dith=Yujie_dataset_clean$Ald,
                                          al_ox=Yujie_dataset_clean$Alo,
                                          smect_vermic=Yujie_dataset_clean$Smectite),
                         fraction=data.frame())

  attributes(Yujie_soilcarbon)$file_name<-Yujie_file
  Yujie_data_nofraction<-Yujie_soilcarbon[-5]
  Yujie_flat<-flatten(soilcarbon_data = Yujie_data_nofraction)
  Yujie_database<-Yujie_flat
  Yujie_database[]<-lapply(Yujie_database, function(x) stringi::stri_trans_general(as.character(x), "latin-ascii"))
  Yujie_database[]<-lapply(Yujie_database, type.convert)

  return(Yujie_database)
}