R/data_file_paths.R

In annack84/STMdevelopment: Develop State-and-Transition Models for the Upper Colorado River Basin

#' Set file paths for specific users' working environments
#'
#' The purpose of this function is to make it easy to run the analyses from
#'  different users working environments. Add new list items as needed to access
#'  other data sets.
#'
#' @param user Character. Options are "Anna" and "Travis" for personal hard
#'  drive and OneDrive folders/files, or VPN if doing everything from the
#'  network. "Duniway_et_al_2024" accesses the data archive of the data that
#'  went into the Semiarid Warm Sandy and Loamy Uplands STM for the Duniway et
#'  al. 2024 manuscript (may only work from Anna's computer).
#'
#' @return List. Use this list in other functions to access data from different
#'  file locations
#' @export data_file_paths
#' @rdname data_file_paths

data_file_paths <- function(user){ # "Anna", "Travis", "Duniway_et_al_2024" or "VPN"
  network_files <- list(plotnet_processed = "V:/PROJECTS/MIKE_DUNIWAY/CURRENT/SWDesertRangelandMonitoring/Data/ProcessedData",
                        nri = "V:/PROJECTS/MIKE_DUNIWAY/CURRENT/SWDesertRangelandMonitoring/Data/ProcessedData/NRI",
                        ESG_map = "V:/PROJECTS/TRAVIS_NAUMAN/ESGs/Analysis/RMD_STMs/ESGs_final.tif",
                        target_ESG_map_folder = "V:/PROJECTS/TRAVIS_NAUMAN/ESGs/Analysis/RMD_STMs/leaflet_map_ESG_rasters",
                        apriori_stms = "V:/PROJECTS/TRAVIS_NAUMAN/ESGs/Analysis/RMD_STMs/S5_ESG_STM_summary_forRMD.csv",
                        species_list = "V:/PROJECTS/TRAVIS_NAUMAN/ESGs/Analysis/RMD_STMs/SpeciesList_WesternUS_AcceptedSymbols_2020-01-06.csv", # update to match Anna's file
                        prodfolder = "V:/PROJECTS/TRAVIS_NAUMAN/ESGs/Data_Nonspatial/Duniway_EDIT_qry",
                        climate = "V:/PROJECTS/TRAVIS_NAUMAN/ESGs/Data_Spatial/shps_SSURGO18",
                        ssurgo = "V:/PROJECTS/TRAVIS_NAUMAN/GIS_Archive/gSSURGO18/gSSURGO_CONUS.gdb",
                        ssurgo_result_fldr = "V:/PROJECTS/TRAVIS_NAUMAN/ESGs/Analysis/RMD_STMs/ssurgo_results",
                        plotnet_splist_location = "V:/PROJECTS/MIKE_DUNIWAY/CURRENT/SWDesertRangelandMonitoring/Data",
                        # need to update to this aim and lmf species list, but the SpeciesState handling gets messy
                        #aimlmf_splist = "V:/PROJECTS/MIKE_DUNIWAY/CURRENT/SWDesertRangelandMonitoring/Data/ProcessedData/AIM/PlotNet_style_calcs_AIMLMF_all/SpeciesList_AIMLMF_20231201.csv",
                        aimlmf_splist ="V:/PROJECTS/MIKE_DUNIWAY/CURRENT/SWDesertRangelandMonitoring/Data/ProcessedData/AIM/Old_AIM_LMF_databases/Terrestrial AIM Data Spring 2020/PlotNet_style_AIMLMF_calcs/SpeciesList_AIM2020UCRBStates.csv",
                        ai_raster = "V:/PROJECTS/ANNA_KNIGHT/GIS/Climate/GlobalAIandPET/global-ai_et0/ai_et0/ai_et0_WesternUSEcoregions.tif",
                        prism_rasters = c("V:/PROJECTS/ANNA_KNIGHT/GIS/Climate/PRISM/ppt/PRISM_ppt_30yr_normal_800mM2_annual_asc/PRISM_ppt_30yr_normal_800mM2_annual_asc.asc",
                                          "V:/PROJECTS/ANNA_KNIGHT/GIS/Climate/PRISM/ppt/PRISM_ppt_30yr_normal_800mM2_monthly_asc/PRISM_ppt_30yr_normal_800mM2_06_asc.asc",
                                          "V:/PROJECTS/ANNA_KNIGHT/GIS/Climate/PRISM/ppt/PRISM_ppt_30yr_normal_800mM2_monthly_asc/PRISM_ppt_30yr_normal_800mM2_07_asc.asc",
                                          "V:/PROJECTS/ANNA_KNIGHT/GIS/Climate/PRISM/ppt/PRISM_ppt_30yr_normal_800mM2_monthly_asc/PRISM_ppt_30yr_normal_800mM2_08_asc.asc",
                                          "V:/PROJECTS/ANNA_KNIGHT/GIS/Climate/PRISM/ppt/PRISM_ppt_30yr_normal_800mM2_monthly_asc/PRISM_ppt_30yr_normal_800mM2_09_asc.asc",
                                          "V:/PROJECTS/ANNA_KNIGHT/GIS/Climate/PRISM/temp/PRISM_tmean_30yr_normal_800mM2_annual_asc/PRISM_tmean_30yr_normal_800mM2_annual_asc.asc",
                                          "V:/PROJECTS/ANNA_KNIGHT/GIS/Climate/PRISM/temp/PRISM_tmax_30yr_normal_800mM2_annual_asc/PRISM_tmax_30yr_normal_800mM2_annual_asc.asc",
                                          "V:/PROJECTS/ANNA_KNIGHT/GIS/Climate/PRISM/temp/PRISM_tmin_30yr_normal_800mM2_annual_asc/PRISM_tmin_30yr_normal_800mM2_annual_asc.asc"
                        ),
                        aero = "V:/PROJECTS/ANNA_KNIGHT/ESG/STM/AERO/AERO_indicators_AIMLMF_20211112.csv",
                        rhem = list(aim = "V:/PROJECTS/ANNA_KNIGHT/ESG/STM/RHEM/Final_5_RHEM_AIM_SoilGrids_NEDslope_21926_09May2022_SubsetNVUTAZCONM_2023-01-31.csv",
                                    lmf = "V:/PROJECTS/ANNA_KNIGHT/ESG/STM/RHEM/Final_5_RHEM_LMF_SoilGrids_NEDslope_21926_09May2022_SubsetNVUTAZCONM_2023-01-31.csv",
                                    nri = "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/ESG/STM/RHEM/contains_NRI_do_not_sync/Final_2_RHEM_NRI_SoilGrids_NEDSlope_32425_09May2022.csv"),
                        soil_rasters = list(clay = c("G:/Base Layers/Soils/UCRB_30m/claytotal_r_0_cm_2D_QRF_bt.tif",
                                                     "G:/Base Layers/Soils/UCRB_30m/claytotal_r_5_cm_2D_QRF_bt.tif",
                                                     "G:/Base Layers/Soils/UCRB_30m/claytotal_r_15_cm_2D_QRF_bt.tif",
                                                     "G:/Base Layers/Soils/UCRB_30m/claytotal_r_30_cm_2D_QRF_bt.tif"),
                                            sand = c("G:/Base Layers/Soils/UCRB_30m/sandtotal_r_0_cm_2D_QRF.tif",
                                                     "G:/Base Layers/Soils/UCRB_30m/sandtotal_r_5_cm_2D_QRF.tif",
                                                     "G:/Base Layers/Soils/UCRB_30m/sandtotal_r_15_cm_2D_QRF.tif",
                                                     "G:/Base Layers/Soils/UCRB_30m/sandtotal_r_30_cm_2D_QRF.tif"),
                                            fragments = c("G:/Base Layers/Soils/UCRB_30m/fragvol_r_0_cm_2D_QRF_bt_ART_SG100covs_bt.tif",
                                                          "G:/Base Layers/Soils/UCRB_30m/fragvol_r_5_cm_2D_QRF_bt_ART_SG100covs_bt.tif",
                                                          "G:/Base Layers/Soils/UCRB_30m/fragvol_r_15_cm_2D_QRF_bt_ART_SG100covs_bt.tif",
                                                          "G:/Base Layers/Soils/UCRB_30m/fragvol_r_30_cm_2D_QRF_bt_ART_SG100covs_bt.tif"),
                                            ec = c("G:/Base Layers/Soils/UCRB_30m/ec_r_0_cm_2D_QRF_bt.tif",
                                                   "G:/Base Layers/Soils/UCRB_30m/ec_r_5_cm_2D_QRF_bt.tif",
                                                   "G:/Base Layers/Soils/UCRB_30m/ec_r_15_cm_2D_QRF_bt.tif",
                                                   "G:/Base Layers/Soils/UCRB_30m/ec_r_30_cm_2D_QRF_bt.tif"),
                                            depthclass = "G:/Base Layers/Soils/UCRB_30m/DepthClass_ensemble.tif"
                        ),
                        sgu_probability_raster = "V:/PROJECTS/ANNA_KNIGHT/ESG/Maps/UCRB_SGUs_ProbMax/UCRB_SGUs_ProbMax.tif"
  )

  if(user=="Anna"){
    file_list <- network_files
    # update paths specific to your computer here
    file_list$plotnet_processed <- "C:/Users/aknight/Documents/Telework_Backups/V_drive/SWDesertRangelandMonitoring/Data/ProcessedData"
    file_list$ESG_map <- "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/ESG/Maps/Eco_Site_Group_Data/ESGs_final.tif"
    file_list$target_ESG_map_folder <- "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/ESG/Maps/Eco_Site_Group_Data"
    file_list$species_list <- "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/ESG/Maps/Eco_Site_Group_Data/SpeciesList_PlotNet_compiled_2021-11-01.csv"
    file_list$apriori_stms <- "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/ESG/STM/ESD_STMs/outputs/state_STM_summary_by_ESG_SandyLoamyRecombined.csv"
    file_list$plotnet_splist_location <- "C:/Users/aknight/Documents/Telework_Backups/V_drive/SWDesertRangelandMonitoring/Data"
    #file_list$aimlmf_splist <- "C:/Users/aknight/Documents/Telework_Backups/V_drive/SWDesertRangelandMonitoring/Data/ProcessedData/AIM/PlotNet_style_calcs_AIMLMF_all/SpeciesList_AIMLMF_20231201.csv"
    file_list$aimlmf_splist <- "C:/Users/aknight/Documents/Telework_Backups/V_drive/SWDesertRangelandMonitoring/Data/ProcessedData/AIM/Old_AIM_LMF_databases/Terrestrial AIM Data Spring 2020/PlotNet_style_AIMLMF_calcs/SpeciesList_AIM2020UCRBStates.csv"
    file_list$nri <- "C:/Users/aknight/Documents/Telework_Backups/U_drive/Projects/NRI_US_limitaccess/NRI/NRI_USGS_formats/NRI_UCRB/Indicators"
    file_list$aero <- "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/ESG/STM/AERO/AERO_indicators_AIMLMF_20211112.csv"
    file_list$ai_raster <- "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/GIS/Climate/GlobalAIandPET/global-ai_et0/ai_et0/ai_et0_WesternUSEcoregions.tif"
    file_list$prism_rasters <- c("C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/GIS/Climate/PRISM/ppt/PRISM_ppt_30yr_normal_800mM2_annual_asc/PRISM_ppt_30yr_normal_800mM2_annual_asc.asc",
                                 "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/GIS/Climate/PRISM/ppt/PRISM_ppt_30yr_normal_800mM2_monthly_asc/PRISM_ppt_30yr_normal_800mM2_06_asc.asc",
                                 "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/GIS/Climate/PRISM/ppt/PRISM_ppt_30yr_normal_800mM2_monthly_asc/PRISM_ppt_30yr_normal_800mM2_07_asc.asc",
                                 "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/GIS/Climate/PRISM/ppt/PRISM_ppt_30yr_normal_800mM2_monthly_asc/PRISM_ppt_30yr_normal_800mM2_08_asc.asc",
                                 "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/GIS/Climate/PRISM/ppt/PRISM_ppt_30yr_normal_800mM2_monthly_asc/PRISM_ppt_30yr_normal_800mM2_09_asc.asc",
                      "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/GIS/Climate/PRISM/temp/PRISM_tmean_30yr_normal_800mM2_annual_asc/PRISM_tmean_30yr_normal_800mM2_annual_asc.asc",
                      "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/GIS/Climate/PRISM/temp/PRISM_tmax_30yr_normal_800mM2_annual_asc/PRISM_tmax_30yr_normal_800mM2_annual_asc.asc",
                      "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/GIS/Climate/PRISM/temp/PRISM_tmin_30yr_normal_800mM2_annual_asc/PRISM_tmin_30yr_normal_800mM2_annual_asc.asc"
                      )
    file_list$rhem$aim <- "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/ESG/STM/RHEM/Final_5_RHEM_AIM_SoilGrids_NEDslope_21926_09May2022_SubsetNVUTAZCONM_2023-01-31.csv"
    file_list$rhem$lmf <- "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/ESG/STM/RHEM/Final_5_RHEM_LMF_SoilGrids_NEDslope_21926_09May2022_SubsetNVUTAZCONM_2023-01-31.csv"
    file_list$soil_rasters$clay <- gsub(x=file_list$soil_rasters$clay, pattern = "G:/Base Layers/Soils/UCRB_30m", replacement = "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/GIS/Soils")
    file_list$soil_rasters$sand <- gsub(x=file_list$soil_rasters$sand, pattern = "G:/Base Layers/Soils/UCRB_30m", replacement = "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/GIS/Soils")
    file_list$soil_rasters$fragments <- gsub(x=file_list$soil_rasters$fragments, pattern = "G:/Base Layers/Soils/UCRB_30m", replacement = "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/GIS/Soils")
    file_list$soil_rasters$depthclass <- gsub(x=file_list$soil_rasters$depthclass, pattern = "G:/Base Layers/Soils/UCRB_30m", replacement = "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/GIS/Soils")
    file_list$sgu_probability_raster <- "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/ESG/Maps/UCRB_SGUs_ProbMax/UCRB_SGUs_ProbMax.tif"
  }

  if(user=="Duniway_et_al_2024"){
    # This one is an archive of the data used in the STM paper, Duniway et al. 2024
    file_list <- network_files
    file_list$plotnet_processed <- "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/ESG/STM/Data/Plot_data_used_Duniway_et_al_2024/PlotNet/Indicators"
    file_list$ESG_map <- "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/ESG/Maps/Eco_Site_Group_Data/ESGs_final.tif"
    file_list$target_ESG_map_folder <- "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/ESG/Maps/Eco_Site_Group_Data"
    file_list$species_list <- "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/ESG/STM/Data/Plot_data_used_Duniway_et_al_2024/SpeciesLists/SpeciesList_PlotNet_compiled_2021-11-01.csv"
    file_list$apriori_stms <- "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/ESG/STM/Data/Plot_data_used_Duniway_et_al_2024/state_STM_summary_by_ESG_SandyLoamyRecombined.csv"
    file_list$plotnet_splist_location <- "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/ESG/STM/Data/Plot_data_used_Duniway_et_al_2024/PlotNet"
    file_list$aimlmf_splist <- "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/ESG/STM/Data/Plot_data_used_Duniway_et_al_2024/SpeciesLists/SpeciesList_AIM2020UCRBStates.csv"
    file_list$nri <- "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/ESG/STM/Data/Plot_data_used_Duniway_et_al_2024/NRI_do_not_sync"
    file_list$aero <- "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/ESG/STM/Data/Plot_data_used_Duniway_et_al_2024/AERO_indicators_AIMLMF_20211112.csv"
    file_list$ai_raster <- "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/GIS/Climate/GlobalAIandPET/global-ai_et0/ai_et0/ai_et0_WesternUSEcoregions.tif"
    file_list$prism_rasters <- c("C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/GIS/Climate/PRISM/ppt/PRISM_ppt_30yr_normal_800mM2_annual_asc/PRISM_ppt_30yr_normal_800mM2_annual_asc.asc",
                                 "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/GIS/Climate/PRISM/ppt/PRISM_ppt_30yr_normal_800mM2_monthly_asc/PRISM_ppt_30yr_normal_800mM2_06_asc.asc",
                                 "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/GIS/Climate/PRISM/ppt/PRISM_ppt_30yr_normal_800mM2_monthly_asc/PRISM_ppt_30yr_normal_800mM2_07_asc.asc",
                                 "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/GIS/Climate/PRISM/ppt/PRISM_ppt_30yr_normal_800mM2_monthly_asc/PRISM_ppt_30yr_normal_800mM2_08_asc.asc",
                                 "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/GIS/Climate/PRISM/ppt/PRISM_ppt_30yr_normal_800mM2_monthly_asc/PRISM_ppt_30yr_normal_800mM2_09_asc.asc",
                                 "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/GIS/Climate/PRISM/temp/PRISM_tmean_30yr_normal_800mM2_annual_asc/PRISM_tmean_30yr_normal_800mM2_annual_asc.asc",
                                 "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/GIS/Climate/PRISM/temp/PRISM_tmax_30yr_normal_800mM2_annual_asc/PRISM_tmax_30yr_normal_800mM2_annual_asc.asc",
                                 "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/GIS/Climate/PRISM/temp/PRISM_tmin_30yr_normal_800mM2_annual_asc/PRISM_tmin_30yr_normal_800mM2_annual_asc.asc"
    )
    file_list$rhem$aim <- "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/ESG/STM/Data/Plot_data_used_Duniway_et_al_2024/Final_5_RHEM_AIM_SoilGrids_NEDslope_21926_09May2022_SubsetNVUTAZCONM_2023-01-31.csv"
    file_list$rhem$lmf <- "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/ESG/STM/Data/Plot_data_used_Duniway_et_al_2024/Final_5_RHEM_LMF_SoilGrids_NEDslope_21926_09May2022_SubsetNVUTAZCONM_2023-01-31.csv"
    file_list$rhem$nri <- "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/ESG/STM/Data/Plot_data_used_Duniway_et_al_2024/NRI_do_not_sync/RHEM/Final_2_RHEM_NRI_SoilGrids_NEDSlope_32425_09May2022.csv"
    file_list$soil_rasters$clay <- gsub(x=file_list$soil_rasters$clay, pattern = "G:/Base Layers/Soils/UCRB_30m", replacement = "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/GIS/Soils")
    file_list$soil_rasters$sand <- gsub(x=file_list$soil_rasters$sand, pattern = "G:/Base Layers/Soils/UCRB_30m", replacement = "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/GIS/Soils")
    file_list$soil_rasters$fragments <- gsub(x=file_list$soil_rasters$fragments, pattern = "G:/Base Layers/Soils/UCRB_30m", replacement = "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/GIS/Soils")
    file_list$soil_rasters$depthclass <- gsub(x=file_list$soil_rasters$depthclass, pattern = "G:/Base Layers/Soils/UCRB_30m", replacement = "C:/Users/aknight/Documents/Telework_Backups/V_drive/ANNA_KNIGHT/GIS/Soils")
  }

  if(user=="Travis"){
    file_list <- network_files
    # update paths specific to your computer here
    file_list$ESG_map <- "C:/Users/tnauman/OneDrive - DOI/USGS/BLM_projects/BLM_CO_ESGs/ESGs_UCRB/ESG_UCRB_manuscript/datarelease/ESGs_final.tif"
    file_list$prodfolder <- "C:/Users/tnauman/OneDrive - DOI/USGS/BLM_projects/BLM_CO_ESGs/ESGs_UCRB/EDIT_prod"
    file_list$climate <- "C:/Users/tnauman/OneDrive - DOI/USGS/BLM_projects/BLM_CO_ESGs/ESGs_UCRB/shps_SSURGO18"
    file_list$ssurgo <- "C:/models/gSSURGO18/gSSURGO_CONUS.gdb"
    file_list$ssurgo_result_fldr <- "C:/Users/tnauman/OneDrive - DOI/USGS/BLM_projects/BLM_CO_ESGs/ESGs_UCRB/climateOptimize/ssurgo_results"
  }

  if(user=="VPN"){ # if using VPN to connect to the network, don't change any file paths
    file_list <- network_files
  }
  return(file_list)
}