added example scripts/test_all.R - start of for vignette

R/list_outputs.R

@@ -143,8 +143,9 @@ higher_res <- function(x, y) {
 
 # split calculation string for variable addition/subtraction into signs & vars 
 split_sign <- function(string) {
+  print(string)
   # add spaces around +- signs
-  string <- gsub(
+  string <- gsub("-",
     " - ",
     gsub("+", " + ", string, fixed = TRUE),
     fixed = TRUE

inst/extdata/run/lu_1500_2016/pft_npp.bin.json

 {
   "sim_name" : "lu_1500_2016",
-  "source" : "LPJmL C Version 5.7.5",
-  "history" : "/p/projects/open/Fabian/LPJmL_versions/LPJmL57_add_isimip_outputs//bin/lpjml /p/projects/open/Fabian/runs/metrics_double_cell//configurations/config_lu_1500_2016.json",
+  "source" : "LPJmL C Version 5.8.1",
+  "history" : "/p/projects/open/Fabian/LPJmL_versions/LPJmL58//bin/lpjml /p/projects/open/Fabian/runs/metrics_double_cell//configurations/config_lu_1500_2016.json",
   "variable" : "pft_npp",
   "firstcell" : 47459,
   "ncell" : 2,
@@ -34,5 +34,7 @@
   "order" : "cellseq",
   "bigendian" : false,
   "format" : "raw",
+  "grid" : {"filename" : "grid.bin.json", "format" : "meta"},
+  "ref_area" : {"filename" : "terr_area.bin.json", "format" : "meta"},
   "filename" : "pft_npp.bin"
 }

inst/extdata/run/pnv_1500_2016/pft_npp.bin.json

 {
   "sim_name" : "pnv_1500_2016",
-  "source" : "LPJmL C Version 5.7.5",
-  "history" : "/p/projects/open/Fabian/LPJmL_versions/LPJmL57_add_isimip_outputs//bin/lpjml /p/projects/open/Fabian/runs/metrics_double_cell//configurations/config_pnv_1500_2016.json",
+  "source" : "LPJmL C Version 5.8.1",
+  "history" : "/p/projects/open/Fabian/LPJmL_versions/LPJmL58//bin/lpjml /p/projects/open/Fabian/runs/metrics_double_cell//configurations/config_pnv_1500_2016.json",
   "variable" : "pft_npp",
   "firstcell" : 47459,
   "ncell" : 2,
@@ -34,5 +34,7 @@
   "order" : "cellseq",
   "bigendian" : false,
   "format" : "raw",
+  "grid" : {"filename" : "grid.bin.json", "format" : "meta"},
+  "ref_area" : {"filename" : "terr_area.bin.json", "format" : "meta"},
   "filename" : "pft_npp.bin"
 }

scripts/test_all.R

@@ -7,7 +7,7 @@ devtools::load_all("/p/projects/open/Fabian/LPJbox/biospheremetrics_review_paper
 
 run_folder <- paste0(system.file("extdata","run","lu_1500_2016",package = "biospheremetrics"),"/")
 pnv_folder <- paste0(system.file("extdata","run","pnv_1500_2016",package = "biospheremetrics"),"/")
-out_folder <- tempdir()
+out_folder <- paste0(tempdir(),"/")
 
 vars_metrics <- data.frame(
   row.names = c("grid","fpc", "fpc_bft", "cftfrac", "firec", "npp", "runoff",
@@ -38,13 +38,6 @@ vars_metrics <- data.frame(
               "timber_harvestc.bin.json","rootmoist.bin.json")
 )
 
-# read grid
-grid <- read_io(paste0(run_folder, "grid.bin.json"))
-# calculate cell area
-lat <- grid$data[, , 2]
-lon <- grid$data[, , 1]
-cellarea <- calc_cellarea(grid)
-
 ################# calculate BioCol ################
 # 16GB of RAM are enough to calculate BioCol for a smaller analysis window (~40 years)
 # for longer spans (500 years) - use separate script ("read_in_BioCol_data.R") 
@@ -56,7 +49,6 @@ lat <- grid[, , 2]
 lon <- grid[, , 1]
 cellarea <- drop(lpjmlkit::read_io(filename = paste0(run_folder,"terr_area.bin.json"))$data) # in m2
 
-
 paletteNew = c("white",RColorBrewer::brewer.pal(9,"YlOrRd"))
 
 
@@ -69,114 +61,45 @@ biocol <- calc_biocol(
   path_lu = run_folder,
   path_pnv = pnv_folder,
   gridbased = TRUE,
-  start_year = 1980,
+  start_year = 1500,
   stop_year = 2016,
   reference_npp_time_span = 1510:1539,
-  reference_npp_file = "/p/projects/open/Fabian/runs/metrics_202308/output/pnv_1500_2016/npp.bin.json",
+  reference_npp_file = paste0(pnv_folder,"npp.bin.json"),
   read_saved_data = FALSE,
-  save_data = FALSE,
+  save_data = TRUE,
   npp_threshold = 1,
-  data_file = "/p/projects/open/Fabian/Metrics/data/BioCol_202308_1980-2016.RData",
+  data_file = paste0(out_folder, "BioCol_test_202401_1980-2016.RData"),
   external_fire = FALSE,
-  external_wood_harvest = TRUE,
-  external_fire_file = "/p/projects/open/Fabian/LPJbox/human_ignition_fraction.RData",
-  external_wood_harvest_file = "/p/projects/open/LanduseData/LUH2_v2h/wood_harvest_biomass_sum_1500-2016_extended_67420.RData",
+  external_wood_harvest = FALSE,
+  external_fire_file = "",
+  external_wood_harvest_file = "",
   varnames = vars_metrics,
   grass_scaling = FALSE,
   include_fire = FALSE
 )
 
-plot_biocol(
+biospheremetrics::plot_biocol_ts(
   biocol_data = biocol,
-  path_write = paste0(out_folder,"BioCol_test/"),
-  plotyears = c(1980,2014),
+  file = paste0(out_folder,"plots/BioCol_overtime.png"),
+  plot_years = c(1510,2016),
+  first_year = 1510,
   min_val = 0,
-  max_val = 90,
+  max_val = 0.005,
   legendpos = "left",
-  start_year = 1980,
-  mapyear = 2000,
-  highlightyear = 2000,
+  highlight_years = NA,
   eps = FALSE
 )
 
-
-
 ecorisk <- ecorisk_wrapper(
   path_ref = pnv_folder,
   path_scen = run_folder,
   read_saved_data = FALSE,
   nitrogen = TRUE,
-  varnames = vars_ecorisk,
+  varnames = vars_metrics,
   weighting = "equal",
-  save_data = "/p/projects/open/Jannes/tests/metrics/ecorisk_202306_data.RData",
-  save_ecorisk = "/p/projects/open/Jannes/tests/metrics/ecorisk_202306_gamma.RData",
+  save_data = paste0(out_folder, "ecorisk_test_202401_data.RData"),
+  save_ecorisk = paste0(out_folder, "ecorisk_test_202401_gamma.RData"),
   time_span_reference = c(1550:1579),
-  time_span_scenario = c(1985:2014),
+  time_span_scenario = c(1987:2016),
   dimensions_only_local = FALSE
 )
-
-# plot ecorisk
-plot_ecorisk_map(
-  ecorisk$ecorisk_total,
-  file = paste0(out_folder, "EcoRisk/ecorisk.png"),
-  title = "ecorisk"
-)
-
-plot_ecorisk_map(
-  ecorisk$vegetation_structure_change,
-  file = paste0(out_folder, "EcoRisk/vs.png"),
-  title = "vegetation structure change"
-)
-
-plot_ecorisk_map(
-  ecorisk$local_change,
-  file = paste0(out_folder, "EcoRisk/lc.png"),
-  title = "local change"
-)
-
-plot_ecorisk_map(
-  ecorisk$global_importance,
-  file = paste0(out_folder, "EcoRisk/gi.png"),
-  title = "global importance"
-)
-
-plot_ecorisk_map(
-  ecorisk$ecosystem_balance,
-  file = paste0(out_folder, "EcoRisk/eb.png"),
-  title = "ecosystem balance")
-
-plot_ecorisk_map(
-  ecorisk$carbon_stocks,
-  file = paste0(out_folder, "EcoRisk/cs.png"),
-  title = "carbon_stocks"
-)
-
-plot_ecorisk_map(
-  ecorisk$carbon_fluxes,
-  file = paste0(out_folder, "EcoRisk/cf.png"),
-  title = "carbon_fluxes"
-)
-
-plot_ecorisk_map(
-  ecorisk$water_stocks,
-  file = paste0(out_folder, "EcoRisk/ws.png"),
-  title = " water_stocks"
-)
-
-plot_ecorisk_map(
-  ecorisk$water_fluxes,
-  file = paste0(out_folder, "EcoRisk/wf.png"),
-  title = " water_fluxes"
-)
-
-plot_ecorisk_map(
-  ecorisk$nitrogen_stocks,
-  file = paste0(out_folder, "EcoRisk/ns.png"),
-  title = " nitrogen_stocks"
-)
-
-plot_ecorisk_map(
-  ecorisk$nitrogen_fluxes,
-  file = paste0(out_folder, "EcoRisk/nf.png"),
-  title = " nitrogen_fluxes"
-)