updaten vignette

R/biocol.R

@@ -627,9 +627,10 @@ calc_biocol <- function(
     external_wood_harvest = FALSE,
     grass_scaling = FALSE,
     npp_threshold = 20,
-    grass_harvest_file = "grazing_data.RData",
-    external_fire_file = "human_ignition_fraction.RData",
-    external_wood_harvest_file = "wood_harvest_biomass_sum_1500-2014_67420.RData") {
+    grass_harvest_file = NULL,
+    external_fire_file = NULL,
+    external_wood_harvest_file = NULL) {
+  
   metric_files <- system.file(
     "extdata",
     "metric_files.yml",
@@ -665,6 +666,7 @@ calc_biocol <- function(
     cftfrac = paste0(path_pnv, outputs$cftfrac$name, ".", file_extension),
     fpc = paste0(path_pnv, outputs$fpc$name, ".", file_extension)
   )
+  if (is.null(reference_npp_file)) reference_npp_file <- files_baseline$npp
   files_reference <- list(
     npp = reference_npp_file
   )

scripts/test_all.R

@@ -16,7 +16,6 @@ biocol <- biospheremetrics::calc_biocol(
   start_year = 1500,
   stop_year = 2016,
   reference_npp_time_span = 1510:1539,
-  reference_npp_file = paste0(pnv_folder,"npp.bin.json"),
   read_saved_data = FALSE,
   save_data = FALSE
 )

vignette/biospheremetrics.Rmd

@@ -44,4 +44,21 @@ list_outputs(metric = "ecorisk_nitrogen")
 list_outputs(metric = "ecorisk_nitrogen")
 ```
 
-Note that `starwars` is a tibble, a modern reimagining of the data frame. It's particularly useful for large datasets because it only prints the first few rows. You can learn more about tibbles at <https://tibble.tidyverse.org>; in particular you can convert data frames to tibbles with `as_tibble()`.
+## Demo case
+
+The package contains some demo LPJmL simulation data for two cells. 
+Define the folders for run (simulation with climate change and land-use) and
+pnv (potential natural vegetation - climate change, but no land-use) and a 
+temporary output folder, if you want to test to write to files.
+```{r}
+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 <- paste0(tempdir(),"/")
+```
+## BioCol
+
+```{r}
+```
+```{r}
+```
+## Example use