preparing merge with master

.Rbuildignore

 ^.*\.Rproj$
 ^\.Rproj\.user$
+^\.buildlibrary$
+^\.pre-commit-config\.yaml$
+^Makefile$
+^workflow$

R/biospheremetrics-package.R

+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+## usethis namespace: end
+NULL

biospheremetrics.Rproj

@@ -16,3 +16,5 @@ BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
 PackageRoxygenize: rd,collate,namespace,vignette
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes

inst/extdata/metric_files.yml

@@ -265,10 +265,10 @@ file_name:
     nfert_agr: ["nfert_agr"]
     nmanure_agr: ["nmanure_agr"]
     npp: ["npp", "mnpp"]
-    pft_harvestc: ["pft_harvestc"]
+    pft_harvestc: ["pft_harvestc","pft_harvest"]
     pft_lai: ["pft_lai", "mpft_lai"]
     pft_npp: ["pft_npp"]
-    pft_rharvestc: ["pft_rharvestc"]
+    pft_rharvestc: ["pft_rharvestc","pft_rharvest"]
     prec: ["prec","mprec"]
     res_storage: ["res_storage"]
     rivervol: ["rivervol"]

man/biospheremetrics-package.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/biospheremetrics-package.R
+\docType{package}
+\name{biospheremetrics-package}
+\alias{biospheremetrics}
+\alias{biospheremetrics-package}
+\title{biospheremetrics: Biosphere integrity metrics for LPJmL}
+\description{
+Functions to compute Biosphere integrity metrics BioCol and EcoRisk based on output from LPJmL.
+}
+\seealso{
+Useful links:
+\itemize{
+  \item \url{https://github.com/stenzelf/biospheremetrics}
+}
+
+}
+\author{
+\strong{Maintainer}: Fabian Stenzel \email{stenzel@pik-potsdam.de} (\href{https://orcid.org/0000-0002-5109-0048}{ORCID})
+
+Authors:
+\itemize{
+  \item Jannes Breier \email{jannesbr@pik-potsdam.de} (\href{https://orcid.org/0000-0002-9055-6904}{ORCID})
+  \item Johanna Braun \email{jobraun@pik-potsdam.de} (\href{https://orcid.org/0000-0002-8809-1044}{ORCID})
+}
+
+}
+\keyword{internal}

man/calc_biocol.Rd

@@ -23,6 +23,7 @@ calc_biocol(
   grass_harvest_file = NULL,
   external_fire_file = NULL,
   external_wood_harvest_file = NULL,
+  replace_input_file_names = NULL,
   suppressWarnings = TRUE
 )
 }
@@ -81,6 +82,11 @@ fraction c(cell,month,year) since 1500}
 \item{external_wood_harvest_file}{path to R-file containing processed
 timeline of maps for LUH2_v2h woodharvest}
 
+\item{replace_input_file_names}{list with alternative names for output
+identifiers to replace the ones in inst/ext_files/metric_files.yml.
+e.g. list(npp="mnpp") would replace the expected output for npp with
+mnpp followed by the automatically detected file extension (.bin.json)}
+
 \item{suppressWarnings}{suppress warnings when reading files (default: TRUE)}
 }
 \value{

man/ecorisk_wrapper.Rd

@@ -18,6 +18,7 @@ ecorisk_wrapper(
   overtime = FALSE,
   window = 30,
   debug = FALSE,
+  replace_input_file_names = NULL,
   external_variability = FALSE,
   c2vr = NULL,
   suppressWarnings = TRUE
@@ -55,6 +56,11 @@ local change, global change and ecosystem balance (default FALSE)}
 
 \item{debug}{write out all nitrogen state variables (default FALSE)}
 
+\item{replace_input_file_names}{list with alternative names for output
+identifiers to replace the ones in inst/ext_files/metric_files.yml.
+e.g. list(npp="mnpp") would replace the expected output for npp with
+mnpp followed by the automatically detected file extension (.bin.json)}
+
 \item{external_variability}{use externally supplied variability for the
 reference period? experimental! (default: FALSE)}
 

man/read_calc_biocol.Rd

@@ -101,9 +101,10 @@ timeline of maps for LUH2_v2h woodharvest}
 \value{
 list data object containing BioCol and components as arrays: 
         biocol_overtime, biocol_overtime_abs, biocol_overtime_abs_frac_piref, 
-        biocol_overtime_frac_piref, biocol_overtime_frac, 
-        biocol_overtime_abs_frac, npp_harv_overtime, npp_luc_overtime, 
-        npp_act_overtime, npp_pot_overtime, npp_eco_overtime, 
+        biocol_overtime_abs_frac, biocol_overtime_pos,
+        biocol_overtime_pos_frac_piref,biocol_overtime_pos_frac,
+        biocol_overtime_frac_piref, biocol_overtime_frac, npp_harv_overtime, 
+        npp_luc_overtime,npp_act_overtime, npp_pot_overtime,npp_eco_overtime, 
         harvest_grasslands_overtime, harvest_bioenergy_overtime, 
         harvest_cft_overtime, rharvest_cft_overtime, fire_overtime, 
         timber_harvest_overtime, wood_harvest_overtime, biocol, biocol_frac, 

vignettes/biospheremetrics.R

+## ---- include = FALSE---------------------------------------------------------
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+
+## -----------------------------------------------------------------------------
+biospheremetrics::list_outputs(metric = "ecorisk_nitrogen")
+
+## -----------------------------------------------------------------------------
+biospheremetrics::list_outputs(metric = "ecorisk_nitrogen")
+
+## -----------------------------------------------------------------------------
+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(),"/")
+