Groundwork luluc (Biomee)

.github/workflows/test-coverage.yaml

@@ -45,7 +45,7 @@ jobs:
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

NEWS.md

@@ -2,8 +2,12 @@
 
 * new BiomeE behavior to recycle last year of forcing if requested simulation time span (`nyeartrend`) is longer than 
 available forcing data
-* Breaking change: biomee drivers' `init_cohort$init_n_cohorts` column has been phased out and must not be present in  
+* Breaking changes in biomee drivers
+  * `init_cohort$init_n_cohorts` column has been phased out and must not be present in  
 drivers to protect against data corruption.
+  * `update_annualLAImax` flag was removed and the behavior is now slightly altered since `LAImax` and `underLAImax` are set and kept constant at the start of the simulation:
+    * `LAImax` takes value `max(LAI_light, 0.5)`
+    * `underLAImax` takes value `min(LAImax, 1.2)`
 
 # rsofun v5.0.0
 

R/cost_likelihood_biomee.R

@@ -50,7 +50,7 @@ cost_likelihood_biomee <- function(
 ){
 
   # predefine variables for CRAN check compliance
-  GPP <- LAI <- Density12 <- plantC <- error <- NULL
+  GPP <- LAI <- Density12 <- plantC <- NULL
 
   # Add changed model parameters to drivers, overwriting where necessary.
   drivers$params_species[[1]]$phiRL[]  <- par[1]
@@ -65,21 +65,9 @@ cost_likelihood_biomee <- function(
     parallel = FALSE
   )
 
-  # did we spin up
-  spin_up <- drivers$params_siml[[1]]$spinup
-
-  # drop spinup years if activated
-  # see below
-  if (spin_up){
-    spin_up_years <- drivers$params_siml[[1]]$spinupyears + 1
-  } else {
-    spin_up_years <- 0
-  }
-
-  # Aggregate variables from the model df taking the last 500 yrs
-  # if spun up
+  # Aggregate variables from the model df taking the last 50 yrs (up to)
   df <- df$data[[1]]$output_annual_tile |>
-    utils::tail(500 - spin_up_years) |>
+    utils::tail(50) |>
     dplyr::summarise(
       GPP = mean(GPP),
       LAI = stats::quantile(LAI, probs = 0.95, na.rm=TRUE),

R/data.R

@@ -190,16 +190,14 @@
 #'   \item{params_siml}{Simulation parameters as a data.frame, including
 #'   the following data:
 #'     \describe{
-#'       \item{spinup}{Flag indicating whether this simulation does spin-up.}
-#'       \item{spinupyears}{Number of spin-up years.}
+#'       \item{spinup}{Flag indicating whether this simulation does spin-up (deprecated).}
+#'       \item{spinupyears}{Number of spin-up years. Set to 0 for no spinup.}
 #'       \item{recycle}{Number of first N years of forcing data.frame that are recycled for spin-up.}
 #'       \item{firstyeartrend}{Year of first transient year (AD) (optional). Is only used to set years in output data frames. Defaults to 0 if not provided.}
 #'       \item{nyeartrend}{Number of transient years (optional). Determines the length of simulation output after spin-up. Defaults to number of years contained in the forcing data. (If longer than forcing data, last year of forcing is repeated until the end (spin-down).)}
 #'       \item{steps_per_day}{Time resolution of the forcing (day-1).}
 #'       \item{do_U_shaped_mortality}{Flag indicating whether U-shaped
 #'         mortality is used.}
-#'       \item{update_annualLAImax}{Flag indicating whether updating
-#'         LAImax according to mineral N in soil.}
 #'       \item{do_closedN_run}{Flag indicating whether doing N closed
 #'         runs to recover N balance enforcing 0.2 kg N m-2 in the inorganic N pool.}
 #'       \item{code_method_photosynth}{String specifying the method of photosynthesis
@@ -285,7 +283,7 @@
 #'       \item{betaOFF}{Critical soil moisture for phenology offset.}
 #'       \item{seedlingsize}{Initial size of seedlings, in kg C per individual.}
 #'       \item{LNbase}{Basal leaf N per unit area, in kg N m\eqn{^{-2}}.}
-#'       \item{lAImax}{Maximum crown LAI (leaf area index).}
+#'       \item{lAImax}{Maximum crown LAI (leaf area index) (not used, see LAI_light).}
 #'       \item{Nfixrate0}{Reference N fixation rate (kg N kg C\eqn{^{-1}} root).}
 #'       \item{NfixCost0}{Carbon cost of N fixation (kg C kg N\eqn{^{-1}}).}
 #'       \item{phiCSA}{Ratio of sapwood area to leaf area.}
@@ -356,16 +354,14 @@
 #' Dataset. https://doi.org/10.18140/FLX/1440134
 "biomee_validation"
 
-#' rsofun BiomeE (P-model) output data
-#'
-#' Example output dataset from a BiomeE-model run (p-model)
-#' See \code{\link{run_biomee_f_bysite}} for a detailed 
-#' description of the outputs.
-"biomee_p_model_output"
-
 #' rsofun BiomeE (gs_leuning) output data
 #'
-#' Example output dataset from a BiomeE-model run (gs_leuning)
-#' See \code{\link{run_biomee_f_bysite}} for a detailed 
-#' description of the outputs.
+#' Example output dataset from a BiomeE-model run using divers \code{\link{biomee_gs_leuning_drivers}}
+#' See \code{\link{run_biomee_f_bysite}} for a detailed description of the outputs.
 "biomee_gs_leuning_output"
+
+#' rsofun BiomeE (P-model) output data
+#'
+#' Example output dataset from a BiomeE-model run using divers \code{\link{biomee_p_model_drivers}}
+#' See \code{\link{run_biomee_f_bysite}} for a detailed description of the outputs.
+"biomee_p_model_output"