From f0d9bb19735ccf2b3dbe66aab8f4a1723380dd5a Mon Sep 17 00:00:00 2001
From: marcadella <mayeul.marcadella@unibe.ch>
Date: Thu, 19 Dec 2024 14:01:28 +0100
Subject: [PATCH] Fix issue with runread_biomee not being able to deal with
 missing columns.

---
 R/run_biomee_f_bysite.R | 10 ++++++----
 R/runread_biomee_f.R    | 23 +++++++++++++++--------
 2 files changed, 21 insertions(+), 12 deletions(-)

diff --git a/R/run_biomee_f_bysite.R b/R/run_biomee_f_bysite.R
index 81d52375..f0045ab5 100644
--- a/R/run_biomee_f_bysite.R
+++ b/R/run_biomee_f_bysite.R
@@ -242,12 +242,12 @@ run_biomee_f_bysite <- function(
     n_annual_trans = as.integer(n_annual_trans)
   )
 
-  out <- build_out(biomeeout, init_lu$name)
+  out <- build_out(biomeeout, init_lu$name, sitename)
 
   return(out)
 }
 
-build_out <- function(biomeeout, lu_names){
+build_out <- function(biomeeout, lu_names, sitename){
   # If simulation is very long, output gets massive.
   # E.g., In a 3000 years-simulation 'biomeeout' is 11.5 GB.
   # In such cases (here, more than 5 GB), ignore hourly and daily outputs at tile and cohort levels
@@ -332,8 +332,10 @@ build_params_siml <- function(params_siml, forcing_years, makecheck){
   `%nin%` <- Negate(`%in%`)
   if ("spinup" %nin% names(params_siml))
     params_siml$spinup <- params_siml$spinupyears > 0
-  else if (params_siml$spinup != (params_siml$spinupyears > 0))
-    warning("Warning: spinup in driver is deprecated. Please set spinupyears to 0 to disable spinup.")
+  else if (params_siml$spinup != (params_siml$spinupyears > 0)) {
+    warning("Warning: spinup flag is deprecated. Please set spinupyears to 0 to disable spinup.")
+    params_siml$spinup <- (params_siml$spinupyears > 0)
+  }
 
   # Default value for nyeartrend
   if ('nyeartrend' %nin% names(params_siml)) {
diff --git a/R/runread_biomee_f.R b/R/runread_biomee_f.R
index 9f7fcb32..5c7bf1c5 100644
--- a/R/runread_biomee_f.R
+++ b/R/runread_biomee_f.R
@@ -43,8 +43,10 @@ runread_biomee_f <- function(
   params_tile <- params_species <- init_cohort <- init_soil <-
   init_lu <- luc_forcing <- . <- NULL
 
-  if (parallel != (ncores > 0))
-    warning("Warning: parallel in driver is deprecated. Please set ncores to 0 to disable parallel execution.")
+  if (parallel != (ncores > 0)) {
+    warning("Warning: parallel flag is deprecated. Please set ncores to 0 to disable parallel execution.")
+    parallel <- (ncores > 0)
+  }
 
   parameters <- c(
     "sitename",
@@ -59,6 +61,14 @@ runread_biomee_f <- function(
     "luc_forcing"
   )
 
+  # Add potentially missing columns using NULL
+  `%nin%` <- Negate(`%in%`)
+  empty_col <- vector("list", nrow(drivers))
+  if ('init_lu' %nin% colnames(drivers))
+    drivers <- dplyr::mutate(drivers, 'init_lu'=empty_col)
+  if ('luc_forcing' %nin% colnames(drivers))
+    drivers <- dplyr::mutate(drivers, 'luc_forcing'=empty_col)
+
   df <- drivers %>%
     dplyr::select(any_of(parameters))
   
@@ -70,8 +80,6 @@ runread_biomee_f <- function(
         packages = c("dplyr", "purrr", "rsofun")
       )
 
-    # TODO: init_lu and luc_forcing are commented out because otherwise an error
-    # is thrown when they are not provided by the user. Needs to be fixed somehow.
     df <- df %>%
       multidplyr::partition(cl) %>%
       dplyr::mutate('data' = purrr::pmap(list(
@@ -82,14 +90,13 @@ runread_biomee_f <- function(
         params_tile,
         params_species,
         init_cohort,
-        init_soil#,
-        #init_lu,
-        #luc_forcing
+        init_soil,
+        init_lu,
+        luc_forcing
       ), run_biomee_f_bysite)) %>%
       dplyr::collect()
     
   } else {
-    
     df <- df %>%
       dplyr::mutate('data' = purrr::pmap(
         .,