Release 2026.3.1 (#259)

Bug fixes: ChemClass variable was missing as input in two functions, and
Fakelib was not read in correctly in parallel functions
Enhancement: Rescale FRACinf in k_Leaching if inputs are very high

Author: anne-hids

R/fParallel.R

@@ -76,10 +76,29 @@ solveInParallelSteadyState <- function(max_runs_per_slice,
   registerDoParallel(cl)
 
   # Define the worker function for each slice
-  processSlice <- function(i) {
+  processSlice <- function(i, SBooDataLocation) {
     # Load fakelib
     if (!is.null(SBooDataLocation) && !is.na(SBooDataLocation) && SBooDataLocation != "") {
-      source(file.path(SBooDataLocation, "baseScripts/fakeLib.R"))
+      # code take from fakeLib.R in SBooScripts/basescripts
+      library(tidyverse)
+      library(ggdag) #for plotting DAG graphs
+      library(R6)
+      library(rlang)
+      #path to the SBoo package
+      Path2PackageSource <- file.path(SBooDataLocation,"../SBoo")
+      #source all R files and load data from the package
+      Dfiles <- list.files(paste(Path2PackageSource, "data", sep = "/"), pattern = "\\.rda$")
+      Rded <- lapply(Dfiles, function(x) {
+        Dfilename <- paste(Path2PackageSource, "data", x, sep = "/")
+        if (exists("verbose") && verbose) cat(Dfilename, "\n")
+        load(Dfilename, envir = global_env())
+      })
+      Rfiles <- list.files(paste(Path2PackageSource, "R", sep = "/"), pattern = "\\.R$")
+      sourced <- lapply(Rfiles, function(x) {
+        Rfilename <- paste(Path2PackageSource, "R", x, sep = "/")
+        if (exists("verbose") && verbose) cat(Rfilename, "\n")
+        source(Rfilename)
+      })
     } else {
       source("baseScripts/fakeLib.R")}
 
@@ -113,7 +132,7 @@ solveInParallelSteadyState <- function(max_runs_per_slice,
 
   # Execute in parallel using foreach
   combinedResults <- foreach(i = seq_len(nSlices)) %dopar% {
-    processSlice(i)
+    processSlice(i, SBooDataLocation)
   }
 
   # Stop the cluster
@@ -222,10 +241,29 @@ solveInParallelDynamic <- function(max_runs_per_slice,
   cl <- parallel::makeCluster(nCores)
   doParallel::registerDoParallel(cl)
 
-  processSlice <- function(i) {
+  processSlice <- function(i, SBooDataLocation) {
     # Load fakelib
     if (!is.null(SBooDataLocation) && !is.na(SBooDataLocation) && SBooDataLocation != "") {
-      source(file.path(SBooDataLocation, "baseScripts/fakeLib.R"))
+      # code take from fakeLib.R in SBooScripts/basescripts
+      library(tidyverse)
+      library(ggdag) #for plotting DAG graphs
+      library(R6)
+      library(rlang)
+      #path to the SBoo package
+      Path2PackageSource <- file.path(SBooDataLocation,"../SBoo")
+      #source all R files and load data from the package
+      Dfiles <- list.files(paste(Path2PackageSource, "data", sep = "/"), pattern = "\\.rda$")
+      Rded <- lapply(Dfiles, function(x) {
+        Dfilename <- paste(Path2PackageSource, "data", x, sep = "/")
+        if (exists("verbose") && verbose) cat(Dfilename, "\n")
+        load(Dfilename, envir = global_env())
+      })
+      Rfiles <- list.files(paste(Path2PackageSource, "R", sep = "/"), pattern = "\\.R$")
+      sourced <- lapply(Rfiles, function(x) {
+        Rfilename <- paste(Path2PackageSource, "R", x, sep = "/")
+        if (exists("verbose") && verbose) cat(Rfilename, "\n")
+        source(Rfilename)
+      })
     } else {
       source("baseScripts/fakeLib.R")}
 
@@ -266,7 +304,7 @@ solveInParallelDynamic <- function(max_runs_per_slice,
   # browser()
   # Define parallel execution and combine results with `foreach`
   combinedResults <- foreach(i = seq_len(nSlices)) %dopar% {
-    processSlice(i)
+    processSlice(i, SBooDataLocation)
   }
 
   stopCluster(cl)

R/k_Leaching.R

@@ -6,19 +6,23 @@
 #'@param SpeciesName considered species 
 #'@param penetration_depth_s penetration depth for correction factor, based on Hollander et al. (2007) https://doi.org/10.1016/j.envpol.2006.09.018 [m]
 #'@param Kscompw dimensionless partitioning coefficient soil-water [-]
-#'@return Leaching of aggregated (A) or free (S) enp species from natural soil #[s-1]
+#'@description Note: The fraction infiltration (FRACinf) is rescaled to the rest of inflow from rain based on the fraction rain going to runoff (FRACrun). 
+#'@return Leaching rate constant of compound from  soil out of the system (e.g. no deep(er) soil layer considered). [s-1]
 #'@export
-k_Leaching <- function(FRACinf, RAINrate, VertDistance, SpeciesName, 
+k_Leaching <- function(FRACinf,FRACrun, RAINrate, VertDistance, SpeciesName, 
                        penetration_depth_s, Kscompw){ #k_ Leaching
 
   if(SpeciesName %in%  c("Aggregated", "Nanoparticle") ){
     #Correction factor depth dependent soil concentration
     CORRleach <- f_CORRsoil(VertDistance, relevant_depth_s=0.5, penetration_depth_s) 
-    
+    #If due to extreme inputs, FRACinf and FRACrun are both too large, scale FRACinf to mass conserve rain
+    if((FRACinf + FRACrun) > 1) {FRACinf = 1-FRACrun}
     #Leaching of aggregated (A) and free (S) enp species from natural soil [s-1]
     return( (FRACinf * RAINrate * CORRleach) / VertDistance )
   } else if( SpeciesName %in% c("Molecular")) {
-    CORRleach <- f_CORRsoil(VertDistance, relevant_depth_s=0.5, penetration_depth_s=0.1) 
+    CORRleach <- f_CORRsoil(VertDistance, relevant_depth_s=0.5, penetration_depth_s=0.1)
+    #If due to extreme inputs, FRACinf and FRACrun are both too large, scale FRACinf to conserve rain
+    if((FRACinf + FRACrun) > 1) {FRACinf = 1-FRACrun}
     return(FRACinf*RAINrate/Kscompw*CORRleach/VertDistance)
   } else return(NA)
 

R/v_KocAltDorC.R

@@ -9,7 +9,7 @@
 #' @param pKa Dissociation constant of (conjugated) acid (default = 7)
 
 #' @export
-KocAltDorC <- function (Kow, a, b, pKa, KocAlt){
+KocAltDorC <- function (Kow, a, b, pKa, KocAlt, ChemClass){
 
     if (is.na(KocAlt) || KocAlt == "NA") { 
       if (is.na(pKa) || pKa == "NA"){

R/v_KocDorC.R

@@ -8,7 +8,7 @@
 #' @param Koc Organic Carbon partitioning coefficient in
 #' @param pKa Dissociation constant of (conjugated) acid (default = 7)
 #' @export
-KocDorC <- function (Kow, a, b, Koc){
+KocDorC <- function (Kow, a, b, Koc, ChemClass){
 
     if (is.na(Koc) || Koc == "NA") { 
       switch(ChemClass,

R/v_KswDorC.R

@@ -10,7 +10,7 @@
 #' @param pKa Dissociation constant of (conjugated) acid (default = 70
 #' @param Ksw soil water partitioning coefficient in data
 #' @export
-KswDorC <- function (KocDorC, CorgStandard, all.rhoMatrix, Ksw){
+KswDorC <- function (KocDorC, CorgStandard, all.rhoMatrix, Ksw, ChemClass){
   RHOsolid <- all.rhoMatrix$rhoMatrix[all.rhoMatrix$SubCompart == "naturalsoil"]
 
   if (is.na(Ksw) || Ksw == "NA") {