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create initial values to fill WQ_input.csv's #36

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create initial values to fill WQ_input.csv's #36

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21 changes: 19 additions & 2 deletions R/create_input_tables.R
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Original file line number Diff line number Diff line change
Expand Up @@ -129,9 +129,26 @@ create_input_tables <- function(folder = ".", config_file, folder_out = folder,
}else{
groups <- i
}


file.to.write <- input_table[input_table$module == i, -1]

for(j in groups){
write.csv(input_table[input_table$module == i, -1],

if (any(names(lst_config[[i]]) == 'initial')){
label <- i
key <- names(lst_config[[i]][['initial']])

for (p in key){
idx <- which(file.to.write$subprocess == p)
file.to.write$value[idx] = as.numeric(lst_config[[i]][['initial']][p])

file.to.write$value <- as.double(file.to.write$value)
}

}

file.to.write$value <- as.double(file.to.write$value)
write.csv(file.to.write,
paste0(folder_out, "/", j, ".csv"),
row.names = FALSE)
}
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9 changes: 6 additions & 3 deletions inst/extdata/example_input_files/LakeEnsemblR_WQ.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ config_files:
PCLake: PCLake/parameters.txt
run_settings:
bio-shading: true
ode_method: Euler # Options: Euler, RK2, RK4, Pat1, PatRK2, PatRK4, ModPat1, ModPatRK2, ModPatRK4, ExtModPat1, ExtModPatRK2; default = Euler
ode_method: Euler # Options: Euler, RK2, RK4, Pat1, PatRK2, PatRK4, ModPat1, ModPatRK2, ModPatRK4, ExtModPat1, ExtModPatRK2; default = Euler
split_factor: 1
bottom_everywhere: true
repair_state: true
Expand All @@ -23,6 +23,9 @@ input:
oxygen:
use: true
par_file: oxygen.csv
initial:
initial_oxygen: 300
piston_velocity: 5
carbon:
use: true
par_file: carbon.csv
Expand All @@ -43,7 +46,7 @@ silicon:
par_file: silicon.csv
phytoplankton:
use: true
groups:
groups:
diatoms:
par_file: diatoms.csv
cyanobacteria:
Expand All @@ -55,7 +58,7 @@ zooplankton:
groups:
zooplankton:
par_file: zooplankton.csv
fish:
fish:
use: false
groups:
benthivores:
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