Add in boolean for using data for initial pests/pathogens in soil.

R/calibrate.R

@@ -199,7 +199,8 @@ calibrate <- function(infected_years_file,
                       multiple_random_seeds = FALSE,
                       file_random_seeds = NULL,
                       use_soils = FALSE,
-                      soil_starting_pest_file = "") {
+                      soil_starting_pest_file = "",
+                      start_with_soil_populations = FALSE) {
 
   # add all data to config list
   config <- c()
@@ -293,6 +294,7 @@ calibrate <- function(infected_years_file,
   config$file_random_seeds <- file_random_seeds
   config$use_soils <- use_soils
   config$soil_starting_pest_file <- soil_starting_pest_file
+  config$start_with_soil_populations <- start_with_soil_populations
 
   # call configuration function to perform data checks and transform data into
   # format used in pops c++

R/configuration.R

@@ -194,22 +194,26 @@ configuration <- function(config) {
 
   # check that soils raster has the same crs, resolutin, and extent.
   if (config$use_soils) {
-    if (config$function_name %in% aws_bucket_list) {
-      soils_check <-
-        secondary_raster_checks(
-          config$soil_starting_pest_file, infected, config$use_s3, config$bucket)
-    } else {
-      soils_check <- secondary_raster_checks(config$soil_starting_pest_file, infected)
-    }
-    if (soils_check$checks_passed) {
-      soil_pests <- soils_check$raster
-      config$soil_pests <- terra::as.matrix(soil_pests, wide = TRUE)
-    } else {
-      config$failure <- soils_check$failed_check
-      if (config$failure == file_exists_error) {
-        config$failure <- detailed_file_exists_error(config$soil_starting_pest_file)
+    if (config$start_with_soil_populations) {
+      if (config$function_name %in% aws_bucket_list) {
+        soils_check <-
+          secondary_raster_checks(
+            config$soil_starting_pest_file, infected, config$use_s3, config$bucket)
+      } else {
+        soils_check <- secondary_raster_checks(config$soil_starting_pest_file, infected)
       }
-      return(config)
+      if (soils_check$checks_passed) {
+        soil_pests <- soils_check$raster
+        config$soil_pests <- terra::as.matrix(soil_pests, wide = TRUE)
+      } else {
+        config$failure <- soils_check$failed_check
+        if (config$failure == file_exists_error) {
+          config$failure <- detailed_file_exists_error(config$soil_starting_pest_file)
+        }
+        return(config)
+      }
+    } else {
+      config$soil_pests <- zero_matrix
     }
   } else {
     config$soil_pests <- zero_matrix

R/pops_multirun.R

@@ -108,7 +108,8 @@ pops_multirun <- function(infected_file,
                           multiple_random_seeds = FALSE,
                           file_random_seeds = NULL,
                           use_soils = FALSE,
-                          soil_starting_pest_file = "") {
+                          soil_starting_pest_file = "",
+                          start_with_soil_populations = FALSE) {
   config <- c()
   config$random_seed <- random_seed
   config$infected_file <- infected_file
@@ -192,6 +193,7 @@ pops_multirun <- function(infected_file,
   config$file_random_seeds <- file_random_seeds
   config$use_soils <- use_soils
   config$soil_starting_pest_file <- soil_starting_pest_file
+  config$start_with_soil_populations <- start_with_soil_populations
 
   config <- configuration(config)
 

R/validate.R

@@ -124,7 +124,8 @@ validate <- function(infected_years_file,
                      multiple_random_seeds = FALSE,
                      file_random_seeds = NULL,
                      use_soils = FALSE,
-                     soil_starting_pest_file = "") {
+                     soil_starting_pest_file = "",
+                     start_with_soil_populations = FALSE) {
   config <- c()
   config$infected_years_file <- infected_years_file
   config$infected_file <- infected_file
@@ -211,6 +212,7 @@ validate <- function(infected_years_file,
   config$file_random_seeds <- file_random_seeds
   config$use_soils <- use_soils
   config$soil_starting_pest_file <- soil_starting_pest_file
+  config$start_with_soil_populations <- start_with_soil_populations
 
   config <- configuration(config)