add soils file and use soils to all r functions.

DESCRIPTION

@@ -17,7 +17,7 @@ Authors@R:
              family = "Petrasova", 
              role = c("aut"),
              comment = c(ORCID = "0000-0002-5120-5538")))
-Depends: R (>= 3.3.0)
+Depends: R (>= 4.0.0)
 Imports: 
     raster (>= 3.5-15),
     terra (>= 1.5-17),
@@ -26,7 +26,6 @@ Imports:
     foreach,
     parallel,
     doParallel,
-    iterators,
     landscapemetrics,
     lubridate,
     sp,
@@ -41,7 +40,6 @@ URL: http://www.github.com/ncsu-landscape-dynamics/rpops
 Encoding: UTF-8
 LazyData: true
 SystemRequirements: 
-    C++11,
     GNU make
 Suggests: 
     testthat,

R/calibrate.R

@@ -197,7 +197,9 @@ calibrate <- function(infected_years_file,
                       dispersers_to_soils_percentage = 0,
                       quarantine_directions = "",
                       multiple_random_seeds = FALSE,
-                      random_seeds = NULL) {
+                      random_seeds = NULL,
+                      use_soils = FALSE,
+                      soil_starting_pest_file = "") {
 
   # add all data to config list
   config <- c()
@@ -289,7 +291,8 @@ calibrate <- function(infected_years_file,
   config$dispersers_to_soils_percentage <- dispersers_to_soils_percentage
   config$multiple_random_seeds <- multiple_random_seeds
   config$random_seeds <-random_seeds
-
+  config$use_soils <- use_soils
+  config$soil_starting_pest_file <- soil_starting_pest_file
 
   # call configuration function to perform data checks and transform data into
   # format used in pops c++

R/configuration.R

@@ -302,6 +302,28 @@ configuration <- function(config) {
     return(config)
   }
 
+  # check that soils raster has the same crs, resolutin, and extent.
+  if (config$use_soils) {
+    if (config$function_name %in% c("casestudy_creation", "model_api")) {
+      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)
+      }
+      return(config)
+    }
+  } else {
+    config$soil_pests <- zero_matrix
+  }
+
   # check that survival_rates raster has the same crs, resolution, and extent
   if (config$use_survival_rates == TRUE) {
     if (config$function_name %in% c("casestudy_creation", "model_api")) {

R/pops.r

@@ -193,6 +193,8 @@
 #' of dispersers that fall to the soil and survive.
 #' @param soil_starting_pest_file path to the raster file with the starting
 #' amount of pest or pathogen.
+#' @param use_soils boolean to indicate if pests establish in the soil and spread out from there.
+#' Typically used for soil borne pathogens.
 #' @param multiple_random_seeds boolean to indicate if the model should use multiple random seeds
 #' (allows for performing uncertainty partitioning) or a single random seed (backwards
 #' compatibility option). Default is FALSE.
@@ -293,7 +295,9 @@ pops <- function(infected_file,
                  dispersers_to_soils_percentage = 0,
                  quarantine_directions = "",
                  multiple_random_seeds = FALSE,
-                 random_seeds = NULL) {
+                 random_seeds = NULL,
+                 use_soils = FALSE,
+                 soil_starting_pest_file = "") {
 
   config <- c()
   config$random_seed <- random_seed
@@ -378,6 +382,8 @@ pops <- function(infected_file,
   config$dispersers_to_soils_percentage <- dispersers_to_soils_percentage
   config$multiple_random_seeds <- multiple_random_seeds
   config$random_seeds <-random_seeds
+  config$use_soils <- use_soils
+  config$soil_starting_pest_file <- soil_starting_pest_file
 
   config <- configuration(config)
 

R/pops_multirun.R

@@ -106,7 +106,9 @@ pops_multirun <- function(infected_file,
                           dispersers_to_soils_percentage = 0,
                           quarantine_directions = "",
                           multiple_random_seeds = FALSE,
-                          random_seeds = NULL) {
+                          random_seeds = NULL,
+                          use_soils = FALSE,
+                          soil_starting_pest_file = "") {
   config <- c()
   config$random_seed <- random_seed
   config$infected_file <- infected_file
@@ -188,6 +190,8 @@ pops_multirun <- function(infected_file,
   config$dispersers_to_soils_percentage <- dispersers_to_soils_percentage
   config$multiple_random_seeds <- multiple_random_seeds
   config$random_seeds <-random_seeds
+  config$use_soils <- use_soils
+  config$soil_starting_pest_file <- soil_starting_pest_file
 
   config <- configuration(config)
 
@@ -196,8 +200,8 @@ pops_multirun <- function(infected_file,
   }
 
   config$crs <- terra::crs(config$host)
-  # i <- NULL
 
+  i <- NULL
   cl <- parallel::makeCluster(config$core_count)
   doParallel::registerDoParallel(cl)
 

R/validate.R

@@ -122,7 +122,9 @@ validate <- function(infected_years_file,
                      dispersers_to_soils_percentage = 0,
                      quarantine_directions = "",
                      multiple_random_seeds = FALSE,
-                     random_seeds = NULL) {
+                     random_seeds = NULL,
+                     use_soils = FALSE,
+                     soil_starting_pest_file = "") {
   config <- c()
   config$infected_years_file <- infected_years_file
   config$infected_file <- infected_file
@@ -207,6 +209,8 @@ validate <- function(infected_years_file,
   config$dispersers_to_soils_percentage <- dispersers_to_soils_percentage
   config$multiple_random_seeds <- multiple_random_seeds
   config$random_seeds <-random_seeds
+  config$use_soils <- use_soils
+  config$soil_starting_pest_file <- soil_starting_pest_file
 
   config <- configuration(config)