From 7f565f0ea97febdda52bd158e75749f09c428c93 Mon Sep 17 00:00:00 2001
From: cyborginhas <67606742+cyborginhas@users.noreply.github.com>
Date: Mon, 12 Feb 2024 12:30:28 -0500
Subject: [PATCH] Updated pest_host_table_list to include susceptibility and
 mortality rate means and sd (#197)

* added in random seeds

* Update scripts to consider pest_host_table with susceptibility and mortality rate means and sd rather than mean only

* fixed typo

* fixed tests

---------

Co-authored-by: Chris Jones <cjones1688@gmail.com>
---
 R/calibrate.R                                 |  1 +
 R/checks.R                                    | 43 ++++++++++++-------
 R/configuration.R                             |  4 +-
 R/error_messages.R                            | 21 ++++++---
 R/helpers.R                                   | 42 ++++++++++++++++--
 R/lists.R                                     |  4 +-
 R/pops.r                                      | 11 +++--
 R/pops_multirun.R                             |  1 +
 R/validate.R                                  |  1 +
 inst/extdata/competency_table_2host.csv       |  4 +-
 inst/extdata/competency_table_multihost.csv   |  4 +-
 inst/extdata/competency_table_singlehost.csv  |  4 +-
 inst/extdata/pest_host_table.csv              |  8 ++--
 inst/extdata/pest_host_table_2host.csv        |  6 +--
 inst/extdata/pest_host_table_singlehost.csv   |  4 +-
 .../pest_host_table_singlehost010tl1.csv      |  4 +-
 .../extdata/pest_host_table_singlehost025.csv |  4 +-
 .../pest_host_table_singlehost025tl3.csv      |  4 +-
 .../pest_host_table_singlehost_nomort.csv     |  4 +-
 renv.lock                                     |  2 +-
 tests/testthat/test-pops.r                    | 43 +++++++++++--------
 21 files changed, 145 insertions(+), 74 deletions(-)

diff --git a/R/calibrate.R b/R/calibrate.R
index ee6cf2ff..66f45477 100644
--- a/R/calibrate.R
+++ b/R/calibrate.R
@@ -331,6 +331,7 @@ calibrate <- function(infected_years_file,
         config <- host_pool_setup(config)
       }
       config$competency_table_list <- competency_table_list_creator(config$competency_table)
+      config$pest_host_table_list <- pest_host_table_list_creator(config$pest_host_table)
 
       data <- pops_model(
         random_seed = config$random_seed,
diff --git a/R/checks.R b/R/checks.R
index a6a4573b..36fd62db 100644
--- a/R/checks.R
+++ b/R/checks.R
@@ -332,6 +332,14 @@ multihost_checks <-
     failed_check <- competency_value_error
   }
 
+  if (!checks_passed && identical(names(competency_table)
+                                  [(length(names(competency_table)) - 1):
+                                      length(names(competency_table))],
+                                  competency_table_colnames)) {
+    checks_passed <- FALSE
+    failed_check <- competency_table_wrong_columns
+  }
+
   if (!checks_passed && (length(infected_file_list) + 1) <= nrow(competency_table)) {
     checks_passed <- FALSE
     failed_check <- competency_table_row_length_error
@@ -339,32 +347,37 @@ multihost_checks <-
     competency_table_list <- competency_table_list_creator(competency_table)
   }
 
-  if (!checks_passed && length(infected_file_list) != nrow(pest_host_table)) {
+  if (!checks_passed && identical(names(pest_host_table), pest_host_table_colnames)) {
     checks_passed <- FALSE
-    failed_check <- pest_host_table_row_length_error
+    failed_check <- pest_host_table_wrong_columns
   }
 
-  if (!checks_passed && all(pest_host_table$susceptibility >= 0) &&
-      all(pest_host_table$susceptibility <= 1) && all(pest_host_table$mortality_rate >= 0) &&
-      all(pest_host_table$mortality_rate <= 1)) {
+  if (!checks_passed && all(pest_host_table$susceptibility_mean <= 1) &&
+      all(pest_host_table$susceptibility_mean >= 0) &&
+      all(pest_host_table$susceptibility_sd <= 1) &&
+      all(pest_host_table$susceptibility_sd >= 0)) {
     checks_passed <- FALSE
-    failed_check <- pest_host_table_value_error
+    failed_check <- pest_host_susceptbility_value_error
   }
 
-  if (!checks_passed && identical(names(pest_host_table), pest_host_table_list)) {
+  if (!checks_passed && all(pest_host_table$mortality_rate_mean <= 1) &&
+      all(pest_host_table$mortality_rate_mean >= 0) &&
+      all(pest_host_table$mortality_rate_sd <= 1) &&
+      all(pest_host_table$mortality_rate_sd >= 0)) {
     checks_passed <- FALSE
-    failed_check <- pest_host_table_wrong_columns
+    failed_check <- pest_host_mortality_rate_value_error
+  }
+
+  if (!checks_passed && length(infected_file_list) != nrow(pest_host_table)) {
+    checks_passed <- FALSE
+    failed_check <- pest_host_table_row_length_error
   } else {
     host_names <- pest_host_table$host
-    pest_host_table <- pest_host_table[, 2:4]
-    pest_host_table_list <- split(pest_host_table, seq_len(nrow(pest_host_table)))
-    for (i in seq_along(pest_host_table_list)) {
-      pest_host_table_list[[i]] <- unname(pest_host_table_list[[i]])
-      pest_host_table_list[[i]] <- as.vector(t(pest_host_table_list[[i]]))
-    }
+    pest_host_table <- pest_host_table[, -1]
+    pest_host_table_list <- pest_host_table_list_creator(pest_host_table)
   }
 
-  if (any(pest_host_table$mortality_rate > 0)) {
+  if (any(pest_host_table$mortality_rate_mean > 0)) {
     mortality_on <- TRUE
   } else {
     mortality_on <- FALSE
diff --git a/R/configuration.R b/R/configuration.R
index 6f15150f..dcef2490 100644
--- a/R/configuration.R
+++ b/R/configuration.R
@@ -667,11 +667,11 @@ configuration <- function(config) {
 
     mortality_tracker <- list(zero_matrix)
     if (config$mortality_on) {
-      if (config$pest_host_table$mortality_rate[i] <= 0) {
+      if (config$pest_host_table$mortality_rate_mean[i] <= 0) {
         mortality_length <- 1
       } else {
         mortality_length <-
-          1 / config$pest_host_table$mortality_rate[i] +
+          1 / config$pest_host_table$mortality_rate_mean[i] +
           config$pest_host_table$mortality_time_lag[i]
       }
       for (mt in 2:(mortality_length)) {
diff --git a/R/error_messages.R b/R/error_messages.R
index 99febb95..d783d749 100644
--- a/R/error_messages.R
+++ b/R/error_messages.R
@@ -184,18 +184,25 @@ competency_table_row_length_error <-
   "competency_table needs to have at least 1 more row than the number of hosts being modeled which
   is represented by the number of file in the host_file_list"
 
+competency_table_wrong_columns <-
+  "Check column order and headings. The competency table requires a column for each
+  host species, followed by a competency_mean column and competency_sd column"
+
 competency_value_error <-
   "competency_table competency_mean and competency_sd values must be between 0 and 1"
 
-pest_host_table_row_length_error <-
-  "pest_host_table doesn't have the same number of rows as number of files in host_file_list"
-
 pest_host_table_wrong_columns <-
-  "pest_host_table must the 4 columns named and order: host, susceptibility, mortality_rate,
-  mortality_time_lag"
+  "pest_host_table must the 6 columns named and order: host, susceptibility_mean,
+  susceptibility_sd, mortality_rate_mean, mortality_rate_sd, mortality_time_lag"
 
-pest_host_table_value_error <-
-  "pest_host_table susceptiblity and mortality_rate must be between 0 and 1"
+pest_host_susceptbility_value_error <-
+  "pest_host_table susceptiblity_mean and susceptibility_sd values must be between 0 and 1"
+
+pest_host_mortality_rate_value_error <-
+  "pest_host_table mortality_rate_mean and mortality_rate_sd values must be between 0 and 1"
+
+pest_host_table_row_length_error <-
+  "pest_host_table doesn't have the same number of rows as number of files in host_file_list"
 
 multihosts_gt_totpop_error <-
   "All hosts sum to more than the total populations in some cells. Check rasters to ensure that
diff --git a/R/helpers.R b/R/helpers.R
index dc477161..ab0ff1e1 100644
--- a/R/helpers.R
+++ b/R/helpers.R
@@ -271,19 +271,21 @@ combined_sd <- function(v1, v2, m1, m2, n1, n2) {
     (((n1 * n2) * (m1 - m2)^2) / ((n1 + n2) * (n1 + n2 - 1)))
 }
 
+# Reformat competency_table into list (per host composition) with competency values
+# randomly sampled from a normal distribution using mean and sd in competency table
+
 competency_table_list_creator <- function(competency_table) {
   competency_table2 <- competency_table[, 1:(ncol(competency_table) - 1)]
   competencies <-
     rnorm(n = nrow(competency_table), mean = competency_table$competency_mean,
-          sd = competency_table$compentency_sd)
+          sd = competency_table$competency_sd)
   names(competency_table2)[ncol(competency_table2)] <- "competency"
   while (any(competencies > 1) || any(competencies < 0)) {
     competencies <-
       rnorm(n = nrow(competency_table),
-            mean = competency_table$competency_mean, sd = competency_table$compentency_sd)
+            mean = competency_table$competency_mean, sd = competency_table$competency_sd)
   }
   competency_table2$competency <- competencies
-  competency_table2 <- competency_table2
   competency_table_list <- split(competency_table2, seq_len(nrow(competency_table2)))
   for (i in seq_along(competency_table_list)) {
     competency_table_list[[i]] <- unname(competency_table_list[[i]])
@@ -292,6 +294,40 @@ competency_table_list_creator <- function(competency_table) {
   return(competency_table_list)
 }
 
+# Reformat pest_host_table into list (per host species) with susceptibility and
+# mortality rates randomly sampled from a normal distribution using the means and sds i
+# in the pest_host_table
+
+pest_host_table_list_creator <- function(pest_host_table) {
+  pest_host_table2 <- pest_host_table[, !grepl("_sd", colnames(pest_host_table))]
+  susceptibilities <-
+    rnorm(n = nrow(pest_host_table), mean = pest_host_table$susceptibility_mean,
+          sd = pest_host_table$susceptibility_sd)
+  names(pest_host_table2)[1] <- "susceptibility"
+  while (any(susceptibilities > 1) || any(susceptibilities < 0)) {
+    susceptibilities <- rnorm(n = nrow(pest_host_table),
+                              mean = pest_host_table$susceptibility_mean,
+                              sd = pest_host_table$susceptibility_sd)
+  }
+  pest_host_table2$susceptibility <- susceptibilities
+  mortality_rates <-
+    rnorm(n = nrow(pest_host_table), mean = pest_host_table$mortality_rate_mean,
+          sd = pest_host_table$mortality_rate_sd)
+  names(pest_host_table2)[2] <- "mortality_rate"
+  while (any(mortality_rates > 1) || any(mortality_rates < 0)) {
+    mortality_rates <-
+      rnorm(n = nrow(pest_host_table), mean = pest_host_table$mortality_rate_mean,
+            sd = pest_host_table$mortality_rate_sd)
+  }
+  pest_host_table2$mortality_rate <- mortality_rates
+  pest_host_table_list <- split(pest_host_table2, seq_len(nrow(pest_host_table2)))
+  for (i in seq_along(pest_host_table_list)) {
+    pest_host_table_list[[i]] <- unname(pest_host_table_list[[i]])
+    pest_host_table_list[[i]] <- as.vector(t(pest_host_table_list[[i]]))
+  }
+  return(pest_host_table_list)
+}
+
 # Update host pools when uncertainties are used
 host_pool_setup <- function(config) {
   total_infecteds <- config$zero_matrix
diff --git a/R/lists.R b/R/lists.R
index e06e86aa..fbfd9f59 100644
--- a/R/lists.R
+++ b/R/lists.R
@@ -121,4 +121,6 @@ failed_check_list <- c("checks_passed", "failed_check")
 output_frequency_list <-
   c("week", "month", "day", "year", "time_step", "every_n_steps", "final_step")
 csv_list <- c("csv", "txt")
-pest_host_table_list <- c("host", "susceptibility", "mortality_rate", "mortality_time_lag")
+pest_host_table_colnames <- c("host", "susceptibility_mean", "susceptibility_sd",
+                          "mortality_rate_mean", "mortality_rate_sd", "mortality_time_lag")
+competency_table_colnames <- c("competency_mean", "competency_sd")
diff --git a/R/pops.r b/R/pops.r
index 3a7f07b1..c3637d27 100644
--- a/R/pops.r
+++ b/R/pops.r
@@ -187,10 +187,12 @@
 #' @param start_with_soil_populations Boolean to indicate whether to use a starting soil pest or
 #' pathogen population if TRUE then soil_starting_pest_file is required.
 #' @param pest_host_table The file path to a csv that has these columns in this order: host,
-#' susceptibility, mortality rate, and mortality time lag as columns with each row being the
-#' species. Host species must be in the same order in the host_file_list, infected_file_list,
-#' pest_host_table rows, and competency_table columns. The host column is only used for metadata
-#' and labeling output files.
+#' susceptibility_mean, susceptibility_sd, mortality_rate, mortality_rate_mean,
+#' and mortality_time_lag as columns with each row being the species. Host species
+#' must be in the same order in the host_file_list, infected_file_list,
+#' pest_host_table rows, and competency_table columns. The host column is character
+#' string of the species name, and  is only used for metadata  and labeling output files.
+#' Susceptibility and mortality_rate values must be between 0 and 1.
 #' @param competency_table A csv with the hosts as the first n columns (n being the number of hosts)
 #' and the last column being the competency value. Each row is a set of Boolean for host presence
 #' and the competency value (between 0 and 1) for that combination of hosts in a cell.
@@ -382,6 +384,7 @@ pops <- function(infected_file_list,
     config <- host_pool_setup(config)
   }
   config$competency_table_list <- competency_table_list_creator(config$competency_table)
+  config$pest_host_table_list <- pest_host_table_list_creator(config$pest_host_table)
 
   data <- pops_model(random_seed = config$random_seed[1],
                      multiple_random_seeds = config$multiple_random_seeds,
diff --git a/R/pops_multirun.R b/R/pops_multirun.R
index 2eee7256..e87c89ba 100644
--- a/R/pops_multirun.R
+++ b/R/pops_multirun.R
@@ -228,6 +228,7 @@ pops_multirun <- function(infected_file_list,
         config <- host_pool_setup(config)
       }
       config$competency_table_list <- competency_table_list_creator(config$competency_table)
+      config$pest_host_table_list <- pest_host_table_list_creator(config$pest_host_table)
 
       data <- PoPS::pops_model(
         random_seed = config$random_seed[i],
diff --git a/R/validate.R b/R/validate.R
index e10e347b..9f4562be 100644
--- a/R/validate.R
+++ b/R/validate.R
@@ -246,6 +246,7 @@ validate <- function(infected_years_file,
         config <- host_pool_setup(config)
       }
       config$competency_table_list <- competency_table_list_creator(config$competency_table)
+      config$pest_host_table_list <- pest_host_table_list_creator(config$pest_host_table)
 
       data <- pops_model(
         random_seed = config$random_seed[i],
diff --git a/inst/extdata/competency_table_2host.csv b/inst/extdata/competency_table_2host.csv
index 71ea375c..b83db79e 100644
--- a/inst/extdata/competency_table_2host.csv
+++ b/inst/extdata/competency_table_2host.csv
@@ -1,5 +1,5 @@
-oak,tanoak,competency_mean,compentency_sd
+oak,tanoak,competency_mean,competency_sd
 0,0,0,0
 1,0,0,0
 0,1,0.7,0.1
-1,1,0.8,0.05
\ No newline at end of file
+1,1,0.8,0.05
diff --git a/inst/extdata/competency_table_multihost.csv b/inst/extdata/competency_table_multihost.csv
index 16a43fa8..48e0fe46 100644
--- a/inst/extdata/competency_table_multihost.csv
+++ b/inst/extdata/competency_table_multihost.csv
@@ -1,5 +1,5 @@
-oak,tanoak,bay_laurel,competency_mean,compentency_sd
+oak,tanoak,bay_laurel,competency_mean,competency_sd
 0,0,0,0,0
 1,0,0,0,0
 0,1,0,0.7,0.1
-0,0,1,0.8,0.05
\ No newline at end of file
+0,0,1,0.8,0.05
diff --git a/inst/extdata/competency_table_singlehost.csv b/inst/extdata/competency_table_singlehost.csv
index 63951f53..fff6ba12 100644
--- a/inst/extdata/competency_table_singlehost.csv
+++ b/inst/extdata/competency_table_singlehost.csv
@@ -1,3 +1,3 @@
-tanoak,competency_mean,compentency_sd
+tanoak,competency_mean,competency_sd
 0,0,0
-1,1,0.1
\ No newline at end of file
+1,1,0.1
diff --git a/inst/extdata/pest_host_table.csv b/inst/extdata/pest_host_table.csv
index 4d1da095..5533c42a 100644
--- a/inst/extdata/pest_host_table.csv
+++ b/inst/extdata/pest_host_table.csv
@@ -1,4 +1,4 @@
-host,susceptibility,mortality_rate,mortality_time_lag
-oak,0.7,0.1,1
-tanoak,1,0.5,1
-bay laurel,0.5,0,0
\ No newline at end of file
+host,susceptibility_mean,susceptibility_sd,mortality_rate_mean,mortality_rate_sd,mortality_time_lag
+oak,0.7,0.1,0.1,0.02,1
+tanoak,1,0.05,0.5,0.1,1
+bay laurel,0.5,0.06,0,0,0
diff --git a/inst/extdata/pest_host_table_2host.csv b/inst/extdata/pest_host_table_2host.csv
index 843aa802..5b181c15 100644
--- a/inst/extdata/pest_host_table_2host.csv
+++ b/inst/extdata/pest_host_table_2host.csv
@@ -1,3 +1,3 @@
-host,susceptibility,mortality_rate,mortality_time_lag
-oak,0.7,0.1,1
-tanoak,1,0.5,1
\ No newline at end of file
+host,susceptibility_mean,susceptibility_sd,mortality_rate_mean,mortality_rate_sd,mortality_time_lag
+oak,0.7,0.1,0.1,0.02,1
+tanoak,1,0.05,0.5,0.1,1
diff --git a/inst/extdata/pest_host_table_singlehost.csv b/inst/extdata/pest_host_table_singlehost.csv
index c121dc6e..ae932a31 100644
--- a/inst/extdata/pest_host_table_singlehost.csv
+++ b/inst/extdata/pest_host_table_singlehost.csv
@@ -1,2 +1,2 @@
-host,susceptibility,mortality_rate,mortality_time_lag
-oak,0.7,0.5,1
\ No newline at end of file
+host,susceptibility_mean,susceptibility_sd,mortality_rate_mean,mortality_rate_sd,mortality_time_lag
+oak,0.7,0.1,0.5,0.02,1
diff --git a/inst/extdata/pest_host_table_singlehost010tl1.csv b/inst/extdata/pest_host_table_singlehost010tl1.csv
index bbf4ef49..e24ce41b 100644
--- a/inst/extdata/pest_host_table_singlehost010tl1.csv
+++ b/inst/extdata/pest_host_table_singlehost010tl1.csv
@@ -1,2 +1,2 @@
-host,susceptibility,mortality_rate,mortality_time_lag
-oak,0.7,0.1,1
\ No newline at end of file
+host,susceptibility_mean,susceptibility_sd,mortality_rate_mean,mortality_rate_sd,mortality_time_lag
+oak,0.7,0.1,0.1,0.02,1
diff --git a/inst/extdata/pest_host_table_singlehost025.csv b/inst/extdata/pest_host_table_singlehost025.csv
index f76d0695..1067afed 100644
--- a/inst/extdata/pest_host_table_singlehost025.csv
+++ b/inst/extdata/pest_host_table_singlehost025.csv
@@ -1,2 +1,2 @@
-host,susceptibility,mortality_rate,mortality_time_lag
-oak,0.7,0.25,1
\ No newline at end of file
+host,susceptibility_mean,susceptibility_sd,mortality_rate_mean,mortality_rate_sd,mortality_time_lag
+oak,0.7,0.1,0.25,0.02,1
diff --git a/inst/extdata/pest_host_table_singlehost025tl3.csv b/inst/extdata/pest_host_table_singlehost025tl3.csv
index 1361dfa8..586801e2 100644
--- a/inst/extdata/pest_host_table_singlehost025tl3.csv
+++ b/inst/extdata/pest_host_table_singlehost025tl3.csv
@@ -1,2 +1,2 @@
-host,susceptibility,mortality_rate,mortality_time_lag
-oak,0.7,0.25,3
\ No newline at end of file
+host,susceptibility_mean,susceptibility_sd,mortality_rate_mean,mortality_rate_sd,mortality_time_lag
+oak,0.7,0.1,0.25,0.02,3
diff --git a/inst/extdata/pest_host_table_singlehost_nomort.csv b/inst/extdata/pest_host_table_singlehost_nomort.csv
index 94a94f9c..57283fa0 100644
--- a/inst/extdata/pest_host_table_singlehost_nomort.csv
+++ b/inst/extdata/pest_host_table_singlehost_nomort.csv
@@ -1,2 +1,2 @@
-host,susceptibility,mortality_rate,mortality_time_lag
-oak,0.7,0,1
\ No newline at end of file
+host,susceptibility_mean,susceptibility_sd,mortality_rate_mean,mortality_rate_sd,mortality_time_lag
+oak,0.7,0.1,0,0,1
diff --git a/renv.lock b/renv.lock
index b6472fbf..90fbf762 100644
--- a/renv.lock
+++ b/renv.lock
@@ -94,7 +94,7 @@
     },
     "XML": {
       "Package": "XML",
-      "Version": "3.99-0.14",
+      "Version": "3.99-0.16.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
diff --git a/tests/testthat/test-pops.r b/tests/testthat/test-pops.r
index 14b324af..bb56f4ee 100644
--- a/tests/testthat/test-pops.r
+++ b/tests/testthat/test-pops.r
@@ -1361,7 +1361,7 @@ test_that("All kernel types lead to spread", {
   start_date <- "2008-01-01"
   end_date <- "2008-12-31"
   time_step <- "month"
-  parameter_means <- c(3.0, 21, 1, 500, 0, 0, 0, 0)
+  parameter_means <- c(4.0, 21, 1, 500, 0, 0, 0, 0)
   parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
   pest_host_table <-
     system.file("extdata", "pest_host_table_singlehost_nomort.csv", package = "PoPS")
@@ -3539,6 +3539,7 @@ test_that("Using multiple hosts works as expected", {
          start_date = start_date,
          end_date = end_date,
          temp = TRUE,
+         random_seed = 42,
          temperature_coefficient_file = coefficient_file)
 
   test_mat <- terra::as.matrix(terra::rast(infected_file_list[1]), wide = TRUE)
@@ -3547,10 +3548,14 @@ test_that("Using multiple hosts works as expected", {
   expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
   expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
   test_mat <- terra::as.matrix(terra::rast(infected_file_list[2]), wide = TRUE)
-  expect_gte(data$host_pools[[2]]$infected[[1]][[1]], test_mat[[1]])
-  expect_gte(data$host_pools[[2]]$infected[[1]][[2]], test_mat[[2]])
-  expect_gte(data$host_pools[[2]]$infected[[1]][[3]], test_mat[[3]])
-  expect_gte(data$host_pools[[2]]$infected[[1]][[4]], test_mat[[4]])
+  expect_gte(data$host_pools[[2]]$infected[[1]][[1]] + data$host_pools[[2]]$infected[[1]][[1]],
+             test_mat[[1]])
+  expect_gte(data$host_pools[[2]]$infected[[1]][[2]] + data$host_pools[[2]]$infected[[1]][[2]],
+             test_mat[[2]])
+  expect_gte(data$host_pools[[2]]$infected[[1]][[3]] + data$host_pools[[2]]$infected[[1]][[3]],
+             test_mat[[3]])
+  expect_gte(data$host_pools[[2]]$infected[[1]][[4]] + data$host_pools[[2]]$infected[[1]][[4]],
+             test_mat[[4]])
 
   infected_file_list <-
     c(system.file("extdata", "simple2x2", "infected_oak.tif", package = "PoPS"),
@@ -3583,6 +3588,7 @@ test_that("Using multiple hosts works as expected", {
          start_date = start_date,
          end_date = end_date,
          temp = TRUE,
+         random_seed = 42,
          temperature_coefficient_file = coefficient_file)
 
   test_mat <- terra::as.matrix(terra::rast(infected_file_list[1]), wide = TRUE)
@@ -3626,6 +3632,7 @@ test_that("Using multiple hosts works as expected", {
          start_date = start_date,
          end_date = end_date,
          temp = TRUE,
+         random_seed = 42,
          temperature_coefficient_file = coefficient_file)
 
   test_mat <- terra::as.matrix(terra::rast(infected_file_list[1]), wide = TRUE)
@@ -3654,10 +3661,8 @@ test_that("Using multiple hosts with uncertainty works as expected", {
     system.file("extdata", "simple2x2", "total_plants.tif", package = "PoPS")
   start_date <- "2008-01-01"
   end_date <- "2009-12-31"
-  parameter_means <- c(5, 21, 1, 500, 0, 0, 100, 1000)
+  parameter_means <- c(0, 21, 1, 500, 0, 0, 100, 1000)
   parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
-  coefficient_file <-
-    system.file("extdata", "simple2x2", "coefficient_sd.tif", package = "PoPS")
   pest_host_table <-
     system.file("extdata", "pest_host_table.csv", package = "PoPS")
   competency_table <- system.file("extdata", "competency_table_multihost.csv", package = "PoPS")
@@ -3670,10 +3675,10 @@ test_that("Using multiple hosts with uncertainty works as expected", {
          parameter_cov_matrix = parameter_cov_matrix,
          pest_host_table = pest_host_table,
          competency_table = competency_table,
+         random_seed = 42,
          start_date = start_date,
          end_date = end_date,
-         temp = TRUE,
-         temperature_coefficient_file = coefficient_file)
+         use_host_uncertainty = TRUE)
 
   test_mat <- terra::as.matrix(terra::rast(infected_file_list[1]), wide = TRUE)
   expect_gte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])
@@ -3681,10 +3686,14 @@ test_that("Using multiple hosts with uncertainty works as expected", {
   expect_gte(data$host_pools[[1]]$infected[[1]][[3]], test_mat[[3]])
   expect_gte(data$host_pools[[1]]$infected[[1]][[4]], test_mat[[4]])
   test_mat <- terra::as.matrix(terra::rast(infected_file_list[2]), wide = TRUE)
-  expect_gte(data$host_pools[[2]]$infected[[1]][[1]], test_mat[[1]])
-  expect_gte(data$host_pools[[2]]$infected[[1]][[2]], test_mat[[2]])
-  expect_gte(data$host_pools[[2]]$infected[[1]][[3]], test_mat[[3]])
-  expect_gte(data$host_pools[[2]]$infected[[1]][[4]], test_mat[[4]])
+  expect_gte(data$host_pools[[2]]$infected[[1]][[1]] + data$host_pools[[2]]$infected[[1]][[1]],
+             test_mat[[1]])
+  expect_gte(data$host_pools[[2]]$infected[[1]][[2]] + data$host_pools[[2]]$infected[[1]][[2]],
+             test_mat[[2]])
+  expect_gte(data$host_pools[[2]]$infected[[1]][[3]] + data$host_pools[[2]]$infected[[1]][[3]],
+             test_mat[[3]])
+  expect_gte(data$host_pools[[2]]$infected[[1]][[4]] + data$host_pools[[2]]$infected[[1]][[4]],
+             test_mat[[4]])
 
 
   infected_file_list <-
@@ -3699,8 +3708,6 @@ test_that("Using multiple hosts with uncertainty works as expected", {
   end_date <- "2009-12-31"
   parameter_means <- c(5, 21, 1, 500, 0, 0, 100, 1000)
   parameter_cov_matrix <- matrix(0, nrow = 8, ncol = 8)
-  coefficient_file <-
-    system.file("extdata", "simple2x2", "coefficient_sd.tif", package = "PoPS")
   pest_host_table <-
     system.file("extdata", "pest_host_table_2host.csv", package = "PoPS")
   competency_table <- system.file("extdata", "competency_table_2host.csv", package = "PoPS")
@@ -3715,8 +3722,8 @@ test_that("Using multiple hosts with uncertainty works as expected", {
          competency_table = competency_table,
          start_date = start_date,
          end_date = end_date,
-         temp = TRUE,
-         temperature_coefficient_file = coefficient_file)
+         random_seed = 42,
+         use_host_uncertainty = TRUE)
 
   test_mat <- terra::as.matrix(terra::rast(infected_file_list[1]), wide = TRUE)
   expect_gte(data$host_pools[[1]]$infected[[1]][[1]], test_mat[[1]])