Fix 139 (#143)

* added total host to treatments.

* added total_hosts to treatment tests

* lint and typo fixes.

* lint and fix typos

* added total hosts to manage in treatments

* lint and fix total_host to total_hosts in tests

* assigned total hosts in treatment tests in all locations

* added check for total_hosts being treated

* added checks for total_hosts to rest of tests

* remove unnecessary declarations in tests

* lint

* Update README.md

* Update CHANGELOG.md

* made internal variable names more straghtforward

* updated readme

* add missed test of total host update in test on line 87

* lint and add utils to include

* lint

* add new exposed individual in else statement

* match change log to citation in readme

Author: ChrisJones687

CHANGELOG.md

@@ -27,6 +27,7 @@ this repository.
   * requires 2 new parameters mortality_frequency and mortality_frequency_n
 
 ### Changed
+
 - Model class internal attributes and functions are now protected instead of private
   to allow derived classes to access them for greater flexibility.
 - Model class kernels are now created and returned by protected functions.
@@ -38,6 +39,14 @@ this repository.
   * Now moves total_hosts
   * Now moves moratility tracked hosts
   * Adds a new suitable_cell if a movement creates a new location with hosts.
+- Treatments now modify total hosts (Chris Jones)
+- Citation updated to PoPS Frontiers paper (Chris Jones)
+  * Jones, C., Jones, S., Petrasova, A., Petras, V., Gaydos, D., 
+  Skrip, M., Takeuchi, Y., Bigsby, K., and Meentemeyer, R., 2021.
+  Iteratively forecasting biological invasions with PoPS and a little help from 
+  our friends.
+  *Frontiers in Ecology and the Environment* 
+  [DOI: 10.1002/fee.2357](https://doi.org/10.1002/fee.2357)
 
 ## [1.0.2] - 2020-10-09
 

README.md

@@ -20,20 +20,12 @@ required version.
 
 If you use this software or code, please cite the following papers:
 
-* Ross K. Meentemeyer, Nik J. Cunniffe, Alex R. Cook, Joao A. N. Filipe,
-  Richard D. Hunter, David M. Rizzo, and Christopher A. Gilligan, 2011.
-  Epidemiological modeling of invasion in heterogeneous landscapes:
-  spread of sudden oak death in California (1990–2030).
-  *Ecosphere* 2:art17.
-  [DOI: 10.1890/ES10-00192.1](https://doi.org/10.1890/ES10-00192.1)
-
-* Tonini, Francesco, Douglas Shoemaker, Anna Petrasova, Brendan Harmon,
-  Vaclav Petras, Richard C. Cobb, Helena Mitasova,
-  and Ross K. Meentemeyer, 2017.
-  Tangible geospatial modeling for collaborative solutions
-  to invasive species management.
-  *Environmental Modelling & Software* 92: 176-188.
-  [DOI: 10.1016/j.envsoft.2017.02.020](https://doi.org/10.1016/j.envsoft.2017.02.020)
+* Jones, C., Jones, S., Petrasova, A., Petras, V., Gaydos, D., 
+  Skrip, M., Takeuchi, Y., Bigsby, K., and Meentemeyer, R., 2021.
+  Iteratively forecasting biological invasions with PoPS and a little help from 
+  our friends.
+  *Frontiers in Ecology and the Environment* 
+  [DOI: 10.1002/fee.2357](https://doi.org/10.1002/fee.2357)
 
 In case you are using the automatic management feature in rpops or the
 steering version of r.pops.spread (from the branch steering), please

include/pops/model.hpp

@@ -329,7 +329,13 @@ class Model
         // treatments
         if (config_.use_treatments) {
             bool managed = treatments.manage(
-                step, infected, exposed, susceptible, resistant, suitable_cells);
+                step,
+                infected,
+                exposed,
+                susceptible,
+                resistant,
+                total_hosts,
+                suitable_cells);
             if (managed && config_.use_mortality) {
                 // treatments apply to all mortality tracker cohorts
                 for (auto& raster : mortality_tracker) {

include/pops/treatments.hpp

@@ -20,6 +20,7 @@
 #include "raster.hpp"
 #include "date.hpp"
 #include "scheduling.hpp"
+#include "utils.hpp"
 
 #include <map>
 #include <vector>
@@ -87,6 +88,7 @@ class AbstractTreatment
         std::vector<IntegerRaster>& exposed,
         IntegerRaster& susceptible,
         IntegerRaster& resistant,
+        IntegerRaster& total_hosts,
         const std::vector<std::vector<int>>& spatial_indeices) = 0;
     virtual void end_treatment(
         IntegerRaster& susceptible,
@@ -175,29 +177,45 @@ class SimpleTreatment : public BaseTreatment<IntegerRaster, FloatRaster>
         IntegerRaster& infected,
         std::vector<IntegerRaster>& exposed,
         IntegerRaster& susceptible,
-        IntegerRaster&,
+        IntegerRaster& resistant,
+        IntegerRaster& total_hosts,
         const std::vector<std::vector<int>>& suitable_cells) override
     {
         for (auto indices : suitable_cells) {
             int i = indices[0];
             int j = indices[1];
+            int new_exposed_total = 0;
+            int new_infected = 0;
+            int new_susceptible = 0;
+            int new_exposed_individual = 0;
             if (this->application_ == TreatmentApplication::Ratio) {
-                infected(i, j) = infected(i, j) - (infected(i, j) * this->map_(i, j));
+                new_infected = infected(i, j) - (infected(i, j) * this->map_(i, j));
+                infected(i, j) = new_infected;
             }
             else if (this->application_ == TreatmentApplication::AllInfectedInCell) {
-                infected(i, j) = this->map_(i, j) ? 0 : infected(i, j);
+                new_infected = this->map_(i, j) ? 0 : infected(i, j);
+                infected(i, j) = new_infected;
             }
             for (auto& raster : exposed) {
                 if (this->application_ == TreatmentApplication::Ratio) {
-                    raster(i, j) = raster(i, j) - (raster(i, j) * this->map_(i, j));
+                    new_exposed_individual =
+                        raster(i, j) - (raster(i, j) * this->map_(i, j));
+                    raster(i, j) = new_exposed_individual;
+                    new_exposed_total += new_exposed_individual;
                 }
                 else if (
                     this->application_ == TreatmentApplication::AllInfectedInCell) {
-                    raster(i, j) = this->map_(i, j) ? 0 : raster(i, j);
+                    new_exposed_individual =
+                        raster(i, j) - (raster(i, j) * this->map_(i, j));
+                    raster(i, j) = new_exposed_individual;
+                    new_exposed_total += new_exposed_individual;
                 }
             }
-            susceptible(i, j) =
+            new_susceptible =
                 susceptible(i, j) - (susceptible(i, j) * this->map_(i, j));
+            susceptible(i, j) = new_susceptible;
+            total_hosts(i, j) =
+                new_infected + new_susceptible + new_exposed_total + resistant(i, j);
         }
     }
     void end_treatment(
@@ -244,8 +262,10 @@ class PesticideTreatment : public BaseTreatment<IntegerRaster, FloatRaster>
         std::vector<IntegerRaster>& exposed_vector,
         IntegerRaster& susceptible,
         IntegerRaster& resistant,
+        IntegerRaster& total_hosts,
         const std::vector<std::vector<int>>& suitable_cells) override
     {
+        UNUSED(total_hosts);
         for (auto indices : suitable_cells) {
             int i = indices[0];
             int j = indices[1];
@@ -370,13 +390,19 @@ class Treatments
         std::vector<IntegerRaster>& exposed,
         IntegerRaster& susceptible,
         IntegerRaster& resistant,
+        IntegerRaster& total_hosts,
         const std::vector<std::vector<int>>& suitable_cells)
     {
         bool changed = false;
         for (unsigned i = 0; i < treatments.size(); i++) {
             if (treatments[i]->should_start(current)) {
                 treatments[i]->apply_treatment(
-                    infected, exposed, susceptible, resistant, suitable_cells);
+                    infected,
+                    exposed,
+                    susceptible,
+                    resistant,
+                    total_hosts,
+                    suitable_cells);
                 changed = true;
             }
             else if (treatments[i]->should_end(current)) {