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Use rounding for treatments #203

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Use rounding for treatments #203

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1938892
Use rounding for treatments
wenzeslaus Nov 14, 2024
5f25416
update to latest treatments rounding branch
ChrisJones687 Jan 6, 2025
767ccf6
merge with master
ChrisJones687 Jan 6, 2025
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2 changes: 1 addition & 1 deletion inst/cpp/pops-core
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Submodule pops-core updated 9 files
+3 −2 include/pops/actions.hpp
+6 −5 include/pops/host_pool.hpp
+7 −2 include/pops/network.hpp
+4 −4 include/pops/quarantine.hpp
+18 −25 include/pops/treatments.hpp
+6 −4 tests/test_model.cpp
+1 −9 tests/test_network.cpp
+2 −1 tests/test_overpopulation_movements.cpp
+9 −16 tests/test_treatments.cpp
45 changes: 32 additions & 13 deletions inst/include/host_pool.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -515,6 +515,7 @@ class HostPool : public HostPoolInterface<RasterIndex>
* @brief Completely remove any hosts
*
* Removes hosts completely (as opposed to moving them to another pool).
* If mortality is not active, the *mortality* parameter is ignored.
*
* @param row Row index of the cell
* @param col Column index of the cell
Expand All @@ -523,9 +524,6 @@ class HostPool : public HostPoolInterface<RasterIndex>
* @param infected Number of infected hosts to remove.
* @param mortality Number of infected hosts in each mortality cohort.
*
* @note Counts are doubles, so that handling of floating point values is managed
* here in the same way as in the original treatment code.
*
* @note This does not remove resistant just like the original implementation in
* treatments.
*/
Expand Down Expand Up @@ -556,6 +554,11 @@ class HostPool : public HostPoolInterface<RasterIndex>
// Possibly reuse in the I->S removal.
if (infected <= 0)
return;
if (!mortality_tracker_vector_.size()) {
infected_(row, col) -= infected;
reset_total_host(row, col);
return;
}
if (mortality_tracker_vector_.size() != mortality.size()) {
throw std::invalid_argument(
"mortality is not the same size as the internal mortality tracker ("
Expand All @@ -564,8 +567,8 @@ class HostPool : public HostPoolInterface<RasterIndex>
+ std::to_string(row) + ", " + std::to_string(col) + ")");
}

double mortality_total = 0;
for (size_t i = 0; i < mortality.size(); ++i) {
int mortality_total = 0;
for (size_t i = 0; i < mortality_tracker_vector_.size(); ++i) {
if (mortality_tracker_vector_[i](row, col) < mortality[i]) {
throw std::invalid_argument(
"Mortality value [" + std::to_string(i) + "] is too high ("
Expand All @@ -582,20 +585,20 @@ class HostPool : public HostPoolInterface<RasterIndex>
// and once we don't need to keep the exact same double to int results for
// tests. First condition always fails the tests. The second one may potentially
// fail.
if (false && infected != mortality_total) {
if (infected != mortality_total) {
throw std::invalid_argument(
"Total of removed mortality values differs from removed infected "
"count ("
+ std::to_string(mortality_total) + " != " + std::to_string(infected)
+ " for cell (" + std::to_string(row) + ", " + std::to_string(col)
+ ") for cell (" + std::to_string(row) + ", " + std::to_string(col)
+ ")");
}
if (false && infected_(row, col) < mortality_total) {
if (infected_(row, col) < mortality_total) {
throw std::invalid_argument(
"Total of removed mortality values is higher than current number "
"of infected hosts for cell ("
+ std::to_string(row) + ", " + std::to_string(col) + ") is too high ("
"of infected hosts ("
+ std::to_string(mortality_total) + " > " + std::to_string(infected)
+ ") for cell (" + std::to_string(row) + ", " + std::to_string(col)
+ ")");
}
infected_(row, col) -= infected;
Expand Down Expand Up @@ -700,6 +703,8 @@ class HostPool : public HostPoolInterface<RasterIndex>
/**
* @brief Make hosts resistant in a given cell
*
* If mortality is not active, the *mortality* parameter is ignored.
*
* @param row Row index of the cell
* @param col Column index of the cell
* @param susceptible Number of susceptible hosts to make resistant
Expand Down Expand Up @@ -746,6 +751,12 @@ class HostPool : public HostPoolInterface<RasterIndex>
total_resistant += exposed[i];
}
infected_(row, col) -= infected;
total_resistant += infected;
resistant_(row, col) += total_resistant;
if (!mortality_tracker_vector_.size()) {
reset_total_host(row, col);
return;
}
if (mortality_tracker_vector_.size() != mortality.size()) {
throw std::invalid_argument(
"mortality is not the same size as the internal mortality tracker ("
Expand All @@ -755,7 +766,7 @@ class HostPool : public HostPoolInterface<RasterIndex>
}
int mortality_total = 0;
// no simple zip in C++, falling back to indices
for (size_t i = 0; i < mortality.size(); ++i) {
for (size_t i = 0; i < mortality_tracker_vector_.size(); ++i) {
mortality_tracker_vector_[i](row, col) -= mortality[i];
mortality_total += mortality[i];
}
Expand All @@ -771,8 +782,7 @@ class HostPool : public HostPoolInterface<RasterIndex>
+ " for cell (" + std::to_string(row) + ", " + std::to_string(col)
+ "))");
}
total_resistant += infected;
resistant_(row, col) += total_resistant;
reset_total_host(row, col);
}

/**
Expand Down Expand Up @@ -975,6 +985,9 @@ class HostPool : public HostPoolInterface<RasterIndex>
/**
* @brief Get infected hosts in each mortality cohort at a given cell
*
* If mortality is not active, it returns number of all infected individuals
* in the first and only item of the vector.
*
* @param row Row index of the cell
* @param col Column index of the cell
*
Expand All @@ -983,6 +996,12 @@ class HostPool : public HostPoolInterface<RasterIndex>
std::vector<int> mortality_by_group_at(RasterIndex row, RasterIndex col) const
{
std::vector<int> all;

if (!mortality_tracker_vector_.size()) {
all.push_back(infected_at(row, col));
return all;
}

all.reserve(mortality_tracker_vector_.size());
for (const auto& raster : mortality_tracker_vector_)
all.push_back(raster(row, col));
Expand Down
44 changes: 19 additions & 25 deletions inst/include/treatments.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -125,15 +125,15 @@ class BaseTreatment : public AbstractTreatment<HostPool, FloatRaster>
}

// returning double allows identical results with the previous version
double get_treated(int i, int j, int count)
int get_treated(int i, int j, int count)
{
return get_treated(i, j, count, this->application_);
}

double get_treated(int i, int j, int count, TreatmentApplication application)
int get_treated(int i, int j, int count, TreatmentApplication application)
{
if (application == TreatmentApplication::Ratio) {
return count * this->map_(i, j);
return std::lround(count * this->map_(i, j));
}
else if (application == TreatmentApplication::AllInfectedInCell) {
return static_cast<bool>(this->map_(i, j)) ? count : 0;
Expand Down Expand Up @@ -173,20 +173,21 @@ class SimpleTreatment : public BaseTreatment<HostPool, FloatRaster>
for (auto indices : host_pool.suitable_cells()) {
int i = indices[0];
int j = indices[1];
int remove_susceptible = static_cast<int>(std::ceil(this->get_treated(
i, j, host_pool.susceptible_at(i, j), TreatmentApplication::Ratio)));
int remove_infected = static_cast<int>(
std::ceil(this->get_treated(i, j, host_pool.infected_at(i, j))));
int remove_susceptible = this->get_treated(
i, j, host_pool.susceptible_at(i, j), TreatmentApplication::Ratio);
// Treated infected are computed as a sum of treated in mortality groups.
int remove_infected = 0;
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This doesn't remove infected individuals.

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Fails tests and leaves all infected in the cells. The susceptible call above works as it should though.

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This is more complex than I thought yesterday, i.e., it is not a simple oversight. This is an initial value of a sum. The infected ones are computed as a sum of removed individuals from mortality groups (line 184), and then they are passed to HostPool::completely_remove_hosts_at just like before (lines 191-197). The infected is passed as a 5th argument and simply subtracted in that function from the infected raster/matrix.

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ncsu-landscape-dynamics/pops-core#225 now has the update which allows for treatments with no mortality. I added a low level test for that to pops-core.

std::vector<int> remove_mortality;
for (int count : host_pool.mortality_by_group_at(i, j)) {
remove_mortality.push_back(
static_cast<int>(std::ceil(this->get_treated(i, j, count))));
int remove = this->get_treated(i, j, count);
remove_mortality.push_back(remove);
remove_infected += remove;
}
// Will need to use infected directly if not mortality.

std::vector<int> remove_exposed;
for (int count : host_pool.exposed_by_group_at(i, j)) {
remove_exposed.push_back(
static_cast<int>(std::ceil(this->get_treated(i, j, count))));
remove_exposed.push_back(this->get_treated(i, j, count));
}
host_pool.completely_remove_hosts_at(
i,
Expand Down Expand Up @@ -240,26 +241,19 @@ class PesticideTreatment : public BaseTreatment<HostPool, FloatRaster>
for (auto indices : host_pool.suitable_cells()) {
int i = indices[0];
int j = indices[1];
// Given how the original code was written (everything was first converted
// to ints and subtractions happened only afterwards), this needs ints,
// not doubles to pass the r.pops.spread test (unlike the other code which
// did substractions before converting to ints), so the conversion to ints
// happened only later. Now get_treated returns double and floor or ceil is
// applied to the result to get the same results as before.
int susceptible_resistant = static_cast<int>(std::floor(this->get_treated(
i, j, host_pool.susceptible_at(i, j), TreatmentApplication::Ratio)));
int susceptible_resistant = this->get_treated(
i, j, host_pool.susceptible_at(i, j), TreatmentApplication::Ratio);
std::vector<int> resistant_exposed_list;
for (const auto& number : host_pool.exposed_by_group_at(i, j)) {
resistant_exposed_list.push_back(
static_cast<int>(std::floor(this->get_treated(i, j, number))));
resistant_exposed_list.push_back(this->get_treated(i, j, number));
}
int infected = 0;
std::vector<int> resistant_mortality_list;
for (const auto& number : host_pool.mortality_by_group_at(i, j)) {
resistant_mortality_list.push_back(
static_cast<int>(std::floor(this->get_treated(i, j, number))));
int remove = this->get_treated(i, j, number);
resistant_mortality_list.push_back(remove);
infected += remove;
}
int infected = static_cast<int>(
std::floor(this->get_treated(i, j, host_pool.infected_at(i, j))));
host_pool.make_resistant_at(
i,
j,
Expand Down
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