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refactor: Remove unsupported growthRate for demography. #438

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Merged
b-s-code merged 2 commits into from
Sep 10, 2025
Merged

refactor: Remove unsupported growthRate for demography. #438

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1b014b4
Remove growthRate attribute from <demography>.
b-s-code Sep 5, 2025
8027115
Fix whitespace.
b-s-code Sep 8, 2025
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2 changes: 0 additions & 2 deletions model/Population.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -81,8 +81,6 @@ void Population::update()
{
//NOTE: other parts of code are not set up to handle changing population size. Also
// size is assumed to be the _actual and exact_ population size by other code.
//targetPop is the population size at time t allowing population growth
//int targetPop = (int) (size * exp( AgeStructure::rho * sim::ts1().inSteps() ));
int cumPop = 0;

for (auto it = humans.begin(); it != humans.end();) {
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18 changes: 0 additions & 18 deletions model/PopulationAgeStructure.cpp
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Expand Up @@ -36,12 +36,10 @@ namespace OM {
vector<double> AgeStructure::ageGroupBounds;
vector<double> AgeStructure::ageGroupPercent;

double AgeStructure::initialRho = 0.0;
double AgeStructure::mu0;
double AgeStructure::mu1;
double AgeStructure::alpha0;
double AgeStructure::alpha1;
double AgeStructure::rho;

vector<double> AgeStructure::cumAgeProp;

Expand Down Expand Up @@ -137,14 +135,6 @@ void AgeStructure::estimateRemovalRates( const scnXml::Demography& demography ){
for(size_t i = 0;i < ngroups; i++) {
ageGroupPercent[i] = ageGroupPercent[i] * sumperc;
}
/*
RSS between observed and predicted log percentage of population in age groups
is minimised for values of mu1 and alpha1
calls setDemoParameters to calculate the RSS
*/
if( demography.getGrowthRate().present() ){
initialRho = demography.getGrowthRate().get();
}

/* NOTE: unused --- why?
double tol = 0.00000000001;
Expand All @@ -160,14 +150,6 @@ void AgeStructure::estimateRemovalRates( const scnXml::Demography& demography ){
// Static method used by estimateRemovalRates
double AgeStructure::setDemoParameters (double param1, double param2)
{
rho = initialRho;

rho = rho * (0.01 * sim::yearsPerStep());
if (rho != 0.0)
// Issue: in this case the total population size differs from populationSize,
// however, some code currently uses this as the total population size.
throw util::xml_scenario_error ("Population growth rate provided.");

const double IMR = 0.1;
double M_inf = -log (1 - IMR);

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14 changes: 7 additions & 7 deletions model/PopulationAgeStructure.h
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Expand Up @@ -71,19 +71,19 @@ namespace OM
* setDemoParameters()). */
//@{
static vector<double> ageGroupBounds;
static vector<double> ageGroupPercent;
static vector<double> ageGroupPercent;
//@}
static double initialRho;
/** Parameters defining smooth curve of target age-distribution.
*
* Set by estimateRemovalRates() (via setDemoParameters()) and used by
* setupPyramid(). */
//@{
static double mu0;
static double mu1;
static double alpha0;
static double alpha1;
static double rho;
static double mu0;
static double mu1;
static double alpha0;
static double alpha1;
// rho is growth rate of human population.
constexpr static double rho = 0.0;
//@}
//END

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9 changes: 0 additions & 9 deletions schema/demography.xsd
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Expand Up @@ -42,15 +42,6 @@ Licence: GNU General Public Licence version 2 or later (see COPYING) -->
<xs:appinfo>units:Years;min:0;max:100;name:Maximum age of simulated humans;</xs:appinfo>
</xs:annotation>
</xs:attribute>
<xs:attribute name="growthRate" type="xs:double" use="optional">
<xs:annotation>
<xs:documentation>
Growth rate of human population.
(we should be able to implement this with non-zero values)
</xs:documentation>
<xs:appinfo>units:Number;min:0;max:0;name:Growth rate of human population;</xs:appinfo>
</xs:annotation>
</xs:attribute>
</xs:complexType>
<!-- ageGroup -->
<xs:complexType name="DemogAgeGroup">
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