Infections now have an origin type which can be either imported, introduced or indigenous.
The code has been updated to track introduced and indigenous infections separately in the Host, WithinHost and InfectionIncidence model.
The VectorModel has also been updated to track the population of mosquitoes infected from an imported infection and mosquitoes infected from an introduced or indigenous infection separetly.
This pull request adds Imported, Introduced and Indigenous for the following output measures:
nInfect
nPatent
nUncomp
totalInfs
totalPatentInf
SimulatedEIR (only Introduced and Indigenous)
The corresponding new output numbers are defined as follows: Imported: +1000, Introduced: +2000 and Indigenous: +3000
For example nPatent (output measure number 3) can now be tracked as four separate values:
nPatent: 3
nPatent_Imported: 1003
nPatent_Introduced: 2003
nPatent_Indigenous: 3003
Tracking is done by adding the corresponding monitoring options:
<option name="nHost"/> <!-- id 0 -->
<option name="nInfect"/> <!-- id 1 -->
<option name="nInfect_Imported"/> <!-- id 1001 -->
<option name="nInfect_Introduced"/> <!-- id 2001 -->
<option name="nInfect_Indigenous"/> <!-- id 3001 -->
<option name="nPatent"/> <!-- id 3 -->
<option name="nPatent_Imported"/> <!-- id 1003 -->
<option name="nPatent_Introduced"/> <!-- id 2003 -->
<option name="nPatent_Indigenous"/> <!-- id 3003 -->
<option name="totalInfs"/> <!-- id 6 -->
<option name="totalInfs_Imported"/> <!-- id 1006 -->
<option name="totalInfs_Introduced"/> <!-- id 2006 -->
<option name="totalInfs_Indigenous"/> <!-- id 3006 -->
<option name="totalPatentInf"/> <!-- id 8 -->
<option name="totalPatentInf_Imported"/> <!-- id 1008 -->
<option name="totalPatentInf_Introduced"/> <!-- id 2008 -->
<option name="totalPatentInf_Indigenous"/> <!-- id 3008 -->
<option name="nUncomp"/> <!-- id 14 -->
<option name="nUncomp_Imported"/> <!-- id 1014 -->
<option name="nUncomp_Introduced"/> <!-- id 2014 -->
<option name="nUncomp_Indigenous"/> <!-- id 3014 -->
Example:
The simulation in this example lasts 20 years, with a constant importation rate of 1 infection per person per year and a GVI intervention is deployed after 5 years.
Regarding nPatent (and therefore nUncomp), the rule is he following: if a human has an indigenous infection, the human is classified as an indigenous case. If a human does have an indigenous infection but has an introduced infection, the human is classified as an introduced case. If a human only has imported infections, the human is classified as an imported case.
Note that these changes have no impact and predictions will be identical to previous versions as long as there is no imported infection. If imported infections are in place then the model will output slightly different results because of an additional rng call in the code.
The expected results of three tests (which use imported infections) had to be updated because of this.
This pull request adds work on elimination.
Infections now have an origin type which can be either imported, introduced or indigenous.
The code has been updated to track introduced and indigenous infections separately in the Host, WithinHost and InfectionIncidence model.
The VectorModel has also been updated to track the population of mosquitoes infected from an imported infection and mosquitoes infected from an introduced or indigenous infection separetly.
The new equations are detailed in the attached document:OpenMalariaElimination.pdf
This pull request adds Imported, Introduced and Indigenous for the following output measures:
The corresponding new output numbers are defined as follows: Imported: +1000, Introduced: +2000 and Indigenous: +3000
For example nPatent (output measure number 3) can now be tracked as four separate values:
Tracking is done by adding the corresponding monitoring options:
Example:
The simulation in this example lasts 20 years, with a constant importation rate of 1 infection per person per year and a GVI intervention is deployed after 5 years.
Regarding nPatent (and therefore nUncomp), the rule is he following: if a human has an indigenous infection, the human is classified as an indigenous case. If a human does have an indigenous infection but has an introduced infection, the human is classified as an introduced case. If a human only has imported infections, the human is classified as an imported case.
Note that these changes have no impact and predictions will be identical to previous versions as long as there is no imported infection. If imported infections are in place then the model will output slightly different results because of an additional rng call in the code.
The expected results of three tests (which use imported infections) had to be updated because of this.