Add equilibrium solution to P.v model #322
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pwinskill
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Aug 1, 2024
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October 22, 2024 16:15
…e's equilibrium solution. This is accessed during the initial equilibrium calculation in compatability and during the variable creation. The equilibrium solution is found in malariaEquilibriumVivax. Note that we draw individuals from a joint probability distribution over age and het group to generate human state, immunities and number of hypnozoite batches. tests included to check correct equilibrium is generated and maintained. I have also added the An. koliensis parameters as found in Michael White's repo in order to compare equilibrium solutions. Lagged infectivity needs to be saved before the current infectivity is extracted during the biting_process.R. Also, when immunity is boosted through infection, this should incorporate the decrease in immunity from decay (there may be better ways of achieving this).
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/benchmark |
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This is how benchmark results would change (along with a 95% confidence interval in relative change) if 16666ba is merged into dev:
Further explanation regarding interpretation and methodology can be found in the documentation. |
giovannic
requested changes
Oct 23, 2024
| expect_equal(counts, expected, tolerance=1e-3) | ||
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| test_that('vivax ODE stays at equilibrium with low total_M', { |
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This is perhaps redundant? Is there any change in the vector model for vivax?
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I think there was a while when I wasn't sure, but I think you're right: I can take them out.
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| test_that('vivax changing total_M stabilises', { |
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| test_that('Initial states are consistent with equilibrium', { | |||
| skip_on_ci() | |||
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We could run this on the CI? It seems valuable and quick to run. If we're not doing this for falciparum, maybe we should be.
tests/testthat/test-vivax-eq.R
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| test_that('Initial immunities are consistent with equilibrium', { | ||
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tests/testthat/test-vivax-eq.R
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| test_that('vivax equilibrium works with multiple species', { | ||
| skip_on_ci() |
giovannic
approved these changes
Oct 25, 2024
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Added in functionality to start at equilibrium, based on Michael White's equilibrium solution. This is accessed in initial equilibrium calculation in compatability and in variable creation. The equilibrium solution is found in malariaEquilibriumVivax.
Note that we draw individuals from a joint probability distribution over age and het group to generate human state and number of hypnozoite batches.
tests included to check correct equilibrium is generated and maintained.
I have also added the An. koliensis parameters as found in Michael White's repo in order to compare equilibrium solutions.
A few errors were identified. Total infection rates were not being calculated correctly in human_infection.R. Lagged infectivity needs to be saved before the current infectivity is extracted during the biting_process.R. Also, when immunity is boosted through infection, this should incorporate the decrease in immunity from decay (there may be better ways of achieving this).