Mkw hiv mort #26
Mkw hiv mort #26
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mwalte10
commented
Jul 27, 2023
mwalte10
commented
- Integrated the HIV natural history bit for children off treatment
- changed all instances of hC to hc per jeff's comment in leapfrog check in on 25/7
- made all paed model functions have 'child' as the second word to indicate that they are paediatric functions
- removed all instances of hard coding related to age
- separated hc1 from hc2 for output of the hiv stratified population
Co-authored-by: Rob <39248272+r-ash@users.noreply.github.com>
jeff & maggie debugging
src/model_setup.h
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| //Not sure how to do just a single value, ASK ROB | ||
| // !!! TODO: Ask Rob about preferred approach to assigning a single value | ||
| const double ctx_effect = parse_data<double>(data, "ctx_effect", 1)(0); // select the first element of a TensorMap1 and assign to double |
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@r-ash -- please review this. Need to set convention for how to parse a single value
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Added support into the code generation to manage this.
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@r-ash here is the problem with the intermediate data |
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Not sure about the code factor issues here, it is complaining about empty lines but is seemingly referencing an old commit. Those blank lines have been removed. |
| @@ -58,6 +58,7 @@ void save_output(leapfrog::StateSaver<ModelVariant, double> &state_saver, | |||
| int main(int argc, char *argv[]) { | |||
| if (argc < 4) { | |||
| std::cout << | |||
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| @@ -107,6 +108,7 @@ int main(int argc, char *argv[]) { | |||
| ss.hAG, // Age groups HIV 15+ | |||
| 1, // Scale CD4 mortality | |||
| 0.2, // initiation_mortality_weight | |||
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| for (int g = 0; g < adult_ss.NS; ++g) { | ||
| for (int s = 0; s < ss.NS; ++s) { |
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Ah good spot, we should switch elsewhere loop variable to s, I think it might still be g in a lot of places. Doesn't need to be done in this PR though.
src/model_setup.h
Outdated
| //Not sure how to do just a single value, ASK ROB | ||
| // !!! TODO: Ask Rob about preferred approach to assigning a single value | ||
| const double ctx_effect = parse_data<double>(data, "ctx_effect", 1)(0); // select the first element of a TensorMap1 and assign to double |
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Added support into the code generation to manage this.
| for (int s = 0; s < ss.NS; ++s) { | ||
| //less than 5 because there is a cd4 transition between ages 4 and 5 | ||
| for (int a = 1; a < hc_ss.hc2_agestart; ++a) { | ||
| for (int hd = 0; hd < hc_ss.hc1DS; ++hd) { | ||
| for (int cat = 0; cat < hc_ss.hcTT; ++cat) { |
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Loop order here should be NS, hc1AG, hcTT, hc1DS
Codecov ReportPatch coverage:
Additional details and impacted files@@ Coverage Diff @@
## main #26 +/- ##
==========================================
+ Coverage 97.88% 98.28% +0.39%
==========================================
Files 18 18
Lines 1087 1222 +135
==========================================
+ Hits 1064 1201 +137
+ Misses 23 21 -2
☔ View full report in Codecov by Sentry. |
| for (int hd = 0; hd < hc_ss.hc1DS; ++hd) { | ||
| intermediate.children.hc_posthivmort(hd, cat, a, s) = | ||
| state_next.children.hc1_hiv_pop(hd, cat, a, s) * (1 - cpars.hc1_cd4_mort(hd, cat, a)); | ||
| //intermediate.children.hc_posthivmort(hd, cat, a, s) = state_next.children.hc1_hiv_pop(hd, cat, a, s) - (1.0 - cpars.ctx_effect * cpars.ctx_val(time_step)) * state_curr.children.hc1_hiv_pop(hd, cat, a, s) * cpars.hc1_cd4_mort(hd, cat, a); |
