Vivax subpatent duration #250
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… check infectivity is constant. I think only the switch in human_infection.R will be looped during the simulation. The other switches specity initial infectivity and process selection.
…ameter. Typos in parameter.R corrected
… maternal immunity to detectability with rendering
Merge branch 'vivax_pre_eryth_imm' of https://github.com/mrc-ide/malariasimulation into vivax_pre_eryth_imm # Conflicts: # R/parasite_parameters.R
Merge branch 'vivax_subpatent_duration' of https://github.com/mrc-ide/malariasimulation into vivax_subpatent_duration # Conflicts: # tests/testthat/test-vivax.R
…c state is detectable by miscroscopy (e.g. prob = 1). This means that n-detect = p-detect, so might not be incredibly useful...
pwinskill
requested changes
Jun 29, 2023
…tion. Use anti-parasite immunity to calculate subpatent recovery rate for vivax. If vivax: calculate patent infections using anti-parasite immunity, then clinical infections. Added patent incidence to possible age rendering. Created immunity names list outside of render. Improved spacing, typos corrected. Tests for patent rendering and n/p detect outputs.
Added test for vivax infections.
pwinskill
approved these changes
Jul 24, 2023
…t_pcr added: rendering and documentation. Restructured prevalence rendering function. Patent infection incidence added as an output. Made some of the documentation more consistent... Made tests consistent with outputs. Removed severe prevalence rendering documentation
…it wasn't actually producing an output becuase min age was set to numeric(0), rather than 0, so it might as well be fully turned off to avoid confusion. Changed age rendering back to n_age_ after chatting with Pete. test-infection-integration, I removed a couple of lines that don't seem to be contributing to anything.
pwinskill
reviewed
Aug 9, 2023
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Thanks @RJSheppard 🎉. Just a few bits to follow up on from me.
R/render.R
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| } | ||
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| clinically_detected <- state$get_index_of(c('Tr', 'D')) | ||
| detected <- clinically_detected$copy()$or(asymptomatic_detected) | ||
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| lm_detected <- detected <- clinically_detected$copy()$or(asymptomatic_detected) |
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This may be something that bugs me an not anyone else, but can we keep these as two seperate assignments please.
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Ooops - this was actually a mistake (shouldn't have the middle part). I'll fix that.
R/render.R
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| if(parameters$parasite == "falciparum"){ | ||
| # render lm detection (falciparum): integer sample | ||
| renderer$render( | ||
| paste0('n_detect_lm_', lower, '_', upper), | ||
| in_age$copy()$and(lm_detected)$size(), | ||
| timestep | ||
| ) | ||
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| # render lm detection (falciparum): summed probability | ||
| renderer$render( | ||
| paste0('p_detect_lm_', lower, '_', upper), | ||
| in_age$copy()$and(clinically_detected)$size() + sum( | ||
| prob[bitset_index(asymptomatic, in_age)] | ||
| ), | ||
| timestep | ||
| ) | ||
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| } else if (parameters$parasite == "vivax") { | ||
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| # render lm detection (vivax) | ||
| renderer$render( | ||
| paste0('n_detect_lm_', lower, '_', upper), | ||
| in_age$copy()$and(lm_detected)$size(), | ||
| timestep | ||
| ) | ||
| } |
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Can you pull the repeating code out to simplify here:
Suggested change
| if(parameters$parasite == "falciparum"){ | |
| # render lm detection (falciparum): integer sample | |
| renderer$render( | |
| paste0('n_detect_lm_', lower, '_', upper), | |
| in_age$copy()$and(lm_detected)$size(), | |
| timestep | |
| ) | |
| # render lm detection (falciparum): summed probability | |
| renderer$render( | |
| paste0('p_detect_lm_', lower, '_', upper), | |
| in_age$copy()$and(clinically_detected)$size() + sum( | |
| prob[bitset_index(asymptomatic, in_age)] | |
| ), | |
| timestep | |
| ) | |
| } else if (parameters$parasite == "vivax") { | |
| # render lm detection (vivax) | |
| renderer$render( | |
| paste0('n_detect_lm_', lower, '_', upper), | |
| in_age$copy()$and(lm_detected)$size(), | |
| timestep | |
| ) | |
| } | |
| # render lm detection | |
| renderer$render( | |
| paste0('n_detect_lm_', lower, '_', upper), | |
| in_age$copy()$and(lm_detected)$size(), | |
| timestep | |
| ) | |
| if(parameters$parasite == "falciparum"){ | |
| # render lm detection (falciparum): summed probability | |
| renderer$render( | |
| paste0('p_detect_lm_', lower, '_', upper), | |
| in_age$copy()$and(clinically_detected)$size() + sum( | |
| prob[bitset_index(asymptomatic, in_age)] | |
| ), | |
| timestep | |
| ) | |
| } | |
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Sure thing - I think I'd been separating them because the calculations were different, but I've since included an extra if statement earlier that does that calculation at an earlier point.
… white spaces removed.
giovannic
approved these changes
Aug 11, 2023
| renderer, | ||
| names, | ||
| variables | ||
| renderer, |
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This is fine now. But adding spaces can cause needless merge conflicts
Merge branch 'vivax_subpatent_duration' into HEAD # Conflicts: # R/disease_progression.R # R/mortality_processes.R # R/processes.R # data/parasite_parameters.rda # tests/testthat/test-vivax.R
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I've created process function to work out subpatent durations (I thought about coopting the existing functions, but they don't line up closely enough and they model conceptually different things). Introduced maternal ID - used in these functions (birth/death and decay). Falciparum probability of detectability functions no longer used, including in rendering (also altered). Tests to check outputs.