Parameter and output documentation. #299
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…on't think it needs to be multiplied by psi. When these values are drawn in lines 135-140 of biting_process.R they get multiplied by psi in line 144. That means we're effectively multiplying these values by psi^2. I think we can correct this by adjusting the calculation thusly. The two tests at the end would then need adjusting (one way or another) to reflect this change - which could use improving.
… to rendering tests to reflect additional outputs.
…n from another PR.
…od to tidy up. First, n_severe isn't a prevalence output (model.R). I've reorganised the parameter documentation list into an order I think is a bit more intuitive, with consistency between code and documentation.
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giovannic
requested changes
May 8, 2024
R/parameters.R
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| #' please set vaccine strategies with the convenience functions in | ||
| #' `pev_parameters.R:set_pev_epi` | ||
| #' `pev_parameters.R:set_mass_pev` | ||
| #' `pev_parameters.R::set_pev_epi` |
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Is this a thing?
If we're going to make these references more formal shouldn't we use Roxygen syntax?
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| #' `pev_parameters.R::set_pev_epi` | |
| #' \code{\link{set_pev_epi}} |
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Good shout! I'm not super familiar with the syntax, so thanks for pointing this out. I've now changed all the references to other functions to links to the help pages.
pwinskill
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May 10, 2024
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Thanks Richard
Looks like a few of the new links in the docs are upsetting the checks:
❯ checking Rd cross-references ... WARNING
Missing link or links in Rd file 'get_parameters.Rd':
'set_betnets' 'set_epi_outputs'
See section 'Cross-references' in the 'Writing R Extensions' manual.
Otherwise looks great
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I've corrected the set_bednets function spelling, but I think I'll leave the epi outputs in, then merge this one after we merge that branch. |
calculate_eir function correction
dqrng just released a new version, which means we can stop relying on the mrc-ide r-universe as an additional repository.
Depend on dqrng from CRAN again.
… to rendering tests to reflect additional outputs.
…n from another PR.
…de/malariasimulation into lm_pcr_prevalence_explicit
…od to tidy up. First, n_severe isn't a prevalence output (model.R). I've reorganised the parameter documentation list into an order I think is a bit more intuitive, with consistency between code and documentation.
…parameter help page.
…/mrc-ide/malariasimulation into parameter_documentation_ordering
This PR labels detection outputs explicitly as pcr or lm detectable.
giovannic
approved these changes
May 23, 2024
…od to tidy up. First, n_severe isn't a prevalence output (model.R). I've reorganised the parameter documentation list into an order I think is a bit more intuitive, with consistency between code and documentation.
…parameter help page.
…/mrc-ide/malariasimulation into parameter_documentation_ordering
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There are a few parameter documentation things I think it would be good to tidy up. First, n_severe isn't a prevalence output (model.R). I've then reorganised the parameter documentation list into an order I think is a bit more intuitive, with consistency between code and documentation. Nothing has fundamentally changed, just the order, and some small text things to improve clarity, e.g., "probability of detection by light-microscopy when asymptomatic".