Vivax competing hazards main parameters #315
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RJSheppard
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@pwinskill This is a good spot - I think I might have the correct parameter draws data sets somewhere, but need to dig this out and review to make sure it's what I think it should be... (Some of the column headings were mislabeled in the file I'd been sent). |
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I wouldn't want to hold back this PR by discussing the best way to benchmark vivax without adding an hour to our benchmark task. Could we move that functionality to a separate PR? Otherwise, we can merge this once you've updated to dev and @pwinskill is happy with it. |
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I've taken out that functionality and tried to rebase again. I'm hoping that everything works now and that it's ready for merging, but I'm suspicious that it doesn't seem to be merging into the dev branch at the minute? Lots of files seem to have been changed, but these look like they are consistent with dev anyway, so I'm not sure what they're doing...? |
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… parameter sets. These parameter values are associated with the set that fixes b = 0.25 and sigma_squared = 1.67, as recommended by Michael White. These parameters are selected in the get_parameters() function by specifying parasite == "falciparum" or "vivax". The functions then selects the parasite-specific values and combines then withe the non-parasite specific values. In order to allow the vivax code to run without full functionality, we have included additional falciparum parameters in the vivax parameter set. These will be removed in the following stages. Pv parameter draws have been added, with code to read them into the package. Added tests to check parameters are behaving as expected. A new vignette has been started to reflect the P. vivax additions that have been made.
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…These have been corrected.
Added parameters csv file that contains falciparum and vivax specific parameter sets.
These are now selected in the get_parameters() function by specificying parasite == "falciparum" or "vivax". The functions then selects the parasite-specific values and combines then withe the non-parasite specific values.
In order to allow the vivax code to run without full functionality, we have included additional falciparum parameters in the vivax parameter set. These will be removed in the following stages.
Added tests to check parameters are behaving as expected.