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mrc-ide / leapfrog

Multistate population projection model for demographic estimation.
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Paed parameters that need to be extracted #51

Open mwalte10 opened 1 year ago

mwalte10 commented 1 year ago

ART distribution: https://github.com/mrc-ide/leapfrog/blob/clean/R/spectrum-inputs.R#L239-L248 Rates of MTCT: https://github.com/mrc-ide/leapfrog/blob/clean/R/spectrum-inputs.R#L275-L302 Mortality RR by age: https://github.com/mrc-ide/leapfrog/blob/clean/R/spectrum-inputs.R#L275-L302 ART distribution by age: https://github.com/mrc-ide/leapfrog/blob/clean/R/spectrum-inputs.R#L313-L321 Transition between cd4 categories at 14 to 15: https://github.com/mrc-ide/leapfrog/blob/clean/R/spectrum-inputs.R#L313-L321

mwalte10 commented 4 months ago

Whether cotrim was input as a percentage or a number should be added here.

https://github.com/mrc-ide/leapfrog/blob/b579d266c9428766eb73c4de2d6acd60f94adb7c/R/read-spectrum.R#L292-L324

@jeffeaton

jeffeaton commented 4 months ago

Whether cotrim was input as a percentage or a number should be added here.

https://github.com/mrc-ide/leapfrog/blob/b579d266c9428766eb73c4de2d6acd60f94adb7c/R/read-spectrum.R#L292-L324

@jeffeaton

Thanks very much. This function returns a list of two tables, where the first table val$childart is the values entered for cotrim and child ART by age, and the second table val$childart_ispercent has the same dimension and reflects whether each number is a number or percent.

I think that the cotrim as a percentage is the first row of the output of the second table. However, there was an error in the code and it was mostly returning NA values. That is fixed in PR #54.

Can you please merge that and check if the percentage flag makes sense now, or still looks funny?

jeffeaton commented 1 month ago

@mwalte10 -- what is status on this issue now?