SHIPP tool integration #413
Conversation
|
Thanks. Corresponding hintr PR at hivtools/hintr#478 |
-Adds comments & sources -Corrects minor issues w/translation of code -Updates KP calculations based on updated data -Corrects age distribution of MSM to reflect age at sexual debut by country
R/car.R
Outdated
| @@ -74,7 +74,7 @@ scale_gmrf_precision <- function(Q, | |||
| A = matrix(1, ncol = ncol(Q)), | |||
| eps = sqrt(.Machine$double.eps)) { | |||
|
|
|||
| nb <- spdep::mat2listw(abs(Q), style = "M")$neighbours | |||
| nb <- spdep::mat2listw(abs(Q), style = "B")$neighbours | |||
There was a problem hiding this comment.
Note I've updated this using Paddy's fix from #391 which should stop the huge amount of warnings. We can close that PR after this has been merged
There was a problem hiding this comment.
Actually tried that and it broke everything, just suppressing this warning on "M" for now as I can't find an equivalent to this which won't trigger a warning
r-ash
force-pushed
the
agyw-tool-integration
branch
from
65a3d9d
to
1030010
Compare
Errors sounds good, I will add some specific error handling into the excel file generation to return a nicer message should this fail. Note about the warnings, these are not surfaced at the moment for downloads. So fine to add these here if you want but users won't see them until we add some specific handling for this in the front end. It will require a new endpoint in hintr to get these surfaced. In general also after seeing the other warnings I am reluctant to use them. I think people have been trained to ignore the warnings. That said, see the note above about a few floating calls to |
add placeholder for incidence adjustment code
Added KP adjustment to incidence estimates to match Spectrum KP new infection estimates for women & men - results in updated estimates of incidence for other behavioural groups as well
Add KP adjustment for new infections
- Align SHIPP vignette with the methods used - Minor code fixes for adjusting KP new infections to either KP workbook or Goals estimates under the assumption that a consensus KP new infection estimate is never missing
…e/naomi into pse-tool-update-incidence
To do:
agyw_format_naomi()