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Add section that stratifies race into 4 categories
Add new race stratification code
Change from race.cat3 to race.cat throughout
Update EpiStats to generalize race categorization for ARTnet network estimation by allowing user to set `race.level` to a list or vector of race and ethnicity categories as described in ARTnet data (i.e., black, hispanic, white, other, ai/an, asian, mult, nh/pi)
Update NetParams to generalize race categorization for ARTnet network estimation by allowing user to set `race.level` to a list or vector of race and ethnicity categories as described in ARTnet data (i.e., black, hispanic, white, other, ai/an, asian, mult, nh/pi)
Generalize code that assigns numbered race levels Generalize code that assigns initial HIV status
Update capitalization of race labels to work with current code
Correct code so that age is not also updated to be 1 when setting max age for asmr
Comment out language that stops function when we input multiple init.hiv.prev values
Generalize update_asmr() function
Data manipulation that adds new variables to allow for selecting "hispanic" and "other" sub-categories from ARTnet
Update documentation
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Hi @AdrienLeGuillou, for the downstream EpiModel updates, please see this update to mod.acts.R. This was the only changed needed. |
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For the |
To match DESCRIPTION on main branch
Build documentation
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Hi @AdrienLeGuillou - I was able to build the documentation. I think everything is ready for review now. Thanks! |
AdrienLeGuillou
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Awesome work overall thanks!
A few minor elements to modify but nothing much.
Create exported make_race_combo() function that can also be used in EpiModel
Use new make_race_combo() function in NetParams
replace ifelse() with as.integer() for cleaner statement
Replace ifelse() with as.integer() where appropriate for cleaner code
Replace sapply() with vapply() in section renaming race levels
Rename output due to same first letter in some race groups
Replace sapply with vapply and update based on new names for numbers of agents per race group
Add comment for what for loop does in assigning HIV status Update asmr function to ensure column names include asmr
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Hi @AdrienLeGuillou - I addressed the changes you requested. Please let me know if there's anything else that could use updating. Thanks! |
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Apart from the one comment, all is good
Add export flag and build documentation
smjenness
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smjenness
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Everything looks in order. Thanks for this great update!
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@AdrienLeGuillou : if all these most recent updates look good, please feel free to merge. Thanks! |
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Awesome work @clchand23, thanks! |
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New code allows us to specify the race categories for our analysis using
race.levelinbuild_epistats()function.race.levelis a list of race and ethnicity categories that need to match case-sensitive race and ethnicity values in ARTnet. These include "black", "hispanic", "white", "other", "asian", "ai/an", "mult", "nh/pi". Categories can be combined within the list.Examples:
Default (3 categories)
race.level = list("black", "hispanic", c("white", "other")Expand to 4 categories
race.level = list("black", "hispanic", "white", "other")Specify other race groups (Note: when specifying race groups of "asian", "ai/an", "mult", "nh/pi", the "other" race group will be any other group apart from these. When specifying "other" along with "black", "hispanic", and "white", then "other" would include the race groups of "asian", "ai/an", etc.)
race.level = list("hispanic", "asian")Outstanding items: