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Dev hiv ped 24 #31

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Dev hiv ped 24 #31

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Commits on Jun 27, 2022

  1. adding testing for transmission model

    maggie committed Jun 27, 2022
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Commits on Jun 28, 2022

  1. did checks in dplyr

    maggie committed Jun 28, 2022
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Commits on Jun 29, 2022

  1. added age 15 entrants to the no ART group

    maggie committed Jun 29, 2022
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Commits on Jun 30, 2022

  1. reformatted testhat file to use helper functions, so that previous ch… 

    …ecks can be run repeatedly on different build ups of the model
    maggie committed Jun 30, 2022
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  2. took out tests that were causing git to fail

    maggie committed Jun 30, 2022
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  3. added imports

    maggie committed Jun 30, 2022
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Commits on Jul 1, 2022

  1. having eppasm in imports causing failure for dev ubuntu, looks like i… 

    …ts in remotes so hoping that works
    maggie committed Jul 1, 2022
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  2. Revert "added imports" 

    This reverts commit b9eca1c.
    maggie committed Jul 1, 2022
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  3. Revert "having eppasm in imports causing failure for dev ubuntu, look… 

    …s like its in remotes so hoping that works"

This reverts commit af795b6.
    maggie committed Jul 1, 2022
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  4. back to last working imports

    maggie committed Jul 1, 2022
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Commits on Jul 4, 2022

  1. confirmed that demo outputs are the same without hiv deaths

    maggie committed Jul 4, 2022
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  2. trans tests should be checked by jeff, think this might be a number v… 

    … rates issue
    maggie committed Jul 4, 2022
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Commits on Jul 5, 2022

  1. now getting alignment for births, deaths, tot pop, and burden metrics… 

    …, jeff should look at cutoffs
    maggie committed Jul 5, 2022
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  2. added pjnz and removed plotting data

    maggie committed Jul 5, 2022
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  3. now outputting the hiv negative population, changed births so that th… 

    …ey are calculated from this population, need to add in births from hiv pos moms
    maggie committed Jul 5, 2022
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  4. fix white space

    @jeffeaton
    jeffeaton authored Jul 5, 2022
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Commits on Jul 7, 2022

  1. responding to jeffs pr notes

    maggie committed Jul 7, 2022
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  2. merged in entrants

    maggie committed Jul 7, 2022
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  3. added new pjnz file descriptions to the add me, removed one that was … 

    …redundant
    maggie committed Jul 7, 2022
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  4. added purpose

    maggie committed Jul 7, 2022
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  5. fixing test

    maggie committed Jul 7, 2022
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  6. Merge branch 'dev_add_hivp_entrant' of https://github.com/mwalte10/le… 

    …apfrog into dev_add_hivp_entrant
    maggie committed Jul 7, 2022
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Commits on Jul 8, 2022

  1. added return messages to the helper functions and extracted the cutof… 

    …fs and changed them to args to the function. Going to add these to the readme
    maggie committed Jul 8, 2022
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  2. updated readme file

    maggie committed Jul 8, 2022
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  3. added roxygen documentation for helper functions

    maggie committed Jul 8, 2022
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  4. changed threshold

    maggie committed Jul 8, 2022
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Commits on Jul 11, 2022

  1. added in tests to assess leapfrog v eppasm

    maggie committed Jul 11, 2022
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  2. deleted two files that I did not mean to add

    maggie committed Jul 11, 2022
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  3. added in hiv negative population

    maggie committed Jul 11, 2022
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  4. took out a redundant test

    maggie committed Jul 11, 2022
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  5. checked that incrr doesnt seem to affect prevalence

    maggie committed Jul 11, 2022
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Commits on Jul 13, 2022

  1. adding in hiv births, trying to align hiv births between spec and lfr… 

    …og and spec separately from normal births
    maggie committed Jul 13, 2022
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  2. updated thresholds for the births

    maggie committed Jul 13, 2022
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Commits on Jul 19, 2022

  1. .

    maggie committed Jul 19, 2022
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Commits on Jul 22, 2022

  1. added popadjust

    maggie committed Jul 22, 2022
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Commits on Jul 25, 2022

  1. added in population adjust

    maggie committed Jul 25, 2022
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  2. updated readme

    maggie committed Jul 25, 2022
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  3. resolving merge changes

    maggie committed Jul 25, 2022
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  4. resolving merge conflicts

    maggie committed Jul 25, 2022
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  5. trying to get alignment

    maggie committed Jul 25, 2022
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Commits on Jul 27, 2022

  1. added initial ped inputs

    maggie committed Jul 27, 2022
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Commits on Jul 29, 2022

  1. I think that this is working now but somehow adding in the full pAG i… 

    …s causing my R to crash, can move fert rat to just be the 35 dimensions
    maggie committed Jul 29, 2022
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  2. merge

    maggie committed Jul 29, 2022
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Commits on Aug 1, 2022

  1. added in HIV births to the end of the loop over years

    maggie committed Aug 1, 2022
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Commits on Aug 4, 2022

  1. Revert "added in HIV births to the end of the loop over years" 

    This reverts commit 82bad9e.
    maggie committed Aug 4, 2022
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  2. extracted paed incidence from spec, input into spec, distrbuted among… 

    … sex and ages, confirmed aligns with spec
    maggie committed Aug 4, 2022
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  3. trying to add in the hiv strat paed pop, crashing r

    maggie committed Aug 4, 2022
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  4. pushing single cohort file

    maggie committed Aug 4, 2022
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Commits on Aug 5, 2022

  1. added in the read spec object bit

    maggie committed Aug 5, 2022
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Commits on Aug 7, 2022

  1. align infections by age

    @jeffeaton
    jeffeaton committed Aug 7, 2022
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  2. Merge branch 'patch-infections-by-age' into dev_add_hivp_entrant

    @jeffeaton
    jeffeaton committed Aug 7, 2022
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Commits on Aug 8, 2022

  1. merged jeffs changes

    maggie committed Aug 8, 2022
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Commits on Aug 9, 2022

  1. cleaning up integration of RG changes, added thresholds for alignment

    maggie committed Aug 9, 2022
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  2. hiv infections stratified by cd4 init dist

    maggie committed Aug 9, 2022
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Commits on Aug 11, 2022

  1. rebasing git

    maggie committed Aug 11, 2022
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  2. have paed specific storage of hiv population + aging

    maggie committed Aug 11, 2022
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  3. incidence matches but prevalence and deaths dont bc I havent incorpor… 

    …ated natural deaths yet
    maggie committed Aug 11, 2022
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Commits on Aug 15, 2022

  1. removed my version of read_hivproj_param

    maggie committed Aug 15, 2022
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  2. adding testthat to imports rather than suggests, as it seems to be ca… 

    …using problems in git checks
    maggie committed Aug 15, 2022
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Commits on Aug 18, 2022

  1. removed paed = t bc it was breaking

    maggie committed Aug 18, 2022
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  2. added package specifications

    maggie committed Aug 18, 2022
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  3. removed xlsx

    maggie committed Aug 18, 2022
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  4. changed imports per warning

    maggie committed Aug 18, 2022
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