Code

Antimalarial resistance/etf#263

Code

Merged

tbreweric merged 21 commits intodevmrc-ide/malariasimulation:devfrom antimalarial_resistance/etfmrc-ide/malariasimulation:antimalarial_resistance/etfCopy head branch name to clipboardFeb 14, 2024

+1,333-48

Commits

Commits on Feb 9, 2024

• Opened sub-branch of feat/antimalarial_resistance for developing the early treatment failure (ETF) component of the model. Also created a draft vignette for Antimalarial_Resistance on the feat/anti…

  Show description for d8930d8
  

  Thomas Brewer

  authored and

  giovannic

  committed
  d8930d8

• Added first iteration of the set_antimalarial_resistance() function designed to parameterise antimalarial resistance for malariasimulation runs

  

  tbreweric

  authored and

  giovannic

  committed
  8efb863

• Updated the set_antimalarial_resistance() function to allow for multiple-value entries for each parameter (e.g. updates to resistance proportions through time) and included an additional check to m…

  Show description for 74a2a3b
  

  Thomas Brewer

  authored and

  giovannic

  committed
  74a2a3b

• Removed the else{} arguments on the checks, condensed the first check using any(), removed for loops for second and third checks and used any()

  

  Thomas Brewer

  authored and

  giovannic

  committed
  acf145e

• Added additional section for testing different versions of ETF version of model

  

  Thomas Brewer

  authored and

  giovannic

  committed
  856ec1e

• removed the extra versions of calculate_treated() from human_infection and removed additional space from set_antimalarial_resistance() in antimalarial_resistance.R

  

  Thomas Brewer

  authored and

  giovannic

  committed
  da94206

• removed all but resistance first, efficacy second version of calculate treated as part of improvement in development process

  

  tbreweric

  authored and

  giovannic

  committed
  571a20c

• Deleting the development script from the branch (will store development scripts outside of project following advice).

  

  tbreweric

  authored and

  giovannic

  committed
  bfb6aa0

• Amended the calculate_treated() function to remove the loop when assigning the resistance parameters and use a vectorised method. Fixed a typo in the set_antimalarial_resistance() function document…

  Show description for 02e4916
  

  tbreweric

  authored and

  giovannic

  committed
  02e4916

• Added check to number of clinical_infections in calculate_treated() and a step to render this number for testing

  

  tbreweric

  authored and

  giovannic

  committed
  7be84ee

• Removed typos/spaces from antimalarial_resistance.R. Added check for calculate_treated() to separate resistance and non-resistance simulation paths

  

  Thomas Brewer

  authored and

  giovannic

  committed
  fea9da2

• removed comments from calculate_treated() function

  

  tbreweric

  authored and

  giovannic

  committed
  0b1adb6

• removed unnecessary spacing and comments from the calculate_treated() function

  

  tbreweric

  authored and

  giovannic

  committed
  731899e

• Create test-antimalarial-resistance.R and added six tests for the set_antimalarial_resistance() function in antimalarial_resistance.R file. Also amended the existing test for calculate_treated() in…

  Show description for 578c9e5
  

  tbreweric

  authored and

  giovannic

  committed
  578c9e5

• Added test file for new antimalarial resistance functions and added new calculate_treated() tests to test-infection-integration.R. Note - I thought these changes had been included in the previous c…

  Show description for ded0251
  

  tbreweric

  authored and

  giovannic

  committed
  ded0251

• Commiting all changes recommended by Pete/Giovanni except those that involve the function testing (to follow in a subsequent commit).

  

  tbreweric

  authored and

  giovannic

  committed
  d4db8f9

• Commiting the final set of changes and corrections in response to comments on the first PR request

  

  tbreweric

  authored and

  giovannic

  committed
  11e61e1

• Implemented the second round of changes requested in the pull request

  

  Thomas Brewer

  authored and

  giovannic

  committed
  de29495

• Implented the second round of changes requested in the pull request

  

  Thomas Brewer

  authored and

  giovannic

  committed
  4d75b2e

Commits on Feb 12, 2024

• Re-adding the changes recommended by Pete following a reversion to 4d75b2e after a merge error

  tbreweric

  committed
  d51bbf7

Commits on Feb 13, 2024

• Corrected drugs documentation for get_antimalarial_resistance_parameters() function (antimalarial_resistance.R)

  tbreweric

  committed
  2adf823