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Bug/spraying#308

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htopazian wants to merge 68 commits intomastermrc-ide/malariasimulation:masterfrom bug/sprayingmrc-ide/malariasimulation:bug/sprayingCopy head branch name to clipboard

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Commits

Commits on Jul 12, 2023

• Specify timesteps in create process

  pwinskill

  committed
  fd58ea6

Commits on Jul 19, 2023

• Merge pull request #258 from mrc-ide/bug/progress_bar_timesteps

  Show description for 7fa7ea3
  giovannic

  authored
  7fa7ea3

Commits on Sep 18, 2023

• Fix competing hazards for mass and EPI pev:

  Show description for a7c7dd1
  giovannic

  committed
  a7c7dd1

Commits on Sep 22, 2023

• Merge pull request #265 from mrc-ide/bug/competing_vaccination

  Show description for efd3dfc
  giovannic

  authored
  efd3dfc

Commits on Oct 2, 2023

• Fix bug with pev min_wait:

  Show description for e7b5c4d
  giovannic

  committed
  e7b5c4d

Commits on Nov 3, 2023

• Merge pull request #264 from mrc-ide/bug/min_wait

  Show description for 8e0e76e
  giovannic

  authored
  8e0e76e

Commits on Nov 23, 2023

• Custom carrying capacity is set as a relative scaler, not absolute value

  pwinskill

  committed
  5f174c4

Commits on Dec 4, 2023

• Document and make suggested changes to carrying capacity vignette for clarity

  pwinskill

  committed
  a109246

Commits on Dec 6, 2023

• Merge pull request #272 from mrc-ide/carrying_capacity_relative

  Show description for dc922d7
  giovannic

  authored
  dc922d7

Commits on Jan 4, 2024

• Implement time varying coverage for PEV boosters:

  Show description for 73cbfb4
  giovannic

  committed
  73cbfb4

• Fix PEV EPI parameterisation bug

  giovannic

  committed
  d49c8dd

• Implement simplified pev booster interface:

  Show description for 91247b4
  giovannic

  committed
  91247b4

Commits on Jan 9, 2024

• Check that booster_spacing is monotonically increasing

  giovannic

  committed
  45486ad

Commits on Jan 15, 2024

• Changed the calculation of birth_ivm in sample_maternal_immunity(). The function now calculates the maternally-acquired immunity to severe disease (birth_ivm) using the acquired immunity to severe …

  Show description for f1039ea
  tbreweric

  committed
  f1039ea

Commits on Jan 16, 2024

• Merge pull request #270 from mrc-ide/feat/time_boosters

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  giovannic

  authored
  b0ad081

Commits on Jan 18, 2024

• Merge branch 'dev' into bug/maternal_immunity_sampling

  giovannic

  authored
  01a0a1e

Commits on Jan 22, 2024

• Merge pull request #279 from mrc-ide/bug/maternal_immunity_sampling

  Show description for 0359cec
  giovannic

  authored
  0359cec

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…

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  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…

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  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

Commits on Feb 14, 2024

• Merge pull request #263 from mrc-ide/antimalarial_resistance/etf

  Show description for 3ea8ee3
  tbreweric

  authored
  3ea8ee3

Commits on Feb 15, 2024

• Added check for undeveloped antimalarial resistance features (SPC/LPF/LCF/RDP). Included test to ensure check works and amended documentation in get_parameters() to warn users features in development.

  

  Thomas Brewer

  committed
  d16978e

• Merge pull request #282 from mrc-ide/feat/resistance_unused_feature_error

  Show description for 1a5f00a
  tbreweric

  authored
  1a5f00a

Commits on Feb 27, 2024

• Add initial support for saving and restoring simulation state. (#280)

  Show description for c42e2c5
  plietar

  authored
  c42e2c5

Commits on Mar 21, 2024

• Rewrite the exponential decay process in C++. (#285)

  Show description for b3376d3
  plietar

  authored
  b3376d3

Commits on Mar 26, 2024

• Combined ETF and SPC. Need to fix testthat files before PR

  tbreweric

  committed
  2c9932b

Commits on Apr 3, 2024

• Improve correlation tests. (#287)

  Show description for 2a3d4cc
  plietar

  authored
  2a3d4cc

• Fixed errors in unit tests which included amending the create_mortality_process function to include parameters as an input

  

  Thomas Brewer

  committed
  952108c

Commits on Apr 4, 2024

• Added section modelling early treatment failure and slow parasite clearance to the vignette

  tbreweric

  committed
  0cef273

• Made clearer the antimalarial resistance parameter names in set_antimalarial_resistance and get_antimalarial_resistance_parameters, then made additional changes to documentation where necessary to …

  Show description for 5123d6e
  tbreweric

  committed
  5123d6e

Commits on Apr 8, 2024

• Merge branch 'dev' into feat/spc

  tbreweric

  authored
  54456df

Commits on Apr 11, 2024

• Implemented the changes recommended by in first round of PR comments

  tbreweric

  committed
  d9ce4a6

• Merge branch 'feat/spc' of https://github.com/mrc-ide/malariasimulation into feat/spc

  tbreweric

  committed
  086956a

Commits on Apr 15, 2024

• Moved mortality to the end of processes to resolve order of competing hazards.

  RJSheppard

  committed
  5077d4b

Commits on Apr 18, 2024

• Altered check for rate data type in create_disease_progression() function

  tbreweric

  committed
  f58d48f

Commits on Apr 25, 2024

• Update description of the dt parameter. (#288)

  Show description for e9d46e7
  plietar

  authored
  e9d46e7

Commits on Apr 26, 2024

• Merge branch 'dev' into feat/spc

  tbreweric

  authored
  5900751

• Merge pull request #289 from mrc-ide/feat/spc

  Show description for 380d113
  tbreweric

  authored
  380d113

• Clarify some intervention parametrization documentation. (#291)

  Show description for 9debd7f
  plietar

  authored
  9debd7f

Commits on May 1, 2024

• Allow simulation to be restored with new interventions. (#286)

  Show description for e534db7
  plietar

  committed
  e534db7

• Allow correlations to be extended when resuming. (#293)

  Show description for 1111500
  plietar

  committed
  1111500

• Merging dev branch back before merging into main dev branch.

  Show description for a9b495c
  RJSheppard

  committed
  a9b495c

Commits on May 2, 2024

• Merge pull request #292 from mrc-ide/competing_hazards_mortality_order

  Show description for 7e62cc9
  RJSheppard

  authored
  7e62cc9

Commits on May 8, 2024

• I think the calculation for initial EIR values isn't quite right. I don't think it needs to be multiplied by psi. When these values are drawn in lines 135-140 of biting_process.R they get multiplie…

  Show description for b8f3c27
  RJSheppard

  committed
  b8f3c27

Commits on May 9, 2024

• Improved robustness of calculate initial EIR test.

  RJSheppard

  committed
  69fc17f

Commits on May 20, 2024

• Merge pull request #296 from mrc-ide/initial_eir_calculation_correction

  Show description for 6804095
  RJSheppard

  authored
  6804095

• Depend on dqrng from CRAN again.

  Show description for 254bce2
  plietar

  committed
  254bce2

• Fix warnings and deprecations.

  plietar

  committed
  75a0332

Commits on May 21, 2024

• Merge pull request #305 from mrc-ide/dqrng-release

  Show description for 25c0956
  plietar

  authored
  25c0956

• adding in n_spray output

  Show description for 6008a8a
  htopazian

  committed
  6008a8a