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giovannic merged 221 commits intomastermrc-ide/malariasimulation:masterfrom devmrc-ide/malariasimulation:devCopy head branch name to clipboardSep 12, 2024

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Commits on Jul 12, 2023

• Specify timesteps in create process

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Commits on Jul 18, 2023

• Documentation updates

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• mixing matrix row sums == 1 error -> warning

  

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• Reduce mixed transmission with testing

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• rebase rdt_mixing to time_varying_metapop

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• Reduce mixed transmission with testing

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• Remove platform specific build files

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• Add new formula for border test and treat:

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• Update documentation for border check model

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• fixing metapopulation vignette error

  

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• Change test and treat coefficients

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• Update RDT detection model

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• Fix regression tests

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• RDT+

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• Add test case for completely removing transmission

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Commits on Jul 19, 2023

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

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Commits on Sep 6, 2023

• Add asymmetric transmission in mixing:

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Commits on Sep 18, 2023

• Fix competing hazards for mass and EPI pev:

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Commits on Sep 22, 2023

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

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Commits on Oct 2, 2023

• Fix bug with pev min_wait:

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Commits on Nov 3, 2023

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

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Commits on Nov 23, 2023

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

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Commits on Dec 4, 2023

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

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Commits on Dec 6, 2023

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

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Commits on Jan 4, 2024

• Implement time varying coverage for PEV boosters:

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• Fix PEV EPI parameterisation bug

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• Implement simplified pev booster interface:

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Commits on Jan 9, 2024

• Check that booster_spacing is monotonically increasing

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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 …

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Commits on Jan 16, 2024

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

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Commits on Jan 18, 2024

• Merge branch 'dev' into bug/maternal_immunity_sampling

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Commits on Jan 22, 2024

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

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

  

  tbreweric

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• 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…

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

  

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

  

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

  

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

  

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

  

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

  

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

  

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• removed comments from calculate_treated() function

  

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

  

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• 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…

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• 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…

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

  

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

  

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

  

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

  

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Commits on Feb 12, 2024

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

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Commits on Feb 13, 2024

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

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Commits on Feb 14, 2024

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

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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.

  

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

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Commits on Feb 27, 2024

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

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Commits on Mar 21, 2024

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

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Commits on Mar 26, 2024

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

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Commits on Apr 3, 2024

• Improve correlation tests. (#287)

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

  

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Commits on Apr 4, 2024

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

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• 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 …

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Commits on Apr 8, 2024

• Merge branch 'dev' into feat/spc

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Commits on Apr 9, 2024

• Merge pull request #277 from mrc-ide/feat/metapop_asym

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Commits on Apr 11, 2024

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

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

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Commits on Apr 15, 2024

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

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Commits on Apr 18, 2024

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

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Commits on Apr 25, 2024

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

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Commits on Apr 26, 2024

• Merge branch 'dev' into feat/spc

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

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• Clarify some intervention parametrization documentation. (#291)

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Commits on May 1, 2024

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

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

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

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Commits on May 2, 2024

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

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Commits on May 8, 2024

• Function for setting age-structured outputs for incidence, prevalence and immunity. Discrete age groups are set using a list, where vectors within the list result in contiguous age group rendering.

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• 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…

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• Added PCR rendering to prevalence rendering function, adjusting tests to rendering tests to reflect additional outputs.

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• Removed overhanging changes associated with EIR calculation correction from another PR.

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• There are a few parameter documentation things I think it would be good to tidy up. First, n_severe isn't a prevalence output (model.R). I've reorganised the parameter documentation list into an or…

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Commits on May 9, 2024

• Added immunity parameter info to documentation of epi outputs function.

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• Older age groups (older than equilibrium age object) are not correctly initiated. If outside of the age range, they get assigned 1 - the youngest age group. If we limit the max ages during these st…

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• Added proper links to the relevant function documentation in the get_parameter help page.

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• Improved robustness of calculate initial EIR test.

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• competing_hazards.R: Giovanni designed two objects: CompetingOutcome (containing an outcome following resolution and rates that that outcome occurs for each individual in the population) and Compet…

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• Correcting typo in parameter documentation: set_betnets -> set_bednets.

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• Added a stash source_human function to the competing hazards function for use in infection outcome.

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Commits on May 20, 2024

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

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• Corrected vignettes to reflect changes in n_detect_lm outputs.

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• Removed epi_outputs function from documentation so that tests can pass correctly.

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• Depend on dqrng from CRAN again.

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• Fix warnings and deprecations.

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Commits on May 21, 2024

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

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• Changed the initial age distribution to a truncated exponential to remove issues with state and immunity assignment when someone is older than the equilibrium solution.

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• adding in n_spray output

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• fix typo renderer

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• update documentation

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• Update test-vector-control.R

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• add whitespace back in

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Commits on May 22, 2024

• Added PCR rendering to prevalence rendering function, adjusting tests to rendering tests to reflect additional outputs.

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• Removed overhanging changes associated with EIR calculation correction from another PR.

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• Corrected vignettes to reflect changes in n_detect_lm outputs.

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• Removed second psi multiplier from calculate_eir to allow tests to complete.

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

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• Removed mean(psi) multiplier from calculate_eir to allow tests to pass.

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• There are a few parameter documentation things I think it would be good to tidy up. First, n_severe isn't a prevalence output (model.R). I've reorganised the parameter documentation list into an or…

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• Added proper links to the relevant function documentation in the get_parameter help page.

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• Correcting typo in parameter documentation: set_betnets -> set_bednets.

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• Removed epi_outputs function from documentation so that tests can pass correctly.

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

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• competing_hazards.R: Giovanni designed two objects: CompetingOutcome (containing an outcome following resolution and rates that that outcome occurs for each individual in the population) and Compet…

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• Added a stash source_human function to the competing hazards function for use in infection outcome.

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Commits on May 23, 2024

• To correctly render ages and incidence, given the competing hazards solution (any rendering in the infection outcome does not occur), I've split the incidence renderer into three functions: age ren…

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• Removed "age" from age outputs in tests and vignettes.

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• Swap back to explicitly labelled age outputs.

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• Merge pull request #298 from mrc-ide/lm_pcr_prevalence_explicit

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• Function for setting age-structured outputs for incidence, prevalence and immunity. Discrete age groups are set using a list, where vectors within the list result in contiguous age group rendering.

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• Added immunity parameter info to documentation of epi outputs function.

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• Changed age limits back to continuous groups (no discrete age groups will be rendered now). Made the code more easier to read.

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• Rebased with latest dev branch, merging with detect pcr/lm outputs.

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• Merged tip with remote counterpart.

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• There are a few parameter documentation things I think it would be good to tidy up. First, n_severe isn't a prevalence output (model.R). I've reorganised the parameter documentation list into an or…

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• Added proper links to the relevant function documentation in the get_parameter help page.

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• Correcting typo in parameter documentation: set_betnets -> set_bednets.

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• Removed epi_outputs function from documentation so that tests can pass correctly.

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

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• Merge pull request #299 from mrc-ide/parameter_documentation_ordering

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• Merge branch 'dev' into competing_hazards_recovery_infection_resolution

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• Merge branch 'dev' into older_age_state_immunity_init

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• Merge branch 'dev' into new_epi_outputs_function

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• Merge pull request #301 from mrc-ide/older_age_state_immunity_init

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• Merge branch 'dev' into new_epi_outputs_function

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• Correcting rendering tests (merging error).

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• fixing test, removing mortality changes

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

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• fixing test, reverting mortality changes

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• Merge pull request #310 from mrc-ide/bug/spraying

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• Merge pull request #304 from mrc-ide/continuous-benchmarking

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• Merge branch 'dev' into feat/metapopulation_model

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• Merge branch 'dev' into new_epi_outputs_function

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• biting_process renamed as create_biting_process, where functionality now occurs in biting_process.R. Similarly, create_recovery_rates_process functionality is now in disease_progression.R

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• competing_hazards.R: Giovanni designed two objects: CompetingOutcome (containing an outcome following resolution and rates that that outcome occurs for each individual in the population) and Compet…

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• Added a stash source_human function to the competing hazards function for use in infection outcome.

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• To correctly render ages and incidence, given the competing hazards solution (any rendering in the infection outcome does not occur), I've split the incidence renderer into three functions: age ren…

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• Removed "age" from age outputs in tests and vignettes.

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• competing_hazards.R: Giovanni designed two objects: CompetingOutcome (containing an outcome following resolution and rates that that outcome occurs for each individual in the population) and Compet…

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• Added a stash source_human function to the competing hazards function for use in infection outcome.

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• biting_process renamed as create_biting_process, where functionality now occurs in biting_process.R. Similarly, create_recovery_rates_process functionality is now in disease_progression.R

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• Re-added "age" to age outputs.

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

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• Corrected age output names in Demography vignette to enable it to run (e.g., n_age... rather than n_...)

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• Update R/mixing.R

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• Removed redundant commented lines.

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• Add print step to touchstone workflow

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• Export the run_resumable_simulation

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• Merge pull request #323 from mrc-ide/export_resumable_simulation

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• Merge branch 'dev' into feat/metapopulation_model

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• Merge pull request #259 from mrc-ide/feat/metapopulation_model

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• Improve cumsum performance

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• Remove outlining of function

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• Optimize competing hazards.

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• Fix empty occurs case.

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• Simplify competing hazards as a single random draw.

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• Try to optimize competing hazards

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• All all states but S to create_recovery_rates_process

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• Merge remote-tracking branch 'origin/dev' into competing_hazards_recovery_infection_resolution

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• Add a bitset_at implementation that works with a logical index.

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• Fix tests

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• Fix more tests

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• Add tests

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• Function for setting age-structured outputs for incidence, prevalence and immunity. Discrete age groups are set using a list, where vectors within the list result in contiguous age group rendering.

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• Added immunity parameter info to documentation of epi outputs function.

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• Changed age limits back to continuous groups (no discrete age groups will be rendered now). Made the code more easier to read.

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• Rebased with latest dev branch, merging with detect pcr/lm outputs.

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• Function for setting age-structured outputs for incidence, prevalence and immunity. Discrete age groups are set using a list, where vectors within the list result in contiguous age group rendering.

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• Merge branch 'new_epi_outputs_function' of github.com:mrc-ide/malariasimulation into new_epi_outputs_function

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• Merge pull request #297 from mrc-ide/new_epi_outputs_function

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• Default average age is currently 7663. The deterministic model average age is 7665, which seems to make more sense (7665/365=21).

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• Merge pull request #326 from mrc-ide/corrected_average_age

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• Assign names to all processes.

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• Fixes for latest individual.

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• Merge pull request #325 from mrc-ide/named-processes

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• Use new individual features

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• Merge remote-tracking branch 'origin/dev' into competing_hazards_recovery_infection_resolution

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• Fix output test

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• Merge pull request #300 from mrc-ide/competing_hazards_recovery_infection_resolution

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• Add a range check to bitset_index.

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• Merge pull request #331 from mrc-ide/bitset_index_bounds_check

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• pushed R21 profiles

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• Merge branch 'r21_profiles' of https://github.com/mrc-ide/malariasimulation into origin/r21_profiles

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• Redocument and tidy reference for vaccine profiles

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• recovery_rates variable has been renamed as (disease) progression_rates.

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• Minor documentation and performance fixed.

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• Merge pull request #334 from mrc-ide/progression_rates_mass_admin

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• Bump to version 2.0.0

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• Merge branch 'dev' into r21_profiles

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• Merge pull request #333 from mrc-ide/r21_profiles

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• Update readme with hex in same style as malariaverse updates

  

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• format adjustment

  

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• format adjustment

  

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• Merge pull request #336 from mrc-ide/hex

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