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Dev#335

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

+6,320-1,460

Commits

Commits on Jul 12, 2023

• Specify timesteps in create process

  pwinskill

  committed
  fd58ea6

Commits on Jul 18, 2023

• Documentation updates

  giovannic

  committed
  1ba67c0

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

  

  htopazian

  authored and

  giovannic

  committed
  08b1f62

• Reduce mixed transmission with testing

  Show description for c5a7bec
  giovannic

  committed
  c5a7bec

• rebase rdt_mixing to time_varying_metapop

  Show description for 4e14e50
  

  htopazian

  authored and

  giovannic

  committed
  4e14e50

• Reduce mixed transmission with testing

  Show description for 4b54e80
  giovannic

  committed
  4b54e80

• Remove platform specific build files

  giovannic

  committed
  4a58966

• Add new formula for border test and treat:

  Show description for 3236f76
  giovannic

  committed
  3236f76

• Update documentation for border check model

  giovannic

  committed
  8e759c1

• fixing metapopulation vignette error

  

  htopazian

  authored and

  giovannic

  committed
  247432c

• Change test and treat coefficients

  giovannic

  committed
  f3669f5

• Update RDT detection model

  giovannic

  committed
  1d4f4a2

• Fix regression tests

  giovannic

  committed
  e568127

• RDT+

  giovannic

  committed
  0057fda

• Add test case for completely removing transmission

  giovannic

  committed
  a591eb0

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 6, 2023

• Add asymmetric transmission in mixing:

  Show description for ba4bedc
  giovannic

  committed
  ba4bedc

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

  Show description for b0ad081
  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…

  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

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 9, 2024

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

  Show description for 462b0fe
  htopazian

  authored
  462b0fe

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

• 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.

  Show description for 610c5cb
  RJSheppard

  committed
  610c5cb

• 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

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

  RJSheppard

  committed
  b9b923c

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

  RJSheppard

  committed
  1a70ff2

• 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…

  Show description for 6ec5e3d
  RJSheppard

  committed
  6ec5e3d

Commits on May 9, 2024

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

  RJSheppard

  committed
  55d83ea

• 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…

  Show description for d0854db
  RJSheppard

  committed
  d0854db

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

  RJSheppard

  committed
  d1bd2af

• Improved robustness of calculate initial EIR test.

  RJSheppard

  committed
  69fc17f

• 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…

  Show description for b36be83
  RJSheppard

  committed
  b36be83

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

  RJSheppard

  committed
  435180d

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

  RJSheppard

  committed
  0e05f75

Commits on May 20, 2024

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

  Show description for 6804095
  RJSheppard

  authored
  6804095

• Corrected vignettes to reflect changes in n_detect_lm outputs.

  RJSheppard

  committed
  c62decc

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

  RJSheppard

  committed
  ed29688

• 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

• 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.

  RJSheppard

  committed
  40e4f87

• adding in n_spray output

  Show description for 6008a8a
  htopazian

  committed
  6008a8a

• fix typo renderer

  Show description for b0ef327
  

  htopazian

  and

  giovannic

  authored
  b0ef327

• update documentation

  Show description for 7a9966b
  

  htopazian

  and

  giovannic

  authored
  7a9966b

• Update test-vector-control.R

  htopazian

  committed
  f1eb68c

• add whitespace back in

  htopazian

  committed
  7c5232c

Commits on May 22, 2024

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

  RJSheppard

  committed
  d868e19

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

  RJSheppard

  committed
  2f9dd12

• Corrected vignettes to reflect changes in n_detect_lm outputs.

  RJSheppard

  committed
  d28bd2b

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

  RJSheppard

  committed
  5d95b83

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

  RJSheppard

  committed
  21d8f9a

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

  RJSheppard

  committed
  2c1dab3

• 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…

  Show description for 5e559a7
  RJSheppard

  committed
  5e559a7

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

  RJSheppard

  committed
  7f12172

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

  RJSheppard

  committed
  ec16cf6

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

  RJSheppard

  committed
  288e428

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

  RJSheppard

  committed
  6c256ae

• 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…

  Show description for f47bb3e
  RJSheppard

  committed
  f47bb3e

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

  RJSheppard

  committed
  c8c3245

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…

  Show description for c5947ef
  RJSheppard

  committed
  c5947ef

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

  Show description for 4820186
  RJSheppard

  committed
  4820186

• Swap back to explicitly labelled age outputs.

  Show description for d563f6e
  RJSheppard

  committed
  d563f6e

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

  Show description for 69ea7b6
  RJSheppard

  authored
  69ea7b6

• 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.

  Show description for abdcef0
  RJSheppard

  committed
  abdcef0

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

  RJSheppard

  committed
  8786b81

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

  RJSheppard

  committed
  a542d10

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

  RJSheppard

  committed
  482fc83

• Merged tip with remote counterpart.

  Show description for c9c90f5
  RJSheppard

  committed
  c9c90f5

• 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…

  Show description for 23827d2
  RJSheppard

  committed
  23827d2

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

  RJSheppard

  committed
  8a86bee

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

  RJSheppard

  committed
  7dae339

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

  RJSheppard

  committed
  52cc8b5

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

  RJSheppard

  committed
  702fcc4

Commits on May 24, 2024

• Merge branch 'dev' into older_age_state_immunity_init

  RJSheppard

  authored
  4994b82

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

  Show description for 98a7482
  RJSheppard

  authored
  98a7482

• Merge branch 'dev' into competing_hazards_recovery_infection_resolution

  RJSheppard

  authored
  b8980c1

• Merge branch 'dev' into older_age_state_immunity_init

  RJSheppard

  authored
  5eb21fa

• Merge branch 'dev' into new_epi_outputs_function

  RJSheppard

  authored
  8f11a06

• Removed missed merge commit line.

  RJSheppard

  committed
  62791a2

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

  Show description for ab030d7
  RJSheppard

  authored
  ab030d7

• Merge branch 'dev' into new_epi_outputs_function

  RJSheppard

  authored
  09a8c3e

• Correcting rendering tests (merging error).

  RJSheppard

  committed
  1b30562

Commits on May 28, 2024

• adding in n_spray output

  Show description for 47a1741
  htopazian

  committed
  47a1741

• fix typo renderer

  Show description for cde259c
  

  htopazian

  and

  giovannic

  committed
  cde259c

• update documentation

  Show description for 189041b
  

  htopazian

  and

  giovannic

  committed
  189041b

• Update test-vector-control.R

  htopazian

  committed
  c3be9c9

• add whitespace back in

  htopazian

  committed
  c2aea71

• fixing test, removing mortality changes

  htopazian

  committed
  9922527

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

  htopazian

  committed
  732bc0c

• fixing test, reverting mortality changes

  htopazian

  committed
  030b36e

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

  Show description for 46b8311
  htopazian

  authored
  46b8311

Commits on May 30, 2024

• Add GitHub workflow for continuous benchmarking.

  Show description for 3943de1
  plietar

  committed
  3943de1

• Remove raw data upload.

  Show description for 770f5e4
  plietar

  committed
  770f5e4

• Fix reporting of cancelled jobs

  plietar

  committed
  1d40ae0

• Downgrade ubuntu back to 22.04.

  Show description for de27f13
  plietar

  committed
  de27f13

• Add R_GC_MEM_GROW

  plietar

  committed
  bfa9656

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

  Show description for 3ecb72a
  plietar

  committed
  3ecb72a

Commits on Jun 6, 2024

• Merge branch 'dev' into feat/metapopulation_model

  htopazian

  authored
  5746a6b

• update documentation

  htopazian

  committed
  b852847

• fix metapop vignette

  Show description for 24a0253
  htopazian

  committed
  24a0253

Commits on Jun 12, 2024

• Merge branch 'dev' into new_epi_outputs_function

  RJSheppard

  authored
  3989fdc

Commits on Jun 24, 2024

• 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

  Show description for 352fbae
  RJSheppard

  committed
  352fbae

• 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…

  Show description for 8866b5a
  RJSheppard

  committed
  8866b5a

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

  RJSheppard

  committed
  7702e19

• 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…

  Show description for 479c26e
  RJSheppard

  committed
  479c26e

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

  Show description for 6a4311a
  RJSheppard

  committed
  6a4311a

• 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…

  Show description for 13748fd
  RJSheppard

  committed
  13748fd

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

  RJSheppard

  committed
  98c982f

• Removed missed merge commit line.

  RJSheppard

  committed
  16d83d3

• 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

  Show description for c649292
  RJSheppard

  committed
  c649292

• Re-added "age" to age outputs.

  RJSheppard

  committed
  c85ca93

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

  Show description for a6692e3
  RJSheppard

  committed
  a6692e3

Commits on Jun 26, 2024

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

  RJSheppard

  committed
  9142c58

Commits on Jul 1, 2024

• Update R/mixing.R

  Show description for 7bd8c0d
  

  htopazian

  and

  plietar

  authored
  7bd8c0d

• Update R/mixing.R

  Show description for 6d34636
  

  htopazian

  and

  plietar

  authored
  6d34636

Commits on Jul 3, 2024

• Removed redundant commented lines.

  RJSheppard

  committed
  b6787f7

• Remove unnecessary gitignore i386

  giovannic

  committed
  06c1e8d

• Add print step to touchstone workflow

  giovannic

  committed
  5fec286

• Revert "Add print step to touchstone workflow"

  Show description for 598ade0
  giovannic

  committed
  598ade0

• Export the run_resumable_simulation

  Show description for 91f8270
  plietar

  committed
  91f8270

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

  Show description for d05b335
  plietar

  authored
  d05b335

Commits on Jul 4, 2024

• Merge branch 'dev' into feat/metapopulation_model

  giovannic

  authored
  a4f66e2

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

  Show description for e51c6bc
  giovannic

  authored
  e51c6bc

• Improve cumsum performance

  plietar

  committed
  09e6e8c

• Remove outlining of function

  plietar

  committed
  0f21bbc

• Optimize competing hazards.

  Show description for a58e064
  plietar

  committed
  a58e064

• Fix empty occurs case.

  plietar

  committed
  1f7310b

Commits on Jul 10, 2024

• Simplify competing hazards as a single random draw.

  plietar

  committed
  e2242b2

• Try to optimize competing hazards

  plietar

  committed
  4c98559

• All all states but S to create_recovery_rates_process

  plietar

  committed
  0bd7c10

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

  plietar

  committed
  91697ba

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

  Show description for ded6876
  plietar

  committed
  ded6876

• Fix tests

  plietar

  committed
  8f9bcfc

Commits on Jul 11, 2024

• Fix more tests

  plietar

  committed
  f363b94

Commits on Jul 12, 2024

• Add tests

  plietar

  committed
  b339b7a

Commits on Jul 16, 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.

  Show description for b4825c7
  RJSheppard

  committed
  b4825c7

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

  RJSheppard

  committed
  4701748

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

  RJSheppard

  committed
  e004d5b

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

  RJSheppard

  committed
  65e5899

• 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.

  Show description for 0ff9f95
  RJSheppard

  committed
  0ff9f95

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

  Show description for 1886755
  RJSheppard

  committed
  1886755

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

  Show description for 36c4301
  RJSheppard

  authored
  36c4301

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

  RJSheppard

  committed
  1fda585

Commits on Jul 17, 2024

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

  Show description for 342799e
  RJSheppard

  authored
  342799e

Commits on Jul 22, 2024

• Assign names to all processes.

  Show description for 52f4aa0
  plietar

  committed
  52f4aa0

Commits on Jul 25, 2024

• Fixes for latest individual.

  plietar

  committed
  e3091a4

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

  Show description for 8bb953c
  plietar

  authored
  8bb953c

Commits on Jul 27, 2024

• Use new individual features

  plietar

  committed
  f2cacfb

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

  plietar

  committed
  e1bc3c1

• Fix output test

  plietar

  committed
  babc34b

Commits on Aug 20, 2024

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

  Show description for 3e76ce8
  RJSheppard

  authored
  3e76ce8

Commits on Sep 2, 2024

• Add a range check to bitset_index.

  Show description for 4913f03
  plietar

  committed
  4913f03

Commits on Sep 4, 2024

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

  Show description for 83375fe
  plietar

  authored
  83375fe

Commits on Sep 9, 2024

• pushed R21 profiles

  lmhaile

  committed
  6ecab00

Commits on Sep 10, 2024

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

  pwinskill

  committed
  0932eb7

• Redocument and tidy reference for vaccine profiles

  pwinskill

  committed
  c02b450

Commits on Sep 11, 2024

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

  Show description for 4bebd42
  RJSheppard

  committed
  4bebd42

• Minor documentation and performance fixed.

  RJSheppard

  committed
  2556bd6

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

  Show description for 9eef099
  RJSheppard

  authored
  9eef099

• Bump to version 2.0.0

  Show description for 8648c38
  giovannic

  authored
  8648c38

• Merge branch 'dev' into r21_profiles

  giovannic

  authored
  2d84551

Commits on Sep 12, 2024

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

  Show description for db57035
  giovannic

  authored
  db57035

• Update readme with hex in same style as malariaverse updates

  

  pwinskill

  authored and

  giovannic

  committed
  31d8188

• format adjustment

  

  pwinskill

  authored and

  giovannic

  committed
  0207954

• format adjustment

  

  pwinskill

  authored and

  giovannic

  committed
  485ab22

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

  Show description for 9cc9141
  giovannic

  authored
  9cc9141