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Parameter and output documentation.#299

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RJSheppard merged 30 commits intodevmrc-ide/malariasimulation:devfrom parameter_documentation_orderingmrc-ide/malariasimulation:parameter_documentation_orderingCopy head branch name to clipboardMay 24, 2024

+404-363

Commits

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

• 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 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

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

  RJSheppard

  committed
  435180d

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

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

Commits on May 23, 2024

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

  Show description for 69ea7b6
  RJSheppard

  authored
  69ea7b6

• 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