Code

Issue #221: Add marginal model#426

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seabbs merged 62 commits intomainepinowcast/epidist:mainfrom cohort-modelepinowcast/epidist:cohort-modelCopy head branch name to clipboardDec 3, 2024

+1,248-187

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Commits on Nov 29, 2024

• Add cohort model template

  

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• Fix to previous commit (name as cohort_model)

  

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• Generate simulated cohort data

  

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• Add unweighted and weighted direct models

  

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• Thinking about custom family for pcd function

  

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• functions component of stanvars

  

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• Add transformed parameters for cohort model

  

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• Progress on implementing PCD model

  

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• Set q as vector

  

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• Get rid of params input

  

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• This would work, apart from it's the CDF. For the PMF need to import many primarycensored functions..

  

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• Almost working with "import all functions" strategy

  

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• Wrap up on attempt

  

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• Rename to marginal model

  

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• Move towards single wrap function with others imported

  

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• Just running into some C++ errors..

  

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• This doesn't change anything

  

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• Move to marginal model name and lint

  

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• Create aggregate data inside model conversion function for now

  

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• First draft on moving marginal_model into functions

  

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• Run document

  

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• Tests working up to valid Stan code

  

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• Regex version of marginal model

  

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• Use prep_marginal_obs

  

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• Improve assert for marginal model

  

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• Add pkgdown and document

  

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• Clean up scratch implementation

  

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• remove scratch file

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• update data format, formula, and family

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• update stan code

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• basic working version

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• add transformm data methods

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• start exploring the ebola example

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Commits on Dec 2, 2024

• add a helper to find meaningful relative_obs_times

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• get the full ebola vignette working with new variable requirements

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• improve return messages

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• update approx vignette

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• get ebole vignette passing by checking pp and related inputs

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• add marginal model integration tests

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• expand post processing tests

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• add marginal model

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• use the right transform data keyword

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• add ... pass through to make constructors correct

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• fix .summarise_n_by_formula test so error message is as expected

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• drop not required .row_id

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• check using ... properly

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• make the progress messages prettier for reducing data complexit:

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• check post process tests again

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• add a test for the specific transform data method

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• add some tests for the generic transform data method

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• put transform data tests in the correct folder

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Commits on Dec 3, 2024

• add a news update

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• change vignette language to talk about marginal model

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• update the FAQ to use the marginal variables

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• call it transformed_data not trans_data

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• change the error message to make it clear its a epidist limitation

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• update stan docs

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• Update NEWS.md

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• Update NEWS.md

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• Update NEWS.md

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• Update inst/stan/latent_model/functions.stan

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• Update setup.R

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