Code

Vector inputs for ODE models#176

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pratikunterwegs merged 88 commits intomainepiverse-trace/epidemics:mainfrom feature/ode-model-apiepiverse-trace/epidemics:feature/ode-model-apiCopy head branch name to clipboardMar 14, 2024

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Commits on Mar 11, 2024

• Model output processing fn renamed, returns DT

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• Update docs for model output processing fn

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• Default model cpp accepts param vecs, WIP #166

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• Vacamole model cpp accepts param vecs, WIP #166

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• Diphtheria model cpp accepts param vecs, WIP #166

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• Ebola model uses renamed output processing

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• Fn to transpose a list

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• Fns for recycling vectors

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• Update recyclability testing in ODE cpp fns

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• Add cross-checking fns, WIP #175

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• Rm .check_args_model_default(), WIP #175

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• Default model Cpp handles vector of interventions, WIP #167

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• Fns to cross check model elements

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• Simplify checking/prepping default mod args

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• Default model C++ handles lists of vax and populations, WIP #167

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• Add tests for vectorised input, WIP #166, WIP #167

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• Default model fn C++ returns simple DF for scalars, WIP #177

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• Restore tests for scalar args default model C++

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• Skip checks default model R implementation

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• Correct .cross_check_vaccination(), WIP #175

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• Vacamole model C++ accepts lists of components, WIP #167

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• Rename args checker fn for Vacamole

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• Update args checker fn default model

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• Update author list; add @TimTaylor @adamkucharski

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• Update CITATION.cff

  

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• .cross_check_intervention: add check for rate intervs

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• Vacamole: vaccination is optional, use correct internal fn

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• WIP: new test suite for Vacamole model

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• Minor input checks to default model

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• Allow vaccination as NULL for Vacamole

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• Full rewrite tests for default model

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• Full rewrite of tests for Vacamole

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• Remove previous tests for vectorised fn

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• Rename default and Vacamole test files

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• Rename test file for ebola model

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• Refactor diphtheria model to vectorised form, WIP #166, WIP #167

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• Refactor diphtheria args checker, WIP #175

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• Minor corrections to args checkers, WIP #175

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• .output_to_df() takes names from demography, rm get_parameter()

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• Test suite for the diphtheria model, WIP #178

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• Access params without get_parameter()

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• Rm old Rd files

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• More input checks for population()

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• .cross_check_interv checks if contact intervs are allowed

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• Remove wrappers to R-only ODEs; WIP #162

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• Rm .transpose_base(), unify vector recyling fns, no_time_dep() now internal w/ def val

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• Update pkgdown YAML

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• Fix .no_time_dependence() list naming

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• Update function documentation for model params

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• Rmv lang suffixes in model func names; standardise filenames

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• Further renaming of model fns in tests and helper fns

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• Rationalise tests for time-dependence

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• Rename ebola snapshot file

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• Remove benchmarking vignette

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• Rename vignette files; use new fn names

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• Update Readme with fn name

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• Update pkg infrastructure

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• Update tests for new_infections()

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• Add tests for vector recycling tools

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• Minor updates to pkg docs and internal tools

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• Update CITATION.cff

  

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• Update header guards

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• Renaming dummy elements file; document cross-check fns, WIP #175

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• Trigger Readme build

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• Update WORDLIST

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• Remove internal args from model output

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• Add scenario modelling + param uncertainty vignette, fixes #183

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• Automatic readme update

  

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• Update CITATION.cff

  

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• Update dev NEWS and rm {deSolve} from Suggests

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• Update CITATION.cff

  

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• Add motivation for param uncertainty modelling

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• Add tests for effect of cumulative contact intervs, WIP #187

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• Update scenario modelling vignette, WIP #187

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• Use magrittr pipe throughout

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• Add {ggdist} and {purrr} to Suggests

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• Update CITATION.cff

  

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• Pull dummy element creator fns internal, prefix with .

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• Update model docs and comments

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• Update tests for dummy element creators

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• Rm unused params in documentation

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• Scenario modelling vignette adds plots, by_group size

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• Correction to Vacamole vignette from internal .no_vax

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• Add EpiEstim comment, correct R description

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• Automatic readme update

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Commits on Mar 12, 2024

• Add comments on complex input checks

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• Update vignette and WORDLIST

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Commits on Mar 13, 2024

• Correct typo in vignette

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