Code

distribution interface to dist_spec#504

Code

Merged

seabbs merged 136 commits intomainepiforecasts/EpiNow2:mainfrom dist-interfaceepiforecasts/EpiNow2:dist-interfaceCopy head branch name to clipboardMar 12, 2024

+3,774-2,590

Commits

Commits on Feb 20, 2024

• add distribution functions

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• deprecate "empty" distribution

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• make sd S3

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• only generate samples if any params aren't natural

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• update stan model with new dist interface

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• update lognormal parameters

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• return mean function to previous functionality

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• update data

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• deprecate dist_def functions

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• use natural parametrisations in dist_def functions

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• deprecate dist_spec

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• extract_single_dist function

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• update fix_dist to work with compsosite dists

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• extract squash

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• update parameters to extract

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• specify lower bounds in function

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• pass lower bounds to stan model

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• update sample/report functions

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• max squash adjust report

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• update dist functions to new syntax

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• re-create data

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• update get_dist to new syntax

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• fully deprecate get fnuctions

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• create delay inits separately

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• max squash again

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• return correct dist in estimate_truncation

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• few more examples/docs

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• fix tests

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• add documentation to dist interface

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• add input checks

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• sd function to work with composite dists

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• warn when not using natural parameters

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• ensure bounds are respected in stan

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• add empty distribution for legacy reasons

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• add checks to dist_skel

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• use lapply for parameters

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• don't calculate sd if length 1

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• use uncertain reporting in example

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• don't add one to sd

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• return correct parameters

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• dist_skel: calculate rate everywhere

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• update dist_skel examples

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• add missing man file

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• don't run internal examples

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• demote warning to message

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• update syntax everywhere

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• add news item

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• turn sd into an internal function

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• fix distribution documentation

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• remove obselete default

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• spell checking

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• use correct sd function

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• linting

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• remove obsolete tests

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• loop over all parameters

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• update touchstone arguments

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• linting

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• fix regex search/replace gone wrong

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• remove obsolete space

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• update strategy for estimating uncertainty

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• update uncertain parameter transformations

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• add missing sd to parameter sampling

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• update / recompile vignettes

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• update var names

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• rename argument in docs

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• update man pages

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• update test result

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• add reviewer

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• base scaling on variance, not sd

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• re-render vignettes

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• full text capitalisation of distributions

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• separate dist_spec from stan model

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• adjust tests/code for new dist_spec set up

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• re-create examples

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• re-doc

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• update tests

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• new dist_spec in estimate_truncation example

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• update get_seeding_time with updated dist_spec

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• estimate_truncation and seeding time tests

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• update truncation dist in estimate_truncation

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• remove more uses of old dist_spec

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• SD explicitly to zero for fixed

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• give names

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• fix typo

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• fix indent

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• fix another typo

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• squash bugs highlighted by tests

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• remove missing variable

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• linting

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• add missing docs

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• import transpose

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• ensure sd is positive

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• fix estimate_truncation example

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• make tolerance user-settable

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• use purrr::map instead of lapply

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• fix stan dist test

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• fix plotting

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• Apply suggestions from code review

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• rate and scale examples for Gamma

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• capitalise gamma and lognormal

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• change to single hash

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• use bar in normal_cdf

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• remove estraneous backticks

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• remove space before left parenthesis

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Commits on Feb 21, 2024

• split up dist.R

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• move deprecated dist_spec function

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• add examples

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Commits on Feb 26, 2024

• initial design sketch

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Commits on Feb 28, 2024

• make parameter conversion more flexible

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• add test for alternative gama params

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• Merge remote-tracking branch 'origin/main' into dist-interface

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• update syntax in simulate_infections

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• add missing tag

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• update man pages

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• update estimate_secondary tests

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• update simulate_infections for new interface

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• udpate snapshots

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• get_dist deprecation test with natural params

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• update phi syntax

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• hide internal example

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• Merge remote-tracking branch 'origin/main' into dist-interface

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• update deprecations

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• use toString

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• pmf -> NonParametric

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• Merge branch 'main' into dist-interface

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Commits on Feb 29, 2024

• Merge remote-tracking branch 'origin/main' into dist-interface

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• add american spelling

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Commits on Mar 4, 2024

• fix gamma deprecation

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• Merge branch 'main' into dist-interface

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Commits on Mar 6, 2024

• add new functions to pkgdown

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• Merge branch 'main' into dist-interface

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• update vignette

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• recompile vignettes

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Commits on Mar 12, 2024

• Merge branch 'main' into dist-interface

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• Apply suggestions from code review

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• link to design doc

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