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distribution interface to dist_spec #504

Merged
merged 136 commits into from
Mar 12, 2024
Merged

distribution interface to dist_spec #504

merged 136 commits into from
Mar 12, 2024

Commits on Feb 20, 2024

  1. add distribution functions

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  2. deprecate "empty" distribution

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  3. make sd S3

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  4. only generate samples if any params aren't natural

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  5. update stan model with new dist interface

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  6. update lognormal parameters

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  7. return mean function to previous functionality

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  8. update data

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  9. deprecate dist_def functions

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  10. use natural parametrisations in dist_def functions

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  11. deprecate dist_spec

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  12. extract_single_dist function

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  13. update fix_dist to work with compsosite dists

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  14. extract squash

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  15. update parameters to extract

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  16. specify lower bounds in function

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  17. pass lower bounds to stan model

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  18. update sample/report functions

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  19. max squash adjust report

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  20. update dist functions to new syntax

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  21. re-create data

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  22. update get_dist to new syntax

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  23. fully deprecate get fnuctions

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  24. create delay inits separately

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  25. max squash again

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  26. return correct dist in estimate_truncation

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  27. few more examples/docs

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  28. fix tests

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  29. add documentation to dist interface

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  30. add input checks

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  31. sd function to work with composite dists

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  32. warn when not using natural parameters

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  33. ensure bounds are respected in stan

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  34. add empty distribution for legacy reasons

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  35. add checks to dist_skel

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  36. use lapply for parameters

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  37. don't calculate sd if length 1

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  38. use uncertain reporting in example

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  39. don't add one to sd

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  40. return correct parameters

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  41. dist_skel: calculate rate everywhere

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  42. update dist_skel examples

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  43. add missing man file

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  44. don't run internal examples

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  45. demote warning to message

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  46. update syntax everywhere

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  47. add news item

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  48. turn sd into an internal function

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  49. fix distribution documentation

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  50. remove obselete default

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  51. spell checking

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  52. use correct sd function

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  53. linting

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  54. remove obsolete tests

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  55. loop over all parameters

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  56. update touchstone arguments

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  57. linting

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  58. fix regex search/replace gone wrong

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  59. remove obsolete space

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  60. update strategy for estimating uncertainty

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  61. update uncertain parameter transformations

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  62. add missing sd to parameter sampling

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  63. update / recompile vignettes

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  64. update var names

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  65. rename argument in docs

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  66. update man pages

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  67. update test result

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  68. add reviewer 

    Co-authored-by: Sam Abbott <s.e.abbott12@gmail.com>
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  69. base scaling on variance, not sd

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  70. re-render vignettes

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  71. full text capitalisation of distributions

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  72. separate dist_spec from stan model

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  73. adjust tests/code for new dist_spec set up

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  74. re-create examples

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  75. re-doc

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  76. update tests

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  77. new dist_spec in estimate_truncation example

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  78. update get_seeding_time with updated dist_spec

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  79. estimate_truncation and seeding time tests

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  80. update truncation dist in estimate_truncation

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  81. remove more uses of old dist_spec

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  82. SD explicitly to zero for fixed

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  83. give names

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  84. fix typo

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  85. fix indent

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  86. fix another typo

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  87. squash bugs highlighted by tests

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  88. remove missing variable

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  89. linting

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  90. add missing docs

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  91. import transpose

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  92. ensure sd is positive

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  93. fix estimate_truncation example

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  94. make tolerance user-settable

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  95. use purrr::map instead of lapply

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  96. fix stan dist test

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  97. fix plotting

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  98. Apply suggestions from code review 

    Co-authored-by: Sam Abbott <s.e.abbott12@gmail.com>
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  99. rate and scale examples for Gamma 

    Co-authored-by: Sam Abbott <s.e.abbott12@gmail.com>
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  100. capitalise gamma and lognormal 

    Co-authored-by: Sam Abbott <s.e.abbott12@gmail.com>
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  101. change to single hash

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  102. use bar in normal_cdf

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  103. remove estraneous backticks

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  104. remove space before left parenthesis

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Commits on Feb 21, 2024

  1. split up dist.R

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  2. move deprecated dist_spec function

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  3. add examples

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Commits on Feb 26, 2024

  1. initial design sketch

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Commits on Feb 28, 2024

  1. make parameter conversion more flexible

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  2. add test for alternative gama params

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

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  4. update syntax in simulate_infections

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  5. add missing tag

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  6. update man pages

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  7. update estimate_secondary tests

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  8. update simulate_infections for new interface

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  9. udpate snapshots

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  10. get_dist deprecation test with natural params

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  11. update phi syntax

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  12. hide internal example

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

    @sbfnk
    sbfnk committed Feb 28, 2024
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  14. update deprecations

    @sbfnk
    sbfnk committed Feb 28, 2024
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  15. use toString

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    sbfnk committed Feb 28, 2024
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  16. pmf -> NonParametric

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    sbfnk committed Feb 28, 2024
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  17. Merge branch 'main' into dist-interface

    @seabbs
    seabbs authored Feb 28, 2024
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Commits on Feb 29, 2024

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

    @sbfnk
    sbfnk committed Feb 29, 2024
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  2. add american spelling

    @sbfnk
    sbfnk committed Feb 29, 2024
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Commits on Mar 4, 2024

  1. fix gamma deprecation

    @sbfnk
    sbfnk committed Mar 4, 2024
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  2. Merge branch 'main' into dist-interface

    @sbfnk
    sbfnk committed Mar 4, 2024
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Commits on Mar 6, 2024

  1. add new functions to pkgdown

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    sbfnk committed Mar 6, 2024
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  2. Merge branch 'main' into dist-interface

    @sbfnk
    sbfnk committed Mar 6, 2024
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  3. update vignette

    @sbfnk
    sbfnk committed Mar 6, 2024
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  4. recompile vignettes

    @sbfnk
    sbfnk committed Mar 6, 2024
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Commits on Mar 12, 2024

  1. Merge branch 'main' into dist-interface

    @seabbs
    seabbs authored Mar 12, 2024
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  2. Apply suggestions from code review 

    Co-authored-by: Sam Abbott <s.e.abbott12@gmail.com>
    @sbfnk @seabbs
    sbfnk and seabbs authored Mar 12, 2024
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  3. link to design doc

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    sbfnk committed Mar 12, 2024
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