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Update {epiparameter} usage #100

Merged
merged 36 commits into from
Mar 6, 2024
Merged

Update {epiparameter} usage #100

merged 36 commits into from
Mar 6, 2024

Commits on Feb 29, 2024

  1. Update {epiparameter} usage

    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  2. fixing failing checks

    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  3. fixing failing checks

    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  4. Changing parameter description from pathogen to disease

    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  5. Updating epiparameter version in renv::use (from fd250ce to e531c09)

    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  6. Using {epiparameter} instead of {epitrix} when converting summary sta… 

    …tistics to distribution parameters
    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  7. Fixing failing check: issue with line length (111 when it should be <80)

    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  8. Using {epiparameter} instead of {distcrete} to discretise distributio… 

    …n and plot results
    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  9. Removing white space to pass checks

    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  10. Fixing line indentation lintr

    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  11. Removing unused packages lintr

    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  12. Removing author from arguments when using epiparameter_db

    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  13. Updating epiparameter version to discretise normal distribution

    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  14. Change use_epiparameter to use_epiparameter_database

    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  15. Changing hard coded gamma distribution to distribution from params list

    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  16. Removing as.list since distcrete is no longer used

    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  17. Changing epiparameter_disease to disease_name to create epidist o… 

    …bjects when manually providing disease data
    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  18. Changing SI object name to discretise both dist from epiparameter and… 

    … manually supplied
    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  19. Changing si_epiparameter to si_epidist to match SI object name create… 

    …d through epidist_db
    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  20. Taking only parameterised distributions from {epiparameter}

    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  21. Updating code to use r() with an epidist object

    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  22. Updating function to convert parameters with epiparameter

    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  23. Removing rio:: to fix lintr error

    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  24. Remove grateful:: to fix lintr error

    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  25. Creating epidist for manually supplied parameters so that `epiparamet… 

    …er` functions can be used uniformly in subsequent steps
    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  26. Updating distribution mean and sd objects for plotting

    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  27. Update epiparameter use in R0 rmd chunk

    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  28. Updating quantile function from $q to quantile()

    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  29. Changing get_parameters to parenthesis to extract mean and sd from ep… 

    …idist object
    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  30. Removing auto_calc_params

    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  31. Updating authors

    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  32. Removing si_cv as no longer being used

    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  33. Adding ORCID

    @CarmenTamayo @Bisaloo
    CarmenTamayo authored and Bisaloo committed Feb 29, 2024
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  34. Do not explicitly namespace epiparameter 

    To avoid loading it (and its dependencies) before renv::use() even got the chance to run, thus creating version conflicts between already loaded packages and requested versions.
It seems for some reason that explicitly namespaced packages are automatically loaded in Rmd documents
    @Bisaloo
    Bisaloo committed Feb 29, 2024
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Commits on Mar 6, 2024

  1. Get EpiEstim chunk to work with SI passed as epidist

    @Bisaloo
    Bisaloo committed Mar 6, 2024
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  2. Get i2extras to work with SI passed as epidist

    @Bisaloo
    Bisaloo committed Mar 6, 2024
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