Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

ppc_km_overlay(): PPC for (right-)censored data #234

Merged
merged 36 commits into from
Oct 1, 2020
Merged

ppc_km_overlay(): PPC for (right-)censored data #234

merged 36 commits into from
Oct 1, 2020

Commits on Aug 12, 2020

  1. Created ppc_km_overlay(), a function for performing a PPC on right-ce… 

    …nsored data using the Kaplan-Meier estimator. Note that for the replicated data (which is always uncensored), the Kaplan-Meier estimator reduces to "1 - ECDF" with ECDF denoting the ordinary empirical cumulative distribution function.
    @fweber144
    fweber144 committed Aug 12, 2020
    Configuration menu
    Copy the full SHA
    f37a86b View commit details
    Browse the repository at this point in the history

  2. Added a check for package "survival" in ppc_km_overlay().

    @fweber144
    fweber144 committed Aug 12, 2020
    Configuration menu
    Copy the full SHA
    149b2f1 View commit details
    Browse the repository at this point in the history

  3. DESCRIPTION file: Added packages "survival" and "ggfortify" to "Sugge… 

    …sts" list.
    @fweber144
    fweber144 committed Aug 12, 2020
    Configuration menu
    Copy the full SHA
    d4433ff View commit details
    Browse the repository at this point in the history

  4. Added a description of ppc_km_overlay() to the roxygen2 documentation.

    @fweber144
    fweber144 committed Aug 12, 2020
    Configuration menu
    Copy the full SHA
    029f5e0 View commit details
    Browse the repository at this point in the history

  5. Minor improvement in the roxygen2 documentation of ppc_km_overlay().

    @fweber144
    fweber144 committed Aug 12, 2020
    Configuration menu
    Copy the full SHA
    0837f99 View commit details
    Browse the repository at this point in the history

  6. Another minor improvement in the roxygen2 documentation of ppc_km_ove… 

    …rlay().
    @fweber144
    fweber144 committed Aug 12, 2020
    Configuration menu
    Copy the full SHA
    5f9acd7 View commit details
    Browse the repository at this point in the history

  7. Updated the documentation using devtools::document().

    @fweber144
    fweber144 committed Aug 12, 2020
    Configuration menu
    Copy the full SHA
    552a37a View commit details
    Browse the repository at this point in the history

  8. Another minor improvement in the roxygen2 documentation of ppc_km_ove… 

    …rlay(), this time concerning argument 'status_y'. Updated the documentation using devtools::document().
    @fweber144
    fweber144 committed Aug 12, 2020
    Configuration menu
    Copy the full SHA
    e4ed9e3 View commit details
    Browse the repository at this point in the history

  9. Added unit tests for ppc_km_overlay().

    @fweber144
    fweber144 committed Aug 12, 2020
    Configuration menu
    Copy the full SHA
    606cabc View commit details
    Browse the repository at this point in the history

  10. Fixed a bug in the unit tests for ppc_km_overlay() (had to add 'statu… 

    …s_y').
    @fweber144
    fweber144 committed Aug 12, 2020
    Configuration menu
    Copy the full SHA
    d9e5759 View commit details
    Browse the repository at this point in the history

  11. Fixed a bug in the unit tests for ppc_km_overlay() (had to name argum… 

    …ent 'status_y' explicitly).
    @fweber144
    fweber144 committed Aug 12, 2020
    Configuration menu
    Copy the full SHA
    70c0e0e View commit details
    Browse the repository at this point in the history

  12. Ran vdiffr::manage_cases() to validate the ppc_km_overlay() figures f… 

    …or the unit tests.
    @fweber144
    fweber144 committed Aug 12, 2020
    Configuration menu
    Copy the full SHA
    c0116eb View commit details
    Browse the repository at this point in the history

  13. In ppc_km_overlay(): Use aes_() instead of aes() for two reasons: 

      - consistency with the existing code,
  - to prevent the NOTE "no visible binding for global variable" when running R CMD CHECK.
    @fweber144
    fweber144 committed Aug 12, 2020
    Configuration menu
    Copy the full SHA
    d518368 View commit details
    Browse the repository at this point in the history

  14. In ppc_km_overlay(): Use '.data$' in the call to dplyr::mutate() to p… 

    …revent the NOTE "no visible binding for global variable" when running R CMD CHECK.
    @fweber144
    fweber144 committed Aug 12, 2020
    Configuration menu
    Copy the full SHA
    a02442e View commit details
    Browse the repository at this point in the history

  15. In ppc_km_overlay(): Indent the call to dplyr::mutate().

    @fweber144
    fweber144 committed Aug 12, 2020
    Configuration menu
    Copy the full SHA
    4d6ae9d View commit details
    Browse the repository at this point in the history

Commits on Aug 26, 2020

  1. Fix the NOTE "release_questions: missing arguments not allowed in cal… 

    …ls to 'c'" thrown by devtools::check().
    @fweber144
    fweber144 committed Aug 26, 2020
    Configuration menu
    Copy the full SHA
    ce5df55 View commit details
    Browse the repository at this point in the history

  2. Add argument "check_unq" to validate_group() telling it whether or no… 

    …t to error if there is only one unique value.
    @fweber144
    fweber144 committed Aug 26, 2020
    Configuration menu
    Copy the full SHA
    b9d53c5 View commit details
    Browse the repository at this point in the history

  3. Use the new argument "check_unq" of validate_group() in ppc_km_overla… 

    …y().
    @fweber144
    fweber144 committed Aug 26, 2020
    Configuration menu
    Copy the full SHA
    52036c8 View commit details
    Browse the repository at this point in the history

  4. Re-ran roxygen2 to update the documentation.

    @fweber144
    fweber144 committed Aug 26, 2020
    Configuration menu
    Copy the full SHA
    6bdc102 View commit details
    Browse the repository at this point in the history

Commits on Sep 10, 2020

  1. remove check for unique group values

    @jgabry
    jgabry committed Sep 10, 2020
    Configuration menu
    Copy the full SHA
    b9345af View commit details
    Browse the repository at this point in the history

  2. move suggested package checks to top 

    this way we error before doing any computations
    @jgabry
    jgabry committed Sep 10, 2020
    Configuration menu
    Copy the full SHA
    c7cb255 View commit details
    Browse the repository at this point in the history

Commits on Sep 18, 2020

  1. In ppc_km_overlay(): Ensure that the observed data gets plotted last … 

    …by reordering the levels of the factor "strata".
    @fweber144
    fweber144 committed Sep 18, 2020
    Configuration menu
    Copy the full SHA
    34a445e View commit details
    Browse the repository at this point in the history

  2. Re-ran roxygen2 to update the documentation.

    @fweber144
    fweber144 committed Sep 18, 2020
    Configuration menu
    Copy the full SHA
    72cea0e View commit details
    Browse the repository at this point in the history

  3. Update the tests 

    Simply remove those tests which are not up-to-date anymore since argument "group" of validate_group() is now allowed to have a single unique value.
    @fweber144
    fweber144 committed Sep 18, 2020
    Configuration menu
    Copy the full SHA
    5323a1d View commit details
    Browse the repository at this point in the history

  4. Update the expected results for the visual ppc_km_overlay() tests.

    @fweber144
    fweber144 committed Sep 18, 2020
    Configuration menu
    Copy the full SHA
    43fe549 View commit details
    Browse the repository at this point in the history

Commits on Sep 28, 2020

  1. Update NEWS and add Frank Weber as contributor

    @jgabry
    jgabry committed Sep 28, 2020
    Configuration menu
    Copy the full SHA
    079617e View commit details
    Browse the repository at this point in the history

  2. add missing comma in Suggests

    @jgabry
    jgabry committed Sep 28, 2020
    Configuration menu
    Copy the full SHA
    7cd815d View commit details
    Browse the repository at this point in the history

Commits on Sep 30, 2020

  1. Moved ppc_km_overlay() from ppc-distributions.R to ppc-censoring.R to… 

    … create a new documentation page "PPC-censoring".
    @fweber144
    fweber144 committed Sep 30, 2020
    Configuration menu
    Copy the full SHA
    d50b7dd View commit details
    Browse the repository at this point in the history

  2. Adopt the example for censored data.

    @fweber144
    fweber144 committed Sep 30, 2020
    Configuration menu
    Copy the full SHA
    33d5432 View commit details
    Browse the repository at this point in the history

  3. Add a reference for Kaplan and Meier (1958).

    @fweber144
    fweber144 committed Sep 30, 2020
    Configuration menu
    Copy the full SHA
    fe6eb2b View commit details
    Browse the repository at this point in the history

  4. For Kaplan and Meier (1958), follow the citation style from "referenc… 

    …e-loo.R".
    @fweber144
    fweber144 committed Sep 30, 2020
    Configuration menu
    Copy the full SHA
    3836da1 View commit details
    Browse the repository at this point in the history

  5. Re-ran roxygen2 to update the documentation.

    @fweber144
    fweber144 committed Sep 30, 2020
    Configuration menu
    Copy the full SHA
    14bfa1a View commit details
    Browse the repository at this point in the history

Commits on Oct 1, 2020

  1. PPC-overview: Add a link to PPC-censoring.

    @fweber144
    fweber144 committed Oct 1, 2020
    Configuration menu
    Copy the full SHA
    fdd5d47 View commit details
    Browse the repository at this point in the history

  2. PPC-overview: Improve the label for the link to page PPC-censoring.

    @fweber144
    fweber144 committed Oct 1, 2020
    Configuration menu
    Copy the full SHA
    6e06cc7 View commit details
    Browse the repository at this point in the history

  3. Re-ran roxygen2 to update the documentation.

    @fweber144
    fweber144 committed Oct 1, 2020
    Configuration menu
    Copy the full SHA
    b639113 View commit details
    Browse the repository at this point in the history

  4. Add a note requesting suggestions of additional plots for censored data 

    I think to use two paragraphs here we need to add the `@description` tag, otherwise it treats the second paragraph as if it had the `@details` tag.
    @jgabry
    jgabry committed Oct 1, 2020
    Configuration menu
    Copy the full SHA
    bbd7767 View commit details
    Browse the repository at this point in the history