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Feature/restructure #1

Merged
merged 48 commits into from
Oct 20, 2023
Merged

Feature/restructure #1

merged 48 commits into from
Oct 20, 2023

Commits on Sep 5, 2023

  1. - initial test commit

    @wojcieko
    wojcieko committed Sep 5, 2023
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Commits on Sep 15, 2023

  1. - feature restructuring done

    @wojcieko
    wojcieko committed Sep 15, 2023
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  2. - removed helper.R, became superflouos

    @wojcieko
    wojcieko committed Sep 15, 2023
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  3. - updated documentation

    @wojcieko
    wojcieko committed Sep 15, 2023
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Commits on Sep 22, 2023

  1. Create dummy vignette

    @sebastianbossert
    sebastianbossert committed Sep 22, 2023
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  2. - small bug fix for significance test

    @wojcieko
    wojcieko committed Sep 22, 2023
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Commits on Sep 25, 2023

  1. fixed warnings in cmd check

    @Xyarz
    Xyarz committed Sep 25, 2023
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Commits on Sep 29, 2023

  1. First draft vignette - including only test step

    @sebastianbossert
    sebastianbossert committed Sep 29, 2023
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Commits on Oct 4, 2023

  1. - included plot function

    @wojcieko
    wojcieko committed Oct 4, 2023
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  2. -fixed typo in plot function

    @wojcieko
    wojcieko committed Oct 4, 2023
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  3. - getPosterior can now take custom vectors for mu and sd 

    - other small changes
    @wojcieko
    wojcieko committed Oct 4, 2023
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  4. - for single set of simulated data (e.g. observed data), getPosterior… 

    … returns the posterior directly, not the list
    @wojcieko
    wojcieko committed Oct 4, 2023
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Commits on Oct 5, 2023

  1. Inclusion of model fits.

    @sebastianbossert
    sebastianbossert committed Oct 5, 2023
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  2. Addition of (minimum) explanation text to vignette

    @sebastianbossert
    sebastianbossert committed Oct 5, 2023
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Commits on Oct 6, 2023

  1. Merge pull request #2 from Boehringer-Ingelheim/feature/vignettes 

    Feature/vignettes
    @sebastianbossert
    sebastianbossert authored Oct 6, 2023
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  2. Correction of two minor bugs in the vignette file.

    @sebastianbossert
    sebastianbossert committed Oct 6, 2023
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Commits on Oct 9, 2023

  1. Merge branch 'feature/restructure' of https://github.com/Boehringer-I… 

    …ngelheim/BayesianMCPMod into feature/restructure
    @Xyarz
    Xyarz committed Oct 9, 2023
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  2. fixed github action errors

    @Xyarz
    Xyarz committed Oct 9, 2023
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  3. added missing dependency

    @Xyarz
    Xyarz committed Oct 9, 2023
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  4. styled vignette!

    @Xyarz
    Xyarz committed Oct 9, 2023
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  5. added tests

    @Xyarz
    Xyarz committed Oct 9, 2023
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  6. added missing dependency

    @Xyarz
    Xyarz committed Oct 9, 2023
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Commits on Oct 10, 2023

  1. added covr workflow and badges

    @Xyarz
    Xyarz committed Oct 10, 2023
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  2. adjusted covr yaml

    @Xyarz
    Xyarz committed Oct 10, 2023
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  3. added pkgdown yaml

    @Xyarz
    Xyarz committed Oct 10, 2023
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  4. removed error

    @Xyarz
    Xyarz committed Oct 10, 2023
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  5. alter ref

    @Xyarz
    Xyarz committed Oct 10, 2023
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  6. - interim commit to enable pulling latest updated

    @wojcieko
    wojcieko committed Oct 10, 2023
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Commits on Oct 12, 2023

  1. - included bootstrapping credible bands 

    Merge branch 'feature/restructure' of https://github.com/Boehringer-Ingelheim/BayesianMCPMod into feature/restructure

# Conflicts:
#	vignettes/analysis_normal.Rmd
    @wojcieko
    wojcieko committed Oct 12, 2023
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  2. - adapted vignette to new plot function

    @wojcieko
    wojcieko committed Oct 12, 2023
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  3. - fixed changes in plot test file due to re-naming

    @wojcieko
    wojcieko committed Oct 12, 2023
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  4. - devtools::check() pleasing

    @wojcieko
    wojcieko committed Oct 12, 2023
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Commits on Oct 13, 2023

  1. adjusted bootstrapping.R line, error in Vignette as well as created t… 

    …ests for bootstrapping file
    @Xyarz
    Xyarz committed Oct 13, 2023
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  2. - typo correction in bootstrapping function

    @wojcieko
    wojcieko committed Oct 13, 2023
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  3. adjusted tests

    @Xyarz
    Xyarz committed Oct 13, 2023
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  4. - added color for bootstrap credible bands (and median) in plot_model… 

    …Fits()

- changed cr_intv = TRUE as default in plot_modelFits()
- added bootstrap median
- added predict.ModelFits()
- removed superfluous arguments from getModelFitSimple()
- corrected typos
    @wojcieko
    wojcieko committed Oct 13, 2023
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  5. Merge branch 'feature/restructure' of https://github.com/Boehringer-I… 

    …ngelheim/BayesianMCPMod into feature/restructure
    @wojcieko
    wojcieko committed Oct 13, 2023
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  6. adjusted test calls

    @Xyarz
    Xyarz committed Oct 13, 2023
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  7. - corrected typo on bootstrap tests 

    - updated plot function in vignette
    @wojcieko
    wojcieko committed Oct 13, 2023
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  8. Merge branch 'feature/restructure' of https://github.com/Boehringer-I… 

    …ngelheim/BayesianMCPMod into feature/restructure
    @wojcieko
    wojcieko committed Oct 13, 2023
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  9. - introduced S3 methods for modelFits and postList: plot and predict … 

    …for the former, print and summary for the latter
    @wojcieko
    wojcieko committed Oct 13, 2023
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  10. - corrected typo in predict.ModelFit()

    @wojcieko
    wojcieko committed Oct 13, 2023
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Commits on Oct 14, 2023

  1. - added S3 printing methods for BayesianMCP, BayesianMCPMod, modelFits 

    - added separate file for S3 methods
- added function performMayesianMCPMod
- renamed function BMCPMod to perform BayesianMCP
- renamed function BayesMCPMod to BayesMCPi
- unified handling of posterior_list vs posterior in performBayesianMCP and getModelFits
    @wojcieko
    wojcieko committed Oct 14, 2023
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  2. - added function assessDesign() 

    - fixed typo in performBayesianMCPMod
- added functionality to print.BayesianMCPMod
- added getModelData
- to vignette: added automatic numbering, and assessment of trial design
    @wojcieko
    wojcieko committed Oct 14, 2023
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  3. - added new functions getContrMat, getCritProb, getPriorList 

    - changed simulation to output a single data set if !is.null(true_model)
- updated vignette
    @wojcieko
    wojcieko committed Oct 14, 2023
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Commits on Oct 16, 2023

  1. Vignette update (other trial example, making use of newly available f… 

    …unctions,...)
    @sebastianbossert
    sebastianbossert committed Oct 16, 2023
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Commits on Oct 18, 2023

  1. New draft vignette around simulation added

    @sebastianbossert
    sebastianbossert committed Oct 18, 2023
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Commits on Oct 19, 2023

  1. Further updates in vignettes.

    @sebastianbossert
    sebastianbossert committed Oct 19, 2023
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