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Add PBC database as demostration data #44

Merged
merged 13 commits into from
Dec 13, 2024
Merged

Add PBC database as demostration data #44

merged 13 commits into from
Dec 13, 2024

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DougManuel
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This pull request adds the PBC data to demonstrate how to create and use the package. The PBC data is openly accessible and available in the survival package.
Included are:

  • the data: pbc.Rd
  • variables sheet: pbc_variables.csv
  • variable details sheet: pbc_variable_details.csv
  • dataset metadata: pbc_database.yaml. This is new file, and it may require a discussion. At this point, it is a simple meta to describe the data provenance, but this file could potentially be used for a different purposes, such as generating a data dictionary. For now, it is simply introduced as a good data management practice.

note: mtcars is also included in the package, and this data requires similar improvements and additions as is proposed for the pbc data.

reikookamoto
reikookamoto reviewed Nov 19, 2024
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Review the files to ensure they align with the directory structure and organization best practices outlined in the R Packages book

R/pbc_worksheets.R Outdated Show resolved Hide resolved
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DougManuel added a commit that referenced this pull request Nov 26, 2024
@DougManuel
Update data and metadata names for consistency. See #44.
8b18d25 
Starts to transition to pbc data for vignette, but with bugs remaining in derived_variables.Rmd
@DougManuel
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  • Documentation website not yet building on my computer with errors at the end of derived_variables.Rmd.

Bug fixes and improvements in recent commits include:

  1. Renamed data files for a more consistent approach to address bugs and confusion. See #details in data.R.

pbc.rda - Primary Biliary Cirrhosis (PBC) data.
pbc_metadata.rda - Metadata for the PBC data. A list containing the database name and other identification information.
pbc_variables.rda - variables metadata for the PBC dataset. Metadata for each variable in the PBC data. A data frame with 24 rows and 11 columns.
pbc_variable_details.rda - variable_details metadata for the PBC dataset. Metadata for variable category or value label in the PBC data.

recodeflow/R/data.R

Line 7 in dcf600e

#' @details

  1. Updated pbc_variables:
  • Address bugs in NA data, incorrect names and labels, the addition of the age group categorical variables, and derived variable example 'example_der`.
  1. Changed data in derived_variables.Rmd to pbc data.
  1. prep_pbc_data.R updated to generate all .rda data. Remember to execute this file when you change pbc_variables.csv or the other 'raw' data.

@DougManuel DougManuel mentioned this pull request Nov 27, 2024
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The package now passes checks and builds.

@reikookamoto @yulric Do you have any other comments to address?

We now have the PBC data for vignettes and for users to test functions.

We'll need to refresh a few vignettes with minimal examples to use alongside the pbc data.

yulric pushed a commit that referenced this pull request Dec 11, 2024
@DougManuel @yulric
Update data and metadata names for consistency. See #44.
600cf69 
Starts to transition to pbc data for vignette, but with bugs remaining in derived_variables.Rmd
yulric pushed a commit that referenced this pull request Dec 11, 2024
@DougManuel @yulric
Update data and metadata names for consistency. See #44.
db99c94 
Starts to transition to pbc data for vignette, but with bugs remaining in derived_variables.Rmd
yulric pushed a commit that referenced this pull request Dec 11, 2024
@DougManuel @yulric
Update data and metadata names for consistency. See #44.
a06490c 
Starts to transition to pbc data for vignette, but with bugs remaining in derived_variables.Rmd
yulric pushed a commit that referenced this pull request Dec 11, 2024
@DougManuel @yulric
Update data and metadata names for consistency. See #44.
5867c2b 
Starts to transition to pbc data for vignette, but with bugs remaining in derived_variables.Rmd
yulric pushed a commit that referenced this pull request Dec 11, 2024
@DougManuel @yulric
Update data and metadata names for consistency. See #44.
bde9b15 
Starts to transition to pbc data for vignette, but with bugs remaining in derived_variables.Rmd
yulric pushed a commit that referenced this pull request Dec 11, 2024
@DougManuel @yulric
Update data and metadata names for consistency. See #44.
f6649bb 
Starts to transition to pbc data for vignette, but with bugs remaining in derived_variables.Rmd
yulric pushed a commit that referenced this pull request Dec 12, 2024
@DougManuel @yulric
Update data and metadata names for consistency. See #44.
f9e3633 
Starts to transition to pbc data for vignette, but with bugs remaining in derived_variables.Rmd
yulric pushed a commit that referenced this pull request Dec 12, 2024
@DougManuel @yulric
Update data and metadata names for consistency. See #44.
3439ebe 
Starts to transition to pbc data for vignette, but with bugs remaining in derived_variables.Rmd
yulric pushed a commit that referenced this pull request Dec 12, 2024
@DougManuel @yulric
Update data and metadata names for consistency. See #44.
a6af62b 
Starts to transition to pbc data for vignette, but with bugs remaining in derived_variables.Rmd
yulric pushed a commit that referenced this pull request Dec 12, 2024
@DougManuel @yulric
Update data and metadata names for consistency. See #44.
81c0e11 
Starts to transition to pbc data for vignette, but with bugs remaining in derived_variables.Rmd
yulric pushed a commit that referenced this pull request Dec 12, 2024
@DougManuel @yulric
Update data and metadata names for consistency. See #44.
0736cd5 
Starts to transition to pbc data for vignette, but with bugs remaining in derived_variables.Rmd
yulric pushed a commit that referenced this pull request Dec 12, 2024
@DougManuel @yulric
Update data and metadata names for consistency. See #44.
a1fdd8c 
Starts to transition to pbc data for vignette, but with bugs remaining in derived_variables.Rmd
yulric pushed a commit that referenced this pull request Dec 12, 2024
@DougManuel @yulric
Update data and metadata names for consistency. See #44.
5bd94f4 
Starts to transition to pbc data for vignette, but with bugs remaining in derived_variables.Rmd
yulric pushed a commit that referenced this pull request Dec 12, 2024
@DougManuel @yulric
Update data and metadata names for consistency. See #44.
7c55c65 
Starts to transition to pbc data for vignette, but with bugs remaining in derived_variables.Rmd
yulric pushed a commit that referenced this pull request Dec 12, 2024
@DougManuel @yulric
Update data and metadata names for consistency. See #44.
ec32fff 
Starts to transition to pbc data for vignette, but with bugs remaining in derived_variables.Rmd
yulric pushed a commit that referenced this pull request Dec 12, 2024
@DougManuel @yulric
Update data and metadata names for consistency. See #44.
fc70c0f 
Starts to transition to pbc data for vignette, but with bugs remaining in derived_variables.Rmd
yulric pushed a commit that referenced this pull request Dec 12, 2024
@DougManuel @yulric
Update data and metadata names for consistency. See #44.
4a94e21 
Starts to transition to pbc data for vignette, but with bugs remaining in derived_variables.Rmd
DougManuel and others added 6 commits December 13, 2024 14:07
@DougManuel @yulric
adds examples of the variables and variable details worksheet using t…
728b5ab 
…he pbc dataset

* added variables sheet for the pbc dataset
* renamed PBC-variableDetails.csv to follow the naming convention in the
  repo and added fixes to it
  * Fix variable names removing any variables that are not part of the
    dataset
  * Replace empty string wit NA
  * Fix bug with tagged NA for the ascites variable
  * fixed references to the new file
* added metadata for the pbc dataset using the Dublin core standard
* added documentation for all the above elements and the pbc dataset to
  the documentation website
* added code to add the above files to the data directory allowing users
  of the package to access them easily
@yulric
Rbuildignore changes
a2192b4
@yulric
ignore vscode workspace dir
071ad89
@yulric
udpate the authors and maintainers list
5a92d05
@yulric
update roxygen version to use
52f5766
@yulric
documentation fixes and updates to the variable-start.R file
85f85eb
@yulric yulric merged commit d9ef762 into dev Dec 13, 2024
@yulric yulric deleted the PBC-database branch December 13, 2024 19:12
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@yulric yulric Awaiting requested review from yulric

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@DougManuel @reikookamoto @yulric