We warmly welcome contributions to the browseMetadata project! This document provides guidelines for contributing to this repository.
getwd() to check and setwd() to change).devtools::load_all() in the R console. You should see βΉ Loading browseMetadata returned.domain_mapping() in the R console.If you run into issues with branches not seeming to be up to date in the R Studio workspace, consider running remove.packages("browseMetadata") and trying the above steps again, in case a previously installed package library is getting in the way somehow.
Creating .rda Files: To create .rda files in the data directory of the package, use the following command in R:
Generating Documentation Files: To build the documentation files for the package, use the roxygen2 package:
-library(roxygen2)
-roxygenise()This will generate the necessary documentation based on your roxygen comments in the R code.
+devtools::document() This will generates the .Rd files from any updated roxygen comments.
Ensure that your changes do not break any existing functionality. Run any existing tests, and consider adding new tests to cover your changes. Here are some helpful functions to consider:
+codemetar::write_codemeta() ensures the metadata file is up to date.lintr::lint_package(path = ".") checks for adherence to a given style, identifying syntax errors and possible semantic issuesdesc::desc_normalize() to ensure DESCRIPTION file follows a standard structure and stylestyler::style_pkg() ensures consistent code styling that match the guidelines.devtools::check() runs a comprehensive package check.Set your working directory to an empty folder:
-
-setwd("/Users/your-username/test-browseMetadata")R Studio IDE)
@@ -152,12 +149,11 @@ browse_metadata()
This function is easy to run and doesnβt require user interaction. Run it in demo mode using the demo JSON file located in the inst/inputs directory:
-+Upon success, you should see:
--βΉ Three outputs have been saved to your output directory. -βΉ Open the two HTML files in your browser for full-screen viewing.The output files are saved to your working directory. You can change the save location by adjusting the
+output_dirargument. Examples of outputs are available in inst/outputs.+βΉ Three outputs have been saved to your output directory, and two outputs should have opened in your browser.The output files are saved to your project directory. You can change the save location by adjusting the
output_dirargument. Examples of outputs are available in inst/outputs.
Use the outputs from browse_metadata() as a reference when running map_metadata().
To run the mapping function in demo mode, use:
-+In demo mode, the function processes only the first 20 variables from selected tables. Follow the on-screen instructions, and categorise variables into research domains, using the Plot tab as your reference. The demo will simplify domains for ease of use; in a real scenario, you can define more specific domains.
Upon completion, your categorisations, session log, and a summary plot will be saved in your output directory.
@@ -176,7 +172,7 @@
Using a custom metadata input (recommended)
You can run
-map_metadata()andbrowse_metadata()using a custom JSON file instead of the demo input:+new_json_file <- "path/your_new_json.json" demo_domains_file <- system.file("inputs/domain_list_demo.csv", package = "browseMetadata") @@ -218,13 +214,13 @@CitationStickland R (2024). browseMetadata: browse and categorise health metadata. R package version 2.0.2.
A BibTeX entry for LaTeX users:
- +Contributing diff --git a/pkgdown.yml b/pkgdown.yml index 9aa3340..13a7a95 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -4,7 +4,7 @@ pkgdown_sha: ~ articles: browseMetadata: browseMetadata.html HealthMetadata: HealthMetadata.html -last_built: 2024-12-16T09:02Z +last_built: 2024-12-17T11:22Z urls: reference: https://aim-rsf.github.io/browseMetadata/reference article: https://aim-rsf.github.io/browseMetadata/articles diff --git a/reference/BROWSE_bar_NationalCommunityChildHealthDatabase(NCCHD)_V16.0.0.html b/reference/BROWSE_bar_NationalCommunityChildHealthDatabase(NCCHD)_V16.0.0.html index d0413d0..3f76874 100644 --- a/reference/BROWSE_bar_NationalCommunityChildHealthDatabase(NCCHD)_V16.0.0.html +++ b/reference/BROWSE_bar_NationalCommunityChildHealthDatabase(NCCHD)_V16.0.0.html @@ -1955,7 +1955,7 @@
- +