Changelog

Fixed bug in install_sre_gitlab() where it would fail if the desired package didn’t have a previous version installed.

Added new arguments date_format and time_format to read_dat(), dat_to_arrow_formats() etc, to allow overriding the global formats when reading in a dataset. Defaults are the same as in readr functions.

New function health_dict_to_spec() to create a readr column specification from a health dictionary. This allows parsing of most date formats used in the health datasets (#37)
New function flag_across, similar to filter_across, but rather than filtering the dataset it adds a logical column indicating the result of the pattern search across the selected columns (#38)

Deprecate msp_unique and re-export it in the hawkeye package
Deprecate dipr_icd_categories, dipr_icd9_categories and dipr_icd10_categories functions in favour of functionality added to hawkeye package

Add new function filter_across
Changed the internal method to install and update dipr, with new instructions in the README. The new method uses the gitlab API and will enable using dipr to install other SRE gitlab R packages using install_sre_gitlab. (#24)
Add new function get_gitlab_sre_repos
Add new function filter_linked and add Dataset methods for add_linked_status_col function so that it can be used in a arrow workflow.
The template DESCRIPTION file now adds dependent packages to the Depends field rather than the Imports field.
Fixed a bug where the template .Rprofile file used in dipr_create_targets_project() was not included in the package.
Deprecate msp_unique and re-export it in the hawkeye package
New function restore_rstudio_prefs() to help setup RStudio in a new SRE machine (#31)

Added function ocwa_branch_export() (#26) to create a clean branch to prepare the repo for import into OCWA by:
1. Creating a new branch
2. Removing files that can’t be imported - these are listed in the _ocwaignore file in the root of the repo
3. Cleaning README.md to comment out references to images and links that won’t be available in the SRE.
4. Committing the changes from 2 and 3 to the new branch and pushing that to GitHub. This branch can then be used as the basis for an import into OCWA.
Added dipr_create_targets_project which will create a thin package-like targets folder structure.
Adding dipr_document_output_groups as convenience to document datasets
Changes get_core_dat_path() and get_core_dict_path() to accomodate the new structure of provisioned data where the metadata are in the same directory as the data. (#17)
Adds a new data_format argument to dat_to_arrow_formats() and friends, as well as read_dat() and the internal dipr_reader() (#17)
Exposes ... in read_nflt() to allow passing options to readr::read_delim() (#17)
Comments are now removed from nflt files in read_nflt. Comments are by default expected to be denoted by /*, but this is customizable with the comment argument. (#21)

Caching has been removed from dipr (via read_dat) as it was not being used. Removing caching removed significant code complexity

Add convenience function set_gitlab_credentials() to pull up the Git Credential Manager proactively (#6)
Directly use readr now that it use vroom under the hood. Dropping vroom as a direct dependency
Through readr 2.0, read_dat can now directly read two files supplied as a vector of .dat.gz. We have added a second dipr example data set to test this behaviour.
Experimental dat_to_datasets function that is a low memory method to create partitioned Arrow Datasets.
Add species column to internal data
Improved documentation all around

Add age_at_date
Add dipr_icd9_categories and dipr_icd10_categories functions to process icd codes. Thanks to Craig Hutton for this contribution.
Add argument to msp_unique to only use primary icd9 code. This is primarily been done to work around memory bottle necks.

dipr 1.3.1