NEWS.md

In getTBinR: Access and Summarise World Health Organization Tuberculosis Data

getTBinR 0.7.1

Feature updates

• Switched dashboard to default to 2018 data.
• Added a new WHO inspired {ggplot2} theme (theme_who) and colour palette (who_palettes) resolving issue #86. Plus scale_colour and scale_fill_who functions for using the palette. Thanks to @mariabnd for implementing this.
• Added a new function - for_presentation - to switch plots to presentation mode.

Package updates

• Additional testing and examples to support the new WHO inspired theme and colour palettes.
• Additional documentation for the new WHO inspired theme and colour palettes.
• Updated the spelling of organisation to organization in all uses relating to the World Health Organization. Thanks to @mariabnd for spotting this.
• Added @mariabnd as a package contributor.
• Changed verbose to default to FALSE package wide.
• Bumped data availability to 2018.
• Standarised legend to be bottom aligned across the package.
• Dropped tidyverse from suggests as per this issue.
• Fixed legend types as per this issue

Thanks to @mariabnd for contributing to this release.

getTBinR 0.7.0

Feature updates

• Added experimental support for incidence data stratified by age and sex. Current implementation requires data cleaning before use. See the release post for details.

Package updates

• Fixed a bug that was preventing render_country_report from producing a country level report. Added tests to flag this in the future.
• Updated the packages requested for installation by run_tb_dashboard so that render_country_report runs without errors.
• Switched to using ggplot2 best practises (#77).
• Updated the README to make identifying types of badges easier.

getTBinR 0.6.1

Package updates

• Fixed a joining bug for additional datasets that was removing all new data.
• Fixed a joining bug for budgets data that was removing all budgets data.
• Fixed a bug with summarise_tb_burden that caused an error when confidence intervals were not wanted and rates were estimated for countries.

getTBinR 0.6.0

Feature updates

• Added a new summarise_metric function to the package. This function was previously used internally by the TB report. For a given year it returns the value of given metric, along with the regional and global rankings. The average change over the last decade is also supplied. Linked to #57.
• search_data_dict can now be used to search for a dataset by name. All variables in this dataset are then returned.
• Added a new dataframe, available_datasets, that lists the datasets available to be imported into R using the package. This dataframe also gives a short description of each dataset, details the timespan of the dataset, and whether or not it is downloaded by default. Used by get_tb_burden as a URL source for downloading the datasets. Linked to #58.
• get_tb_burden can now import additional datasets (listed in available_datasets), clean them, and then link them with the core dataset. This adds over 400 new variables to the package and provides a near complete list of data used in the WHO Tuberculosis global report. Please open an issue if you find an issue with this dataset.

Package updates

• Jumped to 0.6.0 to signal a major release.
• Updated earliest supported R version based on travis testing - now 3.3.0.
• Added the JOSS paper as the preferred citation for getTBinR and also added this information to the README.
• URL and data save names have been deprecated from all functions and will be removed in a future release. This allows the number of arguments for many functions to be reduced with no loss of functionality (as data is only saved temporally by package functions).
• search_data_dict has improved messaging and no longer returns an error when nothing is found in the data dictionary. From #65.
• search_data_dict has expanded testing to account for new dataset searching and for failing to find results. Linked to #60.
• Dropped usage of dplyr::funs as soft deprecated.
• Added tests for summarise_metric and added to documentation.
• Added tests for additional dataset import in get_tb_burden. #58
• Added available_datasets and new data import to the README and to the getting started vignette.

getTBinR 0.5.8

Package updates

• Added package information to license file - suggested during review for JOSS submission by @rrrlw.
• Updated README introduction to better explain package aim - suggested during review for JOSS submission by @strengejacke
• Improved package DESCRIPTION for CRAN only users - suggested during review for JOSS submission by @rrrlw.
• Used usethis::use_tidy_description to improve DESCRIPTION formatting.
• Added development documentation badge to the README + website.
• Moved to automated pkgdown deployment using travis. Based on this and the dplyr implementation.
• Expanded travis testing grid based on dplyr implementation.
• Updated earliest supported R version based on travis testing - now 3.2.0.
• Used usethis::use_tidy_versions() to set package to dependent on package versions used during development work. Added this to makefile to make automated.
• Added a git commit step to the Makefile use with `make message="your commit message". This will automatically run all build steps that are required and then commit any changes.

getTBinR 0.5.7

Feature updates

• Added support for annual_change to summarise_tb_burden and added validating tests.
• Added support for rates and proportions to summarise_tb_burden and added validating tests.
• Added a new function - plot_tb_burden_summary. Function wraps summarise_tb_burden and allows all in one summary plotting. Inspired by this case study.
• Added a rmarkdown parameterised country level report on TB.
• Added a report generating button to the dashboard generated by run_tb_dashboard.
• Added render_country_report to generate a TB report for a given country.
• Tweaked map_tb_burden to not use geom_path for country outlines.
• Added a smooth argument to plot_tb_burden to allow smooth trend lines to be plotted (derived using ggplot2::geom_smooth).
• Tweaked line thickness in plot_tb_burden to improve plot appearance.
• Added legend argument to all plotting functions to allow control of the legend appearance.
• Added spell checking and list of allowed words.
• Automated package styling using usethis::use_tidy_style() via the styler package. Based on this issue.

Package updates

• Added script to generate hexsticker
• Added hexsticker to README
• Added DOI link to Zenodo.
• Updated tests to account for dplyr 8.0 release and vdiffr updates.
• Added itdepends to package report functionality.

getTBinR 0.5.6

Feature updates

• No new features in this release

Package updates

• Updated custom legend setting in map_tb_burden to work with new version of rlang.
• Updated map_tb_burden tests to work with new version of R lang.
• Added dev to pkgdown site yml for docs prior to release.

getTBinR 0.5.5

Feature updates

• Added a years filter to plot_tb_burden and plot_tb_burden_overview. This allows a range of years to be plotted. The default is all years which was the previous de-facto default.

Package updates

• Updated docs to reflect new year of data.
• Updated examples to use the new year of data as standard.
• Updated README to always use the current year of data.
• Updated all vignettes to reflect new data or be fixed to historic data as appropriate.
• Update site with links out to blog posts using the newest version of pkgdown.

getTBinR 0.5.4

Feature updates

• Added MDR-TB data for 2016, see here for the dataset. The MDR-TB data is automatically joined to the WHO TB burden data.
• Aesthetic updates to map_tb_burden.
• Added new summarise_tb_burden function for summarising metrics across regions, across custom groups and globally.

Package updates

• Improved data cleaning, converting Inf and NaN values to NA when the data is read in.
• Added pgknet report.
• Improved test robustness and scope
• Added vdiffr to test plots when not on CRAN.
• Fixed bug for map_tb_burden which was adding duplicate variables which caused map build to fail.

getTBinR 0.5.3

Feature updates

• Added viridis_palette option to all plotting functions to allow the colour scheme to be set by the user.
• Added ability to handle categories in the legend for map_tb_burden
• Added new case study exploring case fatality rates.

Package updates

• Added improved tests in response to WHO data updates. See here
• Added an additional method for downloading data in response to test failures on CRAN. See here
• Added skip on CRAN for data backend related tests.
• Added Makefile at top level and for data-raw to build the package.

getTBinR 0.5.2

Feature updates

• Improved plotly tool tips in all interactive plots.
• Added option to pass multiple years for interactive maps using the built in plotly frame functionality.

Package updates

• Added retry download option to deal with possible API rate limits in response to this issue.
• Added downloads badge to readme.

getTBinR 0.5.1

Feature updates

• Added annual_change argument to all plotting/mapping functions. Passed to prepare_df_plot. Returns the percentage annual change for the supplied metric.
• Added trans argument to all plotting functions to allow scaling using any ggplot2::continous_scale trans argument.
• Added adaptive axis and legend labels to properly show annual percentage change.
• Added run_tb_dashboard to launch a shiny dashboard for exploring global tuberculosis
• Changed function defaults so that data is automatically downloaded and saved into the temporary directory when get_data functions are called.

Package updates

• Added new examples to display new functionality
• Updated readme with new functionality
• Updated intro vignette with new functionality
• Added a new case studies vignette section
• Added a case study exploring global trends in Tuberculosis incidence rates
• Added a work around using utils::read.csv for downloading the data when fread::data.table fails. Related to this issue.

getTBinR 0.5.0

Feature updates

• Added download_data argument to all functions to make downloading data explicit.
• Added save argument to all functions to make saving the data explicit.
• Added save_name and path arguments to all functions to make location of saving explicit.

Package updates

• Updated documentation to reflect above changes.
• Updated tests to reflect changes.
• Doc improvements ready for CRAN.
• Switched Imported packages from github versions to CRAN versions.
• Switched to saving data only to temporary directory (tempdir())

getTBinR 0.1.0

Feature updates

• Added map_tb_burden function to map TB metrics.

Package updates

• Added a NEWS.md file to track changes to the package.

getTBinR 0.0.5

Feature updates

• Added plot_tb_burden_overview function to plot an overview of the TB burden.

Package updates

• Updated the package site.
• Refactored plotting code.

getTBinR 0.0.1

Feature updates

• Added plot_tb_burden function to plot TB burden

Package updates

• Set up package infrastructure

getTBinR documentation built on July 2, 2020, 12:31 a.m.