Presentation mode

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.

CRAN release

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.

0.6.1 Maintenance release

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.

0.6.0 CRAN Release (including 0.5.8 dev release)

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.

JOSS Review Release

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.

New CRAN Release - Added TB report + summary plot

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.

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.

New CRAN release - fix for rlang breaking changes

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.

New CRAN release - updates for 2017 data.

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.

New CRAN Release - MDR TB data, map updates and a new summary function.

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.

New CRAN Release - Bug fixes, colour options and case study

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 reponse 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.