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Recent Releases of getTBinR

getTBinR - 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.

Scientific Software - Peer-reviewed - HTML
Published by seabbs almost 6 years ago

getTBinR - 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.

Scientific Software - Peer-reviewed - HTML
Published by seabbs over 6 years ago

getTBinR - 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.

Scientific Software - Peer-reviewed - HTML
Published by seabbs almost 7 years ago

getTBinR - 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.

Scientific Software - Peer-reviewed - HTML
Published by seabbs about 7 years ago

getTBinR - 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.

Scientific Software - Peer-reviewed - HTML
Published by seabbs over 7 years ago

getTBinR - New CRAN Release - Added TB report + summary plot

Feature updates

  • Added support for annualchange to summarisetb_burden and added validating tests.
  • Added support for rates and proportions to summarisetbburden and added validating tests.
  • Added a new function - plottbburdensummary. Function wraps summarisetb_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 runtbdashboard.
  • Added rendercountryreport to generate a TB report for a given country.
  • Tweaked maptbburden to not use geom_path for country outlines.
  • Added a smooth argument to plottbburden to allow smooth trend lines to be plotted (derived using - - ggplot2::geom_smooth).
  • Tweaked line thickness in plottbburden 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.

Scientific Software - Peer-reviewed - HTML
Published by seabbs over 7 years ago

getTBinR - 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.

Scientific Software - Peer-reviewed - HTML
Published by seabbs over 7 years ago

getTBinR - 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.

Scientific Software - Peer-reviewed - HTML
Published by seabbs over 7 years ago

getTBinR - 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.

Scientific Software - Peer-reviewed - HTML
Published by seabbs about 8 years ago

getTBinR - 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.

Scientific Software - Peer-reviewed - HTML
Published by seabbs about 8 years ago

getTBinR - New CRAN release - shiny dashboard

Feature updates

  • Added annual_change arguement to all plotting/mapping functions. Passed to prepare_df_plot. Returns the percentage annual change for the supplied metric.
  • Added trans arguement to all plotting functions to allow scaling using any ggplot2::continous_scale trans arguement.
  • 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.

Scientific Software - Peer-reviewed - HTML
Published by seabbs over 8 years ago

getTBinR -

Scientific Software - Peer-reviewed - HTML
Published by seabbs over 8 years ago