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socialmixr (development version)

Breaking changes

  • contact_matrix(counts = TRUE)$matrix is now an array rather than an xtabs object. This matches the existing output format of contact_matrix(counts = FALSE)$matrix (#118).

socialmixr 0.4.0

  • The speed of loading surveys has been increased.
  • An error has been fixed causing NA contact matrices if any 5-year age band in the population data was missing.
  • Results of function calls accessing Zenodo repository are now cached for speedup and to avoid multiple web requests
  • A bug was fixed where ages given as ranges had been set to the average of estimated ones
  • The limits_to_agegroups has been changed to return bracket notated age ranges by default

socialmixr 0.3.2

  • An error in list_surveys() was fixed which stopped this working.

  • contact_matrix() was updated to only accept survey objects, not DOIs and matches the documentation. It is still possible to get a contact matrix from a DOI but it is necessary to go through the get_survey() function.

    # No longer works!
contact_matrix("10.5281/zenodo.1095664")

# Recommended workflow
get_survey("10.5281/zenodo.1095664") |>
  contact_matrix()

  • The efficiency of the contact_matrix() was improved.

socialmixr 0.3.1

  • Tests were updated to prevent failures due to machine precision issues on some platforms (#100)

socialmixr 0.3.0

Major & breaking changes

  • The cite function has been deprecated and replaced with get_citation (#84).
  • the columns argument has been removed from check.survey() (#81).

Internal changes

  • Code quality is now ensured through continuous integration and the lintr package (#69).
  • Cyclomatic complexity of download_survey() has been reduced by externalising the find_common_prefix() function and failing early instead of relying on unnecessary if/else sequences
  • More generous filename checks now pass files named e.g. "..._participants_common..." an not only "...participant_common..."
  • The package now sets a custom user agent when downloading survey data (#82).
  • A problem was fixed where attempted joins of files could lead to blowing up memory use (#75).
  • A problem was fixed where the updated Zenodo API caused downloading to fail (#91).
  • A problem was fixed where the updated Zenodo API caused listing surveys to fail (#96).

socialmixr 0.2.0

Major & breaking changes

  • error argument has been removed from check() and always return warnings. If you want to turn these warnings into errors, please have a look at options(warn = 2)
  • quiet argument has been removed from check(), cite(), contact_matrix(), and get_survey(). If you want to silence diagnostic messages, you should use R idiomatic mechanisms, such as suppressMessages()
  • the n and bootstrap options of contact_matrix() have been deprecated and replaced with a sample.participants argument; bootstrapping is now explained in the vignette instead
  • new matrix_plot() function to plot contact matrix
  • the use of weights has been improved and the corresponding section in the vignette expanded

Minor changes

  • world population data has been updated to 2017 by switching from the wpp2015 to wpp2017 package
  • chkDots() is now used to ensure no argument is silently ignored by S3 methods

Internal changes

  • continuous integration is now done via GitHub Actions
  • improved robustness of survey loading and cleaning
  • get_survey() has been split into separate functions for downloading and processing survey data

socialmixr 0.1.8

  • fixed test
  • fixed order of limits in reduce_agegroups

socialmixr 0.1.7

  • fixed bug when age is given as a range, or when age.limits contains ages not represented in the data
  • limits_to_agegroups now returns an ordered list (thanks @pearsonca)
  • now allows for estimated participant age (thanks @jarvisc1)
  • fixed bug in calculating weights (thanks @alxsrobert)

socialmixr 0.1.6

  • if access to Zenodo fails an informative error message is now given
  • tests that require access to Zenodo now fail if it cannot be accessed
  • fixed bug in interpreting return values of the Zenodo API

socialmixr 0.1.5

  • removed option to call survey by number - use DOI for reproducibility

socialmixr 0.1.4

  • better work with missing and diverse data (e.g., age as factors)
  • 'get_survey' now works with URLs
  • fixed 'list_surveys' to only return the latest version of each data set
  • some small fixes

socialmixr 0.1.3

  • improved handling of DOIs
  • fixed usage of weights
  • more consistency checks and tests
  • performance improvements when weighting
  • 'pop_age' can now be called by the user

socialmixr 0.1.2

  • improved downloading form Zenodo; only a single download is used now
  • improved handling of country names
  • fixed bugs in the "filter" option
  • POLYMOD data set updated to latest v1.1
  • allow user to choose how ages are estimated from age ranges

socialmixr 0.1.1

  • fix: dependency on R >= 3.4.0
  • updated reference handling if a survey is not pulled from Zenodo
  • the 'survey' function can now be used to create a 'survey' object from data frames
  • a few small patches and fixes

socialmixr 0.1.0

  • initial release