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Changelog

Source: NEWS.md

socialmixr (development version)

Breaking changes

  • When age.limits is not specified, it is now inferred from both participant and contact ages, not just participant ages. This may result in more age groups if contacts include ages beyond the participant age range (#230).

  • contact_matrix() now preserves all user-specified age.limits, even when no participants exist in some age groups. Previously, age groups beyond the maximum participant age were silently dropped. Empty age groups now show 0 participants and NA values in the matrix. This may change matrix dimensions for existing code (#144, #231).

  • 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).

Bug fixes

  • A bug was fixed leading to excess contacts with NA age if the lowest age group did not start at 0.

Deprecations

We have soft-deprecated get_survey(), download_survey(), get_citation() and list_surveys() and moved these to contactsurveys. We have also soft-deprecated survey_countries() as this called get_survey() internally. This is part of decoupling these features from socialmixr to reduce dependencies (#207 and #179). These will continue to be supported until we move to a major release (version 1.0.0) of socialmixr. In the meantime, we recommend that users use the contactsurveys package, as these functions have improved caching and support there.

socialmixr 0.4.0

CRAN release: 2024-10-18

  • 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

CRAN release: 2024-04-18

  • 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.

    ```r # No longer works! contact_matrix(“10.5281/zenodo.1095664”)

    CRAN release: 2024-04-18

    get_survey(“10.5281/zenodo.1095664”) |> contact_matrix()

  • The efficiency of the contact_matrix() was improved.

socialmixr 0.3.1

CRAN release: 2023-10-26

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

socialmixr 0.3.0

CRAN release: 2023-10-18

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

CRAN release: 2022-10-27

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

CRAN release: 2020-11-14

  • fixed test
  • fixed order of limits in reduce_agegroups

socialmixr 0.1.7

CRAN release: 2020-08-06

  • 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

CRAN release: 2020-01-10

  • 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

CRAN release: 2019-09-24

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

socialmixr 0.1.4

CRAN release: 2019-07-24

  • 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

CRAN release: 2018-08-09

  • 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

CRAN release: 2018-02-22

  • 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

CRAN release: 2018-01-15

  • 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

CRAN release: 2018-01-08

  • initial release