NEWS.md

In socialmixr: Social Mixing Matrices for Infectious Disease Modelling

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.

```r # 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

socialmixr documentation built on Oct. 18, 2024, 5:14 p.m.