Changelog
Source:NEWS.md
socialmixr (development version)
Breaking changes
-
contact_matrix(counts = TRUE)$matrix
is now an array rather than an xtabs object. This matches the existing output format ofcontact_matrix(counts = FALSE)$matrix
(#118).
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 acceptsurvey
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 theget_survey()
function.```r # No longer works! contact_matrix(“10.5281/zenodo.1095664”)
Recommended workflow
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
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 thefind_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 fromcheck()
and always return warnings. If you want to turn these warnings into errors, please have a look atoptions(warn = 2)
-
quiet
argument has been removed fromcheck()
,cite()
,contact_matrix()
, andget_survey()
. If you want to silence diagnostic messages, you should use R idiomatic mechanisms, such assuppressMessages()
- the
n
andbootstrap
options ofcontact_matrix()
have been deprecated and replaced with asample.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 0.1.7
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