socialmixr 0.5.1

This is a patch release with a bug fix and documentation updates.

• load_survey() no longer fails when merging contact files that lack a
  cont_id column (#278).

• The vignette now points to the
  contactsurveys package
  for downloading surveys from Zenodo, and no longer uses deprecated functions
  (#269).

• Added Nicholas Tierney (@njtierney) as package author (#277).

socialmixr 0.5.0

This release focuses on improved modularity and flexibility for contact matrix
workflows. Key highlights include new standalone functions for age group
assignment and population data retrieval, more intuitive handling of age
limits, and the beginning of a transition to the
contactsurveys package for
survey downloads.

We thank Nicholas Tierney (@njtierney), Lander Willem (@lwillem), Hugo Gruson
(@Bisaloo), Lloyd Chapman (@LloydChapman), James Azam (@jamesmbaazam), and
Abdoelnaser Degoot (@Degoot-AM) for their contributions to this release.

Breaking changes

• 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 (@Bisaloo, #144, #231).

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

• 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).

New features

• as_contact_survey() no longer requires country and year columns. These
  columns are now auto-detected if present, but surveys without them can be
  loaded successfully (#193, #199).

• New assign_age_groups() and survey_country_population() functions allow
  modular pre-processing of survey data (#131, #226).

• Reduced verbosity by removing messages about removing participants/contacts
  with missing ages (#228).

Bug fixes

• clean() now correctly processes age values with units (e.g., "6 months",
  "52 weeks") (@LloydChapman, #250, #256).

• contact_matrix() now warns when a survey contains multiple observations per
  participant, as results will aggregate across all observations (#260).

• load_survey() now correctly loads longitudinal surveys with repeated
  observations per participant (e.g., sday files with wave/studyDay columns).
  Previously, these columns were silently dropped (@njtierney, #192, #194).

• Fixed a bug leading to excess contacts with NA age if the lowest age group
  did not start at 0 (@lwillem, #170).

Deprecations

• Argument names with dots (e.g., age.limits) have been deprecated in favour
  of underscores (e.g., age_limits) in contact_matrix(),
  as_contact_survey(), pop_age(), and clean(). The old argument names
  still work but will produce deprecation warnings (#160).

• get_survey(), download_survey(), get_citation(), list_surveys(), and
  survey_countries() have been soft-deprecated and moved to
  contactsurveys. This is
  part of decoupling these features from socialmixr to reduce dependencies
  (@njtierney, #179, #207). These will continue to work until version 1.0.0.

• The missing_contact_age = "sample" option in contact_matrix() and
  assign_age_groups() has been soft-deprecated. Use "remove" to exclude
  contacts with missing ages, "keep" to retain them as a separate age group,
  or "ignore" to drop only those contacts (#273).

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

v0.1.8

CRAN release 0.1.8