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).