socialmixr 0.6.0

This release adds a pipeline of composable functions for building contact
matrices ([, assign_age_groups(), weigh(), compute_matrix(),
symmetrise(), split_matrix(), per_capita()) and a contact_matrix S3
class. The vignette and README are rewritten around the pipeline (#288).

Breaking changes

• Minimum R version bumped to 4.1.0 (from 3.5.0). Examples in the pipeline
  functions use the native |> pipe, introduced in 4.1.0.

• Terminal age group labels now use [N,Inf) notation instead of N+ when
  bracket notation is used (e.g. [0,5), [5,15), [15,Inf)). This matches
  the contactmatrix package and gives parseable interval notation across all
  age groups. It affects matrix dimnames and the age.group column in
  $participants; code that matches on strings like "15+" will need
  updating to "[15,Inf)". Dash notation (e.g. "15+") is unchanged.

New features

• New [.contact_survey method allows filtering survey objects with
  expressions, e.g. polymod[country == "United Kingdom"] (#161).

• New weigh() function for composable participant weighting: supports
  day-of-week groups, named target vectors, direct numeric columns, and
  population post-stratification (#161).

• New compute_matrix() function computes a contact matrix from a prepared
  survey. It is the final step of the pipeline after assign_age_groups()
  and (optionally) weigh() (#161).

• New post-processing functions symmetrise(), split_matrix(), and
  per_capita() operate on compute_matrix() output. symmetrise() enforces
  reciprocity, split_matrix() decomposes into mean contacts, normalisation,
  and an assortativity matrix, and per_capita() converts to per-capita rates.
  Example workflow (#161):

  uk_pop <- data.frame(
    lower.age.limit = c(0, 5, 15),
    population = c(3500000, 6000000, 50000000)
  )
  polymod[country == "United Kingdom"] |>
    assign_age_groups(age_limits = c(0, 5, 15)) |>
    compute_matrix() |>
    symmetrise(survey_pop = uk_pop)

• Pipeline functions (compute_matrix(), symmetrise(), split_matrix(),
  per_capita()) return a contact_matrix S3 class with print(), plot(),
  and as.matrix() methods. The class inherits from list, so existing code
  using $matrix or $participants continues to work.

• New contact_age_distribution() function extracts the empirical age
  distribution of contacts from a survey. Pass it to
  assign_age_groups(estimated_contact_age = ...) to impute ages from
  ranges by sampling from the reference distribution instead of uniformly.
  This matters for surveys where many contacts have broad age bands, since
  uniform sampling would flatten age-assortativity.

• New agegroups_to_limits() function converts age group labels back to lower
  age limits, the inverse of limits_to_agegroups().

• compute_matrix() gains a weight_threshold parameter to cap extreme
  weights before normalisation, matching the contact_matrix() option (#131).

Bug fixes

• Fixed bug where participants with NA dayofweek were incorrectly weighted
  as weekend days. They now receive an average weight across all days (#131).

• Fixed unmatched-merge warning count when merging files with duplicate keys;
  previously, the count could be wrong (or negative) due to counting join
  pairs rather than distinct matched rows (#289).

• matrix_plot() now restores all graphical parameters (par()) on exit,
  including when the function errors mid-plot. Previously the legend
  parameters (new, pty) and the error handler (err) were left
  modified in the user's session (#307).

Deprecations

• wpp_age() and wpp_countries() are now soft-deprecated. Pass population
  data directly via the survey_pop argument instead. The underlying
  wpp2017 data is also outdated; the wpp2024 package from GitHub provides
  more recent data (#258).

• contact_matrix() now warns when it would look up population data
  automatically via wpp_age(). This automatic lookup happens when
  symmetric, split, per_capita, weigh_age, or return_demography is
  set and countries is given (or the participant data has a country
  column) without an explicit survey_pop. The implicit lookup will be
  removed in a future release; pass survey_pop directly (e.g. from
  survey_country_population() or the wpp2024 package) to silence the
  warning and make the code forwards-compatible.

• get_survey(), download_survey(), list_surveys(), get_citation(), and
  survey_countries() now warn unconditionally when called. These functions
  were soft-deprecated in 0.5.0 and users should switch to the
  contactsurveys package
  (#269).

Internal

• contact_matrix() now uses assign_age_groups() internally, removing
  duplicated code (#227).

• contact_matrix() now uses weigh() internally for all weighting
  (day-of-week, age, and user-defined). The helpers
  warn_multiple_observations() and normalise_weights() were extracted
  so compute_matrix() can share them (#131).

• The vignette and README are rewritten around the pipeline (#288).

• Enabled cyclocomp_linter, line_length_linter, and object_usage_linter.
  Disabled indentation_linter (air handles indentation). Reduced cyclomatic
  complexity of check.contact_survey(), [.contact_survey(),
  find_unique_key(), and try_merge_additional_files() by extracting
  helper functions (#289).