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Social mixing matrices for infectious disease modelling in R

socialmixr is an R package to derive social mixing matrices from survey data.

Installation

The package can be installed using

install.packages("socialmixr")

The current development version can be installed using the remotes package

remotes::install_github("epiforecasts/socialmixr")

Usage

Contact matrices are computed through a small pipeline of composable functions: subsetting the survey, assigning age groups, optionally weighing participants, and computing the matrix. A minimal example using the included POLYMOD data:

library(socialmixr)
data(polymod)

polymod[country == "United Kingdom"] |>
  assign_age_groups(age_limits = c(0, 1, 5, 15)) |>
  compute_matrix()

Post-processing functions symmetrise(), split_matrix() and per_capita() can be piped after compute_matrix() to enforce symmetry, decompose the matrix, or convert to per-capita contact rates.

Documentation

For more on how to use the socialmixr package, see the introduction vignette.

Contributors

All contributions to this project are gratefully acknowledged using the allcontributors package following the allcontributors specification. Contributions of any kind are welcome!

Code

sbfnk, Bisaloo, lwillem, njtierney, alxsrobert, Degoot-AM, pearsonca, jarvisc1, jamesmbaazam, LloydChapman, mariabnd, ukhsa-tt

Issue Authors

bastistician, BlackEdder, Pinzo1, florpi, cchauve, thutran, dlaydon, deusthindwa, krivit, linyang17, cliu822, TimTaylor, NaomiWaterlow, aakhmetz, adamkucharski, chitrams, IsaacStopard, avallecam, maishaoshao, FrancescoBonacina, lucy-gf

Issue Contributors

vikkytom, joshwlambert, bahadzie, coderabbitai

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Version

Install

install.packages('socialmixr')

Monthly Downloads

929

Version

0.7.0

License

MIT + file LICENSE

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/epiforecasts/socialmixr

Homepage

https://epiforecasts.io/socialmixr/

Maintainer

Sebastian Funk

Last Published

August 22nd, 2026

Functions in socialmixr (0.7.0)

Deep copy a contact survey

contact_age_distribution

Extract the empirical age distribution of contacts from a survey

explicit_grouping

Build a grouping triple from an explicit c(part, cnt) entry

Internal function to get survey data

Handle deprecated argument

impute_contact_ages

Impute contact ages

Rebin a population table to a set of age groups

rebin_ages_numeric

Rebin population data to a set of age limits (numeric)

n_participants_per_group

Count participants per grouping combination

Citation for a survey

new_contact_matrix

Create a contact_matrix object

new_contact_survey

n_participants_per_age_group

Count participants per age group

find_unique_key

Find the minimal unique key for a data.table

Get a survey, either from its Zenodo repository, a set of files, or a survey variable

Clean contact survey data

limits_to_age_groups

Convert lower age limits to age groups.

Decompose a contact matrix into mean contacts, normalisation and assortativity

grouping_predicates

Predicates classifying a by entry

Impute ages from ranges (generic helper)

joint_population_vector

Resolve a survey population to a vector aligned with the matrix strata

normalise_country_names

Normalise country names

Social contact data from 8 European countries

flat_level_labels

Build colon-joined tuple labels from a list of level vectors

Flatten a multi-grouping contact matrix to its T x T form

Load a survey from local files

reduce_age_groups

Reduce the number of age groups given a broader set of limits

sample_from_age_distribution

Sample ages from a distribution within [min, max] bands

normalise_weights

Post-stratification weight normalisation

Draws an image plot of a contact matrix with a legend strip and the numeric values in the cells.

resolve_groupings

Resolve grouping specifications to participant/contact column pairs

validate_age_distribution

Validate an age distribution data.frame

impute_participant_ages

Impute participant ages

Change age groups in population data

limits_to_agegroups

Convert lower age limits to age groups (deprecated)

reduce_agegroups

Reduce the number of age groups (deprecated)

warn_multiple_observations

Warn if survey has multiple observations per participant

resolve_one_grouping

Resolve a single by entry to a grouping triple

normalise_weights_to_counts

Normalise a weighted contact array to mean contacts per participant

Get age-specific population data according to the World Population Prospects 2017 edition

is_contact_matrix

Test whether an object is a contact_matrix

Build a grouping triple from a stem string

Weigh survey participants

List all countries and regions for which socialmixr has population data

[.contact_survey

Subset a contact survey

Checks if a character string is a DOI

weighted_matrix_array

Cross-tab contact weights over grouping columns

List all surveys available for download

Contact survey (defunct)

Convert a contact matrix to per-capita rates

survey_countries

List all countries contained in a survey

Symmetrise a contact matrix

survey_country_population

Get survey country population data

Add age column from exact age (generic helper)

Align a population table to a contact matrix's grouping levels

as_contact_survey

Check contact survey data

assign_age_groups

Assign age groups in survey data

Check contact survey data

age_groups_to_limits

Convert age groups to lower age limits

Compute contact matrix from prepared survey data

Generate a contact matrix from diary survey data

download_survey

Download a survey from its Zenodo repository

assemble_survey

Assemble a contact survey with new participant/contact data

abort_if_missing

Abort if grouping columns are absent from a list of available columns

check_grouping_columns

Check that a survey contains the columns required by a list of groupings

default_age_groupings

Default grouping spec corresponding to age groups

agegroups_to_limits

Convert age groups to lower age limits (deprecated)

check_part_cnt_dims_match

Abort if participant and contact dims of a multi-grouping matrix differ