Package: socialmixr 0.7.0

Sebastian Funk

socialmixr: Social Mixing Matrices for Infectious Disease Modelling

Methods for sampling contact matrices from diary data for use in infectious disease modelling, as discussed in Mossong et al. (2008) <doi:10.1371/journal.pmed.0050074>.

Authors:Sebastian Funk [aut, cre], Lander Willem [aut], Hugo Gruson [aut], Nicholas Tierney [aut], Maria Bekker-Nielsen Dunbar [ctb], Carl A. B. Pearson [ctb], Sam Clifford [ctb], Christopher Jarvis [ctb], Alexis Robert [ctb], Niel Hens [ctb], Pietro Coletti [col, dtm], Lloyd Chapman [ctb]

socialmixr_0.7.0.tar.gz
socialmixr_0.7.0.zip(r-4.7-any)socialmixr_0.7.0.zip(r-4.6-any)socialmixr_0.7.0.zip(r-4.5-any)
socialmixr_0.7.0.tgz(r-4.6-any)socialmixr_0.7.0.tgz(r-4.5-any)
socialmixr_0.7.0.tar.gz(r-4.7-any)socialmixr_0.7.0.tar.gz(r-4.6-any)
socialmixr_0.7.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
socialmixr/json (API)

# Install 'socialmixr' in R:

install.packages('socialmixr', repos = c('https://epiforecasts.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/epiforecasts/socialmixr/issues

Pkgdown/docs site:https://epiforecasts.io

Datasets:

polymod - Social contact data from 8 European countries

On CRAN:

10.96 score 44 stars 2 packages 405 scripts 816 downloads 6 mentions 34 exports 37 dependencies

Last updated from:eecd1b614a (on v0.7.0). Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	214
source / vignettes	OK	226
linux-release	OK	181
macos-release	OK	105
macos-oldrel	OK	148
windows-devel	OK	133
windows-release	OK	119
windows-oldrel	OK	124
wasm-release	OK	132

Exports:age_groups_to_limits agegroups_to_limits align_ages as_contact_survey assign_age_groups check clean compute_matrix contact_age_distribution contact_matrix download_survey flatten get_citation get_survey limits_to_age_groups limits_to_agegroups list_surveys load_survey matrix_plot per_capita pop_age rebin_ages reduce_age_groups reduce_agegroups split_matrix survey survey_countries survey_country_population symmetrise weigh weigh_by_age weigh_by_dayofweek wpp_age wpp_countries

Dependencies:askpass backports cachem checkmate cli countrycode cpp11 curl data.table fastmap generics glue httr jsonlite lifecycle lubridate magrittr memoise mime oai openssl pillar pkgconfig plyr purrr R6 Rcpp rlang stringi stringr sys tibble timechange utf8 vctrs wpp2017 xml2

Introduction to socialmixr

Rendered fromsocialmixr.Rmdusingknitr::rmarkdown

Last update: 2026-08-21
Started: 2022-06-16

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Subset a contact survey	[.contact_survey
Convert age groups to lower age limits	age_groups_to_limits
Align a population table to a contact matrix's grouping levels	align_ages
Check contact survey data	as_contact_survey
Assign age groups in survey data	assign_age_groups
Check contact survey data	check check.contact_survey
Clean contact survey data	clean clean.contact_survey
Compute contact matrix from prepared survey data	compute_matrix
Extract the empirical age distribution of contacts from a survey	contact_age_distribution
Generate a contact matrix from diary survey data	contact_matrix
Download a survey from its Zenodo repository	download_survey
Flatten a multi-grouping contact matrix to its T x T form	flatten
Citation for a survey	get_citation
Get a survey, either from its Zenodo repository, a set of files, or a survey variable	get_survey
Checks if a character string is a DOI	is_doi
Convert lower age limits to age groups.	limits_to_age_groups
List all surveys available for download	list_surveys
Load a survey from local files	load_survey
Draws an image plot of a contact matrix with a legend strip and the numeric values in the cells.	matrix_plot
Convert a contact matrix to per-capita rates	per_capita
Social contact data from 8 European countries	polymod
Rebin a population table to a set of age groups	rebin_ages
Reduce the number of age groups given a broader set of limits	reduce_age_groups
Decompose a contact matrix into mean contacts, normalisation and assortativity	split_matrix
Contact survey (defunct)	survey
List all countries contained in a survey	survey_countries
Get survey country population data	survey_country_population
Symmetrise a contact matrix	symmetrise
Weigh survey participants	weigh weigh_by_age weigh_by_dayofweek
Get age-specific population data according to the World Population Prospects 2017 edition	wpp_age
List all countries and regions for which socialmixr has population data	wpp_countries