Social Mixing Matrices for Infectious Disease Modelling

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Documentation for package ‘socialmixr’ version 0.7.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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