Package: socialmixr 0.4.0.9000

Sebastian Funk

socialmixr: Social Mixing Matrices for Infectious Disease Modelling

Provides 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], 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]

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socialmixr.pdf |socialmixr.html✨
socialmixr/json (API)
NEWS

# Install 'socialmixr' in R:

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

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

Datasets:

polymod - Social contact data from 8 European countries

On CRAN:

9.73 score 38 stars 1 packages 197 scripts 919 downloads 6 mentions 16 exports 35 dependencies

Last updated 5 days agofrom:a2a94d7a19. Checks:OK: 7. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Oct 18 2024
R-4.5-win	OK	Oct 18 2024
R-4.5-linux	OK	Oct 18 2024
R-4.4-win	OK	Oct 18 2024
R-4.4-mac	OK	Oct 18 2024
R-4.3-win	OK	Oct 18 2024
R-4.3-mac	OK	Oct 18 2024

Exports:check clean contact_matrix download_survey get_citation get_survey limits_to_agegroups list_surveys load_survey matrix_plot pop_age reduce_agegroups survey survey_countries wpp_age wpp_countries

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

Introduction to socialmixr

Sebastian Funk

Rendered fromsocialmixr.Rmdusingknitr::rmarkdownon Oct 18 2024.

Last update: 2024-10-18
Started: 2022-06-16

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Check contact survey data	check check.survey
Clean contact survey data	clean clean.survey
Generate a contact matrix from diary survey data	contact_matrix
Download a survey from its Zenodo repository	download_survey
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_agegroups
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
Social contact data from 8 European countries	polymod
Change age groups in population data	pop_age
Reduce the number of age groups given a broader set of limits	reduce_agegroups
Contact survey	survey
List all countries contained in a survey	survey_countries
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