Package: epiflows 0.2.2

Pawel Piatkowski

epiflows: Predicting Disease Spread from Flow Data

Provides functions and classes designed to handle and visualise epidemiological flows between locations. Also contains a statistical method for predicting disease spread from flow data initially described in Dorigatti et al. (2017) <doi:10.2807/1560-7917.ES.2017.22.28.30572>. This package is part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.

Authors:Pawel Piatkowski [aut, cre], Paula Moraga [aut], Isobel Blake [ctb, dtc], Thibaut Jombart [aut], VP Nagraj [aut], Zhian N. Kamvar [aut], Salla E. Toikkanen [aut]

epiflows_0.2.2.tar.gz
epiflows_0.2.2.zip(r-4.7)epiflows_0.2.2.zip(r-4.6)epiflows_0.2.2.zip(r-4.5)
epiflows_0.2.2.tgz(r-4.6-any)epiflows_0.2.2.tgz(r-4.5-any)
epiflows_0.2.2.tar.gz(r-4.7-any)epiflows_0.2.2.tar.gz(r-4.6-any)
epiflows_0.2.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
epiflows/json (API)
NEWS

# Install 'epiflows' in R:

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

Bug tracker:https://github.com/reconhub/epiflows/issues

Pkgdown/docs site:https://www.repidemicsconsortium.org

Datasets:

Brazil_epiflows - Yellow Fever Data from Brazil; 2016-12 to 2017-05
YF_Brazil - Yellow Fever Data from Brazil; 2016-12 to 2017-05
YF_coordinates - Yellow Fever Data from Brazil; 2016-12 to 2017-05
YF_flows - Yellow Fever Data from Brazil; 2016-12 to 2017-05
YF_locations - Yellow Fever Data from Brazil; 2016-12 to 2017-05

On CRAN:

outbreak

6.68 score 19 stars 21 scripts 312 downloads 1 mentions 17 exports 87 dependencies

Last updated from:79c8bc5f0d. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	172
source / vignettes	OK	209
linux-release-x86_64	OK	174
macos-release-arm64	OK	134
macos-oldrel-arm64	OK	107
windows-devel	OK	108
windows-release	OK	112
windows-oldrel	OK	99
wasm-release	OK	150

Exports:add_coordinates as.SpatialLinesDataFrame estimate_risk_spread get_coordinates get_flows get_id get_locations get_n get_pop_size get_vars global_vars grid_epiflows make_epiflows map_epiflows set_vars set_vars<-vis_epiflows

Dependencies:askpass base64enc bitops bslib cachem class classInt cli cpp11 crosstalk curl DBI digest dplyr e1071 epicontacts evaluate farver fastmap fontawesome fs generics geosphere ggmap ggplot2 glue gtable highr htmltools htmlwidgets httr igraph isoband jpeg jquerylib jsonlite KernSmooth knitr labeling lattice lazyeval leaflet leaflet.providers lifecycle magrittr MASS Matrix memoise mime openssl pillar pkgconfig plyr png proxy purrr R6 rappdirs raster RColorBrewer Rcpp rlang rmarkdown s2 S7 sass scales sf sp stringi stringr sys terra threejs tibble tidyr tidyselect tinytex units utf8 vctrs viridisLite visNetwork withr wk xfun yaml

00 epiflows: package overview

Rendered fromintroduction.Rmdusingknitr::rmarkdownon May 08 2026.

Last update: 2018-08-14
Started: 2017-09-02

01 Data Preparation

Rendered fromepiflows-class.Rmdusingknitr::rmarkdownon May 08 2026.

Last update: 2018-08-02
Started: 2018-07-30

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Subset `epiflows` objects	[.epiflows
Add/Retrieve location coordinates	add_coordinates get_coordinates get_coordinates.epiflows
Convert to SpatialLinesDataFrame class	as.SpatialLinesDataFrame as.SpatialLinesDataFrame.epiflows
epiflows	epiflows-package epiflows
Travel-related disease cases spreaded to other locations from an infectious location	estimate_risk_spread estimate_risk_spread.default estimate_risk_spread.epiflows
Access flow data	get_flows get_flows.epiflows
Access population identifiers in epiflows objects	get_id
Access flow data	get_locations get_locations.epiflows
get the number of cases per flow	get_n get_n.epiflows
Get population size for each entry in locations	get_pop_size get_pop_size.epiflows
Access location metadata	get_vars get_vars.epiflows set_vars set_vars.epiflows set_vars<- set_vars<-.epiflows
Epiflow Global Variables	epiflows.vars global_vars
Visualise epidemic flows using a grid	grid_epiflows
Create an epiflows object	make_epiflows make_epiflows.data.frame make_epiflows.integer make_epiflows.numeric
Map flows of people between locations	map_epiflows
Various plots for epiflows objects	plot.epiflows
Print method from epiflows objects	print.epiflows
Visualise epidemic flows using visNetwork	vis_epiflows
Yellow Fever Data from Brazil; 2016-12 to 2017-05	Brazil_epiflows YF_Brazil YF_coordinates YF_flows YF_locations