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) . This package is part of the RECON (< http://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.


News

epiflows 0.1

Changes to class

  • epiflows class inherits the epicontacts class. This class is built from two data frames describing a linlist (referred here as locations) and contacts (referred here as flows). This was chosen over the previous implementation of two named vectors of inward and outward flows with a data frame of locations to allow the user to flexibly store more than one focus. An extra element called vars has been added, storing a dictionary of variables that are present in the data frame for use with estimate_risk_spread(). These variables are accessible via global_vars()

Changes to estimate_risk_spread

  • The function is now a generic with a default and an epiflows method.
  • The number of options have been reduced by combining the function and parameter arguments into one.
  • All errors are collected and reported if multiple arguments are missing or misspelled
  • Default varaibles have been set
  • a new parameter, return_all_simulations has been added.

Changes to constructor

  • make_epiflows() is now a generic with methods for data frame, integer, and numeric input.

Changes to plotting

  • plot() defaults to an interactive network plot from visNetwork() if no coordinates are available.
  • map_epiflows() places flows on a map
  • vis_epiflows() places flows on a network
  • grid_epiflows() places flows on a bubble plot/grid

New functions

  • get_flows() returns the flows data frame optionally specifying flows from/to a given location
  • get_locations() returns the locations data frame
  • get_coordinates() returns coordinates or NULL from the locations data frame
  • get_id() returns the identifier of all locations
  • get_n() returns a numeric vector of cases from/to a given location
  • get_pop_size() returns a vector of population sizes for locations
  • get_vars() returns a specified variable from the locations data frame OR returns the defined variables if no arguments are given.
  • set_vars() allows the user to set or reset the global variables.
  • global_vars() can return, set, and reset globally recognized variables
  • as.SpatialLinesDataFrame() converts an epiflows object with coordinates to a SpatialLinesDataFrame class from the sp package.

New data sets

  • Brazil_epiflows is an epiflows object created from the YF_Brazil data
  • YF_flows is the data frame of flows from YF_Brazil
  • YF_locations is the data frame of locations from YF_Brazil
  • YF_coordinates are the coordinates for the locations in YF_Brazil

Removed functions/data

  • get_codes() has been removed in favor of get_id()
  • get_flow_data() has been removed in favor of get_n() and get_flows()
  • get_location_data() has been removed in favor of get_locations()
  • Mex_travel_2009 has been removed

Misc

  • add_coordinates() can now take a data frame input
  • Magrittr pipes are no longer imported.
  • visNetwork is imported
  • vdiffr is used for visual tests
  • continuous integration and automated tests have been set up
  • A new vignette describing the epiflows class has been added
  • README and introduction vignette have been updated.

epiflows 0.0.1.9000

  • Added a NEWS.md file to track changes to the package.

Reference manual

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install.packages("epiflows")

0.2.0 by Pawel Piatkowski, 10 months ago


https://www.repidemicsconsortium.org/epiflows


Report a bug at https://github.com/reconhub/epiflows/issues


Browse source code at https://github.com/cran/epiflows


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]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports epicontacts, leaflet, ggmap, geosphere, ggplot2, tibble, sp, htmlwidgets, stats, htmltools, visNetwork

Suggests testthat, roxygen2, knitr, outbreaks, vdiffr, curl, rmarkdown


See at CRAN