NEWS.md

In reconhub/epiflows: Predicting Disease Spread from Flow Data

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.

reconhub/epiflows documentation built on Sept. 21, 2023, 1:17 p.m.