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)
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
varshas 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
return_all_simulationshas been added.
make_epiflows()is now a generic with methods for data frame, integer, and numeric input.
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
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
NULLfrom 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
SpatialLinesDataFrameclass from the sp package.
Brazil_epiflowsis an epiflows object created from the
YF_flowsis the data frame of flows from
YF_locationsis the data frame of locations from
YF_coordinatesare the coordinates for the locations in
get_codes()has been removed in favor of
get_flow_data()has been removed in favor of
get_location_data()has been removed in favor of
Mex_travel_2009has been removed
add_coordinates()can now take a data frame input
NEWS.mdfile to track changes to the package.