NEWS

epiflows 0.1

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()

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.

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 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.