global_vars: Epiflow Global Variables

In reconhub/epiflows: Predicting Disease Spread from Flow Data

Epiflow Global Variables

Description

The metadata in locations such as population size, duration of stay in a given location, date of first and last cases, etc. can be useful in estimating the risk of spread, but not everyone will code their data with identical column names. To facilitate their use in the function estimate_risk_spread(), the epiflows object stores a dictionary of variables in a place called ⁠$vars⁠. We can tell epiflows what variables are important when we create the object.

Usage

global_vars(..., set = FALSE, reset = FALSE)

Arguments

...	quoted varaibles to add to the default variables
set	when TRUE, the variables provided in ... will be added to the global variables. Defaults to FALSE
reset	when TRUE, the global variables are reset to the default variables listed above. Defaults to FALSE

Details

The default varaibles are:

• coordinates: two columns specifying the lon and lat coordinates

• pop_size: population size of each location

• duration_stay: the average duration of stay for each location

• first_date: the date of first recorded case

• last_date: the date of the last recorded case

• num_cases: the number of cases between the first and last date

See Also

make_epiflows(), get_locations(), get_vars(), set_vars(), get_coordinates()

Examples

# see the default varaibles
global_vars()

# Equivalent
getOption("epiflows.vars")

# create an object, specifying these variables
data("YF_locations")
data("YF_flows")
ef <- make_epiflows(flows         = YF_flows, 
                    locations     = YF_locations, 
                    pop_size      = "location_population",
                    duration_stay = "length_of_stay",
                    num_cases     = "num_cases_time_window",
                    first_date    = "first_date_cases",
                    last_date     = "last_date_cases"
                   )
ef


# You will receive an error if a variable is specified incorrectly
YF_locations$random_variable <- runif(nrow(YF_locations))
try({
  ef <- make_epiflows(flows         = YF_flows, 
                      locations     = YF_locations, 
                      Pop_size      = "location_population",
                      duration_stay = "length_of_stay",
                      num_cases     = "num_cases_time_window",
                      first_date    = "first_date_cases",
                      last_date     = "last_date_cases",
                      random        = "random_variable"
                     )
   })


# If you create a new method and need other varaibles, or just want a shorter
# representation, they can be added to your options:

global_vars("random", set = TRUE)

YF_locations$random_variable <- runif(nrow(YF_locations))
ef <- make_epiflows(flows         = YF_flows, 
                    locations     = YF_locations, 
                    pop_size      = "location_population",
                    duration_stay = "length_of_stay",
                    num_cases     = "num_cases_time_window",
                    first_date    = "first_date_cases",
                    last_date     = "last_date_cases",
                    random        = "random_variable"
                   )

# You can also reset the variables
global_vars(reset = TRUE)

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