global_vars {epiflows} | R Documentation |
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 $vars
.
We can tell epiflows what variables are important when we create the object.
Usage
global_vars(..., set = FALSE, reset = FALSE)
Arguments
... |
quoted varaibles to add to the default variables |
set |
when |
reset |
when |
Details
The default varaibles are:
-
coordinates
: two columns specifying the lon and lat coordinates -
pop_size
: population size of each location -
duration_stay
: the average duration of stay for each location -
first_date
: the date of first recorded case -
last_date
: the date of the last recorded case -
num_cases
: the number of cases between the first and last date
See Also
make_epiflows()
, get_locations()
, get_vars()
, set_vars()
, get_coordinates()
Examples
# see the default varaibles
global_vars()
# Equivalent
getOption("epiflows.vars")
# create an object, specifying these variables
data("YF_locations")
data("YF_flows")
ef <- make_epiflows(flows = YF_flows,
locations = YF_locations,
pop_size = "location_population",
duration_stay = "length_of_stay",
num_cases = "num_cases_time_window",
first_date = "first_date_cases",
last_date = "last_date_cases"
)
ef
# You will receive an error if a variable is specified incorrectly
YF_locations$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)