create_clean_reported_cases {EpiNow2} | R Documentation |
Create Clean Reported Cases
Description
Filters leading zeros, completes dates, and applies an optional threshold at
which point 0 cases are replaced with a user supplied value (defaults to
NA
).
Usage
create_clean_reported_cases(
data,
horizon = 0,
filter_leading_zeros = TRUE,
zero_threshold = Inf,
fill = NA_integer_,
add_breakpoints = TRUE
)
Arguments
data |
A <data.frame> of confirmed cases (confirm) by date
(date). confirm must be numeric and date must be in date format.
|
horizon |
Numeric, defaults to 7. Number of days into the future to
forecast.
|
filter_leading_zeros |
Logical, defaults to TRUE. Should zeros at the
start of the time series be filtered out.
|
zero_threshold |
Numeric defaults
to Inf. Indicates if detected zero cases are meaningful by using a threshold
number of cases based on the 7-day average. If the average is above this
threshold then the zero is replaced using fill .
|
fill |
Numeric, defaults to NA. Value to use to replace NA values or
zeroes that are flagged because the 7-day average is above the
zero_threshold . If the default NA is used then dates with NA values or with
7-day averages above the zero_threshold will be skipped in model fitting.
If this is set to 0 then the only effect is to replace NA values with 0.
|
add_breakpoints |
Logical, defaults to TRUE. Should a breakpoint column
be added to the data frame if it does not exist.
|
Value
A cleaned data frame of reported cases
Examples
## Not run:
create_clean_reported_cases(example_confirmed, 7)
## End(Not run)
[Package
EpiNow2 version 1.5.2
Index]