EVI (version 0.2.0-0)

evirlap: Combining multiple epidemic volatility indices into a multi-early warning index plot

Description

This function returns an overlap graph containing two indices.

1. If index number 1 results in an early warning,then a yellow point will be shown.

2. If index number 2 results in an early warning, then a orange point will be shown.

3. If both indexes result in early warnings, then a red point will be shown.

Usage

evirlap(
  Index1,
  Index2,
  ln = T,
  type = "p",
  size.index = 1,
  Index1.lab = "EVI1",
  Index2.lab = "EVI2",
  Index3.lab = "EVI-",
  Index.country = NULL
)

Value

• evirlap: A graph with two EVI indexes shown simulteounsly.

Arguments

Index1

e.g. output of the deviant() function

Index2

e.g. output of the deviant() function (e.g. method = cEVI)

ln

TRUE or FALSE; If TRUE (the default) the output of the graph will be presented on the logarithmic scale. IF FALSE the output data will be presented on the original scale.

type

By default, points are plotted on EVI graphs. In cases where, changes are very sudden or data sparsely available, type="l" introduces lines on top of points for the "EVI" type of graph.

size.index

Size of the points, default=1

Index1.lab

Text for index 1, "EVI1"

Index2.lab

Text for index 2, "EVI2"

Index3.lab

Text for index conjuction, "EVI-"

Index.country

Label for country/area/region under analysis

Details

The evirlap function can literally combine any two indices with only 2 requirements. The two vectors (Index1, Index2) to be of equal length and to contain either 0s (no warnings) or 1s (warnings).

For each time point the stored variables are:

References

Pateras K, Meletis E, Denwood M, et al. The convergence epidemic index (cEVI) an early warning tool for identifying waves in an epidemic. Inf Dis Mod, (2023)

Examples

# Run basic functions to acquire early warnings results
#data('Italy')
#EVI_output=deviant(new_cases=Italy$Cases, cum=FALSE, method="EVI")
#cEVI_output=deviant(new_cases=Italy$Cases, cum=FALSE, method="cEVI")

# Plot the EVI combination graph
#evirlap(Index1=EVI_output, Index2=cEVI_output, ln=TRUE)
#evirlap(Index1=EVI_output, Index2=cEVI_output, ln=TRUE, type="l") # For the line EVI plot

# Austria first 150 case example
#data('Austria')
#tmp_EVI_at=deviant(new_cases = Austria$Cases)
#tmp_cEVI_at=deviant(new_cases = Austria$Cases,lag_max = 40,method = "cEVI")
#evirlap(Index1 = tmp_EVI_at,Index2 = tmp_cEVI_at)