EVI (version 0.2.0-0)

evi.graphs: This function produces plots of the time series data with the EVI predictions.

Description

Three types of plots are generated: (i) A plot of the confirmed cases with red dots corresponding to time points that an early warning was issued and grey dots corresponding to time points without an early warning indication. (ii) A plot of the confirmed cases with colored dots corresponding to time points with an early warning. Color intensity is increasing with higher positive predictive value (PPV). (iii) A plot of the confirmed cases with colored dots corresponding to time points without an early warning. Color intensity is increasing with higher negative predictive value (NPV).

Usage

evi.graphs(EVI_output, graph = c("EVI"), ln = T, type = "p")

Arguments

EVI_output

output of the deviant() function

graph

Type of graph to be plotted. Options: "EVI", "PPV", "NPV". "EVI" (the default) is giving a plot of the confirmed cases, with red dots corresponding to time points that an early warning was issued and grey dots corresponding to time points without an early warning indication. "PPV" is giving a plot of the confirmed cases with colored dots corresponding to time points with an early warning. Color intensity is increasing with higher PPV. "NPV" is giving a plot of the confirmed cases with colored dots corresponding to time points without an early warning. Color intensity is increasing with higher NPV.

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.

Details

An EVI_output is required as input, derived from the deviant() function.

References

Kostoulas P, Meletis E, Pateras K, et al. The epidemic volatility index, a novel early warning tool for identifying new waves in an epidemic. Sci Rep 11, 23775 (2021). tools:::Rd_expr_doi("10.1038/s41598-021-02622-3") 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

data("Italy")
EVI_output<-deviant(new_cases=Italy$Cases[1:20], cum=FALSE, r_a=7, r=0.2, lag_max=30,method="EVI")
#EVI_output<-deviant(new_cases=Italy$Cases, cum=FALSE, r_a=7, r=0.2, lag_max=30,method="EVI")

evi.graphs(EVI_output=EVI_output, graph="EVI", ln=TRUE)
evi.graphs(EVI_output=EVI_output, graph="PPV", ln=TRUE)
evi.graphs(EVI_output=EVI_output, graph="NPV", ln=TRUE)
evi.graphs(EVI_output=EVI_output, graph="EVI", ln=TRUE, type="l") # For the line EVI plot