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EVI

EVI: the Epidemic Volatility Index as an early-warning tool for epidemic waves

Installation

To install the current source from GitHub use:

install.packages(c("devtools", "remotes"))
require(devtools)
require(remotes)
remotes::install_github("ku-awdc/EVI")

To install a stable version from the drat repository use:

## Will be added once a stable version is available

Basic functions of EVI package

require(EVI)

To load some example data:

data("Italy")

To run EVI analysis on the example data:

deviant(Italy$Cases)

To run EVI analysis when you already have historical data and need an update with the influx of new data you do the following: first you analyze the historical data. Let’s say we have first observed only the 148 cases from the Italian data. We initially run the deviant function:

deviant(Italy$Cases[1:148])

As a new observation (or observations) comes in we need to update our output file by adding the EVI output for the new case(s) as a new row(s). This is done by using the deviant_update function:

deviant_update(Italy$Cases[1:149])

This has as a result an updated output file (the “EVI_output” file) with 149 rows now, after the addition of the row from the analysis of the newly observed data.

To create a plot of the analysed data:

evi.graphs(EVI_output)

The basic two functions of the EVI analysis are deviant() and evi.graphs(). For help on these functions type:

?deviant
?deviant_update
?evi.graphs

Troubleshooting

In case an error during download occur try the following

remotes::install_github("ku-awdc/EVI", force = TRUE, dependecies = TRUE)

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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