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Plot epidemic forecasts produced by epifx

This package provides functions to load and plot the forecasting outputs produced by the Python package epifx, by way of the ggplot2 plotting package for R.

License

This work is made available under the BSD 2-Clause license (see epifxplot/LICENSE).

Requirements

This package requires R 2.15 or newer, and the following packages:

The Cairo package is also suggested for printing plots to disk (e.g., as PDF or PNG files).

Usage

library(epifxplot)

# Identify an epifx output file.
hdf5_file <- '...'

# Plot the forecasts generated at each forecasting date.
p1 <- plot_forecasts(hdf5_file, obs=TRUE)

# Plot the peak timing predictions.
p2 <- plot_peak_timing(hdf5_file, obs=TRUE)

Install

Clone the repository, cd into the root directory, and run:

make install

This will install the package by running R CMD INSTALL epifxplot.