fortify_aggregate.pomp_df: Takes in data from the R pomp package where the output is a...

In skgallagher/EpiCompare: A Pipeline to Analyze and Compare Infectious Disease Epidemics

Description

Takes in data from the R pomp package where the output is a data frame and puts it in SIR format for EpiCompare

Usage

## S3 method for class 'pomp_df'
fortify_aggregate(data, states = c("S", "I", "R"), package_source = NULL)

Arguments

data	Output from a pomp simulation where the output is a data frame, pomp::simulate(), and we have added the name pomp_df to the class names.
states	vector of state names
package_source	optional package name

Details

The default variables that are retained are SIR, but can be modified with the states argument. If codestates = NULL, we will attempt to find all single letter names in POMP and output those.

Value

data frame with the following columns

t

the time

sim

simulation number (factor variable) (optional column)

Xk

where k = 0, ..., K

Examples

out <- fortify_aggregate(pomp_df, package_source = "pomp",
states = c("S", "I", "R"))
head(out)
unique(rowSums(out[, 3:5]))

skgallagher/EpiCompare documentation built on Sept. 14, 2021, 5:45 a.m.