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

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

# S3 method for 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

Value

data frame with the following columns

t

the time

sim

simulation number (factor variable) (optional column)

Xk

where k = 0, ..., K

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.

Examples

out <- fortify_aggregate(pomp_df, package_source = "pomp",
states = c("S", "I", "R"))
head(out)
#>   t sim  X0 X1 X2
#> 1 0   1 950 50  0
#> 2 1   1 946 52  2
#> 3 2   1 944 54  2
#> 4 3   1 941 57  2
#> 5 4   1 937 60  3
#> 6 5   1 931 65  4
unique(rowSums(out[, 3:5]))
#> [1] 1000