SimInf (version 6.2.0)

V<-: Set a template for where to write the V result matrix

Description

Using a sparse V result matrix can save a lot of memory if the model contains many nodes and time-points, but where only a few of the data points are of interest for post-processing.

Usage

V(model) <- value

Arguments

model

The model to set a template for the result matrix V.

value

A data.frame that specify the nodes, time-points and compartments of when to record the real-valued continuous state at tspan. Use NULL to reset the model to record the real-valued continuous state in every node at each time-point in tspan.

Details

Using a sparse V result matrix can save a lot of memory if the model contains many nodes and time-points, but where only a few of the data points are of interest for post-processing. To use this feature, a template has to be defined for which data points to record. This is done using a data.frame that specifies the time-points (column ‘time’) and nodes (column ‘node’) to record the state of the continuous state compartments, see ‘Examples’. The specified time-points, nodes and compartments must exist in the model, or an error is raised. Note that specifying a template only affects which data-points are recorded for post-processing, it does not affect how the solver simulates the trajectory.

Examples

# NOT RUN {
## Create an 'SISe' model with 6 nodes and initialize
## it to run over 10 days.
u0 <- data.frame(S = 100:105, I = 1:6)
model <- SISe(u0 = u0, tspan = 1:10, phi = rep(0, 6),
    upsilon = 0.02, gamma = 0.1, alpha = 1, epsilon = 1.1e-5,
    beta_t1 = 0.15, beta_t2 = 0.15, beta_t3 = 0.15, beta_t4 = 0.15,
    end_t1 = 91, end_t2 = 182, end_t3 = 273, end_t4 = 365)

## Run the model
result <- run(model, threads = 1)

## Display the continuous state variable 'phi' for every node at
## each time-point in tspan.
trajectory(result, compartments = "phi")

## Assume we are only interested in nodes '2' and '4' at the
## time-points '3' and '5'
df <- data.frame(time = c(3, 5, 3, 5),
                 node = c(2, 2, 4, 4),
                 phi = c(TRUE, TRUE, TRUE, TRUE))
V(model) <- df
result <- run(model, threads = 1)
trajectory(result, compartments = "phi")

## It is possible to use an empty 'data.frame' to specify
## that no data-points should be recorded for the trajectory.
V(model) <- data.frame()
result <- run(model, threads = 1)
trajectory(result, compartments = "phi")

## Use 'NULL' to reset the model to record data for every node at
## each time-point in tspan.
V(model) <- NULL
result <- run(model, threads = 1)
trajectory(result, compartments = "phi")
# }