punchcard-set: Set a template for where to record result during a simulation

In stewid/SimInf: A Framework for Data-Driven Stochastic Disease Spread Simulations

Set a template for where to record result during a simulation

Description

Using a sparse 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

punchcard(model) <- value

## S4 replacement method for signature 'SimInf_model'
punchcard(model) <- value

Arguments

model	The model to set a template for where to record result.
value	A data.frame that specify the nodes, time-points and compartments to record the number of individuals at tspan. Use NULL to reset the model to record the number of inidividuals in each compartment in every node at each time-point in tspan.

Details

Using a sparse 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 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

## For reproducibility, call the set.seed() function and specify
## the number of threads to use. To use all available threads,
## remove the set_num_threads() call.
set.seed(123)
set_num_threads(1)

## Create an 'SIR' model with 6 nodes and initialize it to run over 10 days.
u0 <- data.frame(S = 100:105, I = 1:6, R = rep(0, 6))
model <- SIR(u0 = u0, tspan = 1:10, beta = 0.16, gamma = 0.077)

## Run the model.
result <- run(model)

## Display the trajectory with data for every node at each
## time-point in tspan.
trajectory(result)

## 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),
                 S = c(TRUE, TRUE, TRUE, TRUE),
                 I = c(TRUE, TRUE, TRUE, TRUE),
                 R = c(TRUE, TRUE, TRUE, TRUE))
punchcard(model) <- df
result <- run(model)
trajectory(result)

## We can also specify to record only some of the compartments in
## each time-step.
df <- data.frame(time = c(3, 5, 3, 5),
                 node = c(2, 2, 4, 4),
                 S = c(FALSE, TRUE, TRUE, TRUE),
                 I = c(TRUE, FALSE, TRUE, FALSE),
                 R = c(TRUE, FALSE, TRUE, TRUE))
punchcard(model) <- df
result <- run(model)
trajectory(result)

## A shortcut to specify to record all of the compartments in
## each time-step is to only inlude node and time.
df <- data.frame(time = c(3, 5, 3, 5),
                 node = c(2, 2, 4, 4))
punchcard(model) <- df
result <- run(model)
trajectory(result)

## It is possible to use an empty 'data.frame' to specify
## that no data-points should be recorded for the trajectory.
punchcard(model) <- data.frame()
result <- run(model)
trajectory(result)

## Use 'NULL' to reset the model to record data for every node at
## each time-point in tspan.
punchcard(model) <- NULL
result <- run(model)
trajectory(result)

stewid/SimInf documentation built on April 16, 2024, 12:12 a.m.