plot_model: Plot Compartment Populations over Time for a Model Simulation

In bristolmathmodellers/biddmodellingcourse: Practicals and Code for the BIDD Modelling Short Course

Description

Make seperate plots for each model compartment. Assumes model output is structured as that produced from solve_ode.

Usage

plot_model(sim, prev_sim = NULL, model_labels = NULL, facet = TRUE,
  interactive = FALSE)

Arguments

sim	A tibble of model output as formated by solve_ode
prev_sim	A second tibble of model output formated as for sim. Used to compare to model runs.
model_labels	A character vector of model names, defaults to c("Current", "Previous").
facet	Logical, defaults to TRUE. If FALSE then the plot will not be facetted otherwise it will be.
interactive	Logical, defaults to FALSE. If TRUE produces an interative plot.

Value

A Plot of each model compartments population over time.

Examples

## Intialise
N = 100000
I_0 = 1
S_0 = N - I_0
R_0 = 1.1
beta = R_0

##Time for model to run over
tbegin = 0
tend = 50
times <- seq(tbegin, tend, 1)

##Vectorise input
parameters <- as.matrix(c(beta = beta))
inits <- as.matrix(c(S = S_0, I = I_0))

sim <- solve_ode(model = SI_ode, inits, parameters, times, as.data.frame = TRUE)

plot_model(sim, facet = FALSE, interactive = FALSE)

plot_model(sim, facet = TRUE, interactive = FALSE)

## Compare with an updated model run

#'## Intialise
R_0 = 1.3
beta = R_0
parameters <- as.matrix(c(beta = beta))

new_sim <- solve_ode(model = SI_ode, inits, parameters, times, as.data.frame = TRUE)


plot_model(new_sim,sim, facet = FALSE, interactive = FALSE)

plot_model(new_sim, sim, facet = TRUE, interactive = FALSE)

bristolmathmodellers/biddmodellingcourse documentation built on May 28, 2019, 7:13 p.m.