Plot fit of model to data — plotFit • fitR

This function simulates the model under theta, generates observation and plot them against the data. Since simulation and observation processes can be stochastic, nReplicates can be plotted.

plotFit(
  fitmodel,
  theta,
  initState,
  data,
  nReplicates = 1,
  summary = TRUE,
  alpha = min(1, 10/nReplicates),
  allVars = FALSE,
  nonExtinct = NULL,
  observation = TRUE,
  plot = TRUE
)

Arguments

fitmodel: a fitmodel object
theta: named numeric vector. Values of the parameters. Names should match fitmodel$thetaNames.
initState: named numeric vector. Initial values of the state variables. Names should match fitmodel$stateNames.
data: data frame. Observation times and observed data. The time column must be named "time" and the observation column must be named "obs".
nReplicates: numeric, number of replicated simulations.
summary: logical. If TRUE, the mean, median as well as the 50th and 95th percentile of the trajectories are plotted (default). If FALSE, all individual trajectories are plotted (transparency can be set with alpha).
alpha: transparency of the trajectories (between 0 and 1).
allVars: logical, if FALSE only the observations are plotted. Otherwise, all state variables are plotted.
nonExtinct: character vector. Names of the infected states which must be non-zero so the epidemic is still ongoing. When the names of these states are provided, the extinction probability is plotted by computing the proportion of faded-out epidemics over time. An epidemic has faded-out when all the infected states (whose names are provided) are equal to 0. This is only relevant for stochastic models. In addition, if summary == TRUE, the summaries of the trajectories conditioned on non-extinction are shown. Default to NULL.
observation: logical, if TRUE simulated observation are generated by rTrajObs.
plot: if TRUE the plot is displayed, and returned otherwise.

Value

if plot == FALSE, a list of 2 elements is returned:

simulations data.frame of nReplicates simulated observations.
plot the plot of the fit.