plotFit | R Documentation |
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
)
fitmodel |
a |
theta |
named numeric vector. Values of the parameters. Names should
match |
initState |
named numeric vector. Initial values of the state
variables. Names should match |
data |
data frame. Observation times and observed data. The time column
must be named |
nReplicates |
numeric, number of replicated simulations. |
summary |
logical. If |
alpha |
transparency of the trajectories (between 0 and 1). |
allVars |
logical, if |
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 |
observation |
logical, if |
plot |
if |
if plot == FALSE
, a list of 2 elements is returned:
simulations
data.frame
of nReplicates
simulated observations.
plot
the plot of the fit.
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