predict.egf

confint.predict.egf

Computes predicted values of top level nonlinear model parameters.
These are conditional on an estimated nonlinear mixed effects model
and, optionally, new data.

Maximum likelihood estimation of nonlinear mixed effects models of
epidemic growth using Template Model Builder ('TMB'). Enables
joint estimation for collections of disease incidence time series,
including time series that describe multiple epidemic waves.
Supports a set of widely used phenomenological models: exponential,
logistic, Richards (generalized logistic), subexponential,
and Gompertz. Provides methods for interrogating model objects
and several auxiliary functions, including one for computing basic
reproduction numbers from fitted values of the initial exponential
growth rate.
Preliminary versions of this software were applied
in Ma et al. (2014) <doi:10.1007/s11538-013-9918-2> and
in Earn et al. (2020) <doi:10.1073/pnas.2004904117>.

Mikael Jagan

epigrowthfit

Nonlinear Mixed Effects Models of Epidemic Growth

Ben Bolker

Jonathan Dushoff

David Earn

Junling Ma

predict.egf function

<dl><dt>object</dt>
<dd>an <code>egf</code> object.</dd><dt>newdata</dt>
<dd>a data frame containing variables to replace those in the model
 frame. The default is to use the model frame as is, and currently
 that is the only implemented behaviour.</dd><dt>class</dt>
<dd>a logical. If <code>TRUE</code>,
 then the value of the method call call is a <code>predict.egf</code>
 object, not a matrix.</dd><dt>se</dt>
<dd>a logical. If <code>TRUE</code> and if <code>class = TRUE</code>,
 then the result is augmented with approximate delta method
 standard errors.</dd><dt>...</dt>
<dd>additional arguments passed from or to other methods.</dd></dl>

Arguments

Predicted Values — predict.egf

<dl>

<dt>object</dt>
<dd>an <code>egf</code> object.</dd>

<dt>newdata</dt>
<dd>a data frame containing variables to replace those in the model
 frame. The default is to use the model frame as is, and currently
 that is the only implemented behaviour.</dd>

<dt>class</dt>
<dd>a logical. If <code>TRUE</code>,
 then the value of the method call call is a <code>predict.egf</code>
 object, not a matrix.</dd>

<dt>se</dt>
<dd>a logical. If <code>TRUE</code> and if <code>class = TRUE</code>,
 then the result is augmented with approximate delta method
 standard errors.</dd>

<dt>...</dt>
<dd>additional arguments passed from or to other methods.</dd>

</dl>

predict.egf: Predicted Values

Description

Usage

Value

Arguments

See Also