model.frame.egf

model.frame.egf_no_fit

Extracts from a model object any of several data frames used to specify
the model, including the mixed effects model frames.

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

model.frame.egf function

<dl><dt>formula</dt>
<dd>an <code>egf</code> object.</dd><dt>which</dt>
<dd>a character string controlling what is returned:<dl>
 <dt><code>"ts"</code></dt>
<dd>disease incidence time series.</dd></dl></dd> <dt><code>"windows"</code></dt>
<dd>fitting window endpoints.</dd> <dt><code>"parameters"</code></dt>
<dd>the mixed effects model frame corresponding to <code>top</code>.</dd> <dt><code>"extra"</code></dt>
<dd>variables preserved in <code>formula</code> due to setting of
 <code>egf</code> argument <code>select_windows</code>.</dd> <dt><code>"combined"</code></dt>
<dd>the result of concatenating (in the sense of <code>cbind</code>)
 all mixed effects model frames and the data frame corresponding
 to <code>"extra"</code>, then deleting any duplicated variables.</dd> 
</dl><dt>top</dt>
<dd>a character string specifying a top level nonlinear model parameter,
 for <code>which = "parameters"</code>.</dd><dt>full</dt>
<dd>a logical, for <code>which = "ts"</code>. If <code>TRUE</code>, then complete
 time series are returned. Otherwise, only observations belonging
 to fitting windows are returned.</dd><dt>...</dt>
<dd>unused optional arguments.</dd>

Arguments

Extract Model Frames — model.frame.egf

<dl>

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

<dt>which</dt>
<dd>a character string controlling what is returned:<dl>
 <dt><code>"ts"</code></dt>
<dd>disease incidence time series.</dd>

 <dt><code>"windows"</code></dt>
<dd>fitting window endpoints.</dd>

 <dt><code>"parameters"</code></dt>
<dd>the mixed effects model frame corresponding to <code>top</code>.</dd>

 <dt><code>"extra"</code></dt>
<dd>variables preserved in <code>formula</code> due to setting of
 <code>egf</code> argument <code>select_windows</code>.</dd>

 <dt><code>"combined"</code></dt>
<dd>the result of concatenating (in the sense of <code>cbind</code>)
 all mixed effects model frames and the data frame corresponding
 to <code>"extra"</code>, then deleting any duplicated variables.</dd>

 
</dl></dd>

<dt>top</dt>
<dd>a character string specifying a top level nonlinear model parameter,
 for <code>which = "parameters"</code>.</dd>

<dt>full</dt>
<dd>a logical, for <code>which = "ts"</code>. If <code>TRUE</code>, then complete
 time series are returned. Otherwise, only observations belonging
 to fitting windows are returned.</dd>

<dt>...</dt>
<dd>unused optional arguments.</dd>

</dl>

model.frame.egf: Extract Model Frames

Description

Usage

Value

Arguments

See Also