# Nonlinear Mixed Effects Models of Epidemic Growth

## Documentation for package ‘epigrowthfit’ version 0.15.4

- DESCRIPTION file.
- Package NEWS.

## Help Pages

epigrowthfit-package | R Package 'epigrowthfit'
as.list.coef.egf | Extract Coefficients and Random Effect Covariance Parameters
coef.egf | Extract Coefficients and Random Effect Covariance Parameters
coef.egf_no_fit | Extract Coefficients and Random Effect Covariance Parameters
coef.simulate.egf_model | Simulating Incidence Time Series
confint.egf | Confidence Intervals
confint.fitted.egf | Fitted Values
confint.predict.egf | Predicted Values
confint.profile.egf | Univariate Likelihood Profiles
cov2theta | Compute a Packed Representation of a Covariance Matrix
covid19.ontario | COVID-19 in Ontario, Canada
df.residual.egf | Extract the Residual Degrees of Freedom
df.residual.egf_no_fit | Extract the Residual Degrees of Freedom
dgi | Generation Interval Distribution
egf | Fit Nonlinear Mixed Effects Models of Epidemic Growth
egf-class | Description of Objects of Class 'egf'
egf.egf_model | Fit Nonlinear Mixed Effects Models of Epidemic Growth
egf.simulate.egf_model | Simulating Incidence Time Series
egf_control | Define Control Parameters
egf_control_plot | Define Control Parameters for Plotting
egf_has_converged | Test for Convergence
egf_has_random | Test for Random Effects
egf_model | Define a Top Level Nonlinear Model
egf_optimizer | Define an Optimization Method
egf_parallel | Define a Parallelization Method
egf_prior | Prior Distributions
egf_top | Top Level Nonlinear Model Parameter Names
egf_top.egf | Top Level Nonlinear Model Parameter Names
egf_top.egf_model | Top Level Nonlinear Model Parameter Names
egf_top.egf_no_fit | Top Level Nonlinear Model Parameter Names
epigrowthfit | R Package 'epigrowthfit'
epigrowthfit-defunct | Defunct Functions in Package 'epigrowthfit'
epigrowthfit-deprecated | Deprecated Functions in Package 'epigrowthfit'
epigrowthfit-notyet | Not Yet Implemented Functions in Package 'epigrowthfit'
extractAIC.egf | Extract the (Generalized) AIC
finalsize | Compute the Expected Epidemic Final Size
fitted.egf | Fitted Values
fitted.egf_no_fit | Fitted Values
fixef | Details about Fixed Effect Coefficients
fixef.egf | Details about Fixed Effect Coefficients
fixef.egf_no_fit | Details about Fixed Effect Coefficients
formula.egf | Extract Model Formulae
formula.egf_no_fit | Extract Model Formulae
getCall.egf | Extract Model Calls
getCall.egf_no_fit | Extract Model Calls
getCall.simulate.egf_model | Simulating Incidence Time Series
gi | Generation Interval Distribution
InverseWishart | Prior Distributions
labels.coef.egf | Extract Coefficients and Random Effect Covariance Parameters
LKJ | Prior Distributions
logLik.egf | Extract the Log (Marginal) Likelihood
model.frame.egf | Extract Model Frames
model.frame.egf_no_fit | Extract Model Frames
model.matrix.egf | Extract Design Matrices
model.matrix.egf_no_fit | Extract Design Matrices
nobs.egf | Extract the Number of Observations
nobs.egf_no_fit | Extract the Number of Observations
Normal | Prior Distributions
pgi | Generation Interval Distribution
plot.confint.egf | Confidence Intervals
plot.egf | Plot Nonlinear Mixed Effects Models of Epidemic Growth
plot.profile.egf | Univariate Likelihood Profiles
predict.egf | Predicted Values
print.coef.egf | Extract Coefficients and Random Effect Covariance Parameters
print.egf | Printing Model Objects
print.summary.egf | Model Summaries
profile.egf | Univariate Likelihood Profiles
qgi | Generation Interval Distribution
R0 | Compute the Basic Reproduction Number
ranef | Details about Random Effect Coefficients
ranef.egf | Details about Random Effect Coefficients
ranef.egf_no_fit | Details about Random Effect Coefficients
rgi | Generation Interval Distribution
simulate.egf | Simulation and Parametric Bootstrapping
simulate.egf_model | Simulating Incidence Time Series
summary.egf | Model Summaries
terms.egf | Model Terms
terms.egf_no_fit | Model Terms
theta2cov | Compute a Packed Representation of a Covariance Matrix
timescale | Compute the Characteristic Time Scale
vcov.egf | Model Covariance Matrices
Wishart | Prior Distributions