Nonlinear Mixed Effects Models of Epidemic Growth

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Documentation for package ‘epigrowthfit’ version 0.15.4

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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