Package: epigrowthfit 0.15.3

Mikael Jagan

epigrowthfit: Nonlinear Mixed Effects Models of Epidemic Growth

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>.

Authors:Mikael Jagan [aut, cre], Ben Bolker [aut], Jonathan Dushoff [ctb], David Earn [ctb], Junling Ma [ctb]

epigrowthfit_0.15.3.tar.gz
epigrowthfit_0.15.3.tar.gz(r-4.5-noble)epigrowthfit_0.15.3.tar.gz(r-4.4-noble)
epigrowthfit_0.15.3.tgz(r-4.4-emscripten)
epigrowthfit.pdf |epigrowthfit.html✨
epigrowthfit/json (API)
NEWS

# Install 'epigrowthfit' in R:
install.packages('epigrowthfit', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/davidearn/epigrowthfit/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:

1.95 score 45 scripts 154 downloads 24 exports 6 dependencies

Last updated 5 months agofrom:c7e1d3a175. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 16 2024
R-4.5-linux-x86_64OKNov 16 2024

Exports:cov2thetadgiegfegf_controlegf_control_plotegf_has_convergedegf_has_randomegf_modelegf_optimizeregf_parallelegf_topfinalsizefixefInverseWishartLKJNormalpgiqgiR0ranefrgitheta2covtimescaleWishart

Dependencies:latticeMatrixnlmeRcppRcppEigenTMB

Readme and manuals

Help Manual

Help pageTopics
R Package 'epigrowthfit'epigrowthfit-package epigrowthfit
Extract Coefficients and Random Effect Covariance Parametersas.list.coef.egf coef.egf coef.egf_no_fit labels.coef.egf print.coef.egf
Confidence Intervalsconfint.egf plot.confint.egf
Compute a Packed Representation of a Covariance Matrixcov2theta theta2cov
COVID-19 in Ontario, Canadacovid19.ontario
Extract the Residual Degrees of Freedomdf.residual.egf df.residual.egf_no_fit
Fit Nonlinear Mixed Effects Models of Epidemic Growthegf egf.egf_model
Define Control Parametersegf_control
Define Control Parameters for Plottingegf_control_plot
Test for Convergenceegf_has_converged
Test for Random Effectsegf_has_random
Define a Top Level Nonlinear Modelegf_model
Define an Optimization Methodegf_optimizer
Define a Parallelization Methodegf_parallel
Prior Distributionsegf_prior InverseWishart LKJ Normal Wishart
Top Level Nonlinear Model Parameter Namesegf_top egf_top.egf egf_top.egf_model egf_top.egf_no_fit
Description of Objects of Class 'egf'egf-class
Defunct Functions in Package 'epigrowthfit'epigrowthfit-defunct
Deprecated Functions in Package 'epigrowthfit'epigrowthfit-deprecated
Not Yet Implemented Functions in Package 'epigrowthfit'epigrowthfit-notyet
Extract the (Generalized) AICextractAIC.egf
Compute the Expected Epidemic Final Sizefinalsize
Fitted Valuesconfint.fitted.egf fitted.egf fitted.egf_no_fit
Details about Fixed Effect Coefficientsfixef fixef.egf fixef.egf_no_fit
Extract Model Formulaeformula.egf formula.egf_no_fit
Extract Model CallsgetCall.egf getCall.egf_no_fit
Generation Interval Distributiondgi gi pgi qgi rgi
Extract the Log (Marginal) LikelihoodlogLik.egf
Extract Model Framesmodel.frame.egf model.frame.egf_no_fit
Extract Design Matricesmodel.matrix.egf model.matrix.egf_no_fit
Extract the Number of Observationsnobs.egf nobs.egf_no_fit
Plot Nonlinear Mixed Effects Models of Epidemic Growthplot.egf
Predicted Valuesconfint.predict.egf predict.egf
Printing Model Objectsprint.egf
Univariate Likelihood Profilesconfint.profile.egf plot.profile.egf profile.egf
Compute the Basic Reproduction NumberR0
Details about Random Effect Coefficientsranef ranef.egf ranef.egf_no_fit
Simulation and Parametric Bootstrappingsimulate.egf
Simulating Incidence Time Seriescoef.simulate.egf_model egf.simulate.egf_model getCall.simulate.egf_model simulate.egf_model
Model Summariesprint.summary.egf summary.egf
Model Termsterms.egf terms.egf_no_fit
Compute the Characteristic Time Scaletimescale
Model Covariance Matricesvcov.egf