deBInfer: Bayesian Inference for Differential Equations
Version 0.4.1

A Bayesian framework for parameter inference in differential equations. This approach offers a rigorous methodology for parameter inference as well as modeling the link between unobservable model states and parameters, and observable quantities. Provides templates for the DE model, the observation model and data likelihood, and the model parameters and their prior distributions. A Markov chain Monte Carlo (MCMC) procedure processes these inputs to estimate the posterior distributions of the parameters and any derived quantities, including the model trajectories. Further functionality is provided to facilitate MCMC diagnostics and the visualisation of the posterior distributions of model parameters and trajectories.

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AuthorPhilipp H Boersch-Supan [aut, cre], Leah R Johnson [aut], Sadie J Ryan [aut]
Date of publication2016-09-14 21:44:04
MaintainerPhilipp H Boersch-Supan <pboesu@gmail.com>
LicenseGPL-3
Version0.4.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("deBInfer")

Man pages

chytrid: Chytrid fungus data set
debinfer_par: debinfer_par
deinits: Get starting/fixed values of DE initial values
de_mcmc: de_mcmc
depars: Get starting/fixed values of DE parameters
is.debinfer_result: is.debinfer_result
logd_prior: logd_prior
logistic: Logistic growth data set
log_post_params: log_post_params
log_prior_params: log_prior_params
pairs.debinfer_result: Pairwise posterior marginals
plot.debinfer_result: Plot inference outputs
plot.post_sim_list: Plot posterior trajectory
post_prior_densplot: Plot posterior marginals and corresponding priors
post_sim: post_sim
prior_draw_rev: prior_draw_rev
propose_joint_rev: propose_joint
propose_single_rev: propose_single_rev
reshape_post_sim: Reshape posterior model solutions
setup_debinfer: setup_debinfer
solve_de: solve_de
summary.debinfer_result: Summary of the inference results
update_sample_rev: update_sample_rev

Functions

chytrid Man page
de_mcmc Man page Source code
debinfer_par Man page Source code
deinits Man page Source code
depars Man page Source code
is.debinfer_result Man page Source code
log_post_params Man page Source code
log_prior_params Man page Source code
logd_prior Man page Source code
logistic Man page
pairs.debinfer_result Man page Source code
plot.debinfer_result Man page Source code
plot.post_sim_list Man page Source code
post_prior_densplot Man page Source code
post_sim Man page Source code
prior_draw_rev Man page Source code
propose_joint_rev Man page Source code
propose_single_rev Man page Source code
reshape_post_sim Man page Source code
setup_debinfer Man page Source code
solve_de Man page Source code
summary.debinfer_result Man page Source code
update_sample_rev Man page Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/deBInfer_compiled_code.pdf
inst/doc/logistic_ode_example.pdf
inst/doc/chytrid_dede_example.pdf
inst/doc/chytrid_dede_example.R
inst/doc/deBInfer_compiled_code.pdf.asis
inst/doc/logistic_ode_example.R
inst/doc/chytrid_dede_example.Rmd
inst/doc/logistic_ode_example.Rmd
tests
tests/testthat.R
tests/testthat
tests/testthat/test_likelihood_eval.R
tests/testthat/test_inference_logistic.R
tests/testthat/test_debinfer_par.R
NAMESPACE
data
data/logistic.rda
data/chytrid.rda
R
R/setup_mcmc.R
R/de_solver.R
R/de_mcmc_rev.R
R/data_doc.R
R/mcmc_plotting.R
R/debinfer_utils.R
vignettes
vignettes/methods-in-ecology-and-evolution.csl
vignettes/debinfer.bib
vignettes/deBInfer_compiled_code.pdf.asis
vignettes/epsilon-sensitivity.pdf
vignettes/chytrid_dede_example.Rmd
vignettes/logistic_ode_example.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/log_post_params.Rd
man/debinfer_par.Rd
man/pairs.debinfer_result.Rd
man/summary.debinfer_result.Rd
man/plot.debinfer_result.Rd
man/depars.Rd
man/logd_prior.Rd
man/logistic.Rd
man/post_prior_densplot.Rd
man/solve_de.Rd
man/prior_draw_rev.Rd
man/plot.post_sim_list.Rd
man/is.debinfer_result.Rd
man/update_sample_rev.Rd
man/de_mcmc.Rd
man/log_prior_params.Rd
man/propose_joint_rev.Rd
man/propose_single_rev.Rd
man/post_sim.Rd
man/setup_debinfer.Rd
man/reshape_post_sim.Rd
man/chytrid.Rd
man/deinits.Rd
deBInfer documentation built on May 19, 2017, 4:20 p.m.