Hierarchical Modelling of Faecal Egg Counts

An implementation of Bayesian hierarchical models for faecal egg count data to assess anthelmintic efficacy. Bayesian inference is done via MCMC sampling using Stan.


News

eggCounts 2.1, 2.1-1:

  • Improved usability of fecr_stanExtra()

  • Fixed a minor bug in stan2mcmc() for paired model

  • Updated citation information, URL

  • Updated Stan version requirement

eggCounts 2.0:

  • Added individual efficacy model for paired design

  • Added vignette

  • Added functions for selecting priors in small sample size (<10) settings

  • Added simplified model for small sample sizes in paired design

  • Added fecr_stanExtra() to import external models hosted on gitHub

  • Improved function documentations

  • Modified default arguments: nsamples, nburnin, nchain, zeroInflation

  • Fixed parameter sampling issue in using the unpaired model without zero inflation

  • Added simple MCMC convergence diagnostic output based on split chain potential scale reduction factors

  • Added possibility to not save all model parameters in fec_stan() and fecr_stan()

  • Added possibility to simulate with different efficacy in simData2s()

  • Re-named function fecr_probability() to fecr_probs()

  • Added 'plot' argument in fecr_probs() to plot posterior density of reduction

  • Added warnings in using fecrtCI() when all of post-treatment counts are zero

  • Added warnings in using fec_stan() and fecr_stan() when divergent transitions occur

  • Cleaned Stan models code

  • Removed un-used dataset

eggCounts 1.4:

  • Modified default arguments for fec_stan and fecr_stan

  • Optimized package onLoad messages

  • Added plotCounts function

  • Corrected fec_stan help file examples (thanks to Ivailo)

  • Corrected coding error with non-default prior for ziunpaired model (thanks to Anja)

eggCounts 1.3:

  • Fixed bug in printing MCMC summaries for meanEPG

  • Fixed implementation bug of the zero-inflation models that was in v1.2

  • Fixed minor bug in printing warnings

  • Added function to compute probability of reduction based on posterior density

  • Added flexibility to un-constrain reduction between 0 and 1

  • Updated citation information

eggCounts 1.2:

  • Allowed direct extraction of summary output

  • Fixed minor bug in validating correction factors

  • Fixed minor bug in converting multiple mcmc chains

  • Updated citation information

eggCounts 1.1, 1.1-1, 1.1-2:

  • Updated documentation

  • Removed redundant functions

  • Updated LinkingTo version requirements

  • Updated Stan program syntax

  • Fixed minor bug in the mcmc output of the 1-sample zero-inflation model

eggCounts 1.0:

  • MCMC inference migrated from Metropolis-Hastlings algorithm and Gibbs sampler to Stan modelling language.

  • Further improved bug fix of version 0.4.

  • Improved models.

  • Full-support on zero-inflation models.

eggCounts 0.4, 0.4-1:

  • Bug fixes introduced since version 0.1.

  • Further improved bug fix of version 0.3.

  • Alerts the user in case of atypical data through 'NOTE'.

  • Added verboselevel functionality for detailed debugging.

  • Improved help and added tests.

eggCounts 0.2, 0.3:

  • stable release on CRAN

  • Updated package structure: NEWS, ChangeLog and CITATION files.

  • Bug fix: all "zero" draws from rgamma are captured and set to minrgamma=.Machine$double.eps. Thus numerical results are likely to change.

Reference manual

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install.packages("eggCounts")

2.1-2 by Craig Wang, a month ago


https://www.math.uzh.ch/pages/eggcount/


Browse source code at https://github.com/cran/eggCounts


Authors: Craig Wang [aut, cre] , Michaela Paul [aut] , Tea Isler [ctb] , Reinhard Furrer [ctb] , Trustees of Columbia University [cph] (src/init.cpp , tools/make_cc.R , R/stanmodels.R)


Documentation:   PDF Manual  


GPL (>= 3) license


Imports boot, coda, utils, testthat, numbers, lattice, rootSolve

Depends on Rcpp, rstan, methods

Suggests R.rsp, eggCountsExtra, knitr, rmarkdown

Linking to StanHeaders, rstan, BH, Rcpp, RcppEigen

System requirements: GNU make


See at CRAN