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' < https://mc-stan.org/>.


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")

2.3 by Craig Wang, 9 months 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 methods, utils, rstan, boot, coda, numbers, lattice, rootSolve

Depends on Rcpp

Suggests eggCountsExtra, R.rsp, testthat

Linking to rstan, Rcpp, BH, StanHeaders, RcppEigen

System requirements: GNU make


See at CRAN