An implementation of Bayesian hierarchical models for faecal egg count data to assess anthelmintic efficacy. Bayesian inference is done via MCMC sampling using Stan.
Improved usability of fecr_stanExtra()
Fixed a minor bug in stan2mcmc() for paired model
Updated citation information, URL
Updated Stan version requirement
Added individual efficacy model for paired design
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
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)
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
Allowed direct extraction of summary output
Fixed minor bug in validating correction factors
Fixed minor bug in converting multiple mcmc chains
Updated citation information
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
MCMC inference migrated from Metropolis-Hastlings algorithm and Gibbs sampler to Stan modelling language.
Further improved bug fix of version 0.4.
Full-support on zero-inflation models.
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.
stable release on CRAN
Updated package structure: NEWS, ChangeLog and CITATION files.
Bug fix: all "zero" draws from rgamma are captured and
Thus numerical results are likely to change.