Package: inlatools 0.0.3

Thierry Onkelinx

inlatools: Diagnostic Tools for INLA Models

Several functions which can be useful to choose sensible priors and diagnose the fitted model.

Authors:Thierry Onkelinx [aut, cre], Research Institute for Nature and Forest [cph, fnd]

inlatools_0.0.3.tar.gz
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inlatools.pdf |inlatools.html✨
inlatools/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/inbo/inlatools/issues

Pkgdown:https://inbo.github.io

On CRAN:

bayesian-statisticsgplv3inlamixed-modelsmodel-checkingmodel-validation

4.40 score 4 stars 42 scripts 26 exports 52 dependencies

Last updated 3 months agofrom:e711776e83. Checks:OK: 4 ERROR: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 03 2024
R-4.5-linuxOKDec 03 2024
R-4.4-winOKDec 03 2024
R-4.4-macOKDec 03 2024
R-4.3-macERRORDec 05 2024

Exports:dgpoissondispersiondispersion_checkdistribution_checkfast_aggregation_checkfast_distribution_checkfittedgenerate_dataget_anomalyget_observedprec2sdresidualsrgpoissonrzanbinomrzapoisrzinbinomrzipoisselect_changeselect_divergenceselect_polyselect_quantilesimulate_iidsimulate_rwvar_nbinomvar_zinbinom1var_zipois1

Dependencies:assertthatclassclassIntclicolorspacecpp11DBIdplyre1071fansifarverfmeshergenericsggplot2gluegtableINLAisobandKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixMatrixModelsmgcvmunsellnlmepillarpkgconfigproxypurrrR6RColorBrewerRcpprlangs2scalessfspstringistringrtibbletidyrtidyselectunitsutf8vctrsviridisLitewithrwk

Checking the Distribution and Dispersion of a Model

Thierry Onkelinx

Rendered fromdistribution.Rmdusingknitr::rmarkdownon Dec 03 2024.

Last update: 2022-09-14
Started: 2018-12-03

Getting a Grasp on the Random Walk Hyperparameter

Thierry Onkelinx

Rendered fromrwprior.Rmdusingknitr::rmarkdownon Dec 03 2024.

Last update: 2022-09-14
Started: 2019-03-08

Setting a Prior for the Random Intercept Variance and Fixed Effects

Thierry Onkelinx

Rendered fromprior.Rmdusingknitr::rmarkdownon Dec 03 2024.

Last update: 2022-09-14
Started: 2018-12-03

Readme and manuals

Help Manual

Help pageTopics
The generalised Poisson distributiondgpoisson rgpoisson
Calculate a measure for dispersiondispersion
Use simulations to check for overdispersion or underdispersiondispersion_check dispersion_check,inla-method
Use simulations to compare the observed distribution with the modelled distributiondistribution_check distribution_check,inla-method
Fast aggregation check Compare the observed and modelled aggregated values.fast_aggregation_check fast_aggregation_check,inla-method
Use simulations to compare the observed distribution with the modelled distributionfast_distribution_check fast_distribution_check,inla-method fast_distribution_check,list-method
Extract the fitted values from an INLA modelfitted,inla-method
Generate dummy data with several distributionsgenerate_data
Get a set of anomalies of the modelget_anomaly get_anomaly,inla-method
get the observed values from the model objectget_observed
Plot the results from a dispersion checkplot.dispersion_check
Plot the results from a distribution checkplot.distribution_check
Plot Simulated Random Interceptsplot.sim_iid
Plot Simulated Random Walksplot.sim_rw
Convert the posterior marginal of a precision to a standard deviationprec2sd
Calculate the Residuals From an INLA Modelresiduals,inla-method
Zero altered negative binomialrzanbinom
Zero-altered Poissonrzapois
Zero inflated negative binomialrzinbinom
Zero-inflated Poissonrzipois
Select Fast Changing Simulations from an 'sim_rw' Objectselect_change
Select Diverging Simulations from an 'sim_rw' Objectselect_divergence
Select Random Walks Best Matching Some Polygon Coefficientsselect_poly
select the quantiles from an 'sim_rw' objectselect_quantile
simulate data from a second order random walksimulate_iid
simulate data from a second order random walksimulate_rw
Variance of the negative binomial distributionvar_nbinom var_zinbinom1 var_zipois1