Joint Analysis and Imputation of Incomplete Data

Provides joint analysis and imputation of (generalized) linear regression models, (generalized) linear mixed models and parametric survival models with incomplete (covariate) data in the Bayesian framework. The package performs some preprocessing of the data and creates a 'JAGS' model, which will then automatically be passed to 'JAGS' < http://mcmc-jags.sourceforge.net> with the help of the package 'rjags'. It also provides summary and plotting functions for the output.


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The package JointAI provides joint analysis and imputation of linear regression models, generalized linear regression models or linear mixed models with incomplete (covariate) data in the Bayesian framework.

The package performs some preprocessing of the data and creates a JAGS model, which will then automatically be passed to JAGS with the help of the R package rjags.

JointAI also provides summary and plotting functions for the output.

Installation

You can install JointAI from GitHub with:

# install.packages("devtools")
devtools::install_github("NErler/JointAI")

Main functions

Currently, there are three main functions that perform linear, generalized linear or linear mixed regression:

lm_imp()
glm_imp()
lme_imp()

lm_imp() and glm_imp() use specification similar to their complete data counterparts lm() and glm(), whereas lme_imp() uses similar specification as lme() from the package nlme.

Functions summary(), traceplot(), densityplot() provide a summary of the posterior distribution and its visualization.

gr_crit() and mc_error() provide the Gelman-Rubin diagnostic for convergence and the Monte Carlo error of the MCMC sample, respectively.

News

JointAI 0.3.0

Bug fixes

  • monitor_params is now checked to avoid problems when only part of the main parameters is selected
  • categorical imputation models now use min-max trick to prevent probabilities outside [0, 1]
  • initial value generation for logistic analysis model fixed
  • bugfix in re-ordering columns when a function is part of the linear predictor
  • bugfix in intial values for categorical covariates
  • bugfix in finding imputation method when function of variable is specified as auxiliary variable

Minor changes

  • md.pattern() now uses ggplot, which scales better than the previous version
  • lm_imp(), glm_imp() and lme_imp() now ask about overwriting a model file
  • analysis_main = T stays selected when other parameters are followed as well
  • get_MIdat(): argument include added to select if original data are included and id variable .id is added to the dataset
  • subset argument uses same logit as monitor_params argument
  • added switch to hide messages; distinction between messages and warnings
  • lm_imp(), glm_imp() and lme_imp() now take argument trunc in order to truncate the distribution of incomplete variables
  • summary() now omits auxiliary variables from the output
  • imp_par_list is now returned from JointAI models
  • cat_vars is no longer returned from lm_imp(), glm_imp() and lme_imp(), because it is contained in Mlist$refs

Extensions

  • plot_all() function added
  • densplot() and traceplot() optional with ggplot
  • densplot() option to combine chains before plotting
  • example datasets NHANES, simLong and simWide added
  • list_impmodels to print information on the imputation models and hyperparameters
  • parameters() added to display the parameters to be/that were monitored
  • set_refcat() added to guide specification of reference categories
  • extension of possible functions of variables in model formula to (almost all) functions that are available in JAGS
  • added vignettes Minimal Example, Visualizing Incomplete Data, Parameter Selection and Model Specification

JointAI 0.2.0

Bug fixes

  • md_pattern(): does not generate duplicate plot any more
  • corrected names of imputation methods in help file
  • scaling when no continuous covariates are in the model or scaling is deselected fixed
  • initial value specification for coefficient for auxiliary variables fixed
  • get_MIdat(): imputed values are now filled in in the correct order
  • get_MIdat(): variables imputed with lognorm are now included when extracting an imputed dataset
  • get_MIdat(): imputed values of transformed variables are now included in imputed datasets
  • problem with non valid names of factor labels fixed
  • data matrix is now ordered according to order in user-specified meth argument

Minor changes

  • md.pattern(): adaptation to new version of md.pattern() from the mice package
  • internally change all NaN to NA
  • allow for scaling of incomplete covariates with quadratic effects
  • changed hyperparameter for precision in models with logit link from 4/9 to 0.001

Extensions

  • gamma and beta imputation methods implemented

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("JointAI")

0.4.0 by Nicole S. Erler, 2 months ago


https://github.com/nerler/JointAI


Report a bug at https://github.com/nerler/JointAI/issues


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


Authors: Nicole S. Erler [aut, cre]


Documentation:   PDF Manual  


Task views: Missing Data


GPL (>= 2) license


Imports MASS, mcmcse, coda

Depends on rjags

Suggests knitr, rmarkdown, foreign, ggplot2, reshape2

System requirements: JAGS (http://mcmc-jags.sourceforge.net)


See at CRAN