jomo: A Flexible Package for Two-level Joint Modelling Multiple Imputation

Multiple imputation is a tool for parameter estimation and inference with partially observed data, which is used increasingly widely in medical and social research. When the data to be imputed are correlated or have a multilevel structure — repeated observations on patients, school children nested in classes within schools within educational districts — the imputation model needs to include this structure. Here we introduce our joint modelling package for multiple imputation of multilevel data, jomo, which uses a multivariate normal model fitted by Markov Chain Monte Carlo (MCMC). Compared to previous packages for multilevel imputation, e.g. pan, jomo adds the facility to (i) handle and impute categorical variables using a latent normal structure, (ii) impute level-2 variables, and (iii) allow for cluster-specific covariance matrices, including the option to give them an inverse-Wishart distribution at level 2. The package uses C routines to speed up the computations and has been extensively validated in simulation studies both by ourselves and others.

Matteo Quartagno , Simon Grund , James Carpenter

Supplementary materials

Supplementary materials are available in addition to this article. It can be downloaded at

CRAN packages used

jomo, pan, norm, cat, mix, R2MLwiN, mitools, mice, semTools, BaBooN, mitml, Amelia, mi, lavaan.survey, dummies, nlme

CRAN Task Views implied by cited packages

MissingData, OfficialStatistics, SocialSciences, Multivariate, Psychometrics, Bayesian, ChemPhys, Econometrics, Environmetrics, Finance, Spatial, SpatioTemporal


Text and figures are licensed under Creative Commons Attribution CC BY 4.0. The figures that have been reused from other sources don't fall under this license and can be recognized by a note in their caption: "Figure from ...".


For attribution, please cite this work as

Quartagno, et al., "jomo: A Flexible Package for Two-level Joint Modelling Multiple Imputation", The R Journal, 2019

BibTeX citation

  author = {Quartagno, Matteo and Grund, Simon and Carpenter, James},
  title = {jomo: A Flexible Package for Two-level Joint Modelling Multiple Imputation},
  journal = {The R Journal},
  year = {2019},
  note = {},
  doi = {10.32614/RJ-2019-028},
  volume = {11},
  issue = {2},
  issn = {2073-4859},
  pages = {205-228}