Imputation of High-Dimensional Count Data using Side Information

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Documentation for package ‘lori’ version 2.2.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

aravo	Alpine plant communities in Aravo, France: Abundance data and covariates
covmat	covmat
cv.lori	The cv.lori method performs automatic selection of the regularization parameters (lambda1 and lambda2) used in the lori function. These parameters are selected by cross-validation. The classical procedure is to apply cv.lori to the data to select the regularization parameters, and to then impute and analyze the data using the lori function (or mi.lori for multiple imputation).
lori	The lori method implements a method to analyze and impute incomplete count tables. An important feature of the method is that it can take into account main effects of rows and columns, as well as effects of continuous or categorical covariates, and interaction. The estimation procedure is based on minimizing a Poisson loss penalized by a Lasso type penalty (sparse vector of covariate effects) and a nuclear norm penalty inducing a low-rank interaction matrix (a few latent factors summarize the interactions).
mi.lori	The mi.lori performs M multiple imputations using the lori method. Multiple imputation allows to produce estimates of missing values, as well as intervals of variability. The classical procedure is to perform M multiple imputations using the mi.lori method, and to aggregate them using the pool.lori method.
pool.lori	The pool.lori method aggregates lori multiple imputation results. Multiple imputation allows to produce estimates of missing values, as well as intervals of variability. The classical procedure is to perform multiple imputation using the mi.lori method, and to aggregate them using the pool.lori method.
qut	automatic selection of nuclear norm regularization parameter