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
