adj2igraph              Adjacency to igraph
AGP                     American Gut Project
alr                     Additive log-ratio functions
as.data.frame.graph     s3 method for graph to other data types
as.matrix.graph         s3 method for graph to other data types
clr                     Centered log-ratio functions
coat                    COAT
cor2cov                 Convert a symmetric correlation matrix to a
                        covariance matrix given the standard deviation
cov2prec                Covariance matrix to its matrix inverse
                        (Precision matrix)
ebic                    Extended BIC
edge.diss               Edge set dissimilarity
fitdistr                Fit parameters of a marginal distribution to
                        some data vector
get_comm_params         Get the parameters for the OTUs (along mar) of
                        each community
getOptInd               get StARS-optimal network
graph2prec              Convert a symmetric graph (extension of R
                        matrix class)
hmp2                    Human Microbiome Project 2
make_graph              Procedure to generate graph topologies for
                        Gaussian Graphical Models
multi.spiec.easi        multi domain SPIEC-EASI
neff                    N_effective: Compute the exponential of the
                        shannon entropy. linearizes shannon entropy,
                        for a better diveristy metric (effective number
                        of species)
neighborhood.net        Neighborhood net estimates
norm_pseudo             Normalize w/ Pseudocount
norm_rdiric             Normalize via dirichlet sampling
norm_to_total           Total Sum Normalize
prec2cov                Precision matrix (inverse covariance) to a
                        covariance matrix
pulsar.params           pulsar params
pval.sparccboot         SparCC p-vals
qqdplot_comm            qq-plot for theoretical vs observed communities
rmvnegbin               Generate multivariate, Zero-inflated negative
                        binomial data, with counts approximately
                        correlated according to Sigma
rmvnorm                 Draw samples from multivariate, correlated
                        normal distribution with counts correlated
                        according to Sigma
rmvpois                 Generate multivariate poisson data, with counts
                        approximately correlated according to Sigma
rmvzinegbin             Generate multivariate, negative binomial data,
                        with counts approximately correlated according
                        to Sigma
rmvzipois               Generate multivariate, Zero-inflated poisson
                        data, with counts approximately correlated
                        according to Sigma
robustPCA               robust PCA
rzipois                 Draw samples from a zero-inflated poisson
                        distribution
shannon                 compute the shannon entropy from a vector
                        (normalized internally)
sparcc                  sparcc wrapper
sparccboot              Bootstrap SparCC
sparseiCov              Sparse/penalized estimators of covariance
                        matrices
sparseLowRankiCov       Sparse plus Low Rank inverse covariance
spiec.easi              SPIEC-EASI pipeline
stars.roc               stars.roc, stars.pr
symBeta                 sym beta
synth_comm_from_counts
                        synth_comm_from_counts
