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| adj2igraph | Adjacency to igraph |
| 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 |
| band | keywords internal |
| block | keywords internal |
| clr | Centered log-ratio functions |
| cluster | keywords internal |
| cor2cov | Convert a symmetric correlation matrix to a covariance matrix given the standard deviation |
| cov2prec | Covariance matrix to its matrix inverse (Precision matrix) |
| erdos_renyi | keywords internal |
| fitdistr | Fit parameters of a marginal distribution to some data vector |
| getOptBeta | get opt beta |
| getOptMerge | get opt merge |
| get_comm_params | Get the parameters for the OTUs (along mar) of each community |
| graph2prec | Convert a symmetric graph (extension of R matrix class) |
| hub | keywords internal |
| icov.select | Model selection for picking the right 'lambda' penalty. This is identical to huge::huge.stars except that the subsampling loop is replaced with an mclapply function to add parallelization capabilities. |
| make_graph | Procedure to generate graph topologies for Gaussian Graphical Models |
| neff | N_effective: Compute the exponential of the shannon entropy. linearizes shannon entropy, for a better diveristy metric (effective number of species) |
| norm_diric | importFrom VGAM rdiric |
| norm_pseudo | add pseudocount before normalizing a vector |
| norm_to_total | Total sum normalization of a (presumably positive) data vector |
| prec2cov | Precision matrix (inverse covariance) to a covariance matrix |
| pval.sparccboot | get pvals |
| 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 |
| rzipois | Draw samples from a zero-inflated poisson distribution |
| scale_free | keywords internal |
| shannon | compute the shannon entropy from a vector (normalized internally) |
| sparcc | SparCC |
| sparccboot | SparCC bootstraps |
| sparseiCov | Sparse/penalized estimators of covariance matrices |
| spiec.easi | Spiec-Easi pipeline |
| spiec.easi.default | Spiec-Easi pipeline |
| spiec.easi.otu_table | Spiec-Easi pipeline |
| spiec.easi.phyloseq | Spiec-Easi pipeline |
| stars.pr | stars.roc, stars.pr |
| stars.roc | stars.roc, stars.pr |
| symBeta | sym beta |
| synth_comm_from_counts | synth_comm_from_counts |