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| adj2igraph | Adjacency to igraph |
| AGP | American Gut Project |
| alr | Additive log-ratio functions |
| alr.data.frame | Additive log-ratio functions |
| alr.default | Additive log-ratio functions |
| alr.matrix | Additive log-ratio functions |
| amgut1.filt | American Gut Project |
| amgut2.filt.phy | American Gut Project |
| 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 |
| clr.data.frame | Centered log-ratio functions |
| clr.default | Centered log-ratio functions |
| clr.matrix | 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 |
| getOptBeta | get StARS-optimal network |
| getOptCov | get StARS-optimal network |
| getOptiCov | get StARS-optimal network |
| getOptInd | get StARS-optimal network |
| getOptLambda | get StARS-optimal network |
| getOptMerge | get StARS-optimal network |
| getOptNet | get StARS-optimal network |
| getRefit | get StARS-optimal network |
| getStability | get StARS-optimal network |
| get_comm_params | Get the parameters for the OTUs (along mar) of each community |
| graph2prec | Convert a symmetric graph (extension of R matrix class) |
| hmp2 | Human Microbiome Project 2 |
| hmp216S | Human Microbiome Project 2 |
| hmp2prot | 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 |
| spiec.easi.default | SPIEC-EASI pipeline |
| spiec.easi.list | multi domain SPIEC-EASI |
| 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 |
| tril | Functions for triangular matrices |
| triu | Functions for triangular matrices |
| triu2diag | Functions for triangular matrices |