# Sparse Inverse Covariance for Ecological Statistical Inference

## Documentation for package ‘SpiecEasi’ version 2.0.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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