# Sparse Inverse Covariance for Ecological Statistical Inference

## Documentation for package ‘SpiecEasi’ version 0.1.4

- DESCRIPTION file.

## Help Pages

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