Sparse Inverse Covariance for Ecological Statistical Inference

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Documentation for package ‘SpiecEasi’ version 1.1.2

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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