adj2igraph | Adjacency to igraph |
AGP | American Gut Project |
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 |
clr | Centered log-ratio functions |
coat | COAT |
cor2cov | Convert a symmetric correlation matrix to a covariance matrix... |
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 |
get_comm_params | Get the parameters for the OTUs (along mar) of each community |
getOptInd | get StARS-optimal network |
graph2prec | Convert a symmetric graph (extension of R matrix class) |
hmp2 | Human Microbiome Project 2 |
make_graph | Procedure to generate graph topologies for Gaussian Graphical... |
multi.spiec.easi | multi domain SPIEC-EASI |
neff | N_effective: Compute the exponential of the shannon entropy.... |
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,... |
rmvnorm | Draw samples from multivariate, correlated normal... |
rmvpois | Generate multivariate poisson data, with counts approximately... |
rmvzinegbin | Generate multivariate, negative binomial data, with counts... |
rmvzipois | Generate multivariate, Zero-inflated poisson data, with... |
robustPCA | robust PCA |
rzipois | Draw samples from a zero-inflated poisson distribution |
shannon | compute the shannon entropy from a vector (normalized... |
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 |
SpiecEasi-package | SpiecEasi: Sparse Inverse Covariance for Ecological... |
stars.roc | stars.roc, stars.pr |
symBeta | sym beta |
synth_comm_from_counts | synth_comm_from_counts |
triu | Functions for triangular matrices |
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