| aitvar.matrix | compute aitchison variation of a matrix |
| band | keywords internal |
| block | keywords internal |
| cluster | keywords internal |
| coabsenceMat | compute Coabsence |
| coCalc | compute Cooccurance |
| codmeR | codmeR |
| convert_MD_format | keywords internal |
| cooccur | compute Cooccurance |
| cooccurMat | compute Cooccurance |
| cor2cov | Convert a symmetric correlation matrix to a covariance matrix... |
| cov2prec | Covariance matrix to its matrix inverse (Precision matrix) |
| erdos_renyi | keywords internal |
| fastaitvar | compute aitchison variation of matrix cols quickly |
| fitdistr | Fit parameters of a marginal distribution to some data vector |
| fixed_mean_vector | Draw mean vector from a vector of fixed means & pick the... |
| get_comm_params | Get the parameters for the OTUs (rows) of each community |
| graph2prec | Convert a symmetric graph (extension of R matrix class) |
| Hamdist | compute Hamming distance |
| HamdistMat | compute Hamming distance of matrix cols quickly |
| hub | keywords internal |
| log_norm_mean_vector | Draw mean vector from a log-normal vector & find the logsd... |
| make_graph | Procedure to generate graph topologies for Gaussian Graphical... |
| make_precision_mat | Wrapper function for generating a Precision matrix |
| neff | N_effective: Compute the exponential of the shannon entropy.... |
| prec2cov | Precision matrix (inverse covariance) to a covariance matrix |
| proportionality_filter | compute p-vals of proportionality (two ways) via aitchison... |
| qqdplot | deprecated?? |
| 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... |
| rzipois | Draw samples from a zero-inflated poisson distribution |
| scale_free | keywords internal |
| shannon | compute the shannon entropy from a vector (normalized... |
| sim_counts | Simulate count data from various theoretical distributions |
| sparseiCov | Sparse/penalized estimators of covariance matrices |
| sparse_iCov | Sparse/penalized estimators of covariance matrices |
| sparseSigma | One way of generating a sparse, positive definite [square]... |
| sparseSigma_JF | Jonathan Friedman's described method of computing a... |
| synth_comm_from_counts | from count data (ex HMP) fit parameters to OTU margins and... |
| T | compute aitchison variation vector |
| unsparseSigma | deprecated covariance generator |
