ccrepe-package


 ccrepe was developed for use with microbial relative abundance data data, which is both sparse and compositional in nature.


The CCREPE (Compositionality Corrected by REnormalizaion and PErmutation) package is designed to assess the significance of general similarity measures in compositional datasets.  In microbial abundance data, for example, the total abundances of all microbes sum to one; CCREPE is designed to take this constraint into account when assigning p-values to similarity measures between the microbes.  The package has two functions:
ccrepe:    Calculates similarity measures, p-values and q-values for relative abundances of bugs in one or two body sites using bootstrap and permutation matrices of the data.
nc.score:  Calculates species-level co-variation and co-exclusion patterns based on an extension of the checkerboard score to ordinal data.

Emma Schwager

ccrepe

ccrepe_and_nc.score

ccrepe-package function

ccrepe was developed for use with microbial relative abundance data data, which is both sparse and compositional in nature.

A package for analysis of sparse compositional data.Allows calculation of the similarity measure nc-score and calculation of compositionality-corrected p-valuesfor arbitrary similarity scores (including user-defined) applied to compositional data.


 A package for analysis of sparse compositional data.
 Allows calculation of the similarity measure nc-score and calculation of compositionality-corrected p-values
 for arbitrary similarity scores (including user-defined) applied to compositional data.


ccrepe-package: A package for analysis of sparse compositional data. Allows calculation of the similarity measure nc-score and calculation of compositionality-corrected p-values for arbitrary similarity scores (including user-defined) applied to compositional data.

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