R: Oaks amplicon data set

oaks {PLNmodels} | R Documentation

## Oaks amplicon data set

### Description

This data set gives the abundance of 114 taxa (66 bacterial OTU, 48 fungal OTUs) in 116 samples. For each sample, 11 additional covariates are known.

### Usage

    oaks

### Format

A data frame with 13 variables:

- Abundance: A 114 taxa by 116 samples count matrix

- Offset: A 114 taxa by 116 samples offset matrix

- Sample: Unique sample id

- tree: Tree status with respect to the pathogen (susceptible, intermediate or resistant)

- branch: Unique branch id in each tree (4 branches were sampled in each tree, with 10 leaves per branch)

- leafNO: Unique leaf id in each tree (40 leaves were sampled in each tree)

- distTObase: Distance of the sampled leaf to the base of the branch

- distTOtrunk: Distance of the sampled leaf to the base of the tree trunk

- distTOground: Distance of the sampled leaf to the base of the ground

- pmInfection: Powdery mildew infection, proportion of the upper leaf area displaying mildew symptoms

- orientation: Orientation of the branch (South-West SW or North-East NE)

- readsTOTfun: Total number of ITS1 reads for that leaf

- readsTOTbac: Total number of 16S reads for that leaf

### Source

Data from B. Jakuschkin and coauthors.

### References

Jakuschkin, B., Fievet, V., Schwaller, L. et al. Deciphering the Pathobiome: Intra- and Interkingdom Interactions Involving the Pathogen Erysiphe alphitoides . Microb Ecol 72, 870–880 (2016). doi: 10.1007/s00248-016-0777-x

### See Also

`prepare_data()`

### Examples

    data(oaks)
    ## Not run:
    oaks_networks <- PLNnetwork(formula = Abundance ~ 1 + offset(log(Offset)), data = oaks)

    ## End(Not run)

[Package PLNmodels version 0.11.4 Index]