Oaks amplicon data set

Source: R/oaks.R

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.

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)
if (FALSE) { # \dontrun{
oaks_networks <- PLNnetwork(formula = Abundance ~ 1 + offset(log(Offset)), data = oaks)
} # }