oaks: Oaks amplicon data set

oaksR Documentation

Oaks amplicon data set


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.




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


Data from B. Jakuschkin and coauthors.


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). \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1007/s00248-016-0777-x")}

See Also



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

## End(Not run)

PLN-team/PLNmodels documentation built on Sept. 1, 2023, 5:45 p.m.