soil_phylum_small: Small soil phylum data for examples

soil_phylum_smallR Documentation

Small soil phylum data for examples

Description

A small subset of soil_phylo used for examples. A phyloseq object with an OTU table and sample data from a soil microbiome study.

Usage

soil_phylum_small

Format

A phyloseq-class experiment-level object with an OTU table and sample data.

otu_table

OTU table with 7,770 taxa and 119 samples

tax_table

taxonomy table

sam_data

sample data with the following covariates:

  • Plants, values 0 and 1. Index for different plants

  • Day, values 0 (initial sampling point), 1 (12 days after treatment additions), and 2 (82 days after treatment additions). Index for different days of measurement

  • Amdmt, values 0 (no additions), 1 (biochar additions), and 2 (fresh biomass additions). Index for different soil additives.

  • DayAmdmt, values 00, 01, 02, 10, 11, 12, 20, 21, and 22. A single index for the combination of Day and Amdmt with Day as the first digit and Amdmt as the second digit.

  • ID, values A, B, C, D, and F. Index for different soil plots.

References

Whitman, T., Pepe-Ranney, C., Enders, A., Koechli, C., Campbell, A., Buckley, D. H., Lehmann, J. (2016). Dynamics of microbial community composi-tion and soil organic carbon mineralization in soil following addition of pyrogenic andfresh organic matter. The ISME journal, 10(12):2918. <doi: 10.1038/ismej.2016.68>.


corncob documentation built on Aug. 31, 2023, 9:06 a.m.