soil_phylo: (Data) Data frame of soil data from whitman_et_al.

In breakaway: Species Richness Estimation and Modeling

(Data) Data frame of soil data from whitman_et_al.

Description

A phyloseq object with an OTU table and sample data from a soil microbiome study.

Usage

soil_phylo

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>.

breakaway documentation built on Nov. 22, 2022, 5:08 p.m.