soil_phylum_small_otu1: Small soil phylum data for examples, sample data as data...

In corncob: Count Regression for Correlated Observations with the Beta-Binomial

Small soil phylum data for examples, sample data as data frame combined with counts for OTU 1 and sequencing depth.

Description

A small subset of soil_phylo_sample used for examples. A data frame made from the 'phyloseq' object with only sample data and counts for OTU 1.

Usage

soil_phylum_small_otu1

Format

A phyloseq-class experiment-level object with sample data and OTU 1 counts.

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.

• W, counts for OTU1 in each sample. This OTU corresponds with the phylum Proteobacteria.

• M, the sequencing depth for each sample.

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 May 29, 2024, 7:15 a.m.