Here, we explain the method of ecoplate analysis using R script with the following contents. These materials can be used for learning a general multivariate analysis in ecology. Please download the following five files: for_osaka_cer.R, meta_sample.csv, fp.dist_a.csv, fp.dist_b.csv, and online.dissimilarity.
Also visit https://github.com/tksmiki/ecoplate2018_ER
1) Preparation of ecoplate data file
2) Design of the entire R script
3) Reading data file of ecoplate
4) Conversion of raw data of ecoplate
5) Fundamentals of multivariate analysis 1 (PCA, dissimilarity calculation, PCoA)
6) Fundamentals of multivariate analysis 2
Visualization with PCoA using ecoplate data · Test for differences between treatments · Calculation of multifunctionality
7) Multivariate analysis of ecoplate considering chemical dissimilarity between substrates
Material includes an unpublished data, I will share additional data upon e-mail request (tks.miki.ecology@gmail.com).
The statistical tutorial above is based on the following publication.
T Miki, T Yokokawa, P-J Ke, I-F Hsieh, C-h Hsieh, T Kume, K Yoneya, K Matsui (2018) Statistical recipe for quantifying microbial functional diversity from EcoPlate metabolic profiling. Ecological Research (published online) https://doi.org/10.1007/s11284-017-1554-0