bglarkin / wwp_terpenes

Analysis of western white pine (pinus monitcola) terpenes in response to blister rust, fungal endophytes, and ectomycorrhizae.

wwp_terpenes

Analysis of western white pine (Pinus monitcola) terpenes in response to blister rust, fungal endophytes, and ectomycorrhizae.

Source data

The Database directory contains raw csv files which are extracted, transformed, and loaded by data_etl.md. The ETL script is called separately in each analysis script for brevity.

• Raw script: data_etl.R

Global ordination and permutation tests

Ordinations of class centroids for each resistance class of seedlings. Locations based on all terpene compounds. Permutation tests conducted with adonis2() and 1999 permutations.

• Report format: terpenes_globalTests.md
• Raw script: terpenes_globalTests.R

Pairwise comparisons

1. Permutation tests are used to test pairwise multivariate differences in terpene composition within resistance classes and assessments, and between symbiont controls and treatments. The tests are permuted within experimental greenhouse blocks.
2. Permutations tests as in #1, but between induced and control seedlings after the rust inoculation step (rust_inoc vs. rust_ctrl)

• Report format: terpenes_pairwiseTests.md
• Raw script: terpenes_pairwiseTests.R

Indicator terpenes

An indicator species analysis (Borcard et al. 2018) is conducted to identify which terpene compounds associate strongly with particular assessments, resistance classes, or treatments. A post-hoc bootstrap test is conducted to produce visualizations and corroborate the indicator species analysis.

• Report format: terpenes_indicators.md
• Raw script: terpenes_indicators.R

Other files

• gg_style.txt contains adjustments to ggplot themes to make figures consistent within this repository.