10/23/2017
This repository contains code associated with the manuscript “Initial wood trait variation overwhelms endophyte community effects for explaining decay trajectories” (in review)
Author names, institutions and addresses: Marissa Lee 1 Jeff R. Powell 2 Brad Oberle 3 Faride Unda 4 Shawn D. Mansfield 4 Kylie Brice 2 Jessica Rigg 5 *Will K. Cornwell 6 *Amy E. Zanne 1
*co-senior authorship 1 Department of Biological Sciences, The George Washington University, Washington, DC, United States 2 Hawkesbury Institute for the Environment, University of Western Sydney, Hawkesbury, Australia 3 Division of Natural Sciences, New College of Florida, Sarasota, FL, United States 4 Department of Wood Science, University of British Columbia, Vancouver, Canada 5 Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Meanagle, Australia 6 Evolution & Ecology Research Centre, School of Biological Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
Raw DNA sequencing data are available under NCBI BioProject ID PRJNA690172
Code to address three key analyses aims are in R markdown files. A brief description of analyses and associated script are below.
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How do decay trajectories vary between wood species and sizes? 1_decayPatterns.Rmd
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How do wood traits covary? 2a_woodtraits_correlated.Rmd Do wood traits explain decay? 2b_woodtraits_explainDecay.Rmd
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Summarize endophyte communities across wood species and sizes 3a_endoComp_summary.Rmd Does endophyte community composition explain decay? 3b_endoComp_explainDecay.Rmd Does endophyte richness explain decay? 3c_endoDiv_explainDecay.Rmd
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How does including t=0 points affect the decay model fit? Including it affects the liklihood and the model selection criteria, but the curve fits are identical. Excluding t=0 leads to prefering simpler models, which is the same effect as increasing the penalty for model complexity code/testing_time_zero.Rmd
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Do endophyte community dissimilarities correlate strongly with decay trajectory parameters? code/initialDist_vs_decayDist_btwCode.Rmd