R scripts for PERMANOVA, PERMDISP, and cell-stratified bootstrap analyses of soybean responses to salinity and phosphate deficiency

This repository contains the R scripts used for three analyses reported in the associated manuscript: three-factor PERMANOVA, PERMDISP, and cell-stratified nonparametric bootstrap estimation of difference-in-differences effect sizes. The analyses were conducted in R version 4.2.2. The PERMANOVA and PERMDISP analyses used Bray-Curtis dissimilarities with 9,999 permutations. The bootstrap analysis used 5,000 resamples conducted independently within each genotype and treatment combination. Metabolite abundance values were transformed using log2(x + 1), whereas microbial relative abundances were transformed using the arcsine square-root transformation. This repository contains analysis code and documentation only. It does not contain the study input matrices or formal numerical outputs.