Data from: Freshwater phytoplankton communities as complex adaptive systems: multivariate responses to nutrient limitation

This repository is an archive of the data and code used to reproduce the analyses and figure outputs for the paper "Freshwater phytoplankton communities as complex adaptive systems: multivariate responses to nutrient limitation". The main analysis entrypoint is scripts/analysis.R, which regenerates the figure files in figures/ using the primary inputs in data/primary/ together with the archived secondary analysis objects in data/secondary/. Contents data/primary/ data_features.csv: ROI-level feature table with metadata columns (week, treatment, replicate, roi_path) and morphology / fluorescence-texture features (extracted using phenopype) feature_key.csv: lookup table describing each feature column, its feature group, fluorescence channel, and feature type. data/secondary/ Precomputed intermediate results that the plotting workflow loads by default.nThese files are included so the archived workflow can reproduce figures without rerunning every computationally expensive intermediate step. If you want to recompute those intermediates from the primary feature table, inspect the commented code blocks in scripts/analysis.R and uncomment the relevant MFA(...), fwrite(...), and PERMANOVA sections before rerunning the script. Those commented blocks are located immediately before each corresponding load(...) or fread(...) call. data_raw/ species_abundances.csv: time-resolved species abundance table (from Gallego & Narwani [2022]) masks/: PNG masks for individual ROI referenced by roi_path in data_features.csv; these are used as image assets in some figure panels and serve as the underlying object-level archive (generated using phenopype) scripts/ analysis.R: main script that loads data, computes or reloads intermediate objects, and writes the figure outputs. utils.R: helper functions used by the analysis workflow. figures/ Archived figure outputs generated by the analysis script Reproducing all figurs and analyses Set the correct path to your root (i.e., the downloaded repo) in the script, and then run: source("scripts/analysis.R") Or from a shell: Rscript scripts/analysis.R The script will recreate the output directories if needed and write figure files to figures/. Notes The workflow assumes repository-local relative paths. The raw mask archive is large because it preserves ROI-level image objects referenced by the feature matrix. The archive includes precomputed figures and secondary results so readers can distinguish between shipped outputs and regenerated outputs.