Funder multifunctionality

Analysis of how plant functional group removal affects ecosystem multifunctionality across climate gradients in mountain ecosystems (FunCaB/FUNDER experiment, Western Norway).

Purpose

This repo downloads, processes, and analyses data from a macroecological experiment that replicates plant functional group removals (graminoids, forbs, bryophytes) across factorial temperature and precipitation gradients (Vestland Climate Grid). It tests whether biodiversity loss reduces multifunctionality and whether these effects depend on climate context. Ecosystem functions include biomass, decomposition, carbon and nutrient stocks/fluxes, and biodiversity of plants, soil fauna, and microbes.

Workflow

The project uses the targets R package for a reproducible pipeline:

1. Download (R/download_plan.R) — Fetch data from the data repository (biomass, community composition, bryophytes, mesofauna, nematodes, etc.).
2. Transform (R/tranformation_plan.R) — Curate and standardise data; create site × treatment metadata.
3. Multifunctionality (R/multifunctionality_plan.R) — Merge functions, standardise to 0–1, compute average multifunctionality.
4. Analysis (R/analysis_plan.R) — Linear mixed-effects models for effects of functional group richness, treatment identity, temperature, and precipitation.
5. Figures (R/figure_plan.R) — Outputs for the main results.

Pipeline entry point: _targets.R. Run the pipeline with run.R or targets::tar_make().

Results

• results.qmd — Main results document (figures and model tables): effects of functional group number and identity on single functions and average multifunctionality, and how these vary with climate.
• results_new.qmd — Updated results (PCA, heatmaps, model tables).
• SI.qmd — Supplementary information.

Publishing results_new.qmd (shareable page)

1. Run the pipeline, then render into docs/ (output must be basename only; directory via --output-dir):

   quarto render results_new.qmd --output-dir docs --output index.html

   If you get docs/results_new.html instead, run mv docs/results_new.html docs/index.html.

2. Commit docs/index.html and docs/.nojekyll, push to main.

3. GitHub Pages: Settings → Pages → deploy from branch main, folder /docs.
   Site URL: https://audhalbritter.github.io/Funder_multifunctionality/

   Or set Pages source to GitHub Actions and run the workflow Publish results to GitHub Pages (after docs/index.html is committed).

See docs/README.md for details.

Setup

• R project; dependencies managed via renv (renv::restore()).
• Key packages: tidyverse, targets, dataDownloader, dataDocumentation, lme4, lmerTest, vegan, patchwork, gt, etc. (see _targets.R and libraries.R).
• GitHub package: dataDocumentation is from GitHub. Install it with renv::install("audhalbritter/dataDocumentation") so renv records the source; then renv::snapshot() will include it in the lockfile.