Reviewer-response-only condition-factor analysis

# Reviewer-response-only condition-factor analysis ## Purpose This folder contains the exploratory condition-factor analysis requested by Reviewer #1. It is supporting material for the point-by-point response and is not a third prespecified response variable in the manuscript or Supplementary Information. ## Final analytical scope - 21 studies- 59 effect-size observations- Directly reported treatment-level condition-factor summaries with mean, variance information, and sample size- Effect size: `LRR = ln(CF_multispecies / CF_monoculture)`- Shared-control sampling covariance within `Group_ID`- Random intercepts for species nested within species combination, `Group_ID`, and effect-size observation ## Result - Pooled LRR: 0.0086228- 95% CI: -0.0397212 to 0.0569668- p = 0.72665- Back-transformed change: +0.87% (95% CI: -3.89% to +5.86%) ## Files - `df_cf.xlsx`: exact 59-row input used for the analysis- `CF_response_only_data.csv`: analysis-ready data with recomputed confidence limits and explicit response/scope labels- `run_cf_response_analysis.R`: complete analysis and figure script- `CF_model_summary.csv`: numerical model output- `CF_analysis_log.txt`: data checks, model summary, and R session information- `Figure_R1_CF_response_only.png` and `.pdf`: reviewer-response figure The legacy input workbook labels `response_type` as `W` even though all rows are condition-factor records. The analysis does not use that field. The analysis-ready CSV preserves it as `source_response_type` and sets `response_type = CF`; use the corrected CSV, not the legacy label, for archiving and reruns. ## Excluded alternative The expanded merged workbook contains 111 condition-factor records from 38 studies, but all are currently classified as `Pending` or `Excluded`, and 13 lack usable sampling variances. That dataset was therefore not used for the reviewer-facing result. ## Submission action Deposit this folder under a clearly named `reviewer_response_CF` directory in the final Zenodo archive. This preserves reproducibility without expanding the manuscript or Supplementary Information.