Manuscript Analysis Repository

Welcome to the repository containing R code and data analyses for the manuscript:

Long-term biodiversity–stability relationship in temperate mountain forests

This repository makes all analytic scripts, relevant data, and supporting documentation publicly available, supporting transparency and reproducibility of the reported results.

Table of Contents

• [Project Structure]
• [Requirements]
• [Setup Instructions]
• [How to Reproduce Analyses]
• [File Descriptions]
• [Citing This Work]
• [Contact]

Project Structure

├── Bacon_runs
├── Paper_stability.Rproj
├── R
│   ├── 00_setup.R
│   ├── 01_Load_data.R
│   ├── 01_Main_calculations.R
│   ├── 02_Calculate_ROC.R
│   ├── 02_Calculate_disturbance.R
│   ├── 03_Figure_3_Pollen.R
│   ├── 03_Figure_4_PAR.R
│   ├── 03_Figure_5_Index.R
│   ├── 03_Figure_6_RDA.R
│   ├── 03_Table_1.R
│   ├── 03_Table_2.R
│   ├── 04_Figure_S1.R
│   ├── 04_Figure_S2.R
│   ├── 04_Table_S1.R
│   ├── 04_Table_S2.R
│   ├── 04_Table_S3.R
│   ├── 05_Age_depth_bacon.R
│   └── __Init_project__.R
├── README.md
├── data_in
│   ├── CER_CHELSA.xlsx
│   ├── CER_XRF_15-2-1.xlsx
│   ├── CER_XRF_15-2-2.xlsx
│   ├── CER_XRF_GC.xlsx
│   ├── CER_char_corr.xlsx
│   ├── CER_chiro.xlsx
│   ├── CER_chiro_temp.xlsx
│   ├── CER_pollen_corr.xlsx
│   ├── EPD_P_VARS_high3_mod.xlsx
│   ├── _species_dist.csv
│   ├── _taxa_hierarchy.xlsx
│   ├── _taxa_species.xlsx
│   ├── _taxa_synonym.xlsx
│   └── taxa.xlsx
└── data_out
    ├── CER_ROC.rds
    ├── CER_data.RData
    └── CER_disturbance.rds

Requirements

• R version ≥ 4.x

• Optional: RStudio

• Required R packages (see R/__Init_project__.R):

Setup Instructions

1. Clone this repository to your local machine:

   git clone https://github.com/petrkunes/paper-stability.git cd your-repo-name

2. Install R dependencies:

   Open R or RStudio and run:

   source("R/__Init_project__.R")

How to Reproduce Analyses

All main and supplementary analyses are scripted and reproducible.

1. Data Preparation:

   • Load required packages R/00_setup.R.
   • Import and process data by running R/01_Load_data.R.

2. Data Analyses:

• Execute main analyses with R/01_Main_calculations.R.

• (Optional): re-run time consuming Rate of change analysis R/02_Calculate_ROC.R.

• (Optional): re-run time consuming pollen-based disturbance analysis R/02_Calculate_disturbance.R.

2. Figure/Table Generation:

   • Generate publication-ready figures and tables via

     • R/03_Figure_3_Pollen.R

     • R/03_Figure_4_PAR.R

     • R/03_Figure_5_Index.R

     • R/03_Figure_6_RDA.R

     • R/03_Table_1.R

     • R/03_Table_2.R

   • Generate publication ready supplementary material via

     • R/04_Figure_S1.R

     • R/04_Figure_S2.R

     • R/04_Figure_S3.R

     • R/04_Table_S1.R

     • R/04_Table_S2.R

File Descriptions

Folder/File	Description
data_in/	Contains all raw input data
data_in/_species_dist.csv	List of plant species with their disturbance frequency index and frequency of distribution in the vegetation
data_in/_taxa_hierarchy.xlsx	Pollen taxa hierarchical table
data_in/_taxa_species.xlsx	Plant species and pollen taxa harmonization table
data_in/_taxa_synonym.xlsx	Pollen taxa synonym table
data_in/CER_char_corr.xlsx	Sedimentary macroscopic charcoal data from Černé jezero
data_in/CER_CHELSA.xlsx	CHELSA paleoclimate model for the region of Černé jezero
data_in/CER_pollen_corr.xlsx	Sedimentary pollen data from Černé jezero
data_in/CER_XRF_15-2-1.xlsx	Sedimentary XRF data from Černé jezero from separate core drives
data_in/CER_XRF_15-2-2.xlsx	Sedimentary XRF data from Černé jezero from separate core drives
data_in/CER_XRF_GC.xlsx	Sedimentary XRF data from Černé jezero from separate core drives
data_in/EPD_P_VARS_high3_mod.xlsx	EPD synonym and hierarchy table, compiled based on the taxonomy of the EPD-2015 version, with additions made for this study.
data_in/taxa.xlsx	List of pollen taxa used for creating the pollen diagram
R/__Init_project__.R	Installs required R packages (run only once)
R/00_setup.R	Loads required R packages
R/01_Load_data.R	Data import and cleaning steps
R/01_Main_calculations.R	Main numerical analyses
R/02_Calculate_disturbance.R	Re-calculate pollen-based disturbance (optional)
R/02_Calculate_ROC.R	Re-calculate rate of change (optional)
R/03_Figure_3_Pollen.R	Code to generate figures and tables
...
data_out/	Analysis outputs (processed data/figures/tables)
Bacon_runs/	Data folder for Bacon age-depth model
Paper_stability.Rproj	RStudio project file
README.md	This README

Citing This Work

If you use this code or data, please cite the manuscript:

[Manuscript Citation Here]

Contact

For questions or suggestions, please contact:

petr.kunes@natur.cuni.cz

This repository supports reproducible research and adheres to best practices for open science.