Squirrel nut-storage behavior shapes a seedling spatial pattern resembling conspecific negative density dependence in tropical forests

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########### Analyses of Tan et al. of Squirrel nut-storage behavior shapes a seedling spatial pattern ###################################
########### resembling conspecific negative density dependence in tropical forests ####################################
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This file contains the code (for Figure 2, 4, and 5) and data (in .csv, including intermidiate datasets) used for the analyses ,
We have attempted to document all files and workflows as clearly as possible, although minor details may still require further clarification.

If you have any questions regarding the analyses or data organization, please feel free to contact the author.

1. STUDY TITLE
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Squirrel nut-storage behavior shapes a seedling spatial pattern resembling conspecific negative density dependence in tropical forests

2. AUTHOR INFORMATION
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Xuelian Tan
Research Institute of Topical Forestry, Chinese Academy of Forestry, Guangzhou, 510642, China
Email: [e-mail]

3. CONTENT OVERVIEW
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This document package contains three main parts:

1) **Seed analysis**
This part examines the distance distribution patterns of squirrel-stored nuts
around the parent trees and includes the scripts used to generate Figure 2.

2) **Seedling analysis**
This part analyzes the spatial distribution of seedlings in relation to squirrel
nut storage activities and includes the statistical models and plotting scripts
used to generate Figure 4.

3) **Sapling root lesion analysis**
This part evaluates the relationship between sapling distance to the parent tree
and root lesion infection intensity, and includes the scripts used to generate Figure 5.

4. NAMING CONVENTIONS
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The files are organized according to the three analytical components described above.

A. Seed analysis
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- **seed spatial distribution.R**
Main script used to generate Figure 2.

- **NutNumber.csv**
Raw data for the Kernel density curves plot of squirrel-stored nuts across distance.

- **NutNumber2.csv**
Raw or expanded distance dataset used for the kernel density plot of squirrel-stored nuts.

B. Seedling analysis
--------------------
- **seedling spatial distribution.R**
Script for statistical analyses and Figure 4 based on summary statistics.

- **Seedling_summary.csv**
Summary dataset used for plotting Figure 4.

C. Sapling root lesion analysis
-------------------------------
- **fine root lesion analysis.R**
Main script used to fit the mixed-effects model and generate Figure 5.

- **RootLesion_summary.csv**
Raw data containing sapling root lesion measurements and modeling workflow.

5. ANALYTICAL WORKFLOW
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The recommended order for reproducing the analyses is as follows:

1) Run the seed analysis script to reproduce Figure 2.
2) Run the seedling plotting script to reproduce Figure 4.
3) Run the sapling root lesion analysis script to reproduce Figure 5.