README - "Neotropical rivers as interaction corridors: An evaluation of frugivory metanetworks across two biogeographic domains".

This repository contains data and scripts related to the study of frugivory interaction networks between birds and plants across two Neotropical biogeographic domains, specifically comparing the Chaco and Paraná Domains. The data is organized to enable comparative analyses of network structure, modularity, species roles, and connectivity metrics.

📁 data/
    ├── data-birds.xlsx
    ├── data-plants.xlsx
    ├── data-cz-values-interactions-parana.xlsx
    ├── data-METANETWORKS-QC.xlsx
    └── data-METANETWORKS-QS.xlsx

📁 scripts/
    ├── script-metanetwork-plot.txt 
    ├── script-centrality.txt
    ├── script-cz-values-interactions-paranatable.txt
    ├── script-czvalues-vs-status-lifeform.txt
    └── script-heatmap-plot.txt
    ├── script-null-models.txt
    ├── script-upset-plot.txt
    ├── script-beta-harvesine-pearsontest-manteltest.txt


Dataset descriptions

#data-birds.xlsx

Description: Qualitative (presence/absence) list of bird species and their corresponding study site.

Columns: bird species names. 

Rows: study sites

Cells: qualitative information (presence/absence) (0/1)

#data-plants.xlsx

Description: Qualitative list (presence/absence) of plant species and their corresponding study site.

Columns: plant species names.

Cells: qualitative information (presence/absence) (0/1)

#data-cz-values-interactions-parana.xlsx

Description: c-z connectivity values for species in the Paraná metanetwork, based on the framework.

Columns:

interactions: birs-plant interaction names.

c: among-module connectivity

z: within-module connectivity

status: bird status, R = resident, M = migratory

sform: life form of plants, AH = Annual herb, CP = Climbing plant, PB = Parasite bush, S = Shrub, S/H = Shrub/Tree, T = Tree, NN = Unidentified species. 

#data-METANETWORKS-QC.xlsx

Description: Qualitative interaction matrix of bird-plant interactions from six sampling sites within the Chaco and Paraná Domains.

Rows: sampling sites (6)

Columns: interacting species pairs

Cells: qualitative information (presence/absence) (0/1)

#data-METANETWORKS-QS.xlsx

Description: Quantitative interaction matrix of plant–bird interactions from six sampling sites within the Paranaense domain.

Rows: sampling sites (6)

Columns: interacting species pairs

Cells: quantitative information, interaction frequency values


Scripts Overview

1. script-metanetwork-plot.txt
Constructs and plots a meta-network of species interactions across sampling sites. Uses bipartite networks to visualize site-species linkage.

2. script-centrality.txt
Calculates and visualizes species-level centrality metrics (degree, betweenness) from the meta-network. Includes plots by domain (Chaco/Paraná).

3. script-cz-values-interactions-paranatable.txt
Calculates c and z values (within-module and among-module connectivity) and generates tables distinguishing interaction roles within Paraná sites.

4. script-czvalues-vs-status-lifeform.txt
Analyzes the relationship between c–z values and species traits (bird status and plant life forms). Outputs comparative boxplots.

5. script-heatmap-plot.txt
Creates heatmaps representing the beta diversity across sites or modules.

6. script-null-models.txt
Generates null models to assess whether observed network metrics (e.g., connectance) differ from expectations using "r2dtable" and "vaznull" randomization. Outputs Z-scores and p-values.

7. script-upset-plot.txt
Creates upset plots to visualize shared and unique interactions/bird species/plant species across sites. Includes domain-specific color schemes and classification by group.

8. script-beta-harvesine-pearsontest-manteltest.txt
Performs beta diversity analysis of interaction composition across sites. Calculates Jaccard or Sørensen dissimilarity, applies the Haversine formula to compute distances, and conducts Mantel tests.