Datasets y scripts de análisis en R de redes de interacción (frugívora y dispersión de semillas) en los dominios biogeográficos Chaqueño y Paranaense

Abstract

README - Datasets y scripts de análisis en R de redes de interacción (frugívora y dispersión de semillas) en los dominios biogeográficos Chaqueño y Paranaense.

📁 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.