# zhangchunyu-biogeo/angiosperm-biogeographical-spectrum architecture

> Architecture diagram of the GitHub repository zhangchunyu-biogeo/angiosperm-biogeographical-spectrum, generated by GitDiagram from its file tree, README and a sample of source files (last updated 2026-09-28). It is an AI-made overview: check details against the source.

- Interactive diagram: https://gitdiagram.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum
- Repository: https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum

## Overview

This repository contains R analyses and supporting datasets for studying global biogeographical patterns in angiosperm taxonomic traits. The documented workflow is to prepare species-level occurrences and trait proportions for ecoregions, then run individual scripts for statistical analyses and mapping, producing figures and processed data. The README also documents phylogenetic, evolutionary, diversity-null-model, and spatial-SEM analyses. Source excerpts were unavailable, so relationships beyond the documented workflow are omitted; several analysis nodes use the existing Code directory because individual script paths are not shown in the supplied tree.

Main entry points: [`Code`](https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Code) (Occurrence aggregation), [`Data`](https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Data) (Ecoregion data), [`Data/Flora_Evolution_Models`](https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Data/Flora_Evolution_Models) (Evolution model data), [`Data/Taxonomic_Traits_Diversity_Null_Model`](https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Data/Taxonomic_Traits_Diversity_Null_Model) (Null model data)

## Diagram (Mermaid)

```mermaid
flowchart TD

subgraph group_prep["Data preparation"]
  node_prepwork["Occurrence aggregation"]
end

subgraph group_analyses["Statistical analyses"]
  node_scripts["R analysis scripts"]
  node_pca["PCA and visualization"]
  node_pglmm["Phylogenetic models"]
  node_signal["Signal and conservation"]
  node_evolution["Evolutionary models"]
  node_beta["Beta regression"]
end

subgraph group_spatial["Spatial and diversity"]
  node_nulls["Diversity null models"]
  node_gam["GAM mapping"]
  node_sem["Spatial piecewise SEM"]
end

subgraph group_inputs["Research data"]
  node_traitdata[("Trait datasets")]
  node_occurrences[("Occurrence demo data")]
  node_ecodata[("Ecoregion data")]
  node_evolutiondata[("Evolution model data")]
  node_nulldata[("Null model data")]
end

node_researcher(("Researcher"))
node_outputs["Figures and CSVs"]

node_researcher -->|"runs"| node_prepwork
node_prepwork -->|"reads"| node_occurrences
node_prepwork -->|"reads"| node_traitdata
node_prepwork -->|"writes"| node_ecodata
node_researcher -->|"runs"| node_pca
node_researcher -->|"runs"| node_pglmm
node_researcher -->|"runs"| node_signal
node_researcher -->|"runs"| node_evolution
node_researcher -->|"runs"| node_beta
node_researcher -->|"runs"| node_nulls
node_researcher -->|"runs"| node_gam
node_researcher -->|"runs"| node_sem
node_pca -->|"reads"| node_ecodata
node_nulls -->|"reads"| node_nulldata
node_evolution -->|"reads"| node_evolutiondata
node_pca -->|"writes"| node_outputs
node_pglmm -->|"writes"| node_outputs
node_signal -->|"writes"| node_outputs
node_evolution -->|"writes"| node_outputs
node_beta -->|"writes"| node_outputs
node_nulls -->|"writes"| node_outputs
node_gam -->|"writes"| node_outputs
node_sem -->|"writes"| node_outputs

click node_scripts "https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Code"
click node_prepwork "https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Code"
click node_pca "https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Code"
click node_pglmm "https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Code"
click node_signal "https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Code"
click node_evolution "https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Code"
click node_beta "https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Code"
click node_nulls "https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Code"
click node_gam "https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Code"
click node_sem "https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Code"
click node_traitdata "https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Data"
click node_occurrences "https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Data"
click node_ecodata "https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Data"
click node_evolutiondata "https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Data/Flora_Evolution_Models"
click node_nulldata "https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Data/Taxonomic_Traits_Diversity_Null_Model"

classDef toneNeutral fill:#f8fafc,stroke:#334155,stroke-width:1.5px,color:#0f172a
classDef toneBlue fill:#dbeafe,stroke:#2563eb,stroke-width:1.5px,color:#172554
classDef toneAmber fill:#fef3c7,stroke:#d97706,stroke-width:1.5px,color:#78350f
classDef toneMint fill:#dcfce7,stroke:#16a34a,stroke-width:1.5px,color:#14532d
classDef toneRose fill:#ffe4e6,stroke:#e11d48,stroke-width:1.5px,color:#881337
classDef toneIndigo fill:#e0e7ff,stroke:#4f46e5,stroke-width:1.5px,color:#312e81
classDef toneTeal fill:#ccfbf1,stroke:#0f766e,stroke-width:1.5px,color:#134e4a
class node_prepwork toneBlue
class node_scripts,node_pca,node_pglmm,node_signal,node_evolution,node_beta toneAmber
class node_nulls,node_gam,node_sem toneMint
class node_traitdata,node_occurrences,node_ecodata,node_evolutiondata,node_nulldata toneRose
class node_researcher,node_outputs toneIndigo
```

## Components

### Data preparation

- [Occurrence aggregation](https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Code): `Code`

### Statistical analyses

- [R analysis scripts](https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Code): `Code`
- [PCA and visualization](https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Code): `Code`
- [Phylogenetic models](https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Code): `Code`
- [Signal and conservation](https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Code): `Code`
- [Evolutionary models](https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Code): `Code`
- [Beta regression](https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Code): `Code`

### Spatial and diversity

- [Diversity null models](https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Code): `Code`
- [GAM mapping](https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Code): `Code`
- [Spatial piecewise SEM](https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Code): `Code`

### Research data

- [Trait datasets](https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Data): `Data`
- [Occurrence demo data](https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Data): `Data`
- [Ecoregion data](https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Data): `Data`
- [Evolution model data](https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Data/Flora_Evolution_Models): `Data/Flora_Evolution_Models`
- [Null model data](https://github.com/zhangchunyu-biogeo/angiosperm-biogeographical-spectrum/tree/main/Data/Taxonomic_Traits_Diversity_Null_Model): `Data/Taxonomic_Traits_Diversity_Null_Model`

### Other components

- **Researcher**
- **Figures and CSVs**

## Connections

- Researcher → Occurrence aggregation: runs
- Occurrence aggregation → Occurrence demo data: reads
- Occurrence aggregation → Trait datasets: reads
- Occurrence aggregation → Ecoregion data: writes
- Researcher → PCA and visualization: runs
- Researcher → Phylogenetic models: runs
- Researcher → Signal and conservation: runs
- Researcher → Evolutionary models: runs
- Researcher → Beta regression: runs
- Researcher → Diversity null models: runs
- Researcher → GAM mapping: runs
- Researcher → Spatial piecewise SEM: runs
- PCA and visualization → Ecoregion data: reads
- Diversity null models → Null model data: reads
- Evolutionary models → Evolution model data: reads
- PCA and visualization → Figures and CSVs: writes
- Phylogenetic models → Figures and CSVs: writes
- Signal and conservation → Figures and CSVs: writes
- Evolutionary models → Figures and CSVs: writes
- Beta regression → Figures and CSVs: writes
- Diversity null models → Figures and CSVs: writes
- GAM mapping → Figures and CSVs: writes
- Spatial piecewise SEM → Figures and CSVs: writes