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Using N-Dimensional Hypervolumes to Measure Ecosystem Stability

Author: David Bridgwood dmb2417@ic.ac.uk

Description: code for masters project

Dependencies

The following python libraries are required:

  • pandas
  • numpy

The following R packages are required:

  • vegan
  • hypervolume

How to Run

To Do

  • hypervolume svs vs gaussian?
  • general how to do species ordination questions
  • data questions
    • mammals: what do all the comments mean? E100-1 vs E100-2, same or different plot?
  • run_project.py script to walk through all code files
  • link to stability
  • sort out data diectory

Repository Structure


masters_project/
├── Code/
│   │
│   ├── 00_hv_functions.R
│   ├── compare_hv.R
│   ├── sort_data.py
│   └── species_ordination.R
│
├── Data/
│   │
│   ├── family_list.csv
│   │
│   ├── RAW/
│   │   ├── beetles/
│   │   │   ├── family_list.csv
│   │   │   ├── README.txt
│   │   │   └── trap_summaries.csv
│   │   │
│   │   ├── SAFE_toDavidBridgwood_Stability/
│   │   │   ├── Riutta_et_al-2018-Global_Change_Biology_OnlineEarlyVersion.pdf
│   │   │   ├── Riutta_et_al-2018-Global_Change_Biology_SupportingInformation.pdf
│   │   │   ├── SAFE_CarbonPlots_FineRoots_Stock+NPP.xlsx
│   │   │   ├── SAFE_CarbonPlots_Litterfall.xlsx
│   │   │   ├── SAFE_CarbonPlots_Tree+LianaCensus.xlsx
│   │   │   └── SAFE_Maliau_Danum_CarbonPlots_Maps.pdf
│   │   │
│   │   ├── small_mammals/
│   │   │   ├── Grid trapping dates 2011-2016.xlsx
│   │   │   ├── SAFE Map E.png
│   │   │   ├── SAFE Map overview.png
│   │   │   ├── SAFE small mammal Catch Totals 2011-2016.xlsx
│   │   │   └── SAFE small mammals E 2011-2016.xlsx
│   │   │
│   │   └── template_Pfeifer.xlsx
│   │
│   ├── SAFE_CarbonPlots_FineRoots_Stock+NPP.xlsx
│   ├── SAFE_CarbonPlots_Litterfall.xlsx
│   ├── SAFE_CarbonPlots_Tree+LianaCensus.csv
│   ├── SAFE_CarbonPlots_Tree+LianaCensus.xlsx
│   └── small_mammals.csv
│
├── Results/
│   ├── beetles_matrix.csv
│   ├── beetles_sorted.csv
│   ├── mammal_mds_out.Rdata
│   ├── mammals_matrix.csv
│   ├── mammals_sorted.csv
│   ├── mds_out.Rdata
│   ├── trees_matrix.csv
│   └── trees_sorted.csv
│
└── Sandbox/
    ├── code/
    │   ├── beetles_hv.R
    │   ├── sort_beetles_data.py
    │   ├── sort_mammal_data.py
    │   ├── sort_tree_data.py
    │   ├── test_hypvlm.R
    │   └── test_PCA.R
    ├── demo/
    └── Reading
        ├── Papers/
        ├── CMEE-APROJECT!.bib
        ├── Reading.pdf
        └── Reading.tex