SDMs Methods Development

Important

This repository is developed by and for the Science Centre at the Alberta Biodiversity Monitoring Institute (ABMI). It is intended for internal use.

Shared pipeline and static cross-taxa test dataset for methods R&D on ABMI species models.

Contents

• Overview
• Status
• Directory structure
  • 0_data/
  • 1_code/
  • 2_pipeline/
  • 3_output/
• Parity gate
• Naming conventions
• Adding an experiment
• Contributing a taxon module
• Setup
• Related resources
• Contact

Overview

A shared environment for testing methods across taxa. It holds a static cross-taxa test dataset and a companion R&D pipeline: a taxon-agnostic harness, thin taxon-specific modules, and a versioned covariate catalogue.

Because the dataset and pipeline are fixed, R&D questions can be run once across all taxa rather than reimplemented per taxon, and results stay comparable over time.

This repository is for methods research and development. It is not for the final species models and does not generate reporting products.

Status

Component	State
Repository and pipeline structure	In development
Static test dataset	Not yet assembled
Taxon modules	Not yet built
v2.0 parity check (exp_000)	Not yet run

Directory structure

sdm_methods_dev/
├── README.md
│
├── 0_data/                        # read-only inputs; nothing written here by code
│   ├── manifest.md                # dataset version, paths, checksums
│   ├── covariates/                # versioned catalogue (metadata; rasters on server)
│   │   └── catalogue_v1.csv
│   ├── test_dataset/              # frozen: response records, design, evaluation split
│   └── v2_scripts/                # as-received from leads, unmodified
│       ├── birds/
│       ├── mammals/
│       └── plants/
│
├── 1_code/
│   ├── harness/                   # shared, taxon-agnostic
│   │   ├── data_load.R
│   │   ├── data_split.R
│   │   ├── covar_attach.R
│   │   └── eval_metrics.R
│   ├── modules/                   # taxon-specific
│   │   ├── birds/                 
│   │   ├── mammals/
│   │   └── plants/
│   └── experiments/
│       ├── exp_000_parity_v2/
│       │   ├── README.md
│       │   ├── run.R
│       │   ├── 01_script.R
│       │   ├── 02_script.R
│       │   └── 03_script.R
│       ├── exp_001_description/
│       └── exp_002_description/
│
├── 2_pipeline/                    # intermediates, cached; gitignored
│   ├── exp_000_parity_v2/
│   │   └── logs/                  # log files
│   └── exp_001_description/
│
└── 3_output/                      # deliverables; committed
    ├── exp_000_parity_v2/
    │   ├── figures/
    │   ├── tables/
    │   └── report.md
    └── exp_001_description/

0_data/

Read-only. Nothing in this folder is written by code in this repository.

test_dataset/ holds the frozen cross-taxa dataset. Its contents do not change between experiments. Amendments require a version increment and a corresponding update to manifest.md.

covariates/catalogue_v1.csv is a versioned catalogue of covariate layers. It stores metadata and server paths only; rasters live on the ABMI server. Unlike the test dataset, the catalogue is extensible: new covariates can be added under a new catalogue version without invalidating the dataset.

v2_scripts/ holds modelling scripts as received from taxon leads, unmodified, in one subfolder per taxon. Subfolder names match those under 1_code/modules/, so each module has an obvious reference.

manifest.md is the only tracked file in this folder. It records dataset version, file paths, and is what experiment configurations point at.

1_code/

harness/ holds the shared, taxon-agnostic pipeline: loading the frozen dataset, applying the evaluation split, attaching covariates, and computing evaluation metrics. Changes here affect every experiment, past and future, and should be reviewed accordingly.

modules/ holds taxon-specific modelling code. Modules stay thin (just what is needed to run a model): experiment-specific logic belongs in the experiment, not the module. Note that not all taxa need every component, for example QPAD offsets apply to birds but not to plants.

experiments/ holds one folder per R&D question. Each contains a README.md stating the question and design, a run.R entry point, and numbered scripts. Experiments call the harness and modules; they do not reimplement them.

2_pipeline/

Intermediate and cached files, organized by experiment. Gitignored.

3_output/

Committed deliverables, organized by experiment. Because outputs are tracked, comparisons across experiments and over time can be made from the repository alone.

Parity gate

exp_000 is the validation gate. It runs the v2.0 models through this repository's code pipeline and compares the results against the species models v2.0 outputs.

Experiment results will be compared against the results of exp_000.

The minimum acceptable parity target has not yet been defined and will need to be agreed per taxon.

Naming conventions

Item	Convention	Example
Experiments	exp_NNN_short_description	exp_001_covariate_scale

An experiment identifier is used verbatim in 1_code/experiments/, 2_pipeline/, and 3_output/. Derive all three paths from a single variable in run.R rather than typing the identifier per stage.

Adding an experiment

Contributing a taxon module

Setup

Related resources

• code_standards — Science Centre coding conventions
• sciCentRverse — Science Centre R functions

Contact

For any questions regarding the contents of this repository or data access, please contact Brendan Casey at brendan.casey@ualberta.ca.