Code
Lab project data and code will appear at our GitHub organization: jmadinlab. Projects will generally be private until first publication.
Software
| Name | Description | Language |
|---|---|---|
| habtools | The goal of habtools is to collate tools for 3D meshes and digital elevation models (DEM) targeted at biologists and ecologists. Tools calculate metrics like surface area, rugosity, fractal dimension, height range, convexity, sphericity, second moments of volume and more. The initial set of tools came from two research papers. Zawada et al. (2019) examined morphology of coral colony laser scans. Torres-Pulliza et al. (2020) examined complexity of coral reef structure. It is hoped that the number of tools and contributors will grow through time. | R |
Datasets
Datasets are made public following first publication. Datasets are stored in a number of ways, including online databases, FigShare, GitHub and our lab server. Below is a growing list of datasets. This list is currently incomplete and being worked on to make all lab products visible in one location.
| Name | Contact | Description | Access |
|---|---|---|---|
| The Coral Trait Database | Joshua Madin | The Coral Trait Database is a growing compilation of scleractinian coral life history trait, phylogenetic and biogeographic data. As of today, there are 68494 coral observations with 106462 trait entries of 158 traits for 1548 coral species in the database. Most of these entries are for shallow-water, reef-building species. | true |
| Bacterial and archaeal phenotypic trait database | Joshua Madin | A synthesis of phenotypic and quantitative genomic traits is provided for bacteria and archaea, in the form of a scripted, reproducible workflow that standardizes and merges 26 sources. The resulting unified dataset covers 14 phenotypic traits, 5 quantitative genomic traits, and 4 environmental characteristics for approximately 170,000 strain-level and 15,000 species-aggregated records. It spans all habitats including soils, marine and fresh waters and sediments, host-associated and thermal. Trait data can find use in clarifying major dimensions of ecological strategy variation across species. They can also be used in conjunction with species and abundance sampling to characterize trait mixtures in communities and responses of traits along environmental gradients. | true |
| Surface geometry | Damaris Torres-Pulliza | This dataset contains reef surface descriptors of coral reef (rugosity, fractal dimension and height range) for >500 reef patches at Lizard Island and corresponding species abundance and riches data for a subset of patches. | true |
| Trimodal Demography | Joshua Madin | The Trimodal dataset contains growth, survival and reproduction data for 11 species of coral censused yearly for eight years. The data will be published in 2020. | false |