Peter Slaughter

codyn: An r package of community dynamics metrics

Summary New analytical tools applied to long-term data demonstrate that ecological communities are highly dynamic over time. We developed an r package, library(“codyn”), to help ecologists easily implement these metrics and gain broader insights into ecological community dynamics. library(“codyn”) provides temporal diversity indices and community stability metrics. All functions are designed to be easily implemented over multiple replicates. Temporal diversity indices include species turnover, mean rank shifts and rate of community change over time. Community stability metrics calculate overall stability and patterns of species covariance and synchrony over time, and include a null-modelling method to test significance. Finally, library(“codyn”) contains vignettes that describe methods and reproduce figures from published papers to help users contextualize and apply functions to their own data.

ES3: A Demonstration of Transparent Provenance for Scientific Computation

The Earth System Science Server (ES3) is a software environment for data-intensive Earth science, with unique capabilities for automatically and transparently capturing and managing the provenance of arbitrary computations. Transparent acquisition avoids the scientist having to express their computations in specific languages or schemas for provenance to be available. ES3 models provenance as relationships between processes and their input and output files. These relationships are captured by monitoring read and write accesses at various levels in the science software and asynchronously converting them to time-ordered streams of provenance events which are stored in an XML database. An ES3 provenance query returns an XML serialization of a provenance graph, forward or backwards from a specified process or file. We demonstrate ES3 provenance by generating complex data products from Earth satellite imagery.

DataONE: A Data Federation with Provenance Support

DataONE is a federated data network focusing on earth and environmental science data. We present the provenance and search features of DataONE by means of an example involving three earth scientists who interact through a DataONE Member Node. DataONE provenance systems enable reproducible research and facilitate proper attribution of scientific results transitively across generations of derived data products.