Software and Code

The SBC LTER community members are enthusiastic about sharing their scripting expertise. We have an array of scripts and packages developed within our group to facilitate various scientific tasks. These tasks include retrieving data from national databases, assigning taxon to gene markers, and creating data publication tools for research groups. Additionally, we compile student-written codes dedicated to specific articles and research interests. For an extensive list of our GitHub repositories, kindly refer to the SBCLTER GitHub page.

This is a R script for downloading the Santa Barbara Channel daily sst netcdf file from the Physical Oceanography Distributed Active Archive Center, and extracting the sst values for any given locations' coordinates. See the GitHub repository.

These are the R script and the Matlab function harvest hourly HFR data from the UCSD OPENDAP sever. Outputs are east and north velocity. Here are two versions of the scripts and the output are different between these two scripts: Matlab or R script

ensembleTax is an R package that allows incorporation of information from multiple taxonomic assignment algorithms and/or reference databases to compute ensemble taxonomic assignments for ASVs/OTUs generated by common marker gene sequence analyses. You can also access the R package in Cran

This tool uses the R programming language to create an EML document from an Excel metadata workbook (".xlsx") for an ecological data archive. If you plan to publish data on your own and the data repository requires EML document, please check out this tool (with codes and examples) on GitHub and demo video on YouTube