See metadata files associated with simulation outputs in the repository.

The associated modeling code is archived at 10.5281/zenodo.7622893.

The tutorial associated with the publication is published at https://marineomics.github.io/RDAtraitPredictionTutorial.html.

Data collection is ongoing, with updates made semi-annually. For guidance on downloading data subsets, please refer to the BCO-DMO ERDDAP instructions here: https://guide.bco-dmo.org/access-and-reuse/erddap. Decadal subsets available for download from this ERDDAP service include the following download links:

• BATS CTD Data 1988-2000
• BATS CTD Data 2000-2010
• BATS CTD Data 2010-2020
• BATS CTD Data 2020-2023

This dataset contains the OysterFutures larval transport model code, input files, output files, resulting connectivity matrices, and LTRANS User’s Guide which provides extensive information about model structure and input/output files and variables. These files are available below as a large .zip file (6.62 GB).

Each folder in this data set contains a complete model run with code, input, and output files. Folder names correspond to release number (R1-R5, each with a different particle release date) and release replicate number (1-5, each with a different seed value for the random number generators). Please see the LTRANS User’s Guide for parameter descriptions.

Data collection is ongoing, with updates made semi-annually. For guidance on downloading data subsets, please refer to the BCO-DMO ERDDAP instructions here: https://guide.bco-dmo.org/access-and-reuse/erddap. Decadal subsets available for download from this ERDDAP service include:

• Hydro S CTD Data 1988-2000 (Will be linked upon data approval)
• Hydro S CTD Data 2000-2010 (Will be linked upon data approval)
• Hydro S CTD Data 2010-2020 (Will be linked upon data approval)
• Hydro S CTD Data 2020-2023 (Will be linked upon data approval)

From http://northweb.hpl.umces.edu/LTRANS.htm

beta-LTRANS-ADCIRC is based on the Larval TRANSport Lagrangian model (LTRANS v.2b), an off-line particle-tracking model that runs with the stored predictions of a 3D hydrodynamic model. In this case, LTRANS v.2b has been substantially modified to be able to run with the finite-element circulation predictions of ADCIRC. Although LTRANS was built to simulate oyster larvae, it can easily be adapted to simulate passive particles and other planktonic organisms. LTRANS v.2 is written in Fortran 90 and is designed to track the trajectories of particles in three dimensions. It includes a 4th order Runge-Kutta scheme for particle advection and a random displacement model for vertical turbulent particle motion. Reflective boundary conditions, larval behavior, and settlement routines are also included. A brief description of the beta-LTRANS-ADCIRC particle-tracking model can be found here (68 KB .pdf). For more information on LTRANS, please see the LTRANS web page. and the application of LTRANS to oyster larvae transport, see a summary web page with animations, the publications North et al. (2008, 2011), and the LTRANS v.2 User's Guide. Please cite North et al. (2011) when referring to LTRANS v.2b. The updates that were made for LTRANS v.2b are listed here.

Elizabeth North of University of Maryland Center for Environmental Science Horn Point Laboratory implemented beta-LTRANS-ADCIRC. Funding was provided by the National Science Foundation Biological Oceanography Program. Steven Suttles and Jason Spires provided valuable assistance.

beta-LTRANS-ADCIRC Code: beta-LTRANS-ADCIRC Open Source Code. We would appreciate knowing who is using LTRANS. If you would like to share this information with us, please send us your name, contact information, and a brief description of how you plan to use this model to enorth@umces.edu with 'LTRANS-ADCIRC' in the subject line.

Access restrictions: This software is open-source and licensed as stated by MIT/X License, but utilizes external dependencies and program which have different restrictions. Please see the beta-LTRANS-ADCIRC license file and website for more information.

PDF of original beta-LTRANS-ADCIRC webpage: http://dmoserv3.bco-dmo.org/data_docs/EstuarineMetaDyn/betaLTRANS-ADCIRC_website.pdf

Code:

External Dependencies and Programs. beta-LTRANS-ADCIRC requires NetCDF libraries and uses the following programs to calculate random numbers (Mersenne Twister) and fit tension splines (TSPACK). Because beta-LTRANS-ADCIRC reads-in ADCIRC-generated NetCDF (.nc) files, it requires that the appropriate NetCDF libraries be installed on your computer (see files and links below). Also, please note that although the Mersenne Twister and TSPACK programs are included in the beta-LTRANS-ADCIRC in the Random_module.f90 and Tension_module.f90, respectively, they do not share the same license file as beta-LTRANS-ADCIRC Please review and respect their permissions (links and instructions provided below).

From http://northweb.hpl.umces.edu/LTRANS.htm. CHECK FOR UPDATES. NEWER VERSION MAY BE AVAILABLE.

PDF of original LTRANS_v.2b website [2016-09-14]

LTRANS v.2b Model Description

The Larval TRANSport Lagrangian model (LTRANS v.2b) is an off-line particle-tracking model that runs with the stored predictions of a 3D hydrodynamic model, specifically the Regional Ocean Modeling System (ROMS). Although LTRANS was built to simulate oyster larvae, it can easily be adapted to simulate passive particles and other planktonic organisms. LTRANS v.2 is written in Fortran 90 and is designed to track the trajectories of particles in three dimensions. It includes a 4th order Runge-Kutta scheme for particle advection and a random displacement model for vertical turbulent particle motion. Reflective boundary conditions, larval behavior, and settlement routines are also included. A brief description of the LTRANS particle-tracking model can be found here (68 KB .pdf). For more information on LTRANS and the application of LTRANS to oyster larvae transport, see a summary web page with animations, the publications North et al. (2008, 2011), and the LTRANS v.2 User's Guide. Please cite North et al. (2011) when referring to LTRANS v.2b. The updates that were made for LTRANS v.2b are listed here.

The Lagrangian TRANSport (LTRANS v.2b) model is based upon LTRANS v.1 (formerly the Larval TRANSport Lagrangian model). Ian Mitchell made the bug fixes in LTRANS v.2b. Zachary Schlag completed signigicant updates to the code in LTRANS v.2 with input from Elizabeth North, Chris Sherwood, and Scott Peckham. LTRANS v.1 was built by Elizabeth North and Zachary Schlag of University of Maryland Center for Environmental Science Horn Point Laboratory. Funding was provided by the National Science Foundation Biological and Physical Oceanography Programs**, Maryland Department of Natural Resources, NOAA Chesapeake Bay Studies, NOAA Maryland Sea Grant College Program, and NOAA-funded UMCP Advanced Study Institute for the Environment.

A beta version of LTRANS v2b which uses predictions from the circulation model ADCIRC is available here.

LTRANS Code

LTRANS v.2b Open Source Code. We would appreciate knowing who is using LTRANS. If you would like to share this information with us, please send us your name, contact information, and a brief description of how you plan to use LTRANS to enorth@umces.edu. To refer to LTRANS in a peer-reviewed publication, please cite the publication(s) listed in the Description section above.

External Dependencies and Programs. LTRANS v.2b requires NetCDF libraries and uses the following programs to calculate random numbers (Mersenne Twister) and fit tension splines (TSPACK). Because LTRANS v.2 reads-in ROMS-generated NetCDF (.nc) files, it requires that the appropriate NetCDF libraries be installed on your computer (see files and links below). Also, please note that although the Mersenne Twister and TSPACK programs are included in the LTRANS v.2b in the Random_module.f90 and Tension_module.f90, respectively, they do not share the same license file as LTRANS v.2b. Please review and respect their permissions (links and instructions provided below).

LTRANS v.2b Example Input Files. These files can be used to test LTRANS v.2b. They include examples of particle location and habitat polygon input files (.csv) and ROMS grid and history files (.nc) that are needed to run LTRANS v.2b. Many thanks to Wen Long for sharing the ROMS .nc files. The LTRANS v.2b code above is configured to run with these input files. Note: please download the tar (LTRANSv2.tgz) history files (clippped_macroms_his_*.nc) files between the hours of 5 pm and 6 am Eastern Standard Time because of their large size.