What’s Em working on?

I believe there is a clear and present need across all science fields to make workflows more efficient, improve data management, and make our results accessible and digestible to general audiences. The first step toward this is to embrace analysis-to-product workflows in programs like R, and the second step is to share! Please feel free to check out my GitHub for code, make additions/edits, or let me know if you have comments. That’s how we make the best available science!

Communications

AFSC RACE Groundfish and Shellfish Survey Public Data.

This dataset includes zero-filled (presence and absence) observations and catch-per-unit-effort (CPUE) estimates for all identified species at for index stations by the Resource Assessment and Conservation Engineering Division (RACE) Groundfish Assessment Program (GAP) of the Alaska Fisheries Science Center (AFSC). There are no legal restrictions on access to the data. The data from this dataset are shared on the Fisheries One Stop Stop (FOSS) platform. These scripts can be found on GitHub. For more information about codes used in the tables, please refer to the survey code books.

GAP Survey Temperature Maps.

These scripts (GitHub Repository) create the daily temperature and anomaly plots as NOAA Fisheries’ Alaska Fisheries Science Center conducts fisheries independent surveys in Alaska. The scripts pull temperature content from google drive and then push the maps to google drive and our internal communications FTP server for the communications team to post on our website.

R Markdown Reports

Alaska Fisheries Science Center Survey Data Reports.

Reproducibly automate groundfish data reports for all surveys conducted by the AFSC in R Markdown. View the GitHub Repository for this code.

Northern Bering Sea Groundfish and Crab Trawl Survey Community Highlights.

Spies, I, R Haehn-Tam, E Siddon, J Conner, EH Markowitz, C Yeung, J Ianelli

R Packages

{sdmgamindex}: R package for calculating survey indices by age with generalized additive models.

In development: R package for calculating survey indices by age from DATRAS exchange data using Generalized Additive Models.

{FishEconProdOutput}: Measuring Output for U.S. Commercial Fisheries From Theory to Practice.

This package provides guidelines on fishery productivity measurement at the individual fishery and aggregate sector levels. Attention is given to the constructions of output and total factor productivity based on available data and a bottom-up approach. Given that there is no nation-wide standard cost survey, we recommend starting with measuring TFP at the fishery level based on a translog gross output production possibility frontier using index number techniques. Special attention is given to measuring quality-adjusted physical capital inputs in the bottom-up approach.

{GAPsurvey}: At-sea data management tools for RACE GAP surveys.

Tools for working with at-sea survey data for AFSC’s Groundfish Assessment Programs surveys.

R Shiny Applications and Websites

NOAA Fisheries Commerical, Recreational, and Aquaculture Fisheries Economic Impact R Shiny Model.

I/O models are used to assess economic activity such as jobs, income, and sales generated by a given industry sector. This is currently used in industry statistics (such as in FEUS) and management applications (to determine how a change would affect the economy, such as in planning team meetings). The R Package GitHub Repository feeds the R Shiny App.

NOAA Fisheries Marine Mammal Acoustic Thresholds.

NMFS has provided this guidence and R Shiny Web Calculator as an optional tool to provide estimated effect distances (i.e., isopleths) where PTS onset thresholds may be exceeded. Results provided by this calculator do not represent the entirety of the comprehensive effects analysis, but rather serve as one tool to help evaluate the effects of a proposed action on marine mammal hearing and make findings required by NOAA’s various statutes. Input values are the responsibility of the individual user. Code for this tool is available in this (GitHub Repository).

Research

Smithsonian-PMEL Genetics Library Collection.

expanded the availability of genetic reference sequences for benthic invertebrates in the Bering Sea and Aleutian Islands. High-quality, vouchered specimens and DNA samples were collected during standard bottom trawl survey operations and were used to generate mitogenome sequences through the Pacific Marine Environmental Laboratory (PMEL)¹ and verified reference standards for public repositories in the Smithsonian National Museum of Natural History (NMNH)² collections catalog³. These efforts addressed the deficit in verified reference sequences for marine multicellular eukaryote biodiversity. This work serves as an essential foundation for long-term biomonitoring in the region.

Modeling Environmentally Driven Distribution Shifts for Two Demersal, Migratory Species.

Habitat suitability models (HSMs) of summer flounder (Paralichthys dentatus) and black sea bass (Centropristis striata) were created using the fishery-independent Northeast Fisheries Science Center (NEFSC) bottom trawl survey data in generalized additive models and cumulative distribution functions. These analyses were used to probabilistically link where different length classes of these fish would likely be across different environmental variables in spring and fall. These different environmental variables (surface and bottom temperature and salinity, depth, and bottom type) have similar influences on life history of these two demersal, migratory, and commercially important species. Then, the HSMs were used to illustrate how the population’s distribution changed over time by hindcasting over regional ocean modeling systems (ROMS). The ROMS used in this analysis was a 1 Day Averaged ROMS for the Northeast US Coastline from 1958-2020. Learn more on our lab website.