12 Zooplankton Indices
Description: Model-based abundance and annual center of gravity indices for zooplankton groups sampled by NEFSC surveys
Found in: State of the Ecosystem - Indicator Catalog (2025)
Indicator category: Extensive analysis, not yet published
Contributor(s): Abigail Tyrell, Adelle Molina, Sarah Gaichas, and Harvey Walsh
Data steward: Abigail Tyrell abigail.tyrell@noaa.gov
Point of contact: Abigail Tyrell abigail.tyrell@noaa.gov
Public availability statement: Source data are NOT publicly available.
12.1 Methods
12.1.1 Data sources
The Northeast Fisheries Science Center has conducted zooplankton surveys since the 1970s.
The dataset through 2022 used in this analysis was obtained from the Oceanography Branch.
12.1.2 Data analysis
12.1.2.1 VAST models
VAST is a spatio-temporal modeling framework used for index standardization (Thorson and Barnett 2017; Thorson 2019).
Zooplankton models were evaluated using two stages of model selection to determine whether to include
spatial and spatio-temporal random effects, and
“catchability” covariates affecting the observation process: day of year.
Model selection was conducted in 2024 using this script: https://github.com/NOAA-EDAB/zooplanktonindex/blob/main/VASTscripts/VASTunivariate_zoopindex_modselection.R Model selection results are reported at this link: https://noaa-edab.github.io/zooplanktonindex/CopeModSelection.html In the second stage of model selection, the day of year covariate had mixed success. Results of the best models which both converged and had the lowest AIC are reported here: https://noaa-edab.github.io/zooplanktonindex/CopeModResults.html.
Models were run using REML and without bias correction. Two different observation models were applied. The default VAST index standardization (purpose = “index2” in make_settings) uses a Gamma distribution for positive catches and an alternative “Poisson-link delta-model” using log-link for numbers-density and log-link for biomass per number (ObsModel= c(2,1)). For datasets with years where the group of interest was sampled at all stations, we needed to use a different link function, the Poisson-link fixing encounter probability=1 for any year where all samples encounter the species (James T. Thorson 2019). We kept all other settings for index standardization the same, but set (ObsModel= c(2,4)).
We applied the default observation model to Calanus finmarchicus, euphausiids, and large copepod datasets. We applied the alternative observation model to small copepods and zooplankton volume. Based on the model selection results linked above, a day of year catchability covariate was applied when the addition of the covariate had reduced the model AIC and produced a model likely to converge. The two models that incorporated day of year covariates were the spring euphausiid and spring large copepod models.
The script used to run the VAST models is available here: https://github.com/NEFSC/READ-EDAB-VAST_indices/blob/main/zooplankton/zooindex_run_model.R
12.1.3 Data processing
12.1.3.1 Data were aggregated into groups for analysis (names indicate column names in the dataset linked above):
A lookup of these column headings is here: https://www.fisheries.noaa.gov/inport/item/35054
- Calanus finmarchicus (calfin_100m3) = “calfin” ,
- Large copepods (calfin_100m3, mlucens_100m3, calminor_100m3, euc_100m3, calspp_100m3) = “lgcopeALL”,
- Small copepods (all) (ctyp_100m3, pseudo_100m3, tlong_100m3, cham_100m3, para_100m3, acarspp_100m3, clauso, acarlong_100m3, fur_100m3, ost_100m3, temspp_100m3, tort_100m3, paraspp_100m3) = “smallcopeALL” and
- Small copepods (SOE) (ctyp_100m3, pseudo_100m3, tlong_100m3, cham_100m3) = “smallcopeSOE”.
- Euphausiids = “euph_100m3”
- Zoopvolume = “volume_100m3”
12.1.3.3 Years were selected for analysis
The first year of data is 1982. Due to lags in data availability, the published report contains data with a terminal year that is two years earlier than the publication year.
SOE published in 2026: The script that processes input data is available here: https://github.com/NEFSC/READ-EDAB-VAST_indices/blob/main/zooplankton/zooindex_process_input_data.R
SOEs published in 2023-2025: The script that processes input data is available here: https://github.com/NOAA-EDAB/zooplanktonindex/blob/main/data/VASTzoopindex_processinputs.R
catalog link https://noaa-edab.github.io/catalog/zooplankton_index.html