zooper: zooper: A package for integrating zooplankton datasets from...

In InteragencyEcologicalProgram/zooper: Download and Integrate Zooplankton Datasets from the Upper San Francisco Estuary

zooper: A package for integrating zooplankton datasets from the Sacramento San Joaquin Delta

Description

This package contains functions, lookup tables, and 2 built-in pre-combined datasets (one with the zooplankton data and another with the environmental data).

zooper functions

• Zoopsynther

• Zoopdownloader

• Taxnamefinder

• SourceTaxaKeyer

• LCD_Taxa

• Uncountedyears

zooper lookup tables

• crosswalk

• undersampled

• stations

• completeTaxaList

• startDates

zooper pre-combined (with the Zoopdownloader function) zooplankton datasets. These may be out of date

• zoopComb

• zoopEnvComb

Source datasets

Environmental Monitoring Program (EMP)

The EMP zooplankton survey is run by the California Department of Fish and Wildlife. Zooplankton were first collected in 1972. It samples monthly at 17 fixed stations, 2 floating entrapment zone stations, and 3 stations in Carquinez Strait and San Pablo Bay that are only sampled during high outflow and low salinity conditions. EMP samples using micro (43 \mum), meso (160 \mum), and macro (505 \mum) zooplankton nets. Note that additional Amphipod data with quality issues (e.g., vegetation in net) are available in the EMP data publication. Data are available here.

20-mm Survey

The 20-mm survey is run by the California Department of Fish and Wildlife. Zooplankton were first collected in 1995. Zooplankton are collected concurrently with fish samples at 41-55 fixed open-channel stations per year. Samples are collected twice per month between March and July. Only Mesozooplankton are collected with a 160 \mum mesh net. Data are available here.

Fall Midwater Trawl (FMWT) and Summer Townet Survey (STN)

The FMWT and STN are run by the California Department of Fish and Wildlife. FMWT samples are collected monthly between September and December from a subset of the 122 fixed open-channel stations. STN samples are collected monthly between June and August from 40 fixed open-channel stations. Macrozooplankton have been collected since 2007 with a 505 \mum mesh net while mesozooplankton have been collected since 2005 with a 160 \mum mesh net. Data are available here.. Supplemental sampling from the Suisun Marsh Salinity Control Gate study data are also included and those data can be found here.

Fish Restoration Program (FRP)

FRP is run by the California Department of Fish and Wildlife. Zooplankton were first collected in 2015. Samples are collected monthly between March and December in shallow-water habitats near marshes. FRP samples with meso (150 \mum) and macro (500 \mum) zooplankton nets. Data are available here.

Directed Outflow Project Lower Trophic Study (DOP)

The Directed Outflow Project Lower Trophic Study is run by ICF for the United States Bureau of Reclamation. Zooplankton were first collected in fall 2017. Samples were collected once every two weeks in 2017 and weekly thereafter. Sampling is conducted in the fall and, starting in 2019, spring and summer seasons have also been sampled. Three sampling stations per region are randomly selected for 5 regions (Suisun Bay, Suisun Marsh, Lower Sac. River, Cache Slough, Sac Ship Channel). In 2017, stations were sampled in 3 additional regions: West of the Benicia Bridge, Lower San Joaquin, and Upper Sac River. At each station, sample collection is attempted at both shoal (<=10 feet) and channel (>10 feet) habitat. Channels are sampled at the surface and, if deeper than 20 feet, also at the bottom 1/2 to 1/3 of the water column. DOP samples with meso (150 \mum) and macro (500 \mum) zooplankton nets. Data are available here.

Yolo Bypass Fish Monitoring Program (YBFMP)

YBFMP is run by the California Department of Water Resources. Zooplankton were first collected in 1999. Samples are from 2 sites, one in the Yolo Bypass and one in the Sacramento River. In 1999 and 2000, samples were collected for a couple of months each year, and then it increased to roughly winter/spring from 2001-2010. Since 2011, samples are collected twice monthly during most of the year, and weekly when the bypass is inundated. YBFMP samples with micro (50 \mum) and meso (150 \mum) zooplankton nets. Data are available here.

Author(s)

Maintainer: Samuel M Bashevkin [e-mail] (ORCID)

Authors:

• Rosemary Hartman [e-mail] (ORCID)

• Karrin Alstad [e-mail]

• Catarina Pien [e-mail] (ORCID)

See Also

Useful links:

• https://github.com/InteragencyEcologicalProgram/zooper

• Report bugs at https://github.com/InteragencyEcologicalProgram/zooper/issues

InteragencyEcologicalProgram/zooper documentation built on Feb. 6, 2025, 9:01 a.m.