NEWS.md

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

zooper (development version)

• Fixed issue where EMP macro amphipod counts from before 2014 were being converted to unidentified mysids instead of unidentified amphipods, since amphipods were not identified to species before 2014.
• Fixed issue with biomass conversion for macro and micro zooplankton. Previously it was not taking into account the count and instead providing the BPUE if 1 individual were present.
• Added the biomass for the surveys and size classes with the appropriate conversation factors and length data. This feature is still experimental
• Fixed issue with crosswalk that may impact Zoopsynther community output (values in the species column weren't consistent, some were genus species, some just species)
• Updated FRP data
• Fixing malfunctions in the taxonomic consistency over time approach. Uses of that function prior to this fix may not have appropriately resolved for changes in taxonomic consistency over time.
• Added 20mm 2021 and 2022 data
• Broke out turbidity into FNU and NTU. Most surveys use NTU, but 20mm has switched to FNU recently.
• Updated the species name for Eurytemora affinis to Eurytemora carolleeae based on Jungbluth et al 2021
• Jungbluth, M. J., J. Burns, L. Grimaldo, A. Slaughter, A. Katla, and W. Kimmerer. 2021. Feeding habits and novel prey of larval fishes in the northern San Francisco Estuary. Environmental DNA.1-22. https://doi.org/10.1002/edn3.226
• Fixed issue where macrozoop biomass was being incorrectly converted to micrograms, resulting in 100X higher biomass values.
• Added FRP 2022 data and adjusted crosswalk to reflect changes to their taxonomic table.
• Added 2023 FMWT/STN data and adjusted zoopdownloader to reflect new date format

zooper 2.5.1

• Added DOP and STN/FMWT 2022 data

zooper 2.5.0

• Added some missing environmental variables to DOP and removed bottom samples for environmental variables except conductivity.
• Added TowType variable to identify whether each tow was a surface, bottom, oblique, or vertical pump sample.
• Removed crosswalk Inf and -Inf dates and used 2500 and 1800, respectively, instead. For some reason, Inf and -Inf dates were no longer being treated correctly.
• Added DOP to Zoopdownloader test
• Added new co-authors
• Converted undersampled and crosswalk files to csv so it is easier to track changes on git
• Fixed previously incorrect times in EMP data. Previously, times in the EMP data were automatically converted to AM even if they were recorded as PM
• Changed FRP data coordinates to use the sample-specific coordinates instead of the general station location coordinates
• Added DOP data
• Changed data source for FMWT/STN to EDI
• Changed default download method of Zoopdownloader to "auto"
• Updating to newest EMP data.
• Added newest FMWT/STN data, including new station STN 722
• Add option to specify download method in Zoopdownloader function.
• Updated to newest SMSCG data

zooper 2.4.1

• Updated to newest FMWT macro column names.

zooper 2.4.0

• Changed all Acanthocyclops vernalis in crosswalk to Acanthocyclops.
• Added YBFMP data. YBFMP data cannot be used in the Zoopsynther function due to issues with taxonomic and life stage resolution.
• Updated to newest FMWT/SMSCG macro data.

zooper 2.3.1

• Updated EMP EZ station locations

zooper 2.3.0

• Used EMP Macro QAQC flags for amphipod data to set amphipod CPUE to NA whenever issues were detected (vegetation in net)
• Added EMP Amphipod data
• Fixed error where Undersampled taxa were not being flagged, identified by Rosemary Hartman
• Updated EDI download URLs to use pasta links
• Added 2020 SMSCG data
• Added updated 2020 EMP data with corrected depth values and corrected timezones
• Added 2020 EMP data (NOTE there is an outstanding issues with the EMP bottom depth values, two of which are 0 which should be incorrect).

zooper 2.2.0

• Updated to a corrected version of the 20mm dataset.

zooper 2.1.0

• Added tests to ensure no volume values are ever NA.
• Changed the name of the 20mm dataset to "20mm" everywhere for consistency. Previously, the output of Zoopdownloader would have the name as "twentymm", as would the built-in datasets, and the stations dataset.
• Added 2020 20mm data

zooper 2.0.0

• Added some simple progress messages to Zoopdownloader.
• Re-implemented use of the dtplyr package to greatly speed up computation, now that support for dplyr::across has been implemented. dtplyr >1.1.0 must be used for this to work.
• Fixed annoying warning message from Zoopdownloader function that 2 Datetimes failed to parse. Resulting dataset unchanged
• Redirected data downloads (for those datasets not on EDI) toward the new CDFW filelib website (https://filelib.wildlife.ca.gov/Public) instead of the old FTP (ftp://ftp.wildlife.ca.gov) by creating a new function to pull file lists from HTMLs (and a new dependency on rvest), replacing the old function to do the same with FTPs
• Changed internals to apply 3 tries to each attempt to access a URL
• Fixed CDFW FTP URL
• Fixing 20mm bottom depths (formally in feet, now correcting to meters like all other studies are converted).
• Updating with newest 20mm data.
• Added station location for FMWT 520 (=STN 520)

zooper 1.1.1

• Corrected timezone error that was shifting the date of some STN, FMWT, and 20mm samples by 1 day relative to the datetime.
• Updated FMWT station location coordinates to the newest version from the FMWT database.
• Corrected inconsistent capitalization of the STN Mont and Honk stations, resulting in correct coordinates for all those samples.
• Removed EMP Meso Sample corresponding to a mostly empty line at the end of the csv.

zooper 1.1.0

• Updated citation info
• Added 2018 20mm data
• Added tests to ensure column names have not changed.
• Added 2019 EMP, FMWT, and STN data

zooper 1.0.0

• Added SMSCG data
• Changed EMP source to the Environmental Data Initiative instead of the FTP site.
• Updated to newest versions of FMWT and STN data
• Added more flexibility to zoop_downloader so the package will not break when dates are changed in the source dataset filenames.
• Changed Summer Townet acronym from TNS to STN.
• Updated to dplyr 1.0, had to remove dtplyr usage due to incompatibility with dplyr 1.0 "_at" functions and new "across" function. Everything will be slower until dtplyr is updated.

zooper 0.3.0

• Moved to github actions for continuous integration testing.
• Added EMP EZ station latitude and longitude locations for 2004-present.
• Fixed inconsistent Microcystis values in FRP data.
• Fixed typo in Crosswalk table.

zooper 0.2.1

• Updated to newest FMWT & STN data. (04/01/2020)

zooper 0.2.0

• Added an option to the Zoopsynther function to correct for changes in taxonomic resolution over time by enforcing taxonomic consistency over time.
• Made all argument names start with a capital letter for consistency.
• Changed all "Larvae" to "Larva" and "Pupae" to "Pupa" in crosswalk and elsewhere for consistency with other singular life stage names.

zooper 0.1.0

• First stable release.
• Added testthat tests and continuous integration with Travis CI.
• Started incorporating zooper version into shiny app.

zooper 0.0.0.9000

• Added a NEWS.md file to track changes to the package.

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