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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.

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.