Changes in version 2.6.0 - Updated download method to use EDIutils package to handle new requirement for API keys. Added a function to check for an access key and provide instructions if one is not present. - Removed parameter for Redownload_data from Zoopdownloader and reload_data from Zoopsynther, because the EDIutils functions directly read the data but do not save it. - Added EMP and FRP data released in May 2026 - Added EMP data released in June 2025 (sampling from 1972–2023), which no longer includes amphipods in the macro dataset; see the amphipods_notes (EDI 522) for more information. - ~~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 - Added FRP 2023 data and adjusted crosswalk to reflect changes to their table. - Adjusted crosswalk table to reflect the order "Cladocera" being split into several orders. Changes in version 2.5.1 - Added DOP and STN/FMWT 2022 data Changes in version 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 Changes in version 2.4.1 - Updated to newest FMWT macro column names. Changes in version 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. Changes in version 2.3.1 - Updated EMP EZ station locations Changes in version 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). Changes in version 2.2.0 - Updated to a corrected version of the 20mm dataset. Changes in version 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 Changes in version 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) Changes in version 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. Changes in version 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 Changes in version 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. Changes in version 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. Changes in version 0.2.1 - Updated to newest FMWT & STN data. (04/01/2020) Changes in version 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. Changes in version 0.1.0 - First stable release. - Added testthat tests and continuous integration with Travis CI. - Started incorporating zooper version into shiny app. Changes in version 0.0.0.9000 - Added a NEWS.md file to track changes to the package.