Skip to content
This repository was archived by the owner on Aug 9, 2024. It is now read-only.

Latest commit

 

History

History
214 lines (167 loc) · 11.9 KB

CHANGELOG.md

File metadata and controls

214 lines (167 loc) · 11.9 KB

CHANGELOG

All notable changes to this project will be documented in this file.

This project adheres to Semantic Versioning

[v1.5.0] 2023-09-28

Added

  • 2023 Field data

Changed

  • Updated OBIS record to include sea surface temp and salinity, motile sea lice counts as well as genetic stock identification.

[1.4.0] - 2023-06-14

Added

  • 2022 Field and lab data
  • New sea lice time series includes all stages (not only motiles but also chalimus and copepodites) as per the new format for the time series moving forward which includes copepodite stages down to species, chalimus stages (with species not identified in the field but estimated based on proportion of species in the cope and motile stages within each year). This file is in the supplemental_data folder in the tidy_data folder names sealice_all_stages_ts_long.csv

Changed

  • Changed the name of the script that produced the old sea lice time series which was motiles only from historic_sealice_integration.R to historic_motile_sealice_intergration.R.

[1.3.1] - 2022-05-19

Fixed

  • corrected date formatting issues for survey_date, set_time, survey_time_start, survey_time_end which were introduced by googlesheets4 package not handling time of the day as time but rather as date time and therefore was appending or prepending incorrect date or times (eg set_time was 1899-12-30T06:30:00 but now correctly reads 06:30:00)
  • YSI data was blank because of an incorrect file path which is now updated.

[1.3.0] - 2022-04-11

Changed

  • CTD data now only includes data from the downcast, and not the upcast
  • Restructured the repository folders so that one flat and wide data file (jsp_catch_and_bio_data_complete.csv) is joined and available in the root of the repo.

Added

  • 2021 Field season data from field and lab
  • Added fork length, weight, and bycatch to OBIS record
  • Added scientific name of each species to bycatch_mort.csv file
  • Added latitude and longitude for all sites in sites.csv

Fixed

  • Readme file's description of what the workflow is for progressing data through various folders and the function of each script
  • Corrected Pacific Sand Lance scientific name from Ammodytes hexapterus to Ammodytes personatus

[1.2.0] - 2021-03-22

Added

  • 2020 field data results
  • 2020 fish dissection results
  • RNA pathogen results data from Kristi Miller's lab at DFO for 2015 and 2016 sockeye, pink, and chum
  • New column added for sea lice presence absence in fish_field_data.
  • All CTD data collected during juvenile salmon sampling
  • 2018 and 2019 Genetic stock ID
  • 2019 finclip dna sample inventory
  • Data wrangling code and processed-data for OBIS (Ocean Biodiversity Information System)

Fixed

  • Species ID as sockeye was changed based on results of genetic stock ID for:
    • U16451: Coho
    • U17041: Coho
    • U17291: Pink
    • U20467: Coho
    • U20469: Chum
    • U20774: Chum
    • U20864: Chum

Changed

  • Combined the annual-observations-report (time-series) code and data into this repository and deprecated the jsp-time-series repo.

[1.1.0] - 2020-02-14

Added

  • 2019 results to fish_lab_data
  • Sockeye diet results (see: data/sample_results/sockeye_diets) from 302 sockeye caught in 2015 and 2016 from Sam James' MSc. thesis
  • Sample inventory for all tissue samples collected from dissections: RNA:DNA, RNA-pathogens, fatty acid, stable isotope, stomach, scale, otolith, sea lice ID, sea lice microbiome, DNA, extra muscle, and carcass. This is just the complete list of samples taken and does not contain any physical location data. Location data can be found on eLabJournal.
  • Coarse taxonomic analysis of gut contents of some 2019 sockeye (see: data/sample_results/salmon_diets_coarse.csv)

Fixed

  • U20251 species corrected from "CO" to "CK"
  • Updated seine DE607N1 to reflect change in species ID
  • Used zooplankton tow coordinates for seine DE293N1 due to transcribed seine coordinates being on land
  • Added missing lat/long for JE225N1
  • Fixed incorrect lat value for DE526N1
  • Incorrect DNA sample_ids for U3984-U3993 (changed from DH00041-DH00050 to DH00051-DH00060)
  • fish_lab_data comments_protocol that U2208 has no otolith samples, not U2209

Changed

  • Folder sample_results contains sockeye_diets, sealice_lab_fs, and stock_id
  • Added prefixes to quality_flag and quality_log in seine_data, fish_field_data, and fish_lab_data so they don't conflict when merging tables
  • Dissection protocol categories in fish_lab_data renamed for better readibility (also updated in data dictionary)
  • UFN assignment of undissected fish from 2015-2016 now follow the relative order of the SEMSP IDs
  • Updated comments_protocol for: U17095 & U17096 in fish_lab_data to state that these fish do not have gill samples; U5030 has no RNA-muscle sample; U13005 has no RNA-kidney sample
  • quality_level categories now conform with Hakai Data Standards draft document

Removed

  • Deleted seine with no data due to being botched: JE304N1
  • UFNs from stock_id with no results; those samples can now be found in data/sample_inventory/dna_samples.csv
  • Fish SEMSP IDs 2016-06-22-D21-SO-31 to SO-60 and U19102-U19131 because these were trainer fish and not part of the standard processing stream
  • ufn and tissue_type columns from stock_id

[1.0.2] - 2019-10-24

Fixed

  • Fish U20181 species changed from "CO" to "CK"
  • Updated catch statistics for seine DE617N1 to reflect change to U20181 species ID

Added

  • Chum retained for GM that wasn't originally entered into fish_field_data (U22681, JE524N2)

Changed

  • Updated cu_retained for JE524N2 to reflect GM CU added
  • U20841 & U20844 given new package ID because they were pink that were originally packaged with chum

[1.0.1] - 2019-10-21

Fixed

  • Fish U20371 species changed from "CU" to "SO"
  • Updated catch statistics for seine DE612N1 to reflect change to U20371 species ID

[1.0.0] - 2019-10-08

Added

  • 2019 field collection data
  • New tables sites and site_coordinates that contain geographic metadata
  • 2018 fish dissections and sea-louse enumeration
  • Fish that previously did not have fork_length_lab measurements now have a modeled value generated from standard_length_lab measurements using lab data from 2015 to February 2019 (juvenile-salmon repository release 2019-02-21)
  • In site_activity, surveys with no observations (ie., no activity sighted) have a single record where school_number == 0
  • New column 'lice_id_protocol_field' to fish_field_data
  • New table zoop_tax for zooplankton taxonomy samples
  • Added additional metadata to zoop_tows: cast_num, tow_type, line_out, flow_flag, solo_id, solo_depth, tow_split, sample_collected, zoop_tow_comments
  • Added 2018 zooplankton tow & sample metadata
  • Added ctd_drop to survey_data
  • Added more sampling metadata to ysi, updated all records from the EIMS data portal

Changed

  • Species in bycatch_mort no longer use four-letter codes; instead, their common names are fully spelled out
  • In sites, site "J09" renamed to "Bauza Cove"
  • All timestamps reformatted to "yyyy-mm-dd hh:mm Z"
  • In survey_data, renamed "ebb tide" to "ebb" for consistency
  • All fish with only SEMSP IDs (undissected specimens from 2015-16) have now been retroactively assigned UFNs for database consistency

Fixed

  • In survey_data, blank cells for DFO surveys changed to NA (no data)
  • Surveys DE278, DE289, DE293, DE321, DE334, DE348, and DE360 incorrectly had their zone listed as "E"; corrected to "W"
  • In sealice_field, replaced cal & mot counts from 0 to NA for all fish with lice_id_protocol_field == "salmoncoast_motiles"
  • In fish_lab_data, sealice_protocol_lab changed to NA for 2015/2016 fish dissected 2018-07 only for DNA collection

Removed

  • Geographic site metadata from survey_data (migrated to new tables)
  • Removed the following records from sealice_finescale due to no results: U41, U148, U150, U1189, U1375, U1393, U1397, U1411
  • preservation_status no longer an attribute of seine_data, and is being migrated to package_data upon next release
  • In survey_data, ysi_cast_id, ctd_cast_id, secchi, and zoop_sample_id columns (must manually join oceanography data by date, site, etc)
  • photo_number from fish_lab_data
  • 1 chum from seine DE371N1 with no UFN or SEMSP ID (trainer fish)
  • dissection_status from fish_field_data (can determine if a fish has been dissected by joining it with fish_lab_data to see if it has a date_processed value
  • Removed from sealice_lab_fs any UFNs that do not exist in fish_lab_data (discarded due to qc) or do not have results (i.e., unprocessed samples)
  • Removed zooplankton sample IDs from zoop_tows and placed in new table with associated tow IDs
  • ctd_cast_id no longer part of survey_data

[0.2.0] - 2018-10-15

Added

  • 2017 fish dissections and 2018 field collection data
  • New dataset sealice_lab_finescale for sea lice taxonomy data that includes very detailed species, life stages, and sex data, contributed by Sean Godwin and Lauren Portner

Changed

  • Sea licing protocol categories expanded for added clarity of protocol, such as differentiating "lab_finescale" from "lab_motiles"
  • In zoop_tows, volume renamed to corrected_volume to reflect that the volume has been corrected for flowmeter calibrations.
  • seine_id format for a few seine records changed to become more consistent

Removed

  • Sample inventory information, due to becoming quickly outdated.

[0.1.2] - 2018-?-?

Changed

  • In fish_field_data, 'analysis_planned' for fish in packages JP49 and JP50 set to "field loused only" due to fish no longer being available for laboratory dissections

[0.1.1] - 2018-04-19 (?)

Added

  • New dataset surface_activity that quantifies visual observations of fish-related surface activity for 2017 surveys.
  • New records to fish_field_data of fish caught in 2017 that were field liced, but not retained,
  • New column in fish_field_data called 'analysis_planned' to denote whether a fish had been field loused only (and not retained for further analysis), were retained for Sam James's UBC diet study, or were retained for standard SEMSP lab analysis
  • New records in package_data of undissected 2015 non-core pink, chum, coho, and herring that were inventoried in -80 Freezer 1, shelf 2, on 2018-02-05/06
  • New records in sealice_lab_motiles of fish that received finescale motile enumeration and identification Lauren Portner in winter 2018

Changed

  • In fish_lab_data, dissection_protocol of fish U2256-U2260 changed from "lice enumeration only" to "irregular work-up"
  • In fish_field_data, dissection_status of 2015 & 2016-caught sockeye updated to be current as of 2017-12-08, wherein we completed dissections of core site subsamples for 2015/2016
  • In fish_field_data, fish_lab_data, stock_id, and **sealice_lab_motiles, 2-character UFNs now have leading zeroes before the number, e.g. "U1" -> "U01"
  • Updated records in stock_id with proper sample_id and ufn associations (no change to results)

Fixed

  • In survey_data, assigned mixing 'ctd_cast_id' to survyes DE340, DE341, and DE329
  • In stock_id, re-assignment of results due to PBS "off by 1" data entry error for the following records:
    • U515, U299, U300, U307, U308, U317, U318, U319, U328, U331, U332, U333, U408, U409, U410, U466, U467, U468, U470, U491, U492, and U482

[0.1.0] - 2018-?-?

  • This was the first version of the data package and did not receive a hakaisalmon R package version number. The dataset, however, can be found at http://dx.doi.org/10.21966/1.566666 or in the commit history of this package.