Changelog

Source: NEWS.md

hakaisalmon 0.2.0

Data updates

  • Included 2017 fish dissections and 2018 field collection data
  • Sean Godwin and Lauren Portner contributed sea lice taxonomy data that includes very detailed species, life stages, and sex data. This new table is called sealice_lab_finescale.

Structural updates

  • A number of updates were made to sea licing protocol categories, with the addition of lab_finescale and others.
  • In zoop_tows, the volume column was renamed to corrected_volume to reflect that the volume has been corrected for flowmeter calibrations.
  • Most of the inventory information was removed from this package because it becomes out of date so fast. The only remainining inventory information is the sample_container_inventory.
  • seine_id format was changed to be more consistent. Therefore, a small number of seine_ids have changed.

Functions

  • A new function lump_fraser_sockeye_stocks was added, which lumps together the sockeye stock ID categories that the Molecular Genetics Lab at the Pacific Biological Station in Nanaimo uses. The stocks are lumped based on regions in the Fraser River Watershed, and are the categories often used by Chrys Neville to summarize juvenile salmon cohorts.

hakaisalmon 0.1.2

Data updates

  • In fish_field_data, updated analysis_planned for fish in packages JP49 and JP50 to ‘field loused only’ due to fish no longer being available for SEMSP laboratory dissections.

Funtions

  • Created the function log_cumul_abund for the purposes of measuring migration timing. log_cumul_abund takes the cumulative proportion of catch data for each year (make this yourself first) and fits a logistic growth curve to these data and creates predicted values for each day.

hakaisalmon 0.1.1

Data updates

  • Added new table survey_activity that quantifies visual observations of fish-related surface activity for 2017 surveys.
  • Updated dissection_protocol in fish_lab_data from ‘lice enumeration only’ to ‘irregular work-up’ for U2256-U2260
  • Added UFNs of 2017 fish that were field liced but not retained in fish_field_data
  • Added new column to 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
  • Updated dissection_status of 2015 & 2016-caught sockeye to be current as of 2017-12-08 (completed dissections of of the core site subsamples for 2015/16) in fish_field_data
  • Added to package_data: packages of undissected 2015 non-core PI, CU, CO, and HE that were inventoried in -80 Freezer 1, shelf 2, on 2018-02-05/06
  • Changed 2-character UFNs to have leading ‘0’ before the number, e.g. ‘U1’ -> ‘U01’ in in fish_field_data, fish_lab_data, stock_id, and sealice_lab_motiles (and in sample ID inventory)
  • Updated rows in stock_id with proper sample_id and UFN associations (no change to results)
  • Updated sealice_lab_motiles with counts for UFNs processed by Lauren Portner in winter 2018
  • Assigned missing ctd_cast_id to surveys DE340, DE341, and DE329 in survey_data

  • Re-assignment of genetic stock ID due to PBS ‘off by 1’ data entry error for the following UFNs:

    U515 U299 U300 U307 U308 U317 U318 U319 U328 U331 U332 U333 U408 U409 U410 U466 U467 U468 U470 U491 U492 U482
    ————————————–

hakaisalmon 0.1.0

  • 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.