R/data.R
fish_lab_data.RdA dataset containing variables collected from laboratory dissections of fish caught in the field by the Juvenile Salmon Program. A subset of fish_field_data
fish_lab_data
An object of class tbl_df (inherits from tbl, data.frame) with 5602 rows and 19 columns.
The alphanumeric string that uniquely identifies a fish. Primary key to: fish_field_data, sealice_field, and sealice_lab_motiles.
A unique ID for every fish retained that was a concatenation of survey_date, site_id, species, and order the fish was pulled out of the net. In 2017 this was method was abandonded, and instead we assigned seine IDs and UFNs to uniquely identify seines and fish
The date the fish was processed (dissected) in the lab. Blank infers the fish has not be dissected yet. Format: yyyy-mm-dd
Fish were scanned using a handheld CWT read. none = no tag detected. cwt = coded wire tag detected
none = adipose is not clipped. AD = adipose fin was clipped
weight of the fish measured in the lab using Pro Scout scales. Units: grams. 0.1 g precision
The length of the fish measured from the tip of the snout to the caudal peduncle where scales give way to caudal fin rays. Units: millimetres
The length of the fish meadured from the tip of the snout to the fork of the caudal fin. Units: millimetres
Photos of abnormal looking fish were taken. The name of the photo file in the photo database. The file name is also the UFN of the fish.
Comments related to deviations to standard dissection protocols
Comments to describe any abnormal/unique observations about the fish itself (e.g. lesions, non-louse parasites, tissue discolouration, scale loss, etc.)
The initials of the technician who performed the dissection
Categories used to describe the general lab dissection workflow performed on a fish:
Full work-up 1 = procedure for 2015 & 2016 samples (One RNA sample each taken from muscle, gill, brain, spleen, liver, heart, and head kidney; fatty acid, stable isotope, DNA (if no fin clips were taken in the field), stomach, otolith, and scales).
Full work-up 2 = procedure for all samples effective Oct. 2017 (One RNA sample each taken from muscle, gill, brain, spleen, liver, heart, and head kidney; fatty acid, stable isotope, extra muscle stored at -80 degrees Celcius, DNA (if no fin clips were taken in the field), stomach, otolith, and scales).
Full work-up 3 = procedure for fish subsampled for compound specific stable isotope analysis (by David Costalago, Feb. 2018). All samples taken as in full work-up 2, with the addition of a second isotope sample taken.
Work-up excluding cold samples = full work-up 1 without RNA, fatty acid, or stable isotope samples taken.
Irregular work-up = processing with at least one sample type not taken (e.g. no RNA, no DNA, etc.).
Lice enumeration only - in lab = fish was inspected for sea lice only and did not undergo dissection. Lengths and weight recorded.
-20 work up 1 = procedure for dissecting fish that have been previously stored at -20 before dissection. No RNA samples, no fatty acid samples, no extra muscle sample, no sea-lice retention. Reduced sterilization between fish to scrubbing and ethanoling direct contact surfaces with 95
The initials of the technician who quality checked the data
yes = one or more columns has an unresolvable error in data entry (not pertaining to the physical quality of the sample). no = no issues with data quality
Explains why the fish has been flagged
Describes any action taken by QC to address and resolve flagged issues.
The protocol that was followed to collect sealice from the fish. Categories:
lab_motiles_cryo = only motile sea lice were collected
lab_fine_2015 = all life stages, sexes, and species of sea lice were collected (only in 2015)
not_collected = no sea lice were collected
The protocol that was followed for identifying sea lice in the lab. Categories:
lportner_fine = fine-scale identification of all sea lice and life stages that were obtained under
lab_motiles = identification of only motile stages of sea lice