getAge: Get age information for each fish

In nwfsc-assess/PacFIN.Utilities: Generate fishery composition data from PacFIN data for the NWFSC

Get age information for each fish

Description

Get age information for each fish, or row of the data. This functionality was originally in cleanAges(), moved to cleanPacFIN(), and is now compartmentalized here, but called in cleanPacFIN() and stored in the Age column.

Usage

getAge(Pdata, verbose = TRUE, keep, col.bestage = lifecycle::deprecated())

Arguments

Pdata	A data frame of biological samples originating from the Pacific Fishieries Information Network (PacFIN) data warehouse, which originated in 2014. Data are pulled using sql calls, see PullBDS.PacFIN().
verbose	A logical specifying if output should be written to the screen or not. Good for testing and exploring your data but can be turned off when output indicates information that you already know. The printing of output to the screen does not affect any of the returned objects. The default is to always print to the screen, i.e., verbose = TRUE.
keep	A vector of strings, integers, NA, and empty strings (e.g., "") representing the AGE_METHODs you want to keep. All entries will be converted to character values using codify_age_method(). To keep the best age for a given row, at least one of the ageing methods needs to have been performed using one of the methods present in this argument. Often, it is helpful to run getAgeMethod() on the relevant data prior to running this function to see what age methods are currently present.
col.bestage	Deprecated in version 0.2.5.

Details

FISH_AGE_YEARS_FINAL

FISH_AGE_YEARS_FINAL is defined in PacFIN as the “age of specimen (best age or final age)”. If FISH_AGE_YEARS_FINAL does not have an entry, where this should be the best age available, then the user is warned that they should potentially look at the age reads from an individual reader, e.g., 'age1' or 'age2', until the state works out what age read is best and provides this in 'FISH_AGE_YEARS_FINAL'.

How FISH_AGE_YEARS_FINAL is determined can be unclear because it does not always equal the value from one of the age readers. How the value is determined is specific to the lab that conducted the ageing. Sometimes, reconciling multiple age reads to determine the best age will lead to the final age not equaling any of the individual age reads. For example, readers can get together to determine the best read. We assume that those who populated the column know what they are doing; but, please feel free to report errors in PacFIN to GitHub issues or the package maintainer after contacting the state representative.

Ageing methods listed in keep (or derivatives of those) will be used to filter for ages that are of desired method. Any age that was not estimated using one of the desired methods will be replaced with an NA.

Deprecated methods

Previously, getAge() averaged over multiple reads if there was no entry in FINAL_FISH_AGE_IN_YEARS. This functionality has since been removed from the package starting with version 0.2.6.

Washington

Washington uses the following order of operations to assign the best age given there are multiple reads. See issue #49 for a semi-detailed discussion. Note, that they will never report more than three reads because that is the limitation of their database.

• age1 if only one read;

• randomly chosen age between age-read 1 and age-read 2 if the difference between the two reads is less than or equal to three;

• if the difference between two reads is more than three, then the best age is manually keyed in from that designated by a human;

• if three reads are equal, then the value is automatically assigned; and

• if there are three reads and they are not equal then an age reader must choose the final value.

Oregon

Oregon employs a single age reader, or at least has since 2014. Twenty percent of first reads are re-read by the same reader but without knowing any information about the results of the first read.

• age1 if only one read;

• age1 if age1 and age2 agree;

• age3 if age1 and age2 do not agree, where age3 is not a blind read and the reader knows the values reported in age1 and age2 when reading the otolith for a third time.

California

Ageing of otoliths collected in California is performed by the Cooperative Ageing Project, funded through a grant with the Pacific States Marine Fisheries Commission. This same lab also ages the samples collected on the coast-wide surveys as well as some of the samples collected by Oregon when there are too many ages to read for their single age reader.

• age1 if only one read;

• age1 if age1 and age2 agree;

• for younger fish, i.e., less than or equal to age 10, discrepancies can normally be resolved by looking at the otolith and having knowledge of both previous reads;

• for older fish, i.e., older than age 10, discrepancies are resolved and the resolved age is used;

• for older fish where the discrepancy cannot be resolved, age1 is used because it had the freshest otolith and potentially used the better half.

Value

A vector of integer ages in years the same length as the number of rows present in Pdata.

Author(s)

Kelli F. Johnson

nwfsc-assess/PacFIN.Utilities documentation built on March 19, 2024, 11:54 p.m.