codify_sex: Code sexes into standardized strings

In nwfsc-assess/nwfscSurvey: Northwest Fisheries Science Center Survey

Code sexes into standardized strings

Description

Information for sexes can be stored in several forms. codify_sex() works to standardize all possible input values for sex into one of three character values, i.e., F, M, or U. And, codify_sex_SS3() runs codify_sex() on the input and then further standardizes F and M to 3 and all other values to 0 to match grouping of sexed and unsexed fish for Stock Synthesis.

Usage

codify_sex(x)

codify_sex_SS3(x)

Arguments

x	A vector of values used to store sex information. Can be any combination of integers, single characters, or NA values.

Value

A vector of F, M, or U values the same length as x or a vector of 0L or 3L for codify_sex() and codify_sex_SS3(), respectively.

Codifying

Pattern matching is used via grepl() to facilitate matching both standard and potentially erroneous matches. For example, the code can accommodate any number of white space characters before the text string via ⁠"^\\s*⁠. Additionally, only the first letter of the character string is of importance because the code is strictly looking for versions of female, male, and unsexed, ignoring case. All NA values are coded as U for unsexed. A manual produced by Washington Department of Fish and Wildlife, https://wdfw.wa.gov/sites/default/files/publications/01754/wdfw01754.pdf, provides some of the following information regarding how various sampling programs codify sex.

• The Alaska Fisheries Science Center Slope Survey stored sexes uses integers, i.e., male (1), female (2), and unsexed (3).

• Washington followed the same format as the Alaska Fisheries Science Center Slope Survey.

• Oregon and California also use 1 for males and 2 for females; but 9 is used for unknown sex.

Message

A message is printed to the screen if any values do not have a map to F, M, or U. For example, if happy was an entry in x, a summary of the number of times happy was seen in x would be printed to the screen via message and happy would be coded to U such that the returned value is still viable but the user is made aware that something is potentially wrong in x. See for yourself in the examples.

Author(s)

Kelli F. Johnson

Examples

# All values are successfully coded
codify_sex(c("U", "F", "M", 1, 2))
# Some values are not initially successfully coded and
# warning messages are printed to the screen prior to
# changing the uncoded values to "U"
codify_sex(c("U", "F", "M", "both", 1, 2, NA))
codify_sex(c("both", rep(5, 10), "both", 1, 2, NA))

# Change codified sex from letters to integers for Stock Synthesis
codify_sex_SS3(c("M", "U", "K"))

nwfsc-assess/nwfscSurvey documentation built on Nov. 12, 2024, 8:14 p.m.