Code sexes into standardized strings
codify_sex.RdInformation 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.
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.
Examples
# All values are successfully coded
codify_sex(c("U", "F", "M", 1, 2))
#> [1] "U" "F" "M" "M" "F"
# 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))
#> The following unmatched values were found n times in `codify_sex()`:
#> 'both' (n = 1)
#> 'NA' (n = 1)
#> [1] "U" "F" "M" "U" "M" "F" "U"
codify_sex(c("both", rep(5, 10), "both", 1, 2, NA))
#> The following unmatched values were found n times in `codify_sex()`:
#> '5' (n = 10)
#> 'both' (n = 2)
#> 'NA' (n = 1)
#> [1] "U" "U" "U" "U" "U" "U" "U" "U" "U" "U" "U" "U" "M" "F" "U"
# Change codified sex from letters to integers for Stock Synthesis
codify_sex_SS3(c("M", "U", "K"))
#> The following unmatched values were found n times in `codify_sex()`:
#> 'K' (n = 1)
#> [1] 3 0 0