This seems really simple but for some reason, I don't understand the behavior of agrep fuzzy matching involving substitutions. Two substitutions produce a match as expected when all=2 is specified, but not when substitutions=2. Why is this?
# Finds a match as expected
agrep("abcdeX", "abcdef", value = T,
max.distance = list(sub=1, ins=0, del=0))
#> [1] "abcdef"
# Doesn't find a match as expected
agrep("abcdXX", "abcdef", value = T,
max.distance = list(sub=1, ins=0, del=0))
#> character(0)
# Finds a match as expected
agrep("abcdXX", "abcdef", value = T,
max.distance = list(all=2))
#> [1] "abcdef"
# Doesn't find a match UNEXPECTEDLY
agrep("abcdXX", "abcdef", value = T,
max.distance = list(sub=2, ins=0, del=0))
#> character(0)
Created on 2021-06-03 by the reprex package (v2.0.0)
all is an upper limit which always applies, regardless of other max.distance controls (other than cost). It defaults to 10%.
# one characters can change
agrep(pattern = "abcdXX", x = "abcdef", value = TRUE,
max.distance = list(sub = 2, ins = 0, del = 0, all = 0.1))
# character(0)
# two characters can change
agrep(pattern = "abcdXX", x = "abcdef", value = TRUE,
max.distance = list(sub = 2, ins = 0, del = 0, all = 0.2))
# [1] "abcdef"
# one character can change
agrep(pattern = "abcdXX", x = "abcdef", value = TRUE,
max.distance = list(sub = 1, ins = 1, del = 0, all = 0.1))
# character(0)
# two characters can change
agrep(pattern = "abcdXX", x = "abcdef", value = TRUE,
max.distance = list(sub = 1, ins = 1, del = 0, all = 0.2))
# [1] "abcdef"
There's a bit of a gotcha that the fractional mode of setting all switches to the integer mode at 1.
# 8 insertions allowed
agrep(pattern = "abcdXXef", x = "abcdef", value = TRUE,
max.distance = list(sub = 0, ins = 2, del = 0, all = 1 - 1e-9))
# [1] "abcdef"
# 1 insertion allowed
agrep(pattern = "abcdXXef", x = "abcdef", value = TRUE,
max.distance = list(sub = 0, ins = 2, del = 0, all = 1))
# character(0)
When you suppress all by setting it to just less than 1, the limits on the distance mode apply.
# two substitutions allowed
agrep(pattern = "abcdXX",
x = c("abcdef", "abcXdef", "abcefg"), value = TRUE,
max.distance = list(sub = 2, ins = 0, del = 0, all = 1 - 1e-9))
# [1] "abcdef"
The purpose of setting the cost is to allow you to move around the mutation-space at different rates in different directions. This is going to depend on your use case. For example some language dialects might be more likely to add letters. You might chose to let a deletion cost two insertions. By default, all are equally weighted when costs = NULL, i.e. costs = c(ins = 1, del = 1, sub = 1).
EDIT: regarding your comment about why some patterns match and others don't, the 10% refers to the number of characters in the pattern, rounding up.
agrep(pattern = "01234567XX89", x = "0123456789", value = TRUE,
max.distance = list(sub = 0, ins = 2, del = 0))
# [1] "0123456789"
agrep(pattern = "01234567XX", x = "0123456789", value = TRUE,
max.distance = list(sub = 2, ins = 0, del = 0))
# character(0)
num_mutations <- nchar(c("01234567XX89", "01234567XX")) * 0.1
num_mutations
# [1] 1.2 1.0
ceiling(num_mutations)
[1] 2 1
The second pattern is only 10 characters, so only one substitution is allowed.