seq_amatch: Approximate matching for integer sequences.

Description

For a list of integer vectors x, find the closest matches in a list of integer or numeric vectors in table.

Usage

seq_amatch(
  x,
  table,
  nomatch = NA_integer_,
  matchNA = TRUE,
  method = c("osa", "lv", "dl", "hamming", "lcs", "qgram", "cosine", "jaccard", "jw"),
  weight = c(d = 1, i = 1, s = 1, t = 1),
  maxDist = 0.1,
  q = 1,
  p = 0,
  bt = 0,
  nthread = getOption("sd_num_thread")
)
seq_ain(x, table, ...)

Value

seq_amatch returns the position of the closest match of x

in table. When multiple matches with the same minimal distance metric exist, the first one is returned. seq_ain returns a

logical vector of length length(x) indicating wether an element of x approximately matches an element in table.

Arguments

x: (list of) integer or numeric vector(s) to be approximately matched. Will be converted with as.integer.
table: (list of) integer or numeric vector(s) serving as lookup table for matching. Will be converted with as.integer.
nomatch: The value to be returned when no match is found. This is coerced to integer.
matchNA: Should NA's be matched? Default behaviour mimics the behaviour of base match, meaning that NA matches NA. With NA, we mean a missing entry in the list, represented as NA_integer_. If one of the integer sequences stored in the list has an NA entry, this is just treated as another integer (the representation of NA_integer_).
method: Matching algorithm to use. See stringdist-metrics.
weight: For method='osa' or 'dl', the penalty for deletion, insertion, substitution and transposition, in that order. When method='lv', the penalty for transposition is ignored. When method='jw', the weights associated with integers in elements of a, integers in elements of b and the transposition weight, in that order. Weights must be positive and not exceed 1. weight is ignored completely when method='hamming', 'qgram', 'cosine', 'Jaccard', or 'lcs'.
maxDist: Elements in x will not be matched with elements of table if their distance is larger than maxDist. Note that the maximum distance between strings depends on the method: it should always be specified.
q: q-gram size, only when method is 'qgram', 'jaccard', or 'cosine'.
p: Winkler's prefix parameter for Jaro-Winkler distance, with \(0\leq p\leq0.25\). Only when method is 'jw'
bt: Winkler's boost threshold. Winkler's prefix factor is only applied when the Jaro distance is larger than bt. Applies only to method='jw' and p>0.
nthread: Number of threads used by the underlying C-code. A sensible default is chosen, see stringdist-parallelization.
...: parameters to pass to seq_amatch (except nomatch)

Notes

seq_ain is currently defined as

seq_ain(x,table,...) <- function(x,table,...) amatch(x, table, nomatch=0,...) > 0

All input vectors are converted with as.integer. This causes truncation for numeric vectors (e.g. pi will be treated as 3L).

Examples

Run this code


x <- list(1:3,c(3:1),c(1L,3L,4L))
table <- list(
  c(5L,3L,1L,2L)
  ,1:4
)
seq_amatch(x,table,maxDist=2)

# behaviour with missings
seq_amatch(list(c(1L,NA_integer_,3L),NA_integer_), list(1:3),maxDist=1)


if (FALSE) {
# Match sentences based on word order. Note: words must match exactly or they
# are treated as completely different.
#
# For this example you need to have the 'hashr' package installed.
x <- "Mary had a little lamb"
x.words <- strsplit(x,"[[:blank:]]+")
x.int <- hashr::hash(x.words)
table <- c("a little lamb had Mary",
           "had Mary a little lamb")
table.int <- hashr::hash(strsplit(table,"[[:blank:]]+"))
seq_amatch(x.int,table.int,maxDist=3)
}