version 0.1.0

DESCRIPTION

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+Package: tlsh
+Type: Package
+Title: Transitive Locality-Sensitive Hashing (LSH) for Record Linkage
+Version: 0.1.0
+Authors@R: person("Rebecca", "Steorts", email = "beka@stat.duke.edu",
+  role = c("aut", "cre"))
+Depends: R (>= 3.5.0), blink, stats, utils, plyr, igraph, bit64
+Imports:
+Suggests: knitr, ggplot2, rmarkdown
+VignetteBuilder: knitr
+Description: An implementation of the blocking algorithm transitive locality-sensitive hashing (TLSH) in Steorts, Ventura, Sadinle, Fienberg (2014) <DOI:10.1007/978-3-319-11257-2_20>, which is a k-means variant of locality sensitive hashing. The method is illustrated with examples and a vignette. 
+Encoding: UTF-8
+LazyData: true
+License: GPL-3
+RoxygenNote: 7.1.1.9000
+NeedsCompilation: no
+Packaged: 2020-11-02 16:22:06 UTC; rebeccasteorts
+Author: Rebecca Steorts [aut, cre]
+Maintainer: Rebecca Steorts <beka@stat.duke.edu>
+Repository: CRAN
+Date/Publication: 2020-11-06 17:00:02 UTC

MD5

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+395f2eae2242b16010635c0159710d32 *DESCRIPTION
+b308deeacf7be1a89891ae2523b10aed *NAMESPACE
+883a5648af177469263685d621b6968b *R/blocking-evaluations.R
+54acb8a8a2d3db0d8846427f6096e22d *R/minhash_v2.R
+10eb3c9ee8f70eb94b3e60164268dc45 *R/tlsh.R
+b5b601a33c1238f64d7521e55fa5a4ca *build/vignette.rds
+4c8da6ba82b58b79ae31cb933f833730 *inst/doc/tlsh.R
+043c61554a7b1f24e72a3b813bf9cef4 *inst/doc/tlsh.Rmd
+7c94d16e855c117546c0893ddba9edf5 *inst/doc/tlsh.html
+239e26c6ffab4f19c228f2b4965ef831 *man/block.ids.from.blocking.Rd
+68b865ead685190f24280d8bf17d4378 *man/block_setup_v2.Rd
+431dfd43b092d3359adf85ffcb837de9 *man/compare_buckets.Rd
+cf7770443b48e38aa67e4551b58ce8c1 *man/confusion.from.blocking.Rd
+eed4ab096a637c80534def65b5e11a42 *man/eval.blocksetup.Rd
+b634e13566eabb03db9f007c03806fe3 *man/extract_pairs_from_band.Rd
+4154bc7a1e4f546ac23c29bda5995a67 *man/hash_signature.Rd
+8d6a8176be4b368f9eb7bb39aacd90e8 *man/minhash_v2.Rd
+27ebdba13d154cc2051cbb266b2282ee *man/my_hash.Rd
+2be0caecb0d785afb805c7ee861b4c42 *man/primest.Rd
+b28b796a274f35ee917457e8727d3b49 *man/reduction.ratio.Rd
+87093270eb12fdf33bffe80d6bb5c3ba *man/reduction.ratio.from.blocking.Rd
+88bc1a83dda8e41d19bc2f11a4055f3b *man/rhash_funcs.Rd
+eeb46ff58a2f61eed834eec73ada48f8 *man/shingled_record_to_index_vec.Rd
+71ce81206422e086585828a257af8ab3 *man/shingles.Rd
+da525e154d909a4b9ec3184d02867e5f *vignettes/blocks_members.Rdata
+91073e85e36c66cafac6f0b6bb54e1c0 *vignettes/candidate_pairs_graph.Rdata
+043c61554a7b1f24e72a3b813bf9cef4 *vignettes/tlsh.Rmd

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(block.ids.from.blocking)
+export(block_setup_v2)
+export(compare_buckets)
+export(confusion.from.blocking)
+export(eval.blocksetup)
+export(extract_pairs_from_band)
+export(hash_signature)
+export(minhash_v2)
+export(my_hash)
+export(primest)
+export(reduction.ratio)
+export(reduction.ratio.from.blocking)
+export(rhash_funcs)
+export(shingled_record_to_index_vec)
+export(shingles)
+import(bit64)
+import(blink)
+import(igraph)
+import(plyr)
+import(utils)

R/blocking-evaluations.R

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+#' Perform evaluations (recall) for blocking.
+#'
+#' @import blink
+#' @param blocking A list of the blocks
+#' @param true_ids The true identifiers for comparisons
+#' @param recall.only Flag that when true only prints the recall, otherwise
+#' prints many evaluation metrics in a list
+#' @return A vector of that returns the recall and the precision
+#' @export
+#' @examples
+#' r.set <- RLdata500[1:250,c(-2)]
+#' tlsh.blocks <- block_setup_v2(r.set, b=22, save_signature=FALSE, k=2)
+#' confusion.from.blocking(tlsh.blocks, identity.RLdata500, recall.only=TRUE)
+
+confusion.from.blocking <- function(blocking, true_ids, recall.only=FALSE) {
+	# convert blocking into a vector of labels
+	nn <- sum(sapply(blocking,length))
+	block.ids = rep(NA, nn)
+	for(ii in 1:length(blocking))  block.ids[blocking[[ii]]] = ii
+	# For each pair of records, check whether they are in the same block
+
+    candidate.pairs = combn(length(block.ids), 2)
+    same.block <- block.ids[candidate.pairs[1,]] == block.ids[candidate.pairs[2,]]
+    same.truth <- true_ids[candidate.pairs[1,]] == true_ids[candidate.pairs[2,]]
+
+	#same.block <- outer(block.ids,block.ids,"==")
+	# For each pair of records, check whether the true ids match
+	#same.truth <- outer(true_ids,true_ids,"==")
+	# table same-block vs. same-truth
+	confusion <- table(same.block,same.truth, dnn=c("same block?","actually same?"))
+	# In the confusion matrix, rows refer to the blocks and columns refer to the truth
+
+	false.positives <- confusion[2,1]
+	false.negatives <- confusion[1,2]
+	true.positives <- confusion[2,2]
+	true.negatives <- confusion[1,1]
+	recall <- true.positives/(false.negatives + true.positives)
+
+
+	#true.positives <- confusion[2,2]
+	#misses <- confusion[1,2]
+	#recall <- true.positives/(true.positives+misses)
+	#precision <- true.positives/(same.truth)
+	if (recall.only) {
+		return(recall)
+	} else {
+		return(return(list(confusion,
+              recall = true.positives/(false.negatives + true.positives),
+              precision = true.positives/(true.positives + false.positives),
+              fpr = false.positives/(false.positives + true.negatives),
+              fnr = false.negatives/(false.negatives + true.positives),
+              accuracy = (true.positives + true.negatives)/(true.positives + 	true.negatives + false.negatives + false.positives),
+ 			        specificity = true.negatives/(true.negatives + false.positives))))
+	}
+}
+
+#' Returns the block ids associated with a blocking method.
+#'
+#' @import blink
+#' @param blocking A list of the blocks.
+#' @return A list of the blocks ids that corresponds to each block
+#' @export
+#' @examples
+#' tlsh.blocks <- block_setup_v2(r.set = RLdata500[1:250,c(-2,-4)], b=10, save_signature=FALSE, k=1)
+#' block.ids.from.blocking(tlsh.blocks)
+
+block.ids.from.blocking <- function(blocking) {
+	nn <- sum(sapply(blocking,length))
+	block.ids = rep(NA, nn)
+	for(ii in 1:length(blocking))block.ids[blocking[[ii]]] = ii
+	return(block.ids)
+}
+
+#' Returns the reduction ratio associated with a blocking method
+#'
+#' @import blink
+#' @import utils
+#' @param block.labels A list of the blocks labels.
+#' @return The reduction ratio
+#' @export
+#' @examples
+#' tlsh.blocks <- block_setup_v2(r.set = RLdata500[1:50,c(-2)], b=22, save_signature=FALSE, k=2)
+#' block.ids <- block.ids.from.blocking(tlsh.blocks)
+#' reduction.ratio(block.ids)
+
+reduction.ratio <- function(block.labels) 1 - sum(choose(table(block.labels),2)) / choose(length(block.labels),2)
+
+#' Returns the reduction ratio associated with a blocking method
+#'
+#' @import blink
+#' @param blocking The actual blocks
+#' @return The reduction ratio
+#' @export
+#' @examples
+#' tlsh.blocks <- block_setup_v2(r.set = RLdata500[1:50,c(-2,-4)], b=10, save_signature=FALSE, k=1)
+#' reduction.ratio.from.blocking(tlsh.blocks)
+reduction.ratio.from.blocking <- function(blocking) {
+	reduction.ratio(block.ids.from.blocking(blocking))
+}