We present a small example from "Entity Resolution with Emprically Motivated Priors", Bayesian Analysis, (10),4:849-975. We will be using the RecordLinkage package in R and the RLdata500 data set.

The blink package removes duplicate entries from multiple databases using the method outlined in the paper above. We illustrate an example of using this package using a German dataset comprised of first and last name and full date of birth.

Our goals include

- Presenting the RLdata500 dataset with summary information.
- Illustrating how we can format the RLdata500 dataset to work with the blink package
- Examples for setting the tuning parameters for blink
- Running the Gibbs sampler in blink
- Illustrating a few plots and sample output

The RLdata500 dataset exists already in the RecordLinkage package in R. We review this data set for the user.

The RLdata500 data consists of 500 records with 10 percent duplication. Thus, there are 450 unique individuals. There is full information on each record containing first name, last name, and full date of birth.

We first load the Record Linkgae package and load the RLdata500 data set. We also, provide the first few lines of the data.

library(blink) data(RLdata500) head(RLdata500)

Next, we prepare the data for working with the blink package. The methods assume that at least one variable is a categorical variable and one is a string variable. To proceed, we treat first and last name as string variables and full date of birth as the categorical variables.

# X.c contains the categorical variables # X.s contains the string variables # p.c is the number of categorical variables # p.s contains the number of string variables X.c <- RLdata500[c("by","bm","bd")] X.c <- as.matrix(RLdata500[,"bd"],ncol=1) p.c <- ncol(X.c) X.s <- as.matrix(RLdata500[-c(2,4,7)]) p.s <- ncol(X.s)

Now, we give a small example for setting the tuning parameters before running the Gibbs sampler. The details regarding our recommendations can be found in the aforementioned referenced paper.

First, we work with a file number identifier.

# File number identifier # Note: Recall that X.c and X.s include all files "stacked" on top of each other. # The vector below keeps track of which rows of X.c and X.s are in which files. file.num <- rep(c(1,2,3),c(200,150,150))

Next, we work with the parameters that tune the prior on the amount of distortion that goes into the model. (This corresponds to the parameters of a Beta(a,b) distribution.)

# Subjective choices for distortion probability prior a <-1 b <- 999

Then we write a function for the Edit distance between two strings. Other distance functions could be used, such as Jaro-Winkler. Sensitivity of this distance function is discussed in the aforementioned paper.

d <- function(string1,string2){adist(string1,string2)}

For the steepness parameter, we recommend

c <- 1

We now run a test version of the Gibbs sampler using blink, with 10 Gibbs iterations and a maximum size of M=500 (assuming the overall known population size is 500). Note that this is a toy test and one should note that the Gibbs sampler has failed to converged at this point, which should not be suprising.

lam.gs <- rl.gibbs(file.num=file.num,X.s=X.s,X.c=X.c,num.gs=2,a=a,b=b,c=c,d=d, M=500)

Let's read in the estimate linkage structure using 10 Gibbs iterations.

estLink <- lam.gs estPopSize <- apply(estLink , 1, function(x) {length(unique(x))}) plot(density(estPopSize),xlim=c(300,500),main="",lty=1, "Observed Population Size", ylim= c(0,1)) abline(v=450,col="red") abline(v=mean(estPopSize),col="black",lty=2) mean(estPopSize) sd(estPopSize)

Next, we illustrate an example of what we did in the paper for this dataset. Show the same example, show the error rates, show the comparisons with other methods. Show convergence rates.

We have run the Gibbs sampler for approximately 100,000 iterations and read in the output. (If you run this on your own, please do this on a server and not on a laptop since the convergence of this data set is slow due to this particular data set.)

temp <- unzip("../inst/extdata/sampleLinkage2.txt.zip") estLink <- as.matrix(read.table(temp,header=TRUE)) dim(estLink) estPopSize <- apply(estLink , 1, function(x) {length(unique(x))}) plot(density(estPopSize),xlim=c(300,500),main="",lty=1, "Observed Population Size", ylim= c(0,1)) abline(v=450,col="red") abline(v=mean(estPopSize),col="black",lty=2) mean(estPopSize) sd(estPopSize)

Let us now consider the error rates (false negative rate and false positive rate), which are defined in the paper.

# let's calculated the estimated pairwise links # using the blink method est.links.pair <- links(estLink[85000:90000,]) # let's calulated the true links using the # unique identifiers that are stored true.links <- links(matrix(identity.RLdata500,nrow=1)) true.links.pair <- pairwise(true.links) # Correct, incorrect, and missing links comparison <- links.compare(est.links.pair,true.links.pair,counts.only=TRUE) comparison missing.links <- comparison$missing true.links<-comparison$correct false.links <- comparison$incorrect truth.links <- true.links+false.links fpr = false.links/truth.links fnr = missing.links/truth.links fdr = false.links/(true.links+false.links) c(fpr,fnr,fdr)

**Any scripts or data that you put into this service are public.**

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.