recordLink: Probabilistic Patient Record Linkage

Description Usage Arguments Details Value References Examples

View source: R/recordLink.R

Description

Probabilistic Patient Record Linkage

Usage

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recordLink(data1, data2, dates1 = NULL, dates2 = NULL, eps_plus, eps_minus,
  aggreg_2ways = "mean", min_prev = 0.01, data1_cont2diff = NULL,
  data2_cont2diff = NULL, d_max, use_diff = TRUE)

Arguments

data1

either a binary (1 or 0 values only) matrix or binary data frame of dimension n1 x K whose rownames are the observation identifiers.

data2

either a binary (1 or 0 values only) matrix or a binary data frame of dimension n2 x K whose rownames are the observation identifiers.

dates1

matrix or dataframe of dimension n1 x K including the concatenated dates intervals for each corresponding diagnosis codes in data1. Default is NULL in which case dates are not used.

dates2

matrix or dataframe of dimension n2 x K including the concatenated dates intervals for each corresponding diagnosis codes in data2. Default is NULL in which case dates are not used. See details.

eps_plus

discrepancy rate between data1 and data2

eps_minus

discrepancy rate between data2 and data1

aggreg_2ways

a character string indicating how to merge the posterior two probability matrices obtained for each of the 2 databases. Four possibility are currently implemented: "maxnorm", "max", "min", "mean" and "prod". Default is "mean".

min_prev

minimum prevalence for the variables used in matching. Default is 1%.

data1_cont2diff

either a matrix or dataframe of continuous features, such as age, for which the similarity measure uses the difference with data2_cont2diff, whose rownames are . Default is NULL.

data2_cont2diff

either a matrix or dataframe of continuous features, such as age, for which the similarity measure uses the difference with data2_cont1diff, whose rownames are . Default is NULL.

d_max

a numeric vector of length K giving the minimum difference from which it is considered a discrepancy.

use_diff

logical flag indicating whether continuous differentiable variables should be used in the

Details

Dates: the use of dates1 and dates2 requires that at least one date interval matches across dates1 and dates2 for claiming an agreement on a diagnosis code between data1 and data2, in addition of having that very same code recorded in both.

Value

a matrix of size n1 x n2 with the posterior probability of matching for each n1*n2 pair

References

Hejblum BP, Weber G, Liao KP, Palmer N, Churchill S, Szolovits P, Murphy S, Kohane I, Cai T Probabilistic Record Linkage of De-Identified Research Datasets Using Diagnosis Codes, submitted, 2017.

Examples

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set.seed(123)
ncodes <- 500
npat <- 200
incid <- abs(rnorm(n=ncodes, 0.15, 0.07))
bin_codes <- rbinom(n=npat*ncodes, size=1,  prob=rep(incid, npat))
bin_codes_mat <- matrix(bin_codes, ncol=ncodes, byrow = TRUE)
data1_ex <- bin_codes_mat[1:(npat/2+npat/10),]
data2_ex <- bin_codes_mat[c(1:(npat/10), (npat/2+npat/10 + 1):npat), ]
rownames(data1_ex) <- paste0("ID", 1:(npat/2+npat/10), "_data1")
rownames(data2_ex) <- paste0("ID", c(1:(npat/10), (npat/2+npat/10 + 1):npat), "_data2")

## Not run: 
res <- recordLink(data1 = data1_ex, data2 = data2_ex, 
                 use_diff = FALSE, eps_minus = 0.01, eps_plus = 0.01)
round(res[c(1:3, 19:23), c(1:3, 19:23)], 3)

## End(Not run)

borishejblum/ludic documentation built on Jan. 30, 2018, 8:38 p.m.