recordLink: Probabilistic Patient Record Linkage

In borishejblum/ludic: Linkage Using Diagnosis Codes

Description

Probabilistic Patient Record Linkage

Usage

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. Columns should be in the same order as in data1.
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 and Cai T, Probabilistic Record Linkage of De-Identified Research Datasets Using Diagnosis Codes, Scientific Data, 6:180298 (2019). doi: 10.1038/sdata.2018.298.

Examples

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")

if(interactive()){
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)
}

borishejblum/ludic documentation built on Aug. 23, 2021, 3:09 p.m.