Package: ludic 0.2.0

ludic: Linkage Using Diagnosis Codes

Probabilistic record linkage without direct identifiers using only diagnosis codes. Method is detailed in: Hejblum, Weber, Liao, Palmer, Churchill, Szolovits, Murphy, Kohane & Cai (2019) <doi:10.1038/sdata.2018.298> ; Zhang, Hejblum, Weber, Palmer, Churchill, Szolovits, Murphy, Liao, Kohane & Cai (2021) <doi:10.1101/2021.05.02.21256490>.

Authors:Boris P Hejblum [aut, cre], Harrison G Zhang [aut], Tianxi Cai [aut]

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ludic.pdf |ludic.html✨
ludic/json (API)
NEWS

# Install 'ludic' in R:

install.packages('ludic', repos = c('https://borishejblum.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/borishejblum/ludic/issues

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

Datasets:

RA1_11y - Anonymized binarized diagnosis codes from RA study.
RA1_6y - Anonymized binarized diagnosis codes from RA study.
RA2_11y - Anonymized binarized diagnosis codes from RA study.
RA2_6y - Anonymized binarized diagnosis codes from RA study.
silverstandard_truematches - Anonymized binarized diagnosis codes from RA study.

On CRAN:

19 exports 1.10 score 20 dependencies 1 mentions 12 scripts 1.2k downloads

Last updated 3 years agofrom:92507327e2. Checks:OK: 1 NOTE: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 08 2024
R-4.5-win-x86_64	NOTE	Sep 08 2024
R-4.5-linux-x86_64	NOTE	Sep 08 2024
R-4.4-win-x86_64	NOTE	Sep 08 2024
R-4.4-mac-x86_64	NOTE	Sep 08 2024
R-4.4-mac-aarch64	NOTE	Sep 08 2024
R-4.3-win-x86_64	NOTE	Sep 08 2024
R-4.3-mac-x86_64	NOTE	Sep 08 2024
R-4.3-mac-aarch64	NOTE	Sep 08 2024

Exports:agree_C agree_C_sparse atlas comb_pvals em_winkler em_winkler_big expit expit_dev1 logit loglikC_bin loglikC_bin_wDates loglikratioC_diff_arbitrary matchingScore_C matchingScore_C_sparse_big matchProbs_rank_full_C pval_zscore recordLink strsplitC test_han2018

Dependencies:cvar fastICA fBasics fGarch gbutils gss landpred lattice MASS Matrix rbibutils Rcpp RcppArmadillo Rdpack rootSolve spatial stabledist survival timeDate timeSeries

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
ludic	ludic-package ludic
Fast C++ implementation of agreement vector for the element-wise comparison of 2 matrices	agree_C agree_C_sparse
Association testing by combining several matching thresholds	atlas
Fisher's rule for combining several p-values	comb_pvals
Implementation of Winkler's EM algorithm for Fellegi-Sunter matching method	em_winkler em_winkler_big
C++ implementation of the pseudo-likelihood computation	loglikC_bin loglikC_bin_wDates loglikratioC_diff_arbitrary
Fast C++ computation of the final posterior probabilities in the E-M Winkler's method	matchingScore_C matchingScore_C_sparse_big
Compute the matching probabilities for each pair of observations	matchProbs_rank_full_C
Compute p-values for a Z-score	pval_zscore
Anonymized binarized diagnosis codes from RA study.	RA RA1_11y RA1_6y RA2_11y RA2_6y silverstandard_truematches
Probabilistic Patient Record Linkage	recordLink
Association testing using Han & Lahiri estimating equations and jackknife approach	test_han2018