Estimate the false discovery proportion of a record-linkage method via synthetic augmentation
Source:R/FlexRecordLinkage.r
compute_augmRL_FDP_synth.RdRepeatedly augments file B with synthetic records (synthesise()), runs
the chosen record-linkage method link_with_*, and compares the
synthetic-vs-real proportion among linked pairs to estimate the false
discovery proportion, for a range of score thresholds (0.50 to 0.99).
See https://doi.org/10.1002/sim.70292 for the method.
Usage
compute_augmRL_FDP_synth(
synth_method,
encodedA,
encodedB,
PIVs,
n_synth = NULL,
restrict_support_intersection = TRUE,
maxIter4CV = 10,
n_repeats = 10,
RL_method,
...
)Arguments
- synth_method
Passed to
synthesise():"arf","synthpop", or"mice".- encodedA, encodedB
The two encoded data sources as returned by
prepare_data()(encodedAis the smaller one).- PIVs
Character vector, names of the PIVs.
- n_synth
Integer, number of synthetic records to generate per iteration (default: 10% of
nrow(encodedB)).- restrict_support_intersection
Passed to
synthesise().- maxIter4CV
Integer, max number of retries per iteration if no valid FDP estimate is obtained.
- n_repeats
Integer, number of augmentation iterations to average over.
- RL_method
One of
"multilink","fastLink","BRL","reclin2","diyar","fedmatch","FlexRL".- ...
Extra arguments forwarded to the chosen link_with_* wrapper (i.e. to the underlying record-linkage package).
Value
List with FDP_score_estimator, FDP_synth_estimator,
Linked_pairs_augm, Linked_pairs: data frames (n_repeats rows x 50
thresholds, 0.50 to 0.99), and FDP_score_sd, FDP_synth_sd Numeric,
standard deviations of the corresponding estimators over the n_repeats
iterations per threshold (NA when fewer than two valid repeats are
available).
Examples
PIVs_config <- list( V1 = list(dynamics = "stable",
bound_mistakes = c(0.10,0.10),
fix_mistakes = c(NA,NA)),
V2 = list(dynamics = "stable",
bound_mistakes = c(0.10,0.10),
fix_mistakes = c(NA,NA)),
V3 = list(dynamics = "flexible",
bound_mistakes = c(NA,NA),
fix_mistakes = c(NA,NA)),
V4 = list(dynamics = "structured",
bound_mistakes = c(NA,NA),
fix_mistakes = c(0.03,0.03),
cond_hazard_cov = list(cov1=c("Xe", "Xf"),
cov2=c())) )
n_values <- c( 5, 6, 7, 12 )
p_mistake <- list( V1 = c(0.02, 0.02), V2 = c(0.02, 0.02),
V3 = c(0.05, 0.05), V4 = c(0.02, 0.02) )
p_missing <- list( V1 = c(0.005, 0.005), V2 = c(0.005, 0.005),
V3 = c(0.005, 0.005), V4 = c(0.005, 0.005) )
cond_hazard_params <- list( V1 = c(), V2 = c(),
V3 = c(), V4 = log(c(0.7, 0.6, 0.5)) )
gen_data <- simulate_data( PIVs_config, n_values, c(150, 200), 100,
p_mistake, p_missing, cond_hazard_params, TRUE )
prep_data <- prepare_data( gen_data$data1, gen_data$data2, "1", "2",
PIVs_config, TRUE, "entity_id", TRUE )
#> Warning: PIVs 'V4' and 'V3' are associated (Cramer's V = 0.30 in data1, 0.25 in data2); FlexRL assumes conditional independence between PIVs, consider merging or dropping one.
#> '2' is the larger source, saved as B; '1' saved as A.
PIVs <- names(PIVs_config)
compute_augmRL_FDP_synth( "arf", prep_data$encodedA, prep_data$encodedB, PIVs,
NULL, TRUE, 1, 2, "BRL", flds = PIVs,
types = rep("bi",length(PIVs)) )
#> Iteration: 0, Accuracy: 48.61%
#> Warning: PIV 'V1': synthetic records out of the common support were removed.
#> Warning: PIV 'V2': synthetic records out of the common support were removed.
#> Warning: 1 real records were dropped from file B during synthesis; the real/synthetic index split used by the FDP_synth estimator is invalid for data that was not support-restricted by prepare_data().
#> Iteration: 0, Accuracy: 49.24%
#> Warning: PIV 'V1': synthetic records out of the common support were removed.
#> Warning: PIV 'V3': synthetic records out of the common support were removed.
#> Warning: 1 real records were dropped from file B during synthesis; the real/synthetic index split used by the FDP_synth estimator is invalid for data that was not support-restricted by prepare_data().
#> BRL results (average over 2 iterations) (augmented RL task) `compute_augmRL_FDP_synth`
#> Decision rule threshold 0.5 0.55 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95
#> FDP model score estimator (mean) 0.17 0.16 0.16 0.16 0.16 0.16 0.15 0.13 0.1 0
#> FDP model score estimator (sd) 0 0 0 0 0 0 0 0 0 0
#> FDP synth data estimator (mean) 0.1 0 0 0 0 0 0 0 0 0
#> FDP synth data estimator (sd) 0.14 0 0 0 0 0 0 0 0 0
#> Linked pairs (augm. RL) 56 54 54 54 54 54 44 22 1 0
#> Linked pairs (RL) 56 54 54 54 54 54 44 22 1 0
#> $FDP_score_estimator
#> 0.50 0.51 0.52 0.53 0.54 0.55 0.56
#> 1 0.1674343 0.1674343 0.1674343 0.1616667 0.1616667 0.1616667 0.1616667
#> 2 0.1724951 0.1607677 0.1607677 0.1607677 0.1607677 0.1607677 0.1607677
#> 0.57 0.58 0.59 0.60 0.61 0.62 0.63
#> 1 0.1616667 0.1616667 0.1616667 0.1616667 0.1616667 0.1616667 0.1616667
#> 2 0.1607677 0.1607677 0.1607677 0.1607677 0.1607677 0.1607677 0.1607677
#> 0.64 0.65 0.66 0.67 0.68 0.69 0.70
#> 1 0.1616667 0.1616667 0.1616667 0.1616667 0.1616667 0.1616667 0.1616667
#> 2 0.1607677 0.1607677 0.1607677 0.1607677 0.1607677 0.1607677 0.1607677
#> 0.71 0.72 0.73 0.74 0.75 0.76 0.77
#> 1 0.1616667 0.1616667 0.1616667 0.1616667 0.1616667 0.1584829 0.1569935
#> 2 0.1607677 0.1607677 0.1607677 0.1607677 0.1607677 0.1607677 0.1581132
#> 0.78 0.79 0.80 0.81 0.82 0.83 0.84
#> 1 0.1541270 0.1529398 0.1469251 0.1469251 0.1431339 0.1377778 0.1340613
#> 2 0.1555556 0.1519213 0.1495411 0.1473990 0.1438889 0.1385948 0.1306838
#> 0.85 0.86 0.87 0.88 0.89 0.90 0.91 0.92 0.93
#> 1 0.1285507 0.1208889 0.1142222 0.1113889 0.1027778 0.09888889 0 0 0
#> 2 0.1248148 0.1193056 0.1121212 0.1076389 0.1035556 0.09444444 0 0 0
#> 0.94 0.95 0.96 0.97 0.98 0.99
#> 1 0 0 0 0 0 0
#> 2 0 0 0 0 0 0
#>
#> $FDP_synth_estimator
#> 0.50 0.51 0.52 0.53 0.54 0.55 0.56 0.57 0.58 0.59 0.60 0.61
#> 1 0.1949318 0.1949318 0.1949318 0 0 0 0 0 0 0 0 0
#> 2 0.0000000 0.0000000 0.0000000 0 0 0 0 0 0 0 0 0
#> 0.62 0.63 0.64 0.65 0.66 0.67 0.68 0.69 0.70 0.71 0.72 0.73 0.74 0.75 0.76
#> 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> 0.77 0.78 0.79 0.80 0.81 0.82 0.83 0.84 0.85 0.86 0.87 0.88 0.89 0.90 0.91
#> 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> 0.92 0.93 0.94 0.95 0.96 0.97 0.98 0.99
#> 1 0 0 0 0 0 0 0 0
#> 2 0 0 0 0 0 0 0 0
#>
#> $FDP_score_sd
#> 0.50 0.51 0.52 0.53 0.54 0.55
#> 0.0035785142 0.0047140452 0.0047140452 0.0006356819 0.0006356819 0.0006356819
#> 0.56 0.57 0.58 0.59 0.60 0.61
#> 0.0006356819 0.0006356819 0.0006356819 0.0006356819 0.0006356819 0.0006356819
#> 0.62 0.63 0.64 0.65 0.66 0.67
#> 0.0006356819 0.0006356819 0.0006356819 0.0006356819 0.0006356819 0.0006356819
#> 0.68 0.69 0.70 0.71 0.72 0.73
#> 0.0006356819 0.0006356819 0.0006356819 0.0006356819 0.0006356819 0.0006356819
#> 0.74 0.75 0.76 0.77 0.78 0.79
#> 0.0006356819 0.0006356819 0.0016155769 0.0007917782 0.0010101525 0.0007202014
#> 0.80 0.81 0.82 0.83 0.84 0.85
#> 0.0018497901 0.0003351158 0.0005338555 0.0005777016 0.0023882829 0.0026416872
#> 0.86 0.87 0.88 0.89 0.90 0.91
#> 0.0011195857 0.0014856385 0.0026516504 0.0005499719 0.0031426968 0.0000000000
#> 0.92 0.93 0.94 0.95 0.96 0.97
#> 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
#> 0.98 0.99
#> 0.0000000000 0.0000000000
#>
#> $FDP_synth_sd
#> 0.50 0.51 0.52 0.53 0.54 0.55 0.56 0.57
#> 0.1378376 0.1378376 0.1378376 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
#> 0.58 0.59 0.60 0.61 0.62 0.63 0.64 0.65
#> 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
#> 0.66 0.67 0.68 0.69 0.70 0.71 0.72 0.73
#> 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
#> 0.74 0.75 0.76 0.77 0.78 0.79 0.80 0.81
#> 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
#> 0.82 0.83 0.84 0.85 0.86 0.87 0.88 0.89
#> 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
#> 0.90 0.91 0.92 0.93 0.94 0.95 0.96 0.97
#> 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
#> 0.98 0.99
#> 0.0000000 0.0000000
#>
#> $Linked_pairs_augm
#> 0.50 0.51 0.52 0.53 0.54 0.55 0.56 0.57 0.58 0.59 0.60 0.61 0.62 0.63 0.64
#> 1 54 54 54 54 54 54 54 54 54 54 54 54 54 54 54
#> 2 57 55 55 55 55 55 55 55 55 55 55 55 55 55 55
#> 0.65 0.66 0.67 0.68 0.69 0.70 0.71 0.72 0.73 0.74 0.75 0.76 0.77 0.78 0.79
#> 1 54 54 54 54 54 54 54 54 54 54 54 52 51 49 48
#> 2 55 55 55 55 55 55 55 55 55 55 55 55 53 51 48
#> 0.80 0.81 0.82 0.83 0.84 0.85 0.86 0.87 0.88 0.89 0.90 0.91 0.92 0.93 0.94
#> 1 43 43 39 33 29 23 15 10 8 2 1 0 0 0 0
#> 2 46 44 40 34 26 21 16 11 8 5 1 0 0 0 0
#> 0.95 0.96 0.97 0.98 0.99
#> 1 0 0 0 0 0
#> 2 0 0 0 0 0
#>
#> $Linked_pairs
#> 0.50 0.51 0.52 0.53 0.54 0.55 0.56 0.57 0.58 0.59 0.60 0.61 0.62 0.63 0.64
#> 1 55 55 55 54 54 54 54 54 54 54 54 54 54 54 54
#> 2 57 55 55 55 55 55 55 55 55 55 55 55 55 55 55
#> 0.65 0.66 0.67 0.68 0.69 0.70 0.71 0.72 0.73 0.74 0.75 0.76 0.77 0.78 0.79
#> 1 54 54 54 54 54 54 54 54 54 54 54 52 51 49 48
#> 2 55 55 55 55 55 55 55 55 55 55 55 55 53 51 48
#> 0.80 0.81 0.82 0.83 0.84 0.85 0.86 0.87 0.88 0.89 0.90 0.91 0.92 0.93 0.94
#> 1 43 43 39 33 29 23 15 10 8 2 1 0 0 0 0
#> 2 46 44 40 34 26 21 16 11 8 5 1 0 0 0 0
#> 0.95 0.96 0.97 0.98 0.99
#> 1 0 0 0 0 0
#> 2 0 0 0 0 0
#>
compute_augmRL_FDP_synth( "arf", prep_data$encodedA, prep_data$encodedB, PIVs,
NULL, TRUE, 1, 2, "FlexRL", data = prep_data,
StEM_iter = 5, StEM_burnin = 2,
gibbs_iter = 5, gibbs_burnin = 2, n_post_sample = 5 )
#> Iteration: 0, Accuracy: 49.24%
#> Warning: PIV 'V1': synthetic records out of the common support were removed.
#> Warning: PIV 'V3': synthetic records out of the common support were removed.
#> Warning: 1 real records were dropped from file B during synthesis; the real/synthetic index split used by the FDP_synth estimator is invalid for data that was not support-restricted by prepare_data().
#> FlexRL
#> Iteration: 0, Accuracy: 48.1%
#> Warning: PIV 'V1': synthetic records out of the common support were removed.
#> Warning: PIV 'V2': synthetic records out of the common support were removed.
#> Warning: PIV 'V3': synthetic records out of the common support were removed.
#> Warning: PIV 'V4': synthetic records out of the common support were removed.
#> Warning: 1 real records were dropped from file B during synthesis; the real/synthetic index split used by the FDP_synth estimator is invalid for data that was not support-restricted by prepare_data().
#> FlexRL
#> FlexRL results (average over 2 iterations) (augmented RL task) `compute_augmRL_FDP_synth`
#> Decision rule threshold 0.5 0.55 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95
#> FDP model score estimator (mean) 0.11 0.11 0.05 0.05 0.05 0.05 0 0 0 0
#> FDP model score estimator (sd) 0.02 0.02 0.02 0.02 0.02 0.02 0 0 0 0
#> FDP synth data estimator (mean) 0.52 0.52 0.63 0.63 0.63 0.63 0.88 0.88 0.88 0.88
#> FDP synth data estimator (sd) 0.08 0.08 0.12 0.12 0.12 0.12 0.28 0.28 0.28 0.28
#> Linked pairs (augm. RL) 88 88 72 72 72 72 54 54 54 54
#> Linked pairs (RL) 92 92 76 76 76 76 58 58 58 58
#> $FDP_score_estimator
#> 0.50 0.51 0.52 0.53 0.54 0.55 0.56
#> 1 0.12467532 0.12467532 0.12467532 0.12467532 0.12467532 0.12467532 0.12467532
#> 2 0.09245283 0.09245283 0.09245283 0.09245283 0.09245283 0.09245283 0.09245283
#> 0.57 0.58 0.59 0.60 0.61 0.62 0.63
#> 1 0.12467532 0.12467532 0.12467532 0.06349206 0.06349206 0.06349206 0.06349206
#> 2 0.09245283 0.09245283 0.09245283 0.03777778 0.03777778 0.03777778 0.03777778
#> 0.64 0.65 0.66 0.67 0.68 0.69 0.70
#> 1 0.06349206 0.06349206 0.06349206 0.06349206 0.06349206 0.06349206 0.06349206
#> 2 0.03777778 0.03777778 0.03777778 0.03777778 0.03777778 0.03777778 0.03777778
#> 0.71 0.72 0.73 0.74 0.75 0.76 0.77
#> 1 0.06349206 0.06349206 0.06349206 0.06349206 0.06349206 0.06349206 0.06349206
#> 2 0.03777778 0.03777778 0.03777778 0.03777778 0.03777778 0.03777778 0.03777778
#> 0.78 0.79 0.80 0.81 0.82 0.83 0.84 0.85 0.86 0.87 0.88 0.89 0.90
#> 1 0.06349206 0.06349206 0 0 0 0 0 0 0 0 0 0 0
#> 2 0.03777778 0.03777778 0 0 0 0 0 0 0 0 0 0 0
#> 0.91 0.92 0.93 0.94 0.95 0.96 0.97 0.98 0.99
#> 1 0 0 0 0 0 0 0 0 0
#> 2 0 0 0 0 0 0 0 0 0
#>
#> $FDP_synth_estimator
#> 0.50 0.51 0.52 0.53 0.54 0.55 0.56
#> 1 0.5767844 0.5767844 0.5767844 0.5767844 0.5767844 0.5767844 0.5767844
#> 2 0.4613610 0.4613610 0.4613610 0.4613610 0.4613610 0.4613610 0.4613610
#> 0.57 0.58 0.59 0.60 0.61 0.62 0.63
#> 1 0.5767844 0.5767844 0.5767844 0.7136485 0.7136485 0.7136485 0.7136485
#> 2 0.4613610 0.4613610 0.4613610 0.5471956 0.5471956 0.5471956 0.5471956
#> 0.64 0.65 0.66 0.67 0.68 0.69 0.70
#> 1 0.7136485 0.7136485 0.7136485 0.7136485 0.7136485 0.7136485 0.7136485
#> 2 0.5471956 0.5471956 0.5471956 0.5471956 0.5471956 0.5471956 0.5471956
#> 0.71 0.72 0.73 0.74 0.75 0.76 0.77
#> 1 0.7136485 0.7136485 0.7136485 0.7136485 0.7136485 0.7136485 0.7136485
#> 2 0.5471956 0.5471956 0.5471956 0.5471956 0.5471956 0.5471956 0.5471956
#> 0.78 0.79 0.80 0.81 0.82 0.83 0.84
#> 1 0.7136485 0.7136485 1.0796221 1.0796221 1.0796221 1.0796221 1.0796221
#> 2 0.5471956 0.5471956 0.6820119 0.6820119 0.6820119 0.6820119 0.6820119
#> 0.85 0.86 0.87 0.88 0.89 0.90 0.91
#> 1 1.0796221 1.0796221 1.0796221 1.0796221 1.0796221 1.0796221 1.0796221
#> 2 0.6820119 0.6820119 0.6820119 0.6820119 0.6820119 0.6820119 0.6820119
#> 0.92 0.93 0.94 0.95 0.96 0.97 0.98
#> 1 1.0796221 1.0796221 1.0796221 1.0796221 1.0796221 1.0796221 1.0796221
#> 2 0.6820119 0.6820119 0.6820119 0.6820119 0.6820119 0.6820119 0.6820119
#> 0.99
#> 1 1.0796221
#> 2 0.6820119
#>
#> $FDP_score_sd
#> 0.50 0.51 0.52 0.53 0.54 0.55 0.56
#> 0.02278474 0.02278474 0.02278474 0.02278474 0.02278474 0.02278474 0.02278474
#> 0.57 0.58 0.59 0.60 0.61 0.62 0.63
#> 0.02278474 0.02278474 0.02278474 0.01818275 0.01818275 0.01818275 0.01818275
#> 0.64 0.65 0.66 0.67 0.68 0.69 0.70
#> 0.01818275 0.01818275 0.01818275 0.01818275 0.01818275 0.01818275 0.01818275
#> 0.71 0.72 0.73 0.74 0.75 0.76 0.77
#> 0.01818275 0.01818275 0.01818275 0.01818275 0.01818275 0.01818275 0.01818275
#> 0.78 0.79 0.80 0.81 0.82 0.83 0.84
#> 0.01818275 0.01818275 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> 0.85 0.86 0.87 0.88 0.89 0.90 0.91
#> 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> 0.92 0.93 0.94 0.95 0.96 0.97 0.98
#> 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
#> 0.99
#> 0.00000000
#>
#> $FDP_synth_sd
#> 0.50 0.51 0.52 0.53 0.54 0.55 0.56
#> 0.08161668 0.08161668 0.08161668 0.08161668 0.08161668 0.08161668 0.08161668
#> 0.57 0.58 0.59 0.60 0.61 0.62 0.63
#> 0.08161668 0.08161668 0.08161668 0.11769998 0.11769998 0.11769998 0.11769998
#> 0.64 0.65 0.66 0.67 0.68 0.69 0.70
#> 0.11769998 0.11769998 0.11769998 0.11769998 0.11769998 0.11769998 0.11769998
#> 0.71 0.72 0.73 0.74 0.75 0.76 0.77
#> 0.11769998 0.11769998 0.11769998 0.11769998 0.11769998 0.11769998 0.11769998
#> 0.78 0.79 0.80 0.81 0.82 0.83 0.84
#> 0.11769998 0.11769998 0.28115287 0.28115287 0.28115287 0.28115287 0.28115287
#> 0.85 0.86 0.87 0.88 0.89 0.90 0.91
#> 0.28115287 0.28115287 0.28115287 0.28115287 0.28115287 0.28115287 0.28115287
#> 0.92 0.93 0.94 0.95 0.96 0.97 0.98
#> 0.28115287 0.28115287 0.28115287 0.28115287 0.28115287 0.28115287 0.28115287
#> 0.99
#> 0.28115287
#>
#> $Linked_pairs_augm
#> 0.50 0.51 0.52 0.53 0.54 0.55 0.56 0.57 0.58 0.59 0.60 0.61 0.62 0.63 0.64
#> 1 73 73 73 73 73 73 73 73 73 73 59 59 59 59 59
#> 2 102 102 102 102 102 102 102 102 102 102 86 86 86 86 86
#> 0.65 0.66 0.67 0.68 0.69 0.70 0.71 0.72 0.73 0.74 0.75 0.76 0.77 0.78 0.79
#> 1 59 59 59 59 59 59 59 59 59 59 59 59 59 59 59
#> 2 86 86 86 86 86 86 86 86 86 86 86 86 86 86 86
#> 0.80 0.81 0.82 0.83 0.84 0.85 0.86 0.87 0.88 0.89 0.90 0.91 0.92 0.93 0.94
#> 1 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39
#> 2 69 69 69 69 69 69 69 69 69 69 69 69 69 69 69
#> 0.95 0.96 0.97 0.98 0.99
#> 1 39 39 39 39 39
#> 2 69 69 69 69 69
#>
#> $Linked_pairs
#> 0.50 0.51 0.52 0.53 0.54 0.55 0.56 0.57 0.58 0.59 0.60 0.61 0.62 0.63 0.64
#> 1 77 77 77 77 77 77 77 77 77 77 63 63 63 63 63
#> 2 106 106 106 106 106 106 106 106 106 106 90 90 90 90 90
#> 0.65 0.66 0.67 0.68 0.69 0.70 0.71 0.72 0.73 0.74 0.75 0.76 0.77 0.78 0.79
#> 1 63 63 63 63 63 63 63 63 63 63 63 63 63 63 63
#> 2 90 90 90 90 90 90 90 90 90 90 90 90 90 90 90
#> 0.80 0.81 0.82 0.83 0.84 0.85 0.86 0.87 0.88 0.89 0.90 0.91 0.92 0.93 0.94
#> 1 43 43 43 43 43 43 43 43 43 43 43 43 43 43 43
#> 2 73 73 73 73 73 73 73 73 73 73 73 73 73 73 73
#> 0.95 0.96 0.97 0.98 0.99
#> 1 43 43 43 43 43
#> 2 73 73 73 73 73
#>