doConcrete
Arguments
- ConcreteArgs
"ConcreteArgs" object : output of formatArguments()
- x
a ConcreteOut object
- ...
additional arguments to be passed into print methods
- convergence
logical: plot the PnEIC norms for each TMLE small update step
- gweights
logical: plot the densities of the intervention-related nuisance weights for each intervention
- ask
logical: whether or not to prompt for user input before displaying plots
Value
Object with S3 class "ConcreteEst". The fitted object stores TMLE
convergence metadata, including the stopping rule, update trace, and empirical
EIC norm trajectory. Use getTmleDiagnostics() to inspect these diagnostics.
Functions
print(ConcreteEst): print.ConcreteEst print method for "ConcreteEst" classplot(ConcreteEst): plot.ConcreteEst plot method for "ConcreteEst" classprint(ConcreteOut): print.ConcreteOut print method for "ConcreteOut" class
Examples
library(data.table)
library(concrete)
data <- as.data.table(survival::pbc)
data <- data[1:200, .SD, .SDcols = c("id", "time", "status", "trt", "age", "sex")]
data[, trt := sample(0:1, nrow(data), TRUE)]
#> id time status trt age sex
#> <int> <int> <int> <int> <num> <fctr>
#> 1: 1 400 2 0 58.76523 f
#> 2: 2 4500 0 0 56.44627 f
#> 3: 3 1012 2 0 70.07255 m
#> 4: 4 1925 2 0 54.74059 f
#> 5: 5 1504 1 0 38.10541 f
#> ---
#> 196: 196 2363 0 0 57.04038 f
#> 197: 197 2365 0 1 44.62697 f
#> 198: 198 2357 0 1 35.79740 f
#> 199: 199 1592 0 1 40.71732 f
#> 200: 200 2318 0 1 32.23272 f
# formatArguments() returns correctly formatted arguments for doConcrete()
concrete.args <- formatArguments(DataTable = data,
EventTime = "time",
EventType = "status",
Treatment = "trt",
ID = "id",
TargetTime = 2500,
TargetEvent = c(1, 2),
Intervention = makeITT(),
CVArg = list(V = 2))
# doConcrete() returns tmle (and g-formula plug-in) estimates of targeted risks
concrete.est <- doConcrete(concrete.args)
#>
#> Estimating Treatment Propensity:
#>
#> Estimating Hazards:
#> Warning: Loglik converged before variable 1,3 ; coefficient may be infinite.
#> Warning: Loglik converged before variable 3 ; coefficient may be infinite.
#> Trt Time Event PnEIC RelativeCriteria AbsPnEIC
#> <char> <num> <num> <num> <num> <num>
#> 1: A=1 2500 1 -0.007503576 0.001668183 0.007503576
#> 2: A=0 2500 1 0.012855822 0.004800477 0.012855822
#> 3: A=1 2500 2 -0.003757434 0.008589528 0.003757434
#> AbsoluteCriteria StopCriteria RelativeRatio AbsoluteRatio ratio StopRule
#> <num> <num> <num> <num> <num> <char>
#> 1: 0 0.001668183 4.4980545 Inf 4.50 relative
#> 2: 0 0.004800477 2.6780301 Inf 2.68 relative
#> 3: 0 0.008589528 0.4374436 Inf 0.44 relative
#> StopAbsTol
#> <num>
#> 1: 0
#> 2: 0
#> 3: 0
#> Norm PnEIC = 0.01557269
#>
#> Starting TMLE Update:
#> Problem dimension: k = 4
#> Using standard universal LFM approach (iterative small steps)
#> Starting step 1 with update epsilon = 0.1
#> Trt Time Event PnEIC RelativeCriteria AbsPnEIC
#> <char> <num> <num> <num> <num> <num>
#> 1: A=1 2500 1 -0.006298007 0.001666380 0.006298007
#> 2: A=0 2500 2 0.008705936 0.009176792 0.008705936
#> 3: A=0 2500 1 0.003574282 0.004787829 0.003574282
#> AbsoluteCriteria StopCriteria RelativeRatio AbsoluteRatio ratio StopRule
#> <num> <num> <num> <num> <num> <char>
#> 1: 0 0.001666380 3.7794531 Inf 3.78 relative
#> 2: 0 0.009176792 0.9486906 Inf 0.95 relative
#> 3: 0 0.004787829 0.7465350 Inf 0.75 relative
#> StopAbsTol
#> <num>
#> 1: 0
#> 2: 0
#> 3: 0
#> Norm PnEIC = 0.01267847
#> Starting step 2 with update epsilon = 0.1
#> Update increased the active convergence objective, halving OneStepEps
#> Starting step 2 with update epsilon = 0.05
#> Trt Time Event PnEIC RelativeCriteria AbsPnEIC
#> <char> <num> <num> <num> <num> <num>
#> 1: A=1 2500 1 -0.005369281 0.001665150 0.005369281
#> 2: A=0 2500 2 -0.007152786 0.009186461 0.007152786
#> 3: A=0 2500 1 0.003644437 0.004788008 0.003644437
#> AbsoluteCriteria StopCriteria RelativeRatio AbsoluteRatio ratio StopRule
#> <num> <num> <num> <num> <num> <char>
#> 1: 0 0.001665150 3.2245029 Inf 3.22 relative
#> 2: 0 0.009186461 0.7786226 Inf 0.78 relative
#> 3: 0 0.004788008 0.7611593 Inf 0.76 relative
#> StopAbsTol
#> <num>
#> 1: 0
#> 2: 0
#> 3: 0
#> Norm PnEIC = 0.01043122
#> Starting step 3 with update epsilon = 0.05
#> Update increased the active convergence objective, halving OneStepEps
#> Starting step 3 with update epsilon = 0.025
#> Trt Time Event PnEIC RelativeCriteria AbsPnEIC
#> <char> <num> <num> <num> <num> <num>
#> 1: A=1 2500 1 -0.005110785 0.001664829 0.005110785
#> 2: A=0 2500 1 0.001794214 0.004785959 0.001794214
#> 3: A=0 2500 2 0.001459226 0.009180357 0.001459226
#> AbsoluteCriteria StopCriteria RelativeRatio AbsoluteRatio ratio StopRule
#> <num> <num> <num> <num> <num> <char>
#> 1: 0 0.001664829 3.0698555 Inf 3.07 relative
#> 2: 0 0.004785959 0.3748912 Inf 0.37 relative
#> 3: 0 0.009180357 0.1589509 Inf 0.16 relative
#> StopAbsTol
#> <num>
#> 1: 0
#> 2: 0
#> 3: 0
#> Norm PnEIC = 0.005611189
#> Starting step 4 with update epsilon = 0.025
#> Trt Time Event PnEIC RelativeCriteria AbsPnEIC
#> <char> <num> <num> <num> <num> <num>
#> 1: A=1 2500 1 -0.004516020 0.001664131 0.004516020
#> 2: A=0 2500 1 0.001183582 0.004785364 0.001183582
#> 3: A=0 2500 2 -0.001255921 0.009182059 0.001255921
#> AbsoluteCriteria StopCriteria RelativeRatio AbsoluteRatio ratio StopRule
#> <num> <num> <num> <num> <num> <char>
#> 1: 0 0.001664131 2.7137400 Inf 2.71 relative
#> 2: 0 0.004785364 0.2473337 Inf 0.25 relative
#> 3: 0 0.009182059 0.1367799 Inf 0.14 relative
#> StopAbsTol
#> <num>
#> 1: 0
#> 2: 0
#> 3: 0
#> Norm PnEIC = 0.004835683
#> Starting step 5 with update epsilon = 0.025
#> Trt Time Event PnEIC RelativeCriteria AbsPnEIC
#> <char> <num> <num> <num> <num> <num>
#> 1: A=1 2500 1 -0.003932219 0.001663499 0.003932219
#> 2: A=0 2500 2 0.002154573 0.009179947 0.002154573
#> 3: A=0 2500 1 0.000125501 0.004784312 0.000125501
#> AbsoluteCriteria StopCriteria RelativeRatio AbsoluteRatio ratio StopRule
#> <num> <num> <num> <num> <num> <char>
#> 1: 0 0.001663499 2.36382404 Inf 2.36 relative
#> 2: 0 0.009179947 0.23470435 Inf 0.23 relative
#> 3: 0 0.004784312 0.02623178 Inf 0.03 relative
#> StopAbsTol
#> <num>
#> 1: 0
#> 2: 0
#> 3: 0
#> Norm PnEIC = 0.004486477
#> Starting step 6 with update epsilon = 0.025
#> Update increased the active convergence objective, halving OneStepEps
#> Starting step 6 with update epsilon = 0.0125
#> Trt Time Event PnEIC RelativeCriteria AbsPnEIC
#> <char> <num> <num> <num> <num> <num>
#> 1: A=1 2500 1 -0.0036671302 0.001663229 0.0036671302
#> 2: A=0 2500 1 0.0003914089 0.004784588 0.0003914089
#> 3: A=0 2500 2 -0.0007021947 0.009181692 0.0007021947
#> AbsoluteCriteria StopCriteria RelativeRatio AbsoluteRatio ratio StopRule
#> <num> <num> <num> <num> <num> <char>
#> 1: 0 0.001663229 2.20482604 Inf 2.20 relative
#> 2: 0 0.004784588 0.08180618 Inf 0.08 relative
#> 3: 0 0.009181692 0.07647771 Inf 0.08 relative
#> StopAbsTol
#> <num>
#> 1: 0
#> 2: 0
#> 3: 0
#> Norm PnEIC = 0.003755086
#> Starting step 7 with update epsilon = 0.0125
#> Trt Time Event PnEIC RelativeCriteria AbsPnEIC
#> <char> <num> <num> <num> <num> <num>
#> 1: A=1 2500 1 -0.0033781711 0.001662947 0.0033781711
#> 2: A=0 2500 2 0.0004825112 0.009180940 0.0004825112
#> 3: A=0 2500 1 0.0001154230 0.004784317 0.0001154230
#> AbsoluteCriteria StopCriteria RelativeRatio AbsoluteRatio ratio StopRule
#> <num> <num> <num> <num> <num> <char>
#> 1: 0 0.001662947 2.03143684 Inf 2.03 relative
#> 2: 0 0.009180940 0.05255575 Inf 0.05 relative
#> 3: 0 0.004784317 0.02412527 Inf 0.02 relative
#> StopAbsTol
#> <num>
#> 1: 0
#> 2: 0
#> 3: 0
#> Norm PnEIC = 0.003415184
#> Starting step 8 with update epsilon = 0.0125
#> Trt Time Event PnEIC RelativeCriteria AbsPnEIC
#> <char> <num> <num> <num> <num> <num>
#> 1: A=1 2500 1 -0.0030922760 0.001662680 0.0030922760
#> 2: A=0 2500 2 -0.0003410745 0.009181458 0.0003410745
#> 3: A=0 2500 1 0.0001555877 0.004784362 0.0001555877
#> AbsoluteCriteria StopCriteria RelativeRatio AbsoluteRatio ratio StopRule
#> <num> <num> <num> <num> <num> <char>
#> 1: 0 0.001662680 1.85981418 Inf 1.86 relative
#> 2: 0 0.009181458 0.03714819 Inf 0.04 relative
#> 3: 0 0.004784362 0.03252006 Inf 0.03 relative
#> StopAbsTol
#> <num>
#> 1: 0
#> 2: 0
#> 3: 0
#> Norm PnEIC = 0.003115591
#> Starting step 9 with update epsilon = 0.0125
#> Trt Time Event PnEIC RelativeCriteria AbsPnEIC
#> <char> <num> <num> <num> <num> <num>
#> 1: A=1 2500 1 -2.812110e-03 0.001662431 2.812110e-03
#> 2: A=0 2500 2 3.455930e-04 0.009181024 3.455930e-04
#> 3: A=1 2500 2 -5.741848e-05 0.008589298 5.741848e-05
#> AbsoluteCriteria StopCriteria RelativeRatio AbsoluteRatio ratio StopRule
#> <num> <num> <num> <num> <num> <char>
#> 1: 0 0.001662431 1.691565067 Inf 1.69 relative
#> 2: 0 0.009181024 0.037642100 Inf 0.04 relative
#> 3: 0 0.008589298 0.006684886 Inf 0.01 relative
#> StopAbsTol
#> <num>
#> 1: 0
#> 2: 0
#> 3: 0
#> Norm PnEIC = 0.002833866
#> Starting step 10 with update epsilon = 0.0125
#> Trt Time Event PnEIC RelativeCriteria AbsPnEIC
#> <char> <num> <num> <num> <num> <num>
#> 1: A=1 2500 1 -2.538560e-03 0.001662199 2.538560e-03
#> 2: A=0 2500 2 -3.817379e-04 0.009181484 3.817379e-04
#> 3: A=0 2500 1 8.334083e-05 0.004784295 8.334083e-05
#> AbsoluteCriteria StopCriteria RelativeRatio AbsoluteRatio ratio StopRule
#> <num> <num> <num> <num> <num> <char>
#> 1: 0 0.001662199 1.52722948 Inf 1.53 relative
#> 2: 0 0.009181484 0.04157693 Inf 0.04 relative
#> 3: 0 0.004784295 0.01741967 Inf 0.02 relative
#> StopAbsTol
#> <num>
#> 1: 0
#> 2: 0
#> 3: 0
#> Norm PnEIC = 0.002568949
#> Starting step 11 with update epsilon = 0.0125
#> Trt Time Event PnEIC RelativeCriteria AbsPnEIC
#> <char> <num> <num> <num> <num> <num>
#> 1: A=1 2500 1 -2.272520e-03 0.001661985 2.272520e-03
#> 2: A=0 2500 2 5.274996e-04 0.009180912 5.274996e-04
#> 3: A=1 2500 2 -4.399059e-05 0.008589296 4.399059e-05
#> AbsoluteCriteria StopCriteria RelativeRatio AbsoluteRatio ratio StopRule
#> <num> <num> <num> <num> <num> <char>
#> 1: 0 0.001661985 1.367352909 Inf 1.37 relative
#> 2: 0 0.009180912 0.057456127 Inf 0.06 relative
#> 3: 0 0.008589296 0.005121559 Inf 0.01 relative
#> StopAbsTol
#> <num>
#> 1: 0
#> 2: 0
#> 3: 0
#> Norm PnEIC = 0.002334154
#> Starting step 12 with update epsilon = 0.0125
#> Trt Time Event PnEIC RelativeCriteria AbsPnEIC
#> <char> <num> <num> <num> <num> <num>
#> 1: A=1 2500 1 -0.0020164794 0.001661789 0.0020164794
#> 2: A=0 2500 2 -0.0008420416 0.009181782 0.0008420416
#> 3: A=0 2500 1 0.0001238755 0.004784337 0.0001238755
#> AbsoluteCriteria StopCriteria RelativeRatio AbsoluteRatio ratio StopRule
#> <num> <num> <num> <num> <num> <char>
#> 1: 0 0.001661789 1.21343872 Inf 1.21 relative
#> 2: 0 0.009181782 0.09170786 Inf 0.09 relative
#> 3: 0 0.004784337 0.02589189 Inf 0.03 relative
#> StopAbsTol
#> <num>
#> 1: 0
#> 2: 0
#> 3: 0
#> Norm PnEIC = 0.002189066
#> Starting step 13 with update epsilon = 0.0125
#> Update increased the active convergence objective, halving OneStepEps
#> Starting step 13 with update epsilon = 0.00625
#> Trt Time Event PnEIC RelativeCriteria AbsPnEIC
#> <char> <num> <num> <num> <num> <num>
#> 1: A=1 2500 1 -1.897407e-03 0.001661702 1.897407e-03
#> 2: A=0 2500 2 3.260843e-04 0.009181036 3.260843e-04
#> 3: A=0 2500 1 -4.252794e-05 0.004784171 4.252794e-05
#> AbsoluteCriteria StopCriteria RelativeRatio AbsoluteRatio ratio StopRule
#> <num> <num> <num> <num> <num> <char>
#> 1: 0 0.001661702 1.141845895 Inf 1.14 relative
#> 2: 0 0.009181036 0.035517158 Inf 0.04 relative
#> 3: 0 0.004784171 0.008889302 Inf 0.01 relative
#> StopAbsTol
#> <num>
#> 1: 0
#> 2: 0
#> 3: 0
#> Norm PnEIC = 0.001926018
#> Starting step 14 with update epsilon = 0.00625
#> Trt Time Event PnEIC RelativeCriteria AbsPnEIC
#> <char> <num> <num> <num> <num> <num>
#> 1: A=1 2500 1 -1.771510e-03 0.001661611 1.771510e-03
#> 2: A=0 2500 2 -1.874402e-04 0.009181359 1.874402e-04
#> 3: A=0 2500 1 2.862341e-05 0.004784242 2.862341e-05
#> AbsoluteCriteria StopCriteria RelativeRatio AbsoluteRatio ratio StopRule
#> <num> <num> <num> <num> <num> <char>
#> 1: 0 0.001661611 1.066139970 Inf 1.07 relative
#> 2: 0 0.009181359 0.020415300 Inf 0.02 relative
#> 3: 0 0.004784242 0.005982852 Inf 0.01 relative
#> StopAbsTol
#> <num>
#> 1: 0
#> 2: 0
#> 3: 0
#> Norm PnEIC = 0.001781927
#> Starting step 15 with update epsilon = 0.00625
#> Trt Time Event PnEIC RelativeCriteria AbsPnEIC
#> <char> <num> <num> <num> <num> <num>
#> 1: A=1 2500 1 -1.645956e-03 0.001661524 1.645956e-03
#> 2: A=0 2500 2 1.322667e-04 0.009181157 1.322667e-04
#> 3: A=1 2500 2 -2.989555e-05 0.008589294 2.989555e-05
#> AbsoluteCriteria StopCriteria RelativeRatio AbsoluteRatio ratio StopRule
#> <num> <num> <num> <num> <num> <char>
#> 1: 0 0.001661524 0.99063073 Inf 0.99 relative
#> 2: 0 0.009181157 0.01440632 Inf 0.01 relative
#> 3: 0 0.008589294 0.00348056 Inf 0.00 relative
#> StopAbsTol
#> <num>
#> 1: 0
#> 2: 0
#> 3: 0
#> Norm PnEIC = 0.001651624