Bootstrap input dataset and rerun the model to get confidence bounds and aggregated parameters
bootstrapFit(
fit,
nboot = 200,
nSampIndiv,
stratVar,
stdErrType = c("perc", "se"),
ci = 0.95,
pvalues = NULL,
restart = FALSE,
plotHist = FALSE,
fitName = as.character(substitute(fit))
)Arguments
- fit
the nlmixr fit object
- nboot
an integer giving the number of bootstrapped models to be fit; default value is 200
- nSampIndiv
an integer specifying the number of samples in each bootstrapped sample; default is the number of unique subjects in the original dataset
- stratVar
Variable in the original dataset to stratify on; This is useful to distinguish between sparse and full sampling and other features you may wish to keep distinct in your bootstrap
- stdErrType
This gives the standard error type for the updated standard errors; The current possibilities are:
"perc"which gives the standard errors by percentiles (default) or"se"which gives the standard errors by the traditional formula.- ci
Confidence interval level to calculate. Default is 0.95 for a 95% confidence interval
- pvalues
a vector of pvalues indicating the probability of each subject to get selected; default value is NULL implying that probability of each subject is the same
- restart
A boolean to try to restart an interrupted or incomplete boostrap. By default this is
FALSE- plotHist
A boolean indicating if a histogram plot to assess how well the bootstrap is doing. By default this is turned off (
FALSE)- fitName
is the fit name that is used for the name of the boostrap files. By default it is the fit provided though it could be something else.
Value
Nothing, called for the side effects; The original fit is updated with the bootstrap confidence bands
Examples
# \donttest{
one.cmt <- function() {
ini({
## You may label each parameter with a comment
tka <- 0.45 # Log Ka
tcl <- 1 # Log Cl
## This works with interactive models
## You may also label the preceding line with label("label text")
tv <- 3.45
label("log V")
## the label("Label name") works with all models
eta.ka ~ 0.6
eta.cl ~ 0.3
eta.v ~ 0.1
add.sd <- 0.7
})
model({
ka <- exp(tka + eta.ka)
cl <- exp(tcl + eta.cl)
v <- exp(tv + eta.v)
linCmt() ~ add(add.sd)
})
}
fit <- nlmixr(one.cmt, theo_sd, "focei")
#> ℹ parameter labels from comments will be replaced by 'label()'
#> → creating full model...
#> → pruning branches (`if`/`else`)...
#> ✔ done
#> → loading into symengine environment...
#> ✔ done
#> → creating full model...
#> → pruning branches (`if`/`else`)...
#> ✔ done
#> → loading into symengine environment...
#> ✔ done
#> → calculate jacobian
#>
#> → calculate ∂(f)/∂(η)
#>
#> → calculate ∂(R²)/∂(η)
#>
#> → finding duplicate expressions in inner model...
#>
#> → optimizing duplicate expressions in inner model...
#>
#> → finding duplicate expressions in EBE model...
#>
#> → optimizing duplicate expressions in EBE model...
#>
#> → compiling inner model...
#>
#> ✔ done
#> → finding duplicate expressions in FD model...
#>
#> → compiling EBE model...
#>
#> ✔ done
#> → compiling events FD model...
#>
#> ✔ done
#> Key: U: Unscaled Parameters; X: Back-transformed parameters; G: Gill difference gradient approximation
#> F: Forward difference gradient approximation
#> C: Central difference gradient approximation
#> M: Mixed forward and central difference gradient approximation
#> Unscaled parameters for Omegas=chol(solve(omega));
#> Diagonals are transformed, as specified by foceiControl(diagXform=)
#> |-----+---------------+-----------+-----------+-----------+-----------|
#> | #| Objective Fun | tka | tcl | tv | add.sd |
#> |.....................| o1 | o2 | o3 |...........|
#> | 1| 133.56589 | -1.000 | -0.6333 | 1.000 | -0.8333 |
#> |.....................| -0.5425 | -0.3992 | -0.1145 |...........|
#> | U| 133.56589 | 0.4500 | 1.000 | 3.450 | 0.7000 |
#> |.....................| 1.136 | 1.351 | 1.778 |...........|
#> | X| 133.56589 | 1.568 | 2.718 | 31.50 | 0.7000 |
#> |.....................| 1.136 | 1.351 | 1.778 |...........|
#> | G| Gill Diff. | -0.9228 | -1.099 | -3.023 | 1.568 |
#> |.....................| -11.78 | -35.38 | -34.77 |...........|
#> | 2| 122.49084 | -0.9819 | -0.6118 | 1.059 | -0.8640 |
#> |.....................| -0.3121 | 0.2928 | 0.5658 |...........|
#> | U| 122.49084 | 0.4681 | 1.022 | 3.509 | 0.6893 |
#> |.....................| 1.398 | 2.286 | 2.988 |...........|
#> | X| 122.49084 | 1.597 | 2.777 | 33.42 | 0.6893 |
#> |.....................| 1.398 | 2.286 | 2.988 |...........|
#> | F| Forward Diff. | -0.9434 | 13.03 | 68.74 | -4.930 |
#> |.....................| 14.11 | 16.61 | 13.87 |...........|
#> | 3| 685.10853 | -0.9590 | -0.7884 | 0.09939 | -0.8088 |
#> |.....................| -0.3963 | 0.4112 | 0.7175 |...........|
#> | U| 685.10853 | 0.4910 | 0.8449 | 2.549 | 0.7086 |
#> |.....................| 1.302 | 2.446 | 3.258 |...........|
#> | X| 685.10853 | 1.634 | 2.328 | 12.80 | 0.7086 |
#> |.....................| 1.302 | 2.446 | 3.258 |...........|
#> | 4| 121.07098 | -0.9807 | -0.6293 | 0.9672 | -0.8574 |
#> |.....................| -0.3309 | 0.2706 | 0.5472 |...........|
#> | U| 121.07098 | 0.4693 | 1.004 | 3.417 | 0.6916 |
#> |.....................| 1.377 | 2.256 | 2.955 |...........|
#> | X| 121.07098 | 1.599 | 2.729 | 30.48 | 0.6916 |
#> |.....................| 1.377 | 2.256 | 2.955 |...........|
#> | F| Forward Diff. | 2.638 | -7.742 | -54.49 | -3.121 |
#> |.....................| 12.87 | 15.53 | 9.493 |...........|
#> | 5| 118.39726 | -0.9856 | -0.6250 | 1.019 | -0.8462 |
#> |.....................| -0.3736 | 0.2119 | 0.5034 |...........|
#> | U| 118.39726 | 0.4644 | 1.008 | 3.469 | 0.6955 |
#> |.....................| 1.328 | 2.177 | 2.877 |...........|
#> | X| 118.39726 | 1.591 | 2.741 | 32.09 | 0.6955 |
#> |.....................| 1.328 | 2.177 | 2.877 |...........|
#> | F| Forward Diff. | 0.03982 | 0.3472 | 10.92 | -1.065 |
#> |.....................| 7.258 | 11.32 | 6.677 |...........|
#> | 6| 117.98727 | -0.9862 | -0.6227 | 0.9740 | -0.8417 |
#> |.....................| -0.4136 | 0.1435 | 0.4620 |...........|
#> | U| 117.98727 | 0.4638 | 1.011 | 3.424 | 0.6971 |
#> |.....................| 1.283 | 2.084 | 2.803 |...........|
#> | X| 117.98727 | 1.590 | 2.747 | 30.69 | 0.6971 |
#> |.....................| 1.283 | 2.084 | 2.803 |...........|
#> | F| Forward Diff. | 1.116 | -3.218 | -38.20 | 0.7407 |
#> |.....................| 3.039 | 7.258 | 4.321 |...........|
#> | 7| 117.00814 | -0.9847 | -0.6227 | 1.026 | -0.8594 |
#> |.....................| -0.4218 | 0.07312 | 0.4182 |...........|
#> | U| 117.00814 | 0.4653 | 1.011 | 3.476 | 0.6909 |
#> |.....................| 1.273 | 1.989 | 2.726 |...........|
#> | X| 117.00814 | 1.592 | 2.747 | 32.34 | 0.6909 |
#> |.....................| 1.273 | 1.989 | 2.726 |...........|
#> | F| Forward Diff. | -0.2629 | 0.7891 | 16.82 | -1.334 |
#> |.....................| 1.781 | 2.066 | 1.822 |...........|
#> | 8| 116.99951 | -0.9848 | -0.6091 | 1.002 | -0.8443 |
#> |.....................| -0.4153 | 0.01193 | 0.3462 |...........|
#> | U| 116.99951 | 0.4652 | 1.024 | 3.452 | 0.6962 |
#> |.....................| 1.281 | 1.907 | 2.597 |...........|
#> | X| 116.99951 | 1.592 | 2.785 | 31.56 | 0.6962 |
#> |.....................| 1.281 | 1.907 | 2.597 |...........|
#> | F| Forward Diff. | 0.3528 | 2.909 | -6.956 | 0.6620 |
#> |.....................| 3.012 | -2.527 | -2.918 |...........|
#> | 9| 116.95329 | -0.9876 | -0.6388 | 1.014 | -0.8432 |
#> |.....................| -0.4529 | 0.01415 | 0.3526 |...........|
#> | U| 116.95329 | 0.4624 | 0.9945 | 3.464 | 0.6965 |
#> |.....................| 1.238 | 1.910 | 2.609 |...........|
#> | X| 116.95329 | 1.588 | 2.703 | 31.94 | 0.6965 |
#> |.....................| 1.238 | 1.910 | 2.609 |...........|
#> | F| Forward Diff. | -0.3099 | -4.571 | 2.225 | 0.9442 |
#> |.....................| -2.111 | -2.368 | -2.265 |...........|
#> | 10| 116.90989 | -0.9864 | -0.6001 | 1.006 | -0.8520 |
#> |.....................| -0.4576 | 0.03079 | 0.3763 |...........|
#> | U| 116.90989 | 0.4636 | 1.033 | 3.456 | 0.6935 |
#> |.....................| 1.233 | 1.932 | 2.651 |...........|
#> | X| 116.90989 | 1.590 | 2.810 | 31.69 | 0.6935 |
#> |.....................| 1.233 | 1.932 | 2.651 |...........|
#> | F| Forward Diff. | 0.09300 | 5.755 | -2.291 | -0.04211 |
#> |.....................| -1.852 | -0.8516 | -1.085 |...........|
#> | 11| 116.84070 | -0.9857 | -0.6271 | 1.013 | -0.8548 |
#> |.....................| -0.4203 | 0.02920 | 0.3940 |...........|
#> | U| 116.8407 | 0.4643 | 1.006 | 3.463 | 0.6925 |
#> |.....................| 1.275 | 1.930 | 2.683 |...........|
#> | X| 116.8407 | 1.591 | 2.735 | 31.92 | 0.6925 |
#> |.....................| 1.275 | 1.930 | 2.683 |...........|
#> | F| Forward Diff. | -0.01742 | -1.457 | 2.870 | -0.5379 |
#> |.....................| 2.018 | -0.9786 | -0.2287 |...........|
#> | 12| 116.91217 | -0.9860 | -0.6303 | 1.002 | -0.8156 |
#> |.....................| -0.4385 | 0.05061 | 0.3883 |...........|
#> | U| 116.91217 | 0.4640 | 1.003 | 3.452 | 0.7062 |
#> |.....................| 1.254 | 1.959 | 2.672 |...........|
#> | X| 116.91217 | 1.590 | 2.727 | 31.55 | 0.7062 |
#> |.....................| 1.254 | 1.959 | 2.672 |...........|
#> | 13| 116.84102 | -0.9856 | -0.6216 | 1.002 | -0.8528 |
#> |.....................| -0.4278 | 0.03288 | 0.3949 |...........|
#> | U| 116.84102 | 0.4644 | 1.012 | 3.452 | 0.6932 |
#> |.....................| 1.267 | 1.935 | 2.684 |...........|
#> | X| 116.84102 | 1.591 | 2.750 | 31.57 | 0.6932 |
#> |.....................| 1.267 | 1.935 | 2.684 |...........|
#> | 14| 116.82589 | -0.9856 | -0.6244 | 1.008 | -0.8538 |
#> |.....................| -0.4240 | 0.03103 | 0.3944 |...........|
#> | U| 116.82589 | 0.4644 | 1.009 | 3.458 | 0.6928 |
#> |.....................| 1.271 | 1.933 | 2.683 |...........|
#> | X| 116.82589 | 1.591 | 2.743 | 31.75 | 0.6928 |
#> |.....................| 1.271 | 1.933 | 2.683 |...........|
#> | F| Forward Diff. | 0.1123 | -1.009 | -2.046 | -0.5746 |
#> |.....................| 1.758 | -0.8390 | -0.3156 |...........|
#> | 15| 116.81762 | -0.9859 | -0.6219 | 1.013 | -0.8524 |
#> |.....................| -0.4283 | 0.03305 | 0.3952 |...........|
#> | U| 116.81762 | 0.4641 | 1.011 | 3.463 | 0.6933 |
#> |.....................| 1.266 | 1.935 | 2.685 |...........|
#> | X| 116.81762 | 1.591 | 2.749 | 31.90 | 0.6933 |
#> |.....................| 1.266 | 1.935 | 2.685 |...........|
#> | F| Forward Diff. | -0.01800 | -0.02030 | 2.847 | -0.2739 |
#> |.....................| 1.145 | -0.7092 | -0.1303 |...........|
#> | 16| 116.81069 | -0.9860 | -0.6218 | 1.007 | -0.8497 |
#> |.....................| -0.4320 | 0.03562 | 0.3951 |...........|
#> | U| 116.81069 | 0.4640 | 1.011 | 3.457 | 0.6943 |
#> |.....................| 1.262 | 1.939 | 2.684 |...........|
#> | X| 116.81069 | 1.590 | 2.750 | 31.74 | 0.6943 |
#> |.....................| 1.262 | 1.939 | 2.684 |...........|
#> | F| Forward Diff. | 0.08807 | -0.3069 | -2.153 | -0.1145 |
#> |.....................| 0.7425 | -0.5262 | -0.2308 |...........|
#> | 17| 116.80533 | -0.9865 | -0.6218 | 1.011 | -0.8479 |
#> |.....................| -0.4365 | 0.03968 | 0.3931 |...........|
#> | U| 116.80533 | 0.4635 | 1.012 | 3.461 | 0.6949 |
#> |.....................| 1.257 | 1.944 | 2.681 |...........|
#> | X| 116.80533 | 1.590 | 2.750 | 31.84 | 0.6949 |
#> |.....................| 1.257 | 1.944 | 2.681 |...........|
#> | F| Forward Diff. | -0.03522 | -0.08197 | 0.9961 | 0.04165 |
#> |.....................| 0.1105 | -0.3350 | -0.1979 |...........|
#> | 18| 116.80465 | -0.9855 | -0.6206 | 1.009 | -0.8504 |
#> |.....................| -0.4398 | 0.04513 | 0.3914 |...........|
#> | U| 116.80465 | 0.4645 | 1.013 | 3.459 | 0.6940 |
#> |.....................| 1.253 | 1.952 | 2.678 |...........|
#> | X| 116.80465 | 1.591 | 2.753 | 31.79 | 0.6940 |
#> |.....................| 1.253 | 1.952 | 2.678 |...........|
#> | F| Forward Diff. | 0.04682 | 0.1881 | -0.5119 | -0.2081 |
#> |.....................| -0.2275 | 0.03593 | -0.2268 |...........|
#> | 19| 116.80465 | -0.9855 | -0.6206 | 1.009 | -0.8504 |
#> |.....................| -0.4398 | 0.04513 | 0.3914 |...........|
#> | U| 116.80465 | 0.4645 | 1.013 | 3.459 | 0.6940 |
#> |.....................| 1.253 | 1.952 | 2.678 |...........|
#> | X| 116.80465 | 1.591 | 2.753 | 31.79 | 0.6940 |
#> |.....................| 1.253 | 1.952 | 2.678 |...........|
#> calculating covariance matrix
#> done
#> Calculating residuals/tables
#> done
#> Warning: initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=))
#> Warning: ETAs were reset to zero during optimization; (Can control by foceiControl(resetEtaP=.))
#> Warning: last objective function was not at minimum, possible problems in optimization
#> Warning: gradient problems with initial estimate and covariance; see $scaleInfo
RxODE::.rxWithWd(tempdir(), { # Run example in temp dir
bootstrapFit(fit, nboot = 5, restart = TRUE) # overwrites any of the existing data or model files
bootstrapFit(fit, nboot = 7) # resumes fitting using the stored data and model files
# Note this resumes because the total number of bootstrap samples is not 50
bootstrapFit(fit, nboot=50)
# Note the boostrap standard error and variance/covariance matrix is retained.
# If you wish to switch back you can change the covariance matrix by
setCov(fit,"r,s")
# And change it back again
setCov(fit,"boot50")
# This change will affect any simulations with uncertainty in their parameters
# You may also do a chi-square diagnostic plot check for the bootstrap with
bootplot(fit)
})
#>
#> ── Running nlmixr for model index: 1 ───────────────────────────────────────────
#> done
#>
#> ── Running nlmixr for model index: 2 ───────────────────────────────────────────
#> done
#>
#> ── Running nlmixr for model index: 3 ───────────────────────────────────────────
#> done
#>
#> ── Running nlmixr for model index: 4 ───────────────────────────────────────────
#> done
#>
#> ── Running nlmixr for model index: 5 ───────────────────────────────────────────
#> done
#> → creating full model...
#> → pruning branches (`if`/`else`)...
#> ✔ done
#> → loading into symengine environment...
#> ✔ done
#> → creating full model...
#> → pruning branches (`if`/`else`)...
#> ✔ done
#> → loading into symengine environment...
#> ✔ done
#> → calculate jacobian
#>
#> → calculate ∂(f)/∂(η)
#>
#> → calculate ∂(R²)/∂(η)
#>
#> → finding duplicate expressions in inner model...
#>
#> → optimizing duplicate expressions in inner model...
#>
#> → finding duplicate expressions in EBE model...
#>
#> → optimizing duplicate expressions in EBE model...
#>
#> → compiling inner model...
#>
#> ✔ done
#> → finding duplicate expressions in FD model...
#>
#> → compiling EBE model...
#>
#> ✔ done
#> → compiling events FD model...
#>
#> ✔ done
#> Updated original fit object fit
#> ✔ resuming bootstrap data sampling using data at ./nlmixrBootstrapCache_fit_3f329ad5e07a7d94a211676faa119831
#> ✔ resuming bootstrap model fitting using data and models stored at /tmp/RtmpbQXGyc/nlmixrBootstrapCache_fit_3f329ad5e07a7d94a211676faa119831
#>
#> ── Running nlmixr for model index: 6 ───────────────────────────────────────────
#> done
#>
#> ── Running nlmixr for model index: 7 ───────────────────────────────────────────
#> done
#> Updated original fit object fit
#> ✔ resuming bootstrap data sampling using data at ./nlmixrBootstrapCache_fit_3f329ad5e07a7d94a211676faa119831
#> ✔ resuming bootstrap model fitting using data and models stored at /tmp/RtmpbQXGyc/nlmixrBootstrapCache_fit_3f329ad5e07a7d94a211676faa119831
#>
#> ── Running nlmixr for model index: 8 ───────────────────────────────────────────
#> done
#>
#> ── Running nlmixr for model index: 9 ───────────────────────────────────────────
#> done
#>
#> ── Running nlmixr for model index: 10 ──────────────────────────────────────────
#> done
#>
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#> done
#>
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#> done
#>
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#> done
#>
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#> done
#>
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#> done
#>
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#> done
#>
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#> done
#>
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#> done
#>
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#> done
#>
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#> done
#>
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#> done
#>
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#> done
#>
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#> done
#>
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#> done
#>
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#> done
#>
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#> done
#>
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#> done
#>
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#> done
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#> done
#>
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#> done
#>
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#> done
#>
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#> done
#>
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#> done
#>
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#> done
#>
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#> done
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#> done
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#> done
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#> done
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#> done
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#> done
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#> done
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#> done
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#> done
#>
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#> done
#>
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#> done
#>
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#> done
#>
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#> done
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#> done
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#> done
#>
#> ── Running nlmixr for model index: 50 ──────────────────────────────────────────
#> done
#> Updated original fit object fit
#> Updated original fit object fit
#> Updated original fit object fit
#> ✔ resuming bootstrap data sampling using data at ./nlmixrBootstrapCache_fit_3f329ad5e07a7d94a211676faa119831
#> ✔ resuming bootstrap model fitting using data and models stored at /tmp/RtmpbQXGyc/nlmixrBootstrapCache_fit_3f329ad5e07a7d94a211676faa119831
#>
#> ── Loading/Calculating Δ Objective function ────────────────────────────────────
#>
#>
#> ── Running bootstrap estimates on original data for model index: 1 ─────────────
#> Warning: initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=))
#>
#>
#> ── Running bootstrap estimates on original data for model index: 2 ─────────────
#> Warning: initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=))
#>
#>
#> ── Running bootstrap estimates on original data for model index: 3 ─────────────
#> Warning: initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=))
#>
#>
#> ── Running bootstrap estimates on original data for model index: 4 ─────────────
#> Warning: initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=))
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#> Warning: initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=))
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#> Warning: initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=))
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#> Warning: initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=))
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#> ── Running bootstrap estimates on original data for model index: 32 ────────────
#> Warning: initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=))
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#> ── Running bootstrap estimates on original data for model index: 33 ────────────
#> Warning: initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=))
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#> Warning: initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=))
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#> Warning: initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=))
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#> ── Running bootstrap estimates on original data for model index: 36 ────────────
#> Warning: initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=))
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#> ── Running bootstrap estimates on original data for model index: 37 ────────────
#> Warning: initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=))
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#> Warning: initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=))
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#> ── Running bootstrap estimates on original data for model index: 39 ────────────
#> Warning: initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=))
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#> ── Running bootstrap estimates on original data for model index: 40 ────────────
#> Warning: initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=))
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#> ── Running bootstrap estimates on original data for model index: 41 ────────────
#> Warning: initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=))
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#> ── Running bootstrap estimates on original data for model index: 42 ────────────
#> Warning: initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=))
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#> ── Running bootstrap estimates on original data for model index: 43 ────────────
#> Warning: initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=))
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#> ── Running bootstrap estimates on original data for model index: 44 ────────────
#> Warning: initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=))
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#> ── Running bootstrap estimates on original data for model index: 45 ────────────
#> Warning: initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=))
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#> ── Running bootstrap estimates on original data for model index: 46 ────────────
#> Warning: initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=))
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#> ── Running bootstrap estimates on original data for model index: 47 ────────────
#> Warning: initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=))
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#> ── Running bootstrap estimates on original data for model index: 48 ────────────
#> Warning: initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=))
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#> ── Running bootstrap estimates on original data for model index: 49 ────────────
#> Warning: initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=))
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#> ── Running bootstrap estimates on original data for model index: 50 ────────────
#> Warning: initial ETAs were nudged; (can control by foceiControl(etaNudge=., etaNudge2=))
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#> Updated original fit object x
# }