surv2sample: Inference of model-free between-group contrasts with censored...
In surv2sampleComp: Inference for Model-Free Between-Group Parameters for Censored Survival Data
Description
Usage
Arguments
Author(s)
References
Examples
View source: R/surv2sample-ver003.R
Description
Performs inference of several model-free group contrast measures, which include difference/ratio of cumulative incidence rates, quantiles, restricted mean survival times (RMST), and integrated survival rates.
Usage
1
2
3
surv2sample(time, status, arm, npert=1000,
timepoints=c(12, 24, 36, 40), quanprobs=c(0.1, 0.15, 0.2),
tau_start=0, tau, SEED=NULL, procedure="KM", conf.int=0.95)
Arguments
time
The follow-up time.
status
The censoring indicator, 1=event, and 0=censoring.
arm
The indicator for groups to compare 1/0.
npert
The number of resampling. The default is 1000.
timepoints
specifies the time points at which difference and ratio of the survival rates are computed.
quanprobs
specifies the probabilities at which difference and ratio of the corresponding quantiles are computed.
tau_start
The value indicates time point on the follow-up time to calculate the restricted mean survival time beyond the time point. The default is 0.
tau
The value indicates the restricted time point on the follow-up time to calculate the restricted mean survival time. (i.e., the minimum of the largest observed time in each of the two groups)
SEED
A random seed used for the resampling. Default is NULL.
procedure
Specifies the inference procedure. A non-parametric procedure by the method of Kaplan-Meier ("KM") is the default. Another option is a parametric inference procedure by fitting a generalized gamma distribution to each group ("GG").
conf.int
The level for computation of the confidence intervals. The default is 0.95.
Author(s)
Hajime Uno, Miki Horiguchi
References
Tian L, Zhao L, Wei LJ. Predicting the restricted mean event time with the subject's baseline covariates in survival analysis. Biostatistics 2014, 15, 222-233.
Zhao L, Tian L, Uno H, Solomon S, Pfeffer M, Schindler J, Wei LJ. Utilizing the integrated difference of two survival functions to quantify the treatment contrast for designing, monitoring, and analyzing a comparative clinical study. Clinical Trials 2012, 9, 570-577.
Examples
1
2
3
D=pbc.sample()
surv2sample(D$time, D$status, D$group, npert=500, timepoints=c(2,4,6,8),
quanprobs =c(0.2, 0.3), tau=8, procedure="KM")
Example output
$procedure
[1] "KM"
$method
[1] "Perturbation resampling"
$survfit
Call: survfit(formula = Surv(time, status) ~ arm)
n events median 0.95LCL 0.95UCL
arm=0 139 58 8.45 6.57 NA
arm=1 143 55 9.30 8.46 NA
$tau_start
[1] 0
$tau
[1] 8
$time_interval
[1] 8
$npert
[1] 500
$timepoints
[1] 2 4 6 8
$quanprobs
[1] 0.2 0.3
$contrast.all
Est. Lower 95% Upper 95% p-val
RMST Group0-Group1 -0.18940 -0.8049 0.4260 0.546
RMST Group1-Group0 0.18940 -0.4260 0.8049 0.546
RMST Group0/Group1 0.96994 0.8767 1.0730 0.554
RMST Group1/Group0 1.03099 0.9319 1.1406 0.554
Loss time Group0-Group1 0.18940 -0.4260 0.8049 0.546
Loss time Group1-Group0 -0.18940 -0.8049 0.4260 0.546
Loss time Group0/Group1 1.11145 0.7825 1.5786 0.555
Loss time Group1/Group0 0.89973 0.6335 1.2779 0.555
Prob at 2 Group0-Group1 0.00406 -0.0689 0.0771 0.913
Prob at 2 Group1-Group0 -0.00406 -0.0771 0.0689 0.913
Prob at 2 Group0/Group1 1.00454 0.9248 1.0911 0.915
Prob at 2 Group1/Group0 0.99548 0.9165 1.0813 0.915
Prob at 4 Group0-Group1 0.01327 -0.0896 0.1162 0.800
Prob at 4 Group1-Group0 -0.01327 -0.1162 0.0896 0.800
Prob at 4 Group0/Group1 1.01758 0.8901 1.1634 0.799
Prob at 4 Group1/Group0 0.98273 0.8596 1.1235 0.799
Prob at 6 Group0-Group1 -0.04909 -0.1628 0.0646 0.397
Prob at 6 Group1-Group0 0.04909 -0.0646 0.1628 0.397
Prob at 6 Group0/Group1 0.93044 0.7823 1.1066 0.415
Prob at 6 Group1/Group0 1.07476 0.9036 1.2783 0.415
Prob at 8 Group0-Group1 -0.08735 -0.2265 0.0519 0.219
Prob at 8 Group1-Group0 0.08735 -0.0519 0.2265 0.219
Prob at 8 Group0/Group1 0.85623 0.6637 1.1047 0.232
Prob at 8 Group1/Group0 1.16791 0.9052 1.5068 0.232
Quantile at 20 % Group0-Group1 0.19165 -1.6994 2.0827 0.843
Quantile at 20 % Group1-Group0 -0.19165 -2.0827 1.6994 0.843
Quantile at 20 % Group0/Group1 1.06009 0.5962 1.8848 0.842
Quantile at 20 % Group1/Group0 0.94332 0.5306 1.6772 0.842
Quantile at 30 % Group0-Group1 -1.35250 -4.2645 1.5595 0.363
Quantile at 30 % Group1-Group0 1.35250 -1.5595 4.2645 0.363
Quantile at 30 % Group0/Group1 0.79578 0.4988 1.2695 0.338
Quantile at 30 % Group1/Group0 1.25662 0.7877 2.0047 0.338
Ave of t-year event rates Group0-Group1 -0.02978 -0.1180 0.0585 0.508
Ave of t-year event rates Group1-Group0 0.02978 -0.0585 0.1180 0.508
Ave of t-year event rates Group0/Group1 0.95980 0.8468 1.0879 0.521
Ave of t-year event rates Group1/Group0 1.04188 0.9192 1.1809 0.521
Ave percentiles Group0-Group1 -0.58042 -2.7931 1.6323 0.607
Ave percentiles Group1-Group0 0.58042 -1.6323 2.7931 0.607
Ave percentiles Group0/Group1 0.88170 0.5530 1.4058 0.597
Ave percentiles Group1/Group0 1.13418 0.7113 1.8084 0.597
$group0
Est. Lower 95% Upper 95% SE
RMST 6.111 5.629 6.508 0.2255
Loss time 1.889 1.492 2.371 0.2255
Prob at 2 0.899 0.840 0.943 0.0270
Prob at 4 0.768 0.689 0.835 0.0368
Prob at 6 0.657 0.569 0.743 0.0447
Prob at 8 0.520 0.418 0.617 0.0529
Quantile at 20 % 3.381 2.475 4.627 0.5740
Quantile at 30 % 5.270 3.926 6.289 0.6894
Ave of t-year event rates 0.711 0.642 0.770 0.0331
Ave percentiles 4.326 3.285 5.458 0.5819
$group1
Est. Lower 95% Upper 95% SE
RMST 6.301 5.854 6.726 0.2267
Loss time 1.699 1.274 2.146 0.2267
Prob at 2 0.895 0.837 0.937 0.0265
Prob at 4 0.755 0.682 0.823 0.0367
Prob at 6 0.706 0.629 0.782 0.0399
Prob at 8 0.608 0.506 0.700 0.0493
Quantile at 20 % 3.190 2.182 5.057 0.7641
Quantile at 30 % 6.623 3.907 8.144 1.3191
Ave of t-year event rates 0.741 0.675 0.803 0.0325
Ave percentiles 4.906 3.055 6.388 0.9635
$RMST
Est. Lower 95% Upper 95% p-val
RMST Group0-Group1 -0.189 -0.805 0.426 0.546
RMST Group1-Group0 0.189 -0.426 0.805 0.546
RMST Group0/Group1 0.970 0.877 1.073 0.554
RMST Group1/Group0 1.031 0.932 1.141 0.554
$RMLT
Est. Lower 95% Upper 95% p-val
Loss time Group0-Group1 0.189 -0.426 0.805 0.546
Loss time Group1-Group0 -0.189 -0.805 0.426 0.546
Loss time Group0/Group1 1.111 0.783 1.579 0.555
Loss time Group1/Group0 0.900 0.633 1.278 0.555
$contrast.diff10
Est. Lower 95% Upper 95% p-val
RMST Group1-Group0 0.18940 -0.4260 0.8049 0.546
Loss time Group1-Group0 -0.18940 -0.8049 0.4260 0.546
Prob at 2 Group1-Group0 -0.00406 -0.0771 0.0689 0.913
Prob at 4 Group1-Group0 -0.01327 -0.1162 0.0896 0.800
Prob at 6 Group1-Group0 0.04909 -0.0646 0.1628 0.397
Prob at 8 Group1-Group0 0.08735 -0.0519 0.2265 0.219
Quantile at 20 % Group1-Group0 -0.19165 -2.0827 1.6994 0.843
Quantile at 30 % Group1-Group0 1.35250 -1.5595 4.2645 0.363
Ave of t-year event rates Group1-Group0 0.02978 -0.0585 0.1180 0.508
Ave percentiles Group1-Group0 0.58042 -1.6323 2.7931 0.607
$contrast.diff01
Est. Lower 95% Upper 95% p-val
RMST Group0-Group1 -0.18940 -0.8049 0.4260 0.546
Loss time Group0-Group1 0.18940 -0.4260 0.8049 0.546
Prob at 2 Group0-Group1 0.00406 -0.0689 0.0771 0.913
Prob at 4 Group0-Group1 0.01327 -0.0896 0.1162 0.800
Prob at 6 Group0-Group1 -0.04909 -0.1628 0.0646 0.397
Prob at 8 Group0-Group1 -0.08735 -0.2265 0.0519 0.219
Quantile at 20 % Group0-Group1 0.19165 -1.6994 2.0827 0.843
Quantile at 30 % Group0-Group1 -1.35250 -4.2645 1.5595 0.363
Ave of t-year event rates Group0-Group1 -0.02978 -0.1180 0.0585 0.508
Ave percentiles Group0-Group1 -0.58042 -2.7931 1.6323 0.607
$contrast.ratio01
Est. Lower 95% Upper 95% p-val
RMST Group0/Group1 0.970 0.877 1.07 0.554
Loss time Group0/Group1 1.111 0.783 1.58 0.555
Prob at 2 Group0/Group1 1.005 0.925 1.09 0.915
Prob at 4 Group0/Group1 1.018 0.890 1.16 0.799
Prob at 6 Group0/Group1 0.930 0.782 1.11 0.415
Prob at 8 Group0/Group1 0.856 0.664 1.10 0.232
Quantile at 20 % Group0/Group1 1.060 0.596 1.88 0.842
Quantile at 30 % Group0/Group1 0.796 0.499 1.27 0.338
Ave of t-year event rates Group0/Group1 0.960 0.847 1.09 0.521
Ave percentiles Group0/Group1 0.882 0.553 1.41 0.597
$contrast.ratio10
Est. Lower 95% Upper 95% p-val
RMST Group1/Group0 1.031 0.932 1.14 0.554
Loss time Group1/Group0 0.900 0.633 1.28 0.555
Prob at 2 Group1/Group0 0.995 0.916 1.08 0.915
Prob at 4 Group1/Group0 0.983 0.860 1.12 0.799
Prob at 6 Group1/Group0 1.075 0.904 1.28 0.415
Prob at 8 Group1/Group0 1.168 0.905 1.51 0.232
Quantile at 20 % Group1/Group0 0.943 0.531 1.68 0.842
Quantile at 30 % Group1/Group0 1.257 0.788 2.00 0.338
Ave of t-year event rates Group1/Group0 1.042 0.919 1.18 0.521
Ave percentiles Group1/Group0 1.134 0.711 1.81 0.597
$integrated_surv
Est. Lower 95% Upper 95%
Integrated survival rate Group0 0.764 0.704 0.814
Integrated survival rate Group1 0.788 0.732 0.841
$integrated_surv.diff
Est. Lower 95% Upper 95% p-val
Integrated survival rate Group0-Group1 -0.0237 -0.1006 0.0533 0.546
Integrated survival rate Group1-Group0 0.0237 -0.0533 0.1006 0.546
attr(,"class")
[1] "surv2sample"
surv2sampleComp documentation built on May 2, 2019, 12:39 a.m.
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Description Usage Arguments Author(s) References Examples
View source: R/surv2sample-ver003.R
Description
Performs inference of several model-free group contrast measures, which include difference/ratio of cumulative incidence rates, quantiles, restricted mean survival times (RMST), and integrated survival rates.
Usage
1 2 3 | surv2sample(time, status, arm, npert=1000,
timepoints=c(12, 24, 36, 40), quanprobs=c(0.1, 0.15, 0.2),
tau_start=0, tau, SEED=NULL, procedure="KM", conf.int=0.95)
|
Arguments
time |
The follow-up time. |
status |
The censoring indicator, 1=event, and 0=censoring. |
arm |
The indicator for groups to compare 1/0. |
npert |
The number of resampling. The default is 1000. |
timepoints |
specifies the time points at which difference and ratio of the survival rates are computed. |
quanprobs |
specifies the probabilities at which difference and ratio of the corresponding quantiles are computed. |
tau_start |
The value indicates time point on the follow-up time to calculate the restricted mean survival time beyond the time point. The default is 0. |
tau |
The value indicates the restricted time point on the follow-up time to calculate the restricted mean survival time. (i.e., the minimum of the largest observed time in each of the two groups) |
SEED |
A random seed used for the resampling. Default is NULL. |
procedure |
Specifies the inference procedure. A non-parametric procedure by the method of Kaplan-Meier ("KM") is the default. Another option is a parametric inference procedure by fitting a generalized gamma distribution to each group ("GG"). |
conf.int |
The level for computation of the confidence intervals. The default is 0.95. |
Author(s)
Hajime Uno, Miki Horiguchi
References
Tian L, Zhao L, Wei LJ. Predicting the restricted mean event time with the subject's baseline covariates in survival analysis. Biostatistics 2014, 15, 222-233.
Zhao L, Tian L, Uno H, Solomon S, Pfeffer M, Schindler J, Wei LJ. Utilizing the integrated difference of two survival functions to quantify the treatment contrast for designing, monitoring, and analyzing a comparative clinical study. Clinical Trials 2012, 9, 570-577.
Examples
1 2 3 | D=pbc.sample()
surv2sample(D$time, D$status, D$group, npert=500, timepoints=c(2,4,6,8),
quanprobs =c(0.2, 0.3), tau=8, procedure="KM")
|
Example output
$procedure
[1] "KM"
$method
[1] "Perturbation resampling"
$survfit
Call: survfit(formula = Surv(time, status) ~ arm)
n events median 0.95LCL 0.95UCL
arm=0 139 58 8.45 6.57 NA
arm=1 143 55 9.30 8.46 NA
$tau_start
[1] 0
$tau
[1] 8
$time_interval
[1] 8
$npert
[1] 500
$timepoints
[1] 2 4 6 8
$quanprobs
[1] 0.2 0.3
$contrast.all
Est. Lower 95% Upper 95% p-val
RMST Group0-Group1 -0.18940 -0.8049 0.4260 0.546
RMST Group1-Group0 0.18940 -0.4260 0.8049 0.546
RMST Group0/Group1 0.96994 0.8767 1.0730 0.554
RMST Group1/Group0 1.03099 0.9319 1.1406 0.554
Loss time Group0-Group1 0.18940 -0.4260 0.8049 0.546
Loss time Group1-Group0 -0.18940 -0.8049 0.4260 0.546
Loss time Group0/Group1 1.11145 0.7825 1.5786 0.555
Loss time Group1/Group0 0.89973 0.6335 1.2779 0.555
Prob at 2 Group0-Group1 0.00406 -0.0689 0.0771 0.913
Prob at 2 Group1-Group0 -0.00406 -0.0771 0.0689 0.913
Prob at 2 Group0/Group1 1.00454 0.9248 1.0911 0.915
Prob at 2 Group1/Group0 0.99548 0.9165 1.0813 0.915
Prob at 4 Group0-Group1 0.01327 -0.0896 0.1162 0.800
Prob at 4 Group1-Group0 -0.01327 -0.1162 0.0896 0.800
Prob at 4 Group0/Group1 1.01758 0.8901 1.1634 0.799
Prob at 4 Group1/Group0 0.98273 0.8596 1.1235 0.799
Prob at 6 Group0-Group1 -0.04909 -0.1628 0.0646 0.397
Prob at 6 Group1-Group0 0.04909 -0.0646 0.1628 0.397
Prob at 6 Group0/Group1 0.93044 0.7823 1.1066 0.415
Prob at 6 Group1/Group0 1.07476 0.9036 1.2783 0.415
Prob at 8 Group0-Group1 -0.08735 -0.2265 0.0519 0.219
Prob at 8 Group1-Group0 0.08735 -0.0519 0.2265 0.219
Prob at 8 Group0/Group1 0.85623 0.6637 1.1047 0.232
Prob at 8 Group1/Group0 1.16791 0.9052 1.5068 0.232
Quantile at 20 % Group0-Group1 0.19165 -1.6994 2.0827 0.843
Quantile at 20 % Group1-Group0 -0.19165 -2.0827 1.6994 0.843
Quantile at 20 % Group0/Group1 1.06009 0.5962 1.8848 0.842
Quantile at 20 % Group1/Group0 0.94332 0.5306 1.6772 0.842
Quantile at 30 % Group0-Group1 -1.35250 -4.2645 1.5595 0.363
Quantile at 30 % Group1-Group0 1.35250 -1.5595 4.2645 0.363
Quantile at 30 % Group0/Group1 0.79578 0.4988 1.2695 0.338
Quantile at 30 % Group1/Group0 1.25662 0.7877 2.0047 0.338
Ave of t-year event rates Group0-Group1 -0.02978 -0.1180 0.0585 0.508
Ave of t-year event rates Group1-Group0 0.02978 -0.0585 0.1180 0.508
Ave of t-year event rates Group0/Group1 0.95980 0.8468 1.0879 0.521
Ave of t-year event rates Group1/Group0 1.04188 0.9192 1.1809 0.521
Ave percentiles Group0-Group1 -0.58042 -2.7931 1.6323 0.607
Ave percentiles Group1-Group0 0.58042 -1.6323 2.7931 0.607
Ave percentiles Group0/Group1 0.88170 0.5530 1.4058 0.597
Ave percentiles Group1/Group0 1.13418 0.7113 1.8084 0.597
$group0
Est. Lower 95% Upper 95% SE
RMST 6.111 5.629 6.508 0.2255
Loss time 1.889 1.492 2.371 0.2255
Prob at 2 0.899 0.840 0.943 0.0270
Prob at 4 0.768 0.689 0.835 0.0368
Prob at 6 0.657 0.569 0.743 0.0447
Prob at 8 0.520 0.418 0.617 0.0529
Quantile at 20 % 3.381 2.475 4.627 0.5740
Quantile at 30 % 5.270 3.926 6.289 0.6894
Ave of t-year event rates 0.711 0.642 0.770 0.0331
Ave percentiles 4.326 3.285 5.458 0.5819
$group1
Est. Lower 95% Upper 95% SE
RMST 6.301 5.854 6.726 0.2267
Loss time 1.699 1.274 2.146 0.2267
Prob at 2 0.895 0.837 0.937 0.0265
Prob at 4 0.755 0.682 0.823 0.0367
Prob at 6 0.706 0.629 0.782 0.0399
Prob at 8 0.608 0.506 0.700 0.0493
Quantile at 20 % 3.190 2.182 5.057 0.7641
Quantile at 30 % 6.623 3.907 8.144 1.3191
Ave of t-year event rates 0.741 0.675 0.803 0.0325
Ave percentiles 4.906 3.055 6.388 0.9635
$RMST
Est. Lower 95% Upper 95% p-val
RMST Group0-Group1 -0.189 -0.805 0.426 0.546
RMST Group1-Group0 0.189 -0.426 0.805 0.546
RMST Group0/Group1 0.970 0.877 1.073 0.554
RMST Group1/Group0 1.031 0.932 1.141 0.554
$RMLT
Est. Lower 95% Upper 95% p-val
Loss time Group0-Group1 0.189 -0.426 0.805 0.546
Loss time Group1-Group0 -0.189 -0.805 0.426 0.546
Loss time Group0/Group1 1.111 0.783 1.579 0.555
Loss time Group1/Group0 0.900 0.633 1.278 0.555
$contrast.diff10
Est. Lower 95% Upper 95% p-val
RMST Group1-Group0 0.18940 -0.4260 0.8049 0.546
Loss time Group1-Group0 -0.18940 -0.8049 0.4260 0.546
Prob at 2 Group1-Group0 -0.00406 -0.0771 0.0689 0.913
Prob at 4 Group1-Group0 -0.01327 -0.1162 0.0896 0.800
Prob at 6 Group1-Group0 0.04909 -0.0646 0.1628 0.397
Prob at 8 Group1-Group0 0.08735 -0.0519 0.2265 0.219
Quantile at 20 % Group1-Group0 -0.19165 -2.0827 1.6994 0.843
Quantile at 30 % Group1-Group0 1.35250 -1.5595 4.2645 0.363
Ave of t-year event rates Group1-Group0 0.02978 -0.0585 0.1180 0.508
Ave percentiles Group1-Group0 0.58042 -1.6323 2.7931 0.607
$contrast.diff01
Est. Lower 95% Upper 95% p-val
RMST Group0-Group1 -0.18940 -0.8049 0.4260 0.546
Loss time Group0-Group1 0.18940 -0.4260 0.8049 0.546
Prob at 2 Group0-Group1 0.00406 -0.0689 0.0771 0.913
Prob at 4 Group0-Group1 0.01327 -0.0896 0.1162 0.800
Prob at 6 Group0-Group1 -0.04909 -0.1628 0.0646 0.397
Prob at 8 Group0-Group1 -0.08735 -0.2265 0.0519 0.219
Quantile at 20 % Group0-Group1 0.19165 -1.6994 2.0827 0.843
Quantile at 30 % Group0-Group1 -1.35250 -4.2645 1.5595 0.363
Ave of t-year event rates Group0-Group1 -0.02978 -0.1180 0.0585 0.508
Ave percentiles Group0-Group1 -0.58042 -2.7931 1.6323 0.607
$contrast.ratio01
Est. Lower 95% Upper 95% p-val
RMST Group0/Group1 0.970 0.877 1.07 0.554
Loss time Group0/Group1 1.111 0.783 1.58 0.555
Prob at 2 Group0/Group1 1.005 0.925 1.09 0.915
Prob at 4 Group0/Group1 1.018 0.890 1.16 0.799
Prob at 6 Group0/Group1 0.930 0.782 1.11 0.415
Prob at 8 Group0/Group1 0.856 0.664 1.10 0.232
Quantile at 20 % Group0/Group1 1.060 0.596 1.88 0.842
Quantile at 30 % Group0/Group1 0.796 0.499 1.27 0.338
Ave of t-year event rates Group0/Group1 0.960 0.847 1.09 0.521
Ave percentiles Group0/Group1 0.882 0.553 1.41 0.597
$contrast.ratio10
Est. Lower 95% Upper 95% p-val
RMST Group1/Group0 1.031 0.932 1.14 0.554
Loss time Group1/Group0 0.900 0.633 1.28 0.555
Prob at 2 Group1/Group0 0.995 0.916 1.08 0.915
Prob at 4 Group1/Group0 0.983 0.860 1.12 0.799
Prob at 6 Group1/Group0 1.075 0.904 1.28 0.415
Prob at 8 Group1/Group0 1.168 0.905 1.51 0.232
Quantile at 20 % Group1/Group0 0.943 0.531 1.68 0.842
Quantile at 30 % Group1/Group0 1.257 0.788 2.00 0.338
Ave of t-year event rates Group1/Group0 1.042 0.919 1.18 0.521
Ave percentiles Group1/Group0 1.134 0.711 1.81 0.597
$integrated_surv
Est. Lower 95% Upper 95%
Integrated survival rate Group0 0.764 0.704 0.814
Integrated survival rate Group1 0.788 0.732 0.841
$integrated_surv.diff
Est. Lower 95% Upper 95% p-val
Integrated survival rate Group0-Group1 -0.0237 -0.1006 0.0533 0.546
Integrated survival rate Group1-Group0 0.0237 -0.0533 0.1006 0.546
attr(,"class")
[1] "surv2sample"
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