R: Estimate Confounder-Adjusted Survival Time Quantiles

adjusted_surv_quantile {adjustedCurves}

R Documentation

Estimate Confounder-Adjusted Survival Time Quantiles

Description

This function can be utilized to estimate confounder-adjusted survival time quantiles, including the median survival time, given previously estimated adjusted survival curves. May also be used to estimate the difference between or ratio of two adjusted survival time quantiles.

Usage

adjusted_surv_quantile(adjsurv, p=0.5, conf_int=FALSE,
                       conf_level=adjsurv$conf_level,
                       use_boot=FALSE, interpolation="steps",
                       contrast="none", group_1=NULL,
                       group_2=NULL)

Arguments

`adjsurv`	An `adjustedsurv` object created using the `adjustedsurv` function.
`p`	The quantile of interest. To calculate the median survival time, set this parameter to 0.5 (default). Multiple values in form of a numeric vector are allowed.
`conf_int`	Whether to calculate confidence intervals or not. Those are calculated in the same way as the quantiles but using the confidence limit curves. This requires either that `conf_int=TRUE` or `bootstrap=TRUE` was used in the original `adjustedsurv` function call.
`conf_level`	A single number specifying the confidence level of the confidence intervals. By default the previously estimated confidence intervals and thereby the same confidence level that was used in the original `adjustedsurv` call will be used. If `conf_level` is set to a different value, the confidence intervals will be re-calculated first. This works for all methods except `method="km"`.
`use_boot`	Whether to use the bootstrap confidence interval estimates of the survival curves to estimate the confidence intervals of the survival time quantiles or not. Can only be used when `bootstrap=TRUE` was used in the original `adjustedsurv` function call. Ignored if `conf_int=FALSE`.
`interpolation`	Either `"steps"` (default) or `"linear"`. This parameter controls how interpolation is performed. If this argument is set to `"steps"`, the curves will be treated as step functions. If it is set to `"linear"`, the curves wil be treated as if there are straight lines between the point estimates instead. Points that lie between estimated points will be interpolated accordingly.
`contrast`	A single character string, specifying which contrast should be estimated. Needs to be one of `"none"` (estimate no contrasts, just return the adjusted survival time quantile, the default), `"diff"` (estimate the difference) or `"ratio"` (estimate the ratio). When `conf_int=TRUE` is also specified and bootstrapping was performed in the original `adjustedsurv` call, this function will also estimate the corresponding standard error, the confidence interval and a p-value testing whether the difference is equal to 0 (or the ratio is equal to 1). To specify which difference/ratio should be calculated, the `group_1` and `group_2` arguments can be used. By default, the difference/ratio between the first and second level in `variable` is computed.
`group_1`	Optional argument to get a specific difference or ratio. This argument takes a single character string specifying one of the levels of the `variable` used in the original `adjustedsurv` function call. This group will be subtracted from. For example if `group_1="A"` and `group_2="B"` and `contrast=="diff"` the difference `A - B` will be used. If `NULL`, the order of the factor levels in the original data determines the order. Ignored if `contrast="none"`.
`group_2`	Also a single character string specifying one of the levels of `variable`. This corresponds to the right side of the difference/ratio equation. See argument `group_2`. Ignored if `contrast="none"`.

Details

The median survival time is simply the time when half the patients are expected to be alive. The chance of surviving beyond that time is 50 percent. In general, any quantile can be calculated this way. Those can be read directly from the respective survival curve by drawing a straight line from the desired quantile p on the Y-Axis and reading the X-Axis value where this line intersects with the survival curve. The adjusted survival time quantile for group z (corresponding to the variable argument in the adjustedsurv function) is formally defined as:

\hat{Q}_z(p) = min\left(t | \hat{S}_z(t) \leq p\right)

where \hat{S}_z(t) is the estimated counterfactual survival function for z.

If the survival probability never drops below p, the survival time quantile cannot be calculated. This function calculates this quantity automatically.

Confidence intervals

When estimating the adjusted survival time quantiles directly, the confidence intervals are simply read off the survival curves similarly to the point estimates. For example, this means that the lower limit of the confidence interval for some survival time quantile is simply the first point in time at which the curve defined by the lower confidence limit goes below p.

If contrast="none", a different approach is used. Note that this functionality works only with bootstrapping (regardless of whether use_boot is TRUE or FALSE). In this case, the survival time quantiles are calculated for each bootstrap sample separately first. Afterwards, the standard deviation of the resulting estimates is calculated for each group. For differences, the pooled standard error is then estimated as SE_{group_1 - group_2} = \sqrt{SE_{group_1}^2 + SE_{group_2}^2} and used along with the normal approximation to calculate confidence intervals. This is similar to the strategy of Wu (2011). The p-value is also estimated using the pooled standard error and a one-sample two-sided t-test with the null-hypothesis that the difference is equal to 0. The confidence interval and p-value of the ratio is estimated using the method of Fieller (1954).

If one or both of the survival time quantiles used for the difference / ratio calculation could not be estimated from the respective bootstrap sample (due to the curves not extending that far) it is simply discarded.

More than Two Groups

If more than two groups are present in variable, all other comparisons except for group_1 vs. group_2 are ignored. If multiple comparisons are desired, the user needs to call this function multiple times and adjust the group_1 and group_2 arguments accordingly.

Multiple Imputation

If multiple imputation was used in the original function call, the survival time quantiles are read off the final pooled survival curves directly. This also works when using contrast="diff" or contrast="ratio". When using either contrast="diff" or contrast="ratio" in conjunction with conf_int=TRUE (plus bootstrapping), the standard errors of the difference or ratio are estimated for each imputed dataset separately and pooled using Rubins Rule afterwards. The pooled standard errors are then used to perform the same calculations as described above.

Value

Returns a data.frame containing the columns p (the quantiles from the original function call), group (groups in variable) and q_surv (the survival time quantile).

If conf_int=TRUE was used it also includes the confidence limits in the ci_lower and ci_upper columns.

If contrast="diff" was used, the resulting data.frame instead contains the columns p (the quantiles from the original function all) and diff (the difference between the two survival time quantiles). If conf_int=TRUE was used it additionally contains the columns se (the standard deviation of the bootstrap estimates), ci_lower and ci_upper (the confidence interval) and n_boot (the number of bootstrap samples that could be used). The output is similar when using contrast="ratio", except that the diff column is called ratio.

Author(s)

Robin Denz

References

Omer Ben-Aharon, Racheli Magnezi, Moshe Leshno, and Daniel A. Goldstein (2019). "Median Survival or Mean Survival: Which Measure is the Most Appropriate for Patients, Physicians, and Policymakers?" In: The Oncologist 24, pp. 1469-1478

Zhongxue Chen and Guoyi Zhang (2016). "Comparing Survival Curves based on Medians". In: BMC Medical Research Methodology 16.33

Jianrong Wu (2011). "Confidence Intervals for the Difference of Median Failure Times Applied to Censored Tumor Growth Delay Data". In: Statistics in Biopharmaceutical Research 3.3, pp. 488-496

Edgar C. Fieller (1954). "Some Problems in Interval Estimation". In: Journal of the Royal Statistical Society, Series B 16.2, pp. 175-185

Examples

library(adjustedCurves)
library(survival)

# simulate some data as example
set.seed(42)
sim_dat <- sim_confounded_surv(n=50, max_t=1.2)
sim_dat$group <- as.factor(sim_dat$group)

# estimate a cox-regression for the outcome
cox_mod <- coxph(Surv(time, event) ~ x1 + x2 + x3 + x4 + x5 + x6 + group,
                 data=sim_dat, x=TRUE)

# use it to calculate adjusted survival curves with bootstrapping
adjsurv <- adjustedsurv(data=sim_dat,
                        variable="group",
                        ev_time="time",
                        event="event",
                        method="direct",
                        outcome_model=cox_mod,
                        conf_int=TRUE,
                        bootstrap=FALSE)

# calculate adjusted median survival times
adjusted_surv_quantile(adjsurv)

# calculate difference of adjusted median survival times between groups
adjusted_surv_quantile(adjsurv, contrast="diff")

# calculate other quantiles + confidence intervals
adjusted_surv_quantile(adjsurv, conf_int=TRUE, p=c(0.2, 0.4))

[Package adjustedCurves version 0.11.1 Index]