| Title: | Assessing Surrogacy with a Censored Outcome |
| Version: | 1.0 |
| Description: | Identifies the optimal transformation of a surrogate marker and estimates the proportion of treatment explained (PTE) by the optimally-transformed surrogate at an earlier time point when the primary outcome of interest is a censored time-to-event outcome; details are described in Wang et al (2021) <doi:10.1002/sim.9185>. |
| License: | GPL-3 |
| Encoding: | UTF-8 |
| LazyData: | true |
| RoxygenNote: | 7.1.1 |
| Depends: | R (≥ 2.10) |
| Suggests: | testthat, stats |
| NeedsCompilation: | no |
| Packaged: | 2022-09-29 11:19:00 UTC; parastlm |
| Author: | Xuan Wang [aut], Clara-Lea Bonzel [aut], Tianxi Cai [aut], Layla Parast [aut, cre], PARSE LTD [aut] |
| Maintainer: | Layla Parast <parast@austin.utexas.edu> |
| Repository: | CRAN |
| Date/Publication: | 2022-09-29 13:10:01 UTC |
Simulated data for the example.
Description
Simulated data for the example.
Usage
data.example
Format
A data list with 5 elements:
- t.0
time at which the surrogate is measured
- t
time at which the primary outcome is measured
- xob
observed survival time
- s.ob
surrogate information at t.0
- deltaob
event indicator
- aob
treatment indicator
Estimates the proportion of treatment effect explained
Description
Estimates the proportion of treatment effect explained by the optimally transformed surrogate
Usage
pte.survival(xob, s.ob, deltaob, aob, t, t.0, varind = 0, re = 100)
Arguments
xob |
observed survival time |
s.ob |
surrogate information at time t.0 |
deltaob |
event indicator |
aob |
treatment indicator |
t |
time at which the primary outcome is measured |
t.0 |
time at which the surrogate is measured |
varind |
whether to estimate variance (yes=0, no=1) |
re |
number of replications for resampling, if varind=0 |
Value
A list of the following:
pte.est |
The estimated proportion of treatment effect explained (PTE) by the optimally transformed surrogate |
pte.ese |
Standard error estimate for the PTE, provided if var.ind=0 |
g1.est |
Estimated g1 |
g1.ese |
Standard error estimate for ge, provided if var.ind = 0 |
sgrid |
Grid used for the surrogate marker, equally spaced |
gs.est |
Estimated g(s), optimal transformation of s, for the sgrid |
gs.ese |
Standard error estimate for g(s), provided if var.ind = 0 |
Examples
# load the data
data("sysdata")
# time at which the surrogate is measured
t.0 = data.example$t.0
# time at which the primary outcome is measured
t = data.example$t
# observed survival time
xob = data.example$data$xob
# surrogate information at t.0
s.ob = data.example$data$s.ob
# event indicator
deltaob = data.example$data$deltaob
# treatment indicator
aob = data.example$data$aob
# main estimation function
# varind: whether to estimate variance; re:number of replications for resampling
out = pte.survival(xob, s.ob, deltaob, aob, t, t.0, varind=0, re=100)
# estimated PTE
out$pte.est
# estimated g1
out$g1.est
# estimated g2(s) at equally spaced s point
plot(out$sgrid, out$gs.est, type="l", xlab = "Surrogate Marker", ylab = "Optimal Transformation")
#The PTE result indicates that this is a moderate to high surrogate marker in this setting.