Survival Analysis
Chun-Hui Lin
2024-11-22
Last updated: 2024-12-03
Checks: 7 0
Knit directory: demor2/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 5776387 | Chun-Hui Lin | 2024-12-03 | Add power-related files. |
| html | d1baeee | Chun-Hui Lin | 2024-11-27 | Build site. |
| Rmd | 33e3e95 | Chun-Hui Lin | 2024-11-27 | Update survival page (competing risks regression section). |
| html | 32286dd | Chun-Hui Lin | 2024-11-26 | Build site. |
| Rmd | 0a3abb1 | Chun-Hui Lin | 2024-11-26 | Update survival page (median follow-up section). |
| html | 2af34c5 | Chun-Hui Lin | 2024-11-23 | Build site. |
| html | b8b756f | Chun-Hui Lin | 2024-11-23 | Build site. |
| html | b907743 | Chun-Hui Lin | 2024-11-23 | Build site. |
| Rmd | 6843808 | Chun-Hui Lin | 2024-11-23 | Add survival-related files. |
Some notes on conducting survival analyses inspiring by Zabor’s
tutorial using lung
dataset as the example.
Handle date-times stored as character with
lubridatepackage.Identify the order of the year (y), month (m), day (d), hour (h), minute (m) and second (s) elements in your variable and apply the corresponding
ymd_hms()function.%--%operator: equivalent todifftime(), such asas.duration(start.date %--% end.date)/dyears(x = 1).
Time-to-event outcomes: Cox PH regression; if the covariate violates the proportional hazards assumption, consider adding time interaction or stratifying by itself in the model.
- If subjexts have more than one possible events, conduct competing risks regression instead.
Kaplan-Meier Method
gtsummary::tbl_survfit()
Median Survival
survfit(Surv(time, status == 2) ~ sex, lung) %>%
tbl_survfit(prob = 0.5,
label = sex ~ 'Sex',
label_header = "**Median Survival (days)**") %>%
add_p() %>% # equivalent: survdiff()
modify_header(label ~ "") %>%
bold_labels()| Median Survival (days) | p-value1 | |
|---|---|---|
| Sex | 0.001 | |
| 1 | 270 (212, 310) | |
| 2 | 426 (348, 550) | |
| 1 Log-rank test | ||
Median Follow-up
The event of interest is loss-of-follow-up (censored) so we utilized KM method with reversed status indicator.
survfit(Surv(time, status == 1) ~ sex, lung) %>%
tbl_survfit(prob = 0.5,
label = sex ~ 'Sex',
label_header = "**Median Follow-up (days)**") %>%
add_p() %>%
modify_header(label ~ "") %>%
bold_labels()| Median Follow-up (days) | p-value1 | |
|---|---|---|
| Sex | 0.013 | |
| 1 | 840 (806, —) | |
| 2 | 529 (376, —) | |
| 1 Log-rank test | ||
1-year Survival
survfit(Surv(time, status) ~ sex, lung) %>%
tbl_survfit(times = 365.25, # speify 1-year probability
label = sex ~ 'Sex',
label_header = "**1-year Survival (%)**",
estimate_fun = ~ style_percent(.x, digits = 1)) %>%
add_p() %>%
modify_header(label ~ "") %>%
bold_labels()| 1-year Survival (%) | p-value1 | |
|---|---|---|
| Sex | 0.001 | |
| 1 | 33.6 (26.1, 43.3) | |
| 2 | 52.6 (42.1, 65.8) | |
| 1 Log-rank test | ||
survminer::ggsurvplot()
ggsurvplot(survfit(Surv(time, status) ~ sex, lung),
data = lung,
palette = c('#E7B800', '#2E9FDF'), # customize color palettes
linetype = 'strata', # line type by groups
conf.int = T, # add confidence interval
pval = T, # add p-value of log-rank test
surv.median.line = 'hv', # add median survival info
risk.table = T, # add risk table
risk.table.col = 'strata', # number at risk colored by groups
legend.title = 'Sex', # change legend title
legend.labs = c('Male', 'Female'), # change legend labels
xlab = 'Time in days', # customize x-axis label
ggtheme = theme_light())
| Version | Author | Date |
|---|---|---|
| 32286dd | Chun-Hui Lin | 2024-11-26 |
survminer::pairwise_survdiff()
# multiple comparisons of survival curves
pairwise_survdiff(Surv(ttdeath, death) ~ grade, trial)
Pairwise comparisons using Log-Rank test
data: trial and grade
I II
II 0.304 -
III 0.054 0.304
P value adjustment method: BH Cox PH Regression
gtsummary::tbl_regression()
tbl_regression(coxph(Surv(ttdeath, death) ~ trt + age + grade, trial),
exponentiate = T,
estimate_fun = ~ style_ratio(.x, digits = 2),
pvalue_fun = ~ style_pvalue(.x, digits = 2))| Characteristic | HR1 | 95% CI1 | p-value |
|---|---|---|---|
| Chemotherapy Treatment | |||
| Drug A | — | — | |
| Drug B | 1.30 | 0.88, 1.92 | 0.18 |
| Age | 1.01 | 0.99, 1.02 | 0.35 |
| Grade | |||
| I | — | — | |
| II | 1.21 | 0.73, 1.99 | 0.46 |
| III | 1.79 | 1.12, 2.86 | 0.014 |
| 1 HR = Hazard Ratio, CI = Confidence Interval | |||
survival::cox.zph()
# test the proportional hazards assumption of model
cox.zph(coxph(Surv(ttdeath, death) ~ trt + age + grade, trial)) chisq df p
trt 2.053 1 0.15
age 0.163 1 0.69
grade 4.365 2 0.11
GLOBAL 6.666 4 0.15survminer::ggforest()
ggforest()refLabel=argument: customize label for reference levels.
# visualize model by forest plot
ggforest(coxph(Surv(ttdeath, death) ~ trt + age + grade, as.data.frame(trial)),
refLabel = '--')
| Version | Author | Date |
|---|---|---|
| 32286dd | Chun-Hui Lin | 2024-11-26 |
Competing Risks Regression
cmprsk::cuminc()
cuminc(Surv(ttdeath, death_cr) ~ trt, trial) %>%
tbl_cuminc(
times = 12,
label_header = "**{time/12}-year Cumulative Incidence**",
estimate_fun = ~ style_percent(.x, digits = 1)) %>%
add_p() %>%
modify_header(label ~ "") %>%
bold_labels()| 1-year Cumulative Incidence | p-value1 | |
|---|---|---|
| Chemotherapy Treatment | 0.2 | |
| Drug A | 3.06% (0.82%, 7.98%) | |
| Drug B | 8.82% (4.31%, 15.3%) | |
| 1 Gray’s Test | ||
ggsurvfit::ggcuminc()
ggcuminc(cuminc(Surv(ttdeath, death_cr) ~ trt, trial)) +
add_confidence_interval() +
add_risktable() +
scale_ggsurvfit(x_scales = list(breaks = seq(0, 24, 6)))Plotting outcome "death from cancer".
| Version | Author | Date |
|---|---|---|
| d1baeee | Chun-Hui Lin | 2024-11-27 |
cmprsk::crr()
tbl_regression(crr(Surv(ttdeath, death_cr) ~ trt + age, trial),
exponentiate = T,
estimate_fun = ~ style_ratio(.x, digits = 2),
pvalue_fun = ~ style_pvalue(.x, digits = 2))11 cases omitted due to missing values| Characteristic | HR1 | 95% CI1 | p-value |
|---|---|---|---|
| Chemotherapy Treatment | |||
| Drug A | — | — | |
| Drug B | 1.52 | 0.88, 2.62 | 0.13 |
| Age | 1.01 | 0.99, 1.03 | 0.56 |
| 1 HR = Hazard Ratio, CI = Confidence Interval | |||
sessionInfo()R version 4.4.0 (2024-04-24)
Platform: aarch64-apple-darwin20
Running under: macOS 15.1.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Detroit
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggsurvfit_1.1.0 tidycmprsk_1.1.0 cmprsk_2.2-12 MASS_7.3-60.2
[5] gtsummary_2.0.3 survminer_0.4.9 ggpubr_0.6.0 ggplot2_3.5.1
[9] survival_3.7-0 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] tidyselect_1.2.1 dplyr_1.1.4 farver_2.1.2
[4] fastmap_1.2.0 broom.helpers_1.17.0 promises_1.3.0
[7] labelled_2.13.0 digest_0.6.37 lifecycle_1.0.4
[10] processx_3.8.4 magrittr_2.0.3 compiler_4.4.0
[13] rlang_1.1.4 sass_0.4.9 tools_4.4.0
[16] utf8_1.2.4 yaml_2.3.10 gt_0.10.1
[19] data.table_1.16.0 knitr_1.48 ggsignif_0.6.4
[22] labeling_0.4.3 xml2_1.3.6 abind_1.4-5
[25] withr_3.0.1 purrr_1.0.2 grid_4.4.0
[28] fansi_1.0.6 git2r_0.33.0 xtable_1.8-4
[31] colorspace_2.1-1 scales_1.3.0 cli_3.6.3
[34] rmarkdown_2.28 generics_0.1.3 rstudioapi_0.16.0
[37] km.ci_0.5-6 httr_1.4.7 commonmark_1.9.1
[40] cachem_1.1.0 stringr_1.5.1 splines_4.4.0
[43] survMisc_0.5.6 vctrs_0.6.5 hardhat_1.3.1
[46] Matrix_1.7-0 jsonlite_1.8.9 carData_3.0-5
[49] car_3.1-2 callr_3.7.6 patchwork_1.2.0
[52] hms_1.1.3 rstatix_0.7.2 tidyr_1.3.1
[55] jquerylib_0.1.4 glue_1.8.0 ps_1.7.6
[58] cowplot_1.1.3 ggtext_0.1.2 stringi_1.8.4
[61] gtable_0.3.5 later_1.3.2 munsell_0.5.1
[64] tibble_3.2.1 pillar_1.9.0 htmltools_0.5.8.1
[67] R6_2.5.1 KMsurv_0.1-5 rprojroot_2.0.4
[70] evaluate_1.0.0 lattice_0.22-6 haven_2.5.4
[73] markdown_1.12 highr_0.11 backports_1.5.0
[76] cards_0.3.0 gridtext_0.1.5 broom_1.0.7
[79] httpuv_1.6.15 bslib_0.8.0 Rcpp_1.0.13
[82] cardx_0.2.1 gridExtra_2.3 whisker_0.4.1
[85] xfun_0.47 forcats_1.0.0 fs_1.6.4
[88] zoo_1.8-12 getPass_0.2-4 pkgconfig_2.0.3