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+ License, or (at your option) any later version.
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+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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@@ -241,7 +241,7 @@What changes are proposed in this pull request?
If there is an GitHub issue associated with this pull request, please provide link.
Checklist for PR reviewer
-_pkgdown.yml
@@ -71,6 +71,8 @@ usethis::use_spell_check() runs with no spelling errors in documentationrevdepcheck::revdep_check() (https://github.com/r-lib/revdepcheck)When the branch is ready to be merged into master: - [ ] Update NEWS.md with the changes from this pull request under the heading “# tidycmprsk (development version)”. If there is an issue associated with the pull request, reference it in parentheses at the end of the update. - [ ] Increment the version number using usethis::use_version(which = "dev") - [ ] Run usethis::use_spell_check() again - [ ] Approve Pull Request - [ ] Merge the PR. Please use “Squash and merge”.
Sjoberg DD, Fei T (2022). +
Sjoberg DD, Fei T (2023). tidycmprsk: Competing Risks Estimation. -R package version 0.2.0.9001, https://mskcc-epi-bio.github.io/tidycmprsk/. +R package version 0.2.0.9003, https://mskcc-epi-bio.github.io/tidycmprsk/.
@Manual{,
title = {tidycmprsk: Competing Risks Estimation},
author = {Daniel D. Sjoberg and Teng Fei},
- year = {2022},
- note = {R package version 0.2.0.9001},
+ year = {2023},
+ note = {R package version 0.2.0.9003},
url = {https://mskcc-epi-bio.github.io/tidycmprsk/},
}
@@ -94,7 +94,7 @@ Plot risks using using the {ggsurvfit} package.
-library(ggsurvfit)
+library(ggsurvfit)
#> Loading required package: ggplot2
cuminc(Surv(ttdeath, death_cr) ~ trt, trial) %>%
@@ -247,7 +247,7 @@ Dev status
diff --git a/dev/news/index.html b/dev/news/index.html
index 867d629..8ae51ad 100644
--- a/dev/news/index.html
+++ b/dev/news/index.html
@@ -17,7 +17,7 @@
Corrected regression and cuminc() can again handle models with no observed censoring. (#89)
Updates ahead of the {purrr} v1.0 release.
The autoplot.tidycuminc() method has been deprecated in favor of ggsurvfit::ggcuminc(). (#81)
cuminc <- cuminc(Surv(ttdeath, death_cr) ~ trt, trial)
tidy(cuminc)
-#> # A tibble: 228 × 12
-#> time outcome strata estim…¹ std.e…² conf.low conf.…³ n.risk n.event n.cen…⁴
-#> <dbl> <chr> <fct> <dbl> <dbl> <dbl> <dbl> <int> <int> <int>
-#> 1 0 death f… Drug A 0 0 NA NA 98 0 0
-#> 2 3.53 death f… Drug A 0 0 NA NA 98 0 0
-#> 3 7.27 death f… Drug A 0.0102 0.0102 8.84e-4 0.0503 97 1 0
-#> 4 7.38 death f… Drug A 0.0204 0.0144 3.90e-3 0.0652 96 1 0
-#> 5 8.37 death f… Drug A 0.0204 0.0144 3.90e-3 0.0652 95 0 0
-#> 6 10.1 death f… Drug A 0.0204 0.0144 3.90e-3 0.0652 94 0 0
-#> 7 10.3 death f… Drug A 0.0204 0.0144 3.90e-3 0.0652 93 0 0
-#> 8 10.5 death f… Drug A 0.0204 0.0144 3.90e-3 0.0652 92 0 0
-#> 9 11.4 death f… Drug A 0.0306 0.0175 8.17e-3 0.0798 91 1 0
-#> 10 11.8 death f… Drug A 0.0306 0.0175 8.17e-3 0.0798 90 0 0
-#> # … with 218 more rows, 2 more variables: cum.event <int>, cum.censor <int>,
-#> # and abbreviated variable names ¹estimate, ²std.error, ³conf.high, ⁴n.censor
+#> # A tibble: 444 × 12
+#> time outcome strata estimate std.error conf.low conf.high n.risk n.event
+#> <dbl> <chr> <fct> <dbl> <dbl> <dbl> <dbl> <int> <int>
+#> 1 0 death from… Drug A 0 0 NA NA 98 0
+#> 2 3.53 death from… Drug A 0 0 NA NA 98 0
+#> 3 5.33 death from… Drug A 0 0 NA NA 97 0
+#> 4 6.32 death from… Drug A 0 0 NA NA 97 0
+#> 5 7.27 death from… Drug A 0.0102 0.0102 8.84e-4 0.0503 97 1
+#> 6 7.38 death from… Drug A 0.0204 0.0144 3.90e-3 0.0652 96 1
+#> 7 8.37 death from… Drug A 0.0204 0.0144 3.90e-3 0.0652 95 0
+#> 8 8.71 death from… Drug A 0.0204 0.0144 3.90e-3 0.0652 94 0
+#> 9 9.24 death from… Drug A 0.0204 0.0144 3.90e-3 0.0652 94 0
+#> 10 9.73 death from… Drug A 0.0204 0.0144 3.90e-3 0.0652 94 0
+#> # ℹ 434 more rows
+#> # ℹ 3 more variables: n.censor <int>, cum.event <int>, cum.censor <int>
glance(cuminc)
#> # A tibble: 1 × 8
-#> outcome_1 statistic_1 df_1 p.value_1 outcome_2 stati…¹ df_2 p.val…²
-#> <chr> <dbl> <dbl> <dbl> <chr> <dbl> <dbl> <dbl>
-#> 1 death from cancer 1.99 1 0.159 death oth… 0.0886 1 0.766
-#> # … with abbreviated variable names ¹statistic_2, ²p.value_2
+#> outcome_1 statistic_1 df_1 p.value_1 outcome_2 statistic_2 df_2 p.value_2
+#> <chr> <dbl> <dbl> <dbl> <chr> <dbl> <dbl> <dbl>
+#> 1 death from … 1.99 1 0.159 death ot… 0.0886 1 0.766
# restructure glance to one line per outcome
glance(cuminc) %>%
@@ -187,7 +186,7 @@ Examples