Comments (5)
larmarange
commented on July 20, 2024
Experimental support has been added to PR #243
Please note that you need to indicate exponentiate = TRUE
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jalavery
commented on July 20, 2024
Fantastic, thank you for such a quick update @larmarange!
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jalavery
commented on July 20, 2024
I re-ran the test example, and it looks like even with exponentiate = TRUE, the values displayed on the table are the un-exponentiated values. Would you mind please looking into this whenever you have a chance? Thank you!
library(survival)
#> Warning: package 'survival' was built under R version 4.1.3
library(gtsummary)
#> Warning: package 'gtsummary' was built under R version 4.1.3
# case-cohort model using the survival::cch function
# example from survival::cch()
## The complete Wilms Tumor Data
## (Breslow and Chatterjee, Applied Statistics, 1999)
## subcohort selected by simple random sampling.
##
subcoh <- nwtco$in.subcohort
selccoh <- with(nwtco, rel==1|subcoh==1)
ccoh.data <- nwtco[selccoh,]
ccoh.data$subcohort <- subcoh[selccoh]
## central-lab histology
ccoh.data$histol <- factor(ccoh.data$histol,labels=c("FH","UH"))
## tumour stage
ccoh.data$stage <- factor(ccoh.data$stage,labels=c("I","II","III","IV"))
ccoh.data$age <- ccoh.data$age/12 # Age in years
##
## Standard case-cohort analysis: simple random subcohort
##
fit.ccP <- cch(Surv(edrel, rel) ~ stage + histol + age, data =ccoh.data,
subcoh = ~subcohort, id=~seqno, cohort.size=4028)
summary(fit.ccP)
#> Case-cohort analysis,x$method, Prentice
#> with subcohort of 668 from cohort of 4028
#>
#> Call: cch(formula = Surv(edrel, rel) ~ stage + histol + age, data = ccoh.data,
#> subcoh = ~subcohort, id = ~seqno, cohort.size = 4028)
#>
#> Coefficients:
#> Coef HR (95% CI) p
#> stageII 0.735 2.085 1.498 2.900 0.000
#> stageIII 0.597 1.817 1.293 2.552 0.001
#> stageIV 1.384 3.991 2.672 5.963 0.000
#> histolUH 1.498 4.473 3.271 6.117 0.000
#> age 0.043 1.044 0.997 1.094 0.068
# tidy model output: success
broom::tidy(fit.ccP)
#> # A tibble: 5 x 7
#> term estimate std.error statistic p.value conf.low conf.high
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 stageII 0.735 0.168 4.36 1.30e- 5 0.404 1.06
#> 2 stageIII 0.597 0.173 3.44 5.77e- 4 0.257 0.937
#> 3 stageIV 1.38 0.205 6.76 1.40e-11 0.983 1.79
#> 4 histolUH 1.50 0.160 9.38 0 1.19 1.81
#> 5 age 0.0433 0.0237 1.82 6.83e- 2 -0.00324 0.0898
# this now runs
broom.helpers::tidy_plus_plus(fit.ccP, exponentiate = TRUE) %>%
select(term, label, estimate)
#> # A tibble: 7 x 3
#> term label estimate
#> <chr> <chr> <dbl>
#> 1 stageI I 1
#> 2 stageII II 0.735
#> 3 stageIII III 0.597
#> 4 stageIV IV 1.38
#> 5 histolFH FH 1
#> 6 histolUH UH 1.50
#> 7 age age 0.0433
# however, the log(HR) is being displayed as the HR, and the exponentiation seems to not be working
# HR for stage II should be exp(0.74) = 2.08 based on summary(fit.ccP)
# gtsummary::tbl_regression(fit.ccP, exponentiate = TRUE)Created on 2024-01-24 with reprex v2.0.2
Session info
sessioninfo::session_info()
#> - Session info ---------------------------------------------------------------
#> setting value
#> version R version 4.1.2 (2021-11-01)
#> os Windows 10 x64 (build 19045)
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate English_United States.1252
#> ctype English_United States.1252
#> tz America/New_York
#> date 2024-01-24
#> pandoc 3.1.1 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
#>
#> - Packages -------------------------------------------------------------------
#> package * version date (UTC) lib source
#> backports 1.4.1 2021-12-13 [1] CRAN (R 4.1.2)
#> broom 1.0.5 2023-06-09 [1] CRAN (R 4.1.2)
#> broom.helpers 1.14.0.9000 2024-01-24 [1] local
#> cli 3.4.1 2022-09-23 [1] CRAN (R 4.1.3)
#> colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.1.3)
#> digest 0.6.30 2022-10-18 [1] CRAN (R 4.1.3)
#> dplyr 1.1.0 2023-01-29 [1] CRAN (R 4.1.3)
#> ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.0.5)
#> evaluate 0.20 2023-01-17 [1] CRAN (R 4.1.3)
#> fansi 1.0.4 2023-01-22 [1] CRAN (R 4.1.3)
#> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.0.5)
#> forcats 1.0.0 2023-01-29 [1] CRAN (R 4.1.3)
#> fs 1.5.2 2021-12-08 [1] CRAN (R 4.1.3)
#> generics 0.1.3 2022-07-05 [1] CRAN (R 4.1.3)
#> ggplot2 3.4.1 2023-02-10 [1] CRAN (R 4.1.3)
#> glue 1.6.2 2022-02-24 [1] CRAN (R 4.1.2)
#> gt 0.8.0 2022-11-16 [1] CRAN (R 4.1.3)
#> gtable 0.3.1 2022-09-01 [1] CRAN (R 4.1.3)
#> gtsummary * 1.7.0 2023-01-13 [1] CRAN (R 4.1.3)
#> haven 2.5.2 2023-02-28 [1] CRAN (R 4.1.3)
#> hms 1.1.2 2022-08-19 [1] CRAN (R 4.1.3)
#> htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.1.3)
#> knitr 1.42 2023-01-25 [1] CRAN (R 4.1.3)
#> labelled 2.10.0 2022-09-14 [1] CRAN (R 4.1.3)
#> lattice 0.20-45 2021-09-22 [1] CRAN (R 4.1.2)
#> lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.1.3)
#> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.1.3)
#> Matrix 1.5-3 2022-11-11 [1] CRAN (R 4.1.3)
#> munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.0)
#> pillar 1.8.1 2022-08-19 [1] CRAN (R 4.1.3)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.0)
#> purrr 1.0.1 2023-01-10 [1] CRAN (R 4.1.3)
#> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.1.3)
#> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.1.3)
#> R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.1.3)
#> R.utils 2.12.2 2022-11-11 [1] CRAN (R 4.1.3)
#> R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.1)
#> reprex 2.0.2 2022-08-17 [1] CRAN (R 4.1.3)
#> rlang 1.1.1 2023-04-28 [1] CRAN (R 4.1.2)
#> rmarkdown 2.23 2023-07-01 [1] CRAN (R 4.1.2)
#> rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.1.3)
#> scales 1.2.1 2022-08-20 [1] CRAN (R 4.1.3)
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.1.3)
#> stringi 1.7.6 2021-11-29 [1] CRAN (R 4.1.2)
#> stringr 1.5.0 2022-12-02 [1] CRAN (R 4.1.3)
#> styler 1.8.1 2022-11-07 [1] CRAN (R 4.1.3)
#> survival * 3.4-0 2022-08-09 [1] CRAN (R 4.1.3)
#> tibble 3.1.8 2022-07-22 [1] CRAN (R 4.1.3)
#> tidyr 1.3.0 2023-01-24 [1] CRAN (R 4.1.3)
#> tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.1.2)
#> utf8 1.2.3 2023-01-31 [1] CRAN (R 4.1.3)
#> vctrs 0.6.3 2023-06-14 [1] CRAN (R 4.1.2)
#> withr 2.5.0 2022-03-03 [1] CRAN (R 4.1.2)
#> xfun 0.37 2023-01-31 [1] CRAN (R 4.1.3)
#> yaml 2.3.7 2023-01-23 [1] CRAN (R 4.1.3)
#>
#> [1] C:/Program Files/R/R-4.1.2/library
#>
#> ------------------------------------------------------------------------------from broom.helpers.
larmarange
commented on July 20, 2024
Sorry. There was an error in the implementation. Could you check the last version. Now exponentiate is optionnal.
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jalavery
commented on July 20, 2024
Success! Thank you very much.
from broom.helpers.
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