Comments (5)
Experimental support has been added to PR #243
Please note that you need to indicate exponentiate = TRUE
from broom.helpers.
Fantastic, thank you for such a quick update @larmarange!
from broom.helpers.
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.
Sorry. There was an error in the implementation. Could you check the last version. Now exponentiate is optionnal.
from broom.helpers.
Success! Thank you very much.
from broom.helpers.
Related Issues (20)
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- fantastic support of multivariate quantile regression for any quantile HOT 1
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- order of variable levels with marginal tidiers HOT 8
- Release broom.helpers 1.15.0
- Take into account (id) when computing model_get_n() for coxph models
- `marginaleffects::datagridcf()` is deprecated
- Do you know the status of the {margins} pkg? HOT 3
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from broom.helpers.