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Every categorical level should have one reference level for a cox's regression
In the forest plot, there are multiple reference levels
library(survival) library(survminer) require("survival") model <- coxph( Surv(time, status) ~ sex + rx + adhere, data = colon ) ggforest(model) colon <- within(colon, { sex <- factor(sex, labels = c("female", "male")) differ <- factor(differ, labels = c("well", "moderate", "poor")) extent <- factor(extent, labels = c("submuc.", "muscle", "serosa", "contig.")) }) bigmodel <- coxph(Surv(time, status) ~ sex + rx + adhere + differ + extent + node4, data = colon ) p <- ggforest(bigmodel) print(p)
session_info()
R version 3.5.1 (2018-07-02) Platform: x86_64-conda_cos6-linux-gnu (64-bit) Running under: Ubuntu 20.04.6 LTS
Matrix products: default BLAS: /opt/spark/work-dir/environment/lib/R/lib/libRblas.so LAPACK: /opt/spark/work-dir/environment/lib/R/lib/libRlapack.so
locale: [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] RCurl_1.98-1.2 dplyr_0.8.5 survminer_0.4.6 [4] ggpubr_0.2.5 magrittr_2.0.3 ggplot2_3.3.0 [7] survival_3.1-12 arrow_3.0.0 evaluate_0.14 [10] uuid_0.1-4 FoundrySparkR_0.2.0 SparkR_3.2.1 [13] vector_0.0.2 jsonlite_1.6.1 futile.logger_1.4.3
loaded via a namespace (and not attached): [1] zoo_1.8-7 tidyselect_1.1.2 xfun_0.33 [4] purrr_0.3.4 splines_3.5.1 lattice_0.20-41 [7] colorspace_1.4-1 vctrs_0.4.1 generics_0.0.2 [10] survMisc_0.5.5 rlang_1.0.6 pillar_1.4.3 [13] glue_1.6.2 withr_2.2.0 bit64_0.9-7 [16] lambda.r_1.2.4 lifecycle_0.2.0 munsell_0.5.0 [19] ggsignif_0.6.0 gtable_0.3.0 labeling_0.3 [22] knitr_1.28 broom_0.5.6 Rcpp_1.0.6 [25] xtable_1.8-4 scales_1.1.0 backports_1.2.1 [28] formatR_1.7 farver_2.0.3 km.ci_0.5-2 [31] bit_1.1-15.2 gridExtra_2.3 digest_0.6.25 [34] KMsurv_0.1-5 cowplot_1.0.0 grid_3.5.1 [37] bitops_1.0-6 cli_3.4.1 tools_3.5.1 [40] tibble_3.0.1 futile.options_1.0.1 crayon_1.3.4 [43] tidyr_1.0.2 pkgconfig_2.0.3 ellipsis_0.3.0 [46] Matrix_1.2-18 data.table_1.12.8 assertthat_0.2.1 [49] R6_2.4.1 nlme_3.1-147 compiler_3.5.1
# please paste here the result of devtools::session_info()
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Expected behavior
Every categorical level should have one reference level for a cox's regression
Actual behavior
In the forest plot, there are multiple reference levels
Steps to reproduce the problem
session_info()
R version 3.5.1 (2018-07-02)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS
Matrix products: default
BLAS: /opt/spark/work-dir/environment/lib/R/lib/libRblas.so
LAPACK: /opt/spark/work-dir/environment/lib/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RCurl_1.98-1.2 dplyr_0.8.5 survminer_0.4.6
[4] ggpubr_0.2.5 magrittr_2.0.3 ggplot2_3.3.0
[7] survival_3.1-12 arrow_3.0.0 evaluate_0.14
[10] uuid_0.1-4 FoundrySparkR_0.2.0 SparkR_3.2.1
[13] vector_0.0.2 jsonlite_1.6.1 futile.logger_1.4.3
loaded via a namespace (and not attached):
[1] zoo_1.8-7 tidyselect_1.1.2 xfun_0.33
[4] purrr_0.3.4 splines_3.5.1 lattice_0.20-41
[7] colorspace_1.4-1 vctrs_0.4.1 generics_0.0.2
[10] survMisc_0.5.5 rlang_1.0.6 pillar_1.4.3
[13] glue_1.6.2 withr_2.2.0 bit64_0.9-7
[16] lambda.r_1.2.4 lifecycle_0.2.0 munsell_0.5.0
[19] ggsignif_0.6.0 gtable_0.3.0 labeling_0.3
[22] knitr_1.28 broom_0.5.6 Rcpp_1.0.6
[25] xtable_1.8-4 scales_1.1.0 backports_1.2.1
[28] formatR_1.7 farver_2.0.3 km.ci_0.5-2
[31] bit_1.1-15.2 gridExtra_2.3 digest_0.6.25
[34] KMsurv_0.1-5 cowplot_1.0.0 grid_3.5.1
[37] bitops_1.0-6 cli_3.4.1 tools_3.5.1
[40] tibble_3.0.1 futile.options_1.0.1 crayon_1.3.4
[43] tidyr_1.0.2 pkgconfig_2.0.3 ellipsis_0.3.0
[46] Matrix_1.2-18 data.table_1.12.8 assertthat_0.2.1
[49] R6_2.4.1 nlme_3.1-147 compiler_3.5.1
The text was updated successfully, but these errors were encountered: