ggforest ignores interactions and polynomial or spline terms

[fabian-s]

Expected behavior

ggforest shows all estimated coefficients

Actual behavior/Steps to reproduce the problem:

library("survival")
library("survminer")

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."))
  })
model <- coxph(
  Surv(time, status) ~ sex * rx + adhere + differ + extent + node4 + poly(age, 3),
  data = colon)
ggforest(model)
## Warning messages:
## 1: In .get_data(model, data = data) :
##  The `data` argument is not provided. Data will be extracted from model fit.
## 2: Removed 5 rows containing missing values (geom_errorbar). 

So: neither the coefs for the interaction sex:rx nor the coefficients for the polynomials are shown.

The problem is that

survminer/R/ggforest.R

Line 49 in 94fb918

terms <- attr(model$terms, "dataClasses")[-1]

and following

• only yield variable names but should extract all terms
• do not allow for the case that numerical variables have multiple associated coefficients (splines, poly)

---

> devtools::session_info()
Session info -------------------------------------------------------
 setting  value                       
 version  R version 3.4.4 (2018-03-15)
 system   x86_64, linux-gnu           
 ui       RStudio (1.1.447)           
 language en                          
 collate  en_US.UTF-8                 
 tz       Europe/Berlin               
 date     2018-05-04                  

Packages -----------------------------------------------------------
 package    * version    date       source                          
 assertthat   0.2.0      2017-04-11 CRAN (R 3.4.1)                  
 base       * 3.4.4      2018-03-16 local                           
 bindr        0.1.1      2018-03-13 CRAN (R 3.4.3)                  
 bindrcpp     0.2.2      2018-03-29 CRAN (R 3.4.4)                  
 broom        0.4.4      2018-03-29 CRAN (R 3.4.4)                  
 cmprsk       2.2-7      2014-06-17 CRAN (R 3.4.1)                  
 colorspace   1.3-2      2016-12-14 CRAN (R 3.4.3)                  
 compiler     3.4.4      2018-03-16 local                           
 data.table   1.10.4-3   2017-10-27 CRAN (R 3.4.3)                  
 datasets   * 3.4.4      2018-03-16 local                           
 devtools     1.13.5     2018-02-18 CRAN (R 3.4.3)                  
 digest       0.6.15     2018-01-28 CRAN (R 3.4.3)                  
 dplyr        0.7.4      2017-09-28 CRAN (R 3.4.3)                  
 foreign      0.8-69     2017-06-21 CRAN (R 3.4.0)                  
 ggplot2    * 2.2.1      2016-12-30 CRAN (R 3.4.4)                  
 ggpubr     * 0.1.6      2017-11-14 CRAN (R 3.4.3)                  
 glue         1.2.0      2017-10-29 CRAN (R 3.4.3)                  
 graphics   * 3.4.4      2018-03-16 local                           
 grDevices  * 3.4.4      2018-03-16 local                           
 grid         3.4.4      2018-03-16 local                           
 gridExtra    2.3        2017-09-09 CRAN (R 3.4.3)                  
 gtable       0.2.0      2016-02-26 CRAN (R 3.3.0)                  
 km.ci        0.5-2      2009-08-30 CRAN (R 3.4.1)                  
 KMsurv       0.1-5      2012-12-03 CRAN (R 3.4.1)                  
 knitr        1.20       2018-02-20 CRAN (R 3.4.3)                  
 labeling     0.3        2014-08-23 CRAN (R 3.3.0)                  
 lattice      0.20-35    2017-03-25 CRAN (R 3.3.3)                  
 lazyeval     0.2.1      2017-10-29 CRAN (R 3.4.3)                  
 magrittr   * 1.5        2014-11-22 CRAN (R 3.4.3)                  
 Matrix       1.2-14     2018-04-09 CRAN (R 3.4.4)                  
 memoise      1.1.0      2017-04-21 CRAN (R 3.4.3)                  
 methods    * 3.4.4      2018-03-16 local                           
 mnormt       1.5-5      2016-10-15 CRAN (R 3.4.1)                  
 munsell      0.4.3      2016-02-13 CRAN (R 3.3.0)                  
 nlme         3.1-137    2018-04-07 CRAN (R 3.4.4)                  
 parallel     3.4.4      2018-03-16 local                           
 pillar       1.2.2      2018-04-26 CRAN (R 3.4.4)                  
 pkgconfig    2.0.1      2017-03-21 CRAN (R 3.4.1)                  
 plyr         1.8.4      2016-06-08 CRAN (R 3.3.0)                  
 psych        1.8.3.3    2018-03-30 CRAN (R 3.4.4)                  
 purrr        0.2.4      2017-10-18 cran (@0.2.4)                   
 R6           2.2.2      2017-06-17 CRAN (R 3.4.1)                  
 Rcpp         0.12.16    2018-03-13 CRAN (R 3.4.3)                  
 reshape2     1.4.3      2017-12-11 CRAN (R 3.4.3)                  
 rlang        0.2.0.9001 2018-04-17 Github (r-lib/rlang@82b2727)    
 scales       0.5.0.9000 2018-03-28 Github (hadley/scales@d767915)  
 splines      3.4.4      2018-03-16 local                           
 stats      * 3.4.4      2018-03-16 local                           
 stringi      1.1.7      2018-03-12 CRAN (R 3.4.3)                  
 stringr      1.3.0      2018-02-19 CRAN (R 3.4.3)                  
 survival   * 2.42-3     2018-04-16 CRAN (R 3.4.4)                  
 survminer  * 0.4.2      2018-01-31 CRAN (R 3.4.3)                  
 survMisc     0.5.4      2016-11-23 CRAN (R 3.4.3)                  
 tibble       1.4.2      2018-01-22 CRAN (R 3.4.3)                  
 tidyr        0.8.0      2018-01-29 CRAN (R 3.4.3)                  
 tools        3.4.4      2018-03-16 local                           
 utils      * 3.4.4      2018-03-16 local                           
 withr        2.1.2      2018-03-28 Github (jimhester/withr@79d7b0d)
 xtable       1.8-2      2016-02-05 CRAN (R 3.3.0)                  
 yaml         2.1.18     2018-03-08 CRAN (R 3.4.3)                  
 zoo          1.8-1      2018-01-08 CRAN (R 3.4.3)            

[david-awam-jansen]

I am running into a similar issue, has this bean solved?

[DanChaltiel]

I'm also running into this exact issue, and made some kind of workaround.
If you want to use it without waiting for the patch, just add thos prefixes: survminer:::.get_data line 48, generics::tidy line 54 and generics::glance line 55.
Also, you could try to remove the lines 50-51 as a test, as they didn't change anything to me except increasing computing time (but may serve some purpose in very specific cases).

Here are the pull requests, sorry for the duplicate, I'm still quite github-newbie...

[rickyking]

I don't think it resolved. I still can't get the interaction factors.

[kassambara]

solution to show interaction is provided at #496 #496

[mmfalco]

this solution doesn't work if you have both numerical and categorical variables, right?