CODEWITHSUNDEEP
rcox-regressionemmeans
LucaS
LucaS

Reputation: 1303

How to identify relevant strings in this emmeans() output

I am interested in plotting the HR from a coxph() model for a categorical-continuous interaction. Basically estimating the binary HR at multiple values of the continuous predictor and then plotting them. I can do the estimation bit, but I am interested to see if there's an easier way to identify and filter the relevant contrasts from the generation of all pairwise contrasts. The code below produces:

library(survival)
library(emmeans)

# Fit model with covariate-covariate interaction
fit <- coxph(Surv(time, status) ~ trt * karno, data = veteran)
summary(fit)

# Estimate trt HR at different values of karno
emm_df <-  emmeans(fit, ~ trt + karno, at = list(karno = seq(0, 100, by = 5)), type = "unlink") |> pairs(rev = T) |> summary(infer = T)

head(emm_df)
 contrast                  ratio     SE  df asymp.LCL asymp.UCL null z.ratio p.value
 trt2 karno0 / trt1 karno0 2.984 1.8095 Inf    0.2785    31.970    1   1.803  0.9996
 trt1 karno5 / trt1 karno0 0.885 0.0346 Inf    0.7592     1.031    1  -3.139  0.4244
 trt1 karno5 / trt2 karno0 0.296 0.1715 Inf    0.0309     2.848    1  -2.102  0.9922
 trt2 karno5 / trt1 karno0 2.438 1.4338 Inf    0.2445    24.314    1   1.516  1.0000
 trt2 karno5 / trt2 karno0 0.817 0.0263 Inf    0.7206     0.927    1  -6.285  <.0001
 trt2 karno5 / trt1 karno5 2.756 1.5413 Inf    0.3095    24.550    1   1.813  0.9996

How would I filter only those contrasts of trt2/trt1 at the same values of karno? e.g. I only want to keep: trt2 karno0 / trt1 karno0 trt2 karno5 / trt1 karno5 trt2 karno10 / trt1 karno10 etc

It would be even handier if I could convert this variable to numeric on the fly (ready for plotting) e.g. converting those categories above to 0,5,10,etc

Thanks

Upvotes: 4

Views: 89

Answers (2)

Ben Bolker
Ben Bolker

Reputation: 226741

@Aaron's answer is better, but here's a brute force way to transform the character column into the numbers. It's a little clunky, but this will get you a data frame with the karno values of the interaction as the first two (character) columns:

stringr::str_extract_all(emm_df$contrast, "(?<=karno)[0-9]+") |>
   do.call(what = "rbind") |>
   as.data.frame() |>
   setNames(c("karno1", "karno2")) |>
   dplyr::bind_cols(df2 = emm_df)

The key is using stringr::str_extract_all with a lookbehind regular expression to get the bits you want: the rest is just farting around with formats ...

Upvotes: 4

Aaron - mostly inactive
Aaron - mostly inactive

Reputation: 37804

Use the | notation: emmeans(fit, ~ trt | karno, ...)

Upvotes: 4

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