Error message from tidy(coxphFit)

[ghost]

I'm getting the following error message when I try to tidy a coxph fit from the survival package:

Error in seq_len(nrow(x)) : 
  argument must be coercible to non-negative integer
In addition: Warning message:
In seq_len(nrow(x)) : first element used of 'length.out' argument

Here is code to replicate the problem, note I first confirm that tidy works on a regression fit and they attempt it on a coxph fit

library(survival)
library(broom)

# Create data frame for the survival analysis
demoDat <- structure(list(daysFromInvestigation = c(1L, 6L, 7L, 5L, 5L, 
2L, 3L, 1L, 2L, 5L, 1L, 4L, 5L, 7L, 3L, 1L, 6L, 4L, 2L, 6L, 6L, 
7L, 7L, 6L, 4L, 2L, 2L, 4L, 0L, 5L, 5L, 4L, 4L, 1L, 7L, 7L, 1L, 
2L, 0L, 7L, 6L, 7L, 1L, 1L, 2L, 2L, 2L, 1L, 7L, 1L, 2L, 3L, 1L, 
1L, 2L), Sex = structure(c(2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 
2L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 2L, 2L, 
2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 
1L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 2L), .Label = c("F  ", 
"M  "), class = "factor"), dead = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1)), row.names = c(NA, -55L), class = "data.frame", .Names = c("daysFromInvestigation", 
"Sex", "dead"))


# To be sure that I've got the packages loaded and things work, demonstrate with a glm regression
demoFit <- glm(daysFromInvestigation ~ Sex, data=demoDat)
print(demoFit)
tidy(demoFit)

# Works great

# Now do coxph 
demoCoxFit <- coxph(Surv(demoDat$daysFromInvestigation, demoDat$dead) ~ Sex, data = demoDat)

print(demoCoxFit)

Which produces the following:

Call:
coxph(formula = Surv(demoDat$daysFromInvestigation, demoDat$dead) ~ 
    Sex, data = demoDat)


       coef exp(coef) se(coef)     z    p
SexM    0.2      1.22     0.34 0.588 0.56

Likelihood ratio test=0.36  on 1 df, p=0.549  n= 55, number of events= 55 

But when I run tidy on the fit, I get the error message at the beginning of this issue report

tidy(demoCoxFit)

[dgrtwo]

Looks like this was fixed by #36 and #37. They haven't been added to CRAN yet, but for now please try the development version:

devtools::install_github("dgrtwo/broom")

I'm planning to upload broom 0.3.7 to CRAN sometime this week, which will fix this.

[ghost]

That worked, thanks!

[dgrtwo]

broom 0.3.7 now on CRAN, along with this fix!

[github-actions]

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