ci.coords returns a "ret" error for input = "threshold"

[pgcudahy]

Describe the bug When trying to use ci.coords with input="threshold" I get an error regarding ret="threshold"

To Reproduce

values <- c(81.3, 123.3, 42.9, 49.3, 31.9, 12.6, 23.3, 2, 165.8, 3.1, 13.6, 13.6, 10.4, 3.7, 2, 23.8, 47.5, 126.8, 10.3, 18.4)
categories <- c(1, 1, 1, 1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 0, 0, 1, 1, 1, 0, 1)
df <- data.frame(values=values, categories=categories, stringsAsFactors = FALSE)
roc1 <- roc(df$categories, df$values, data=df, plot = FALSE)
coords(roc1, 5, input="threshold")
ci.coords(roc1, 5, input="threshold")

Gives the error

Error in ci.coords.roc(roc1, 5, input = "threshold"): 'threshold' output is only supported for best ROC point ('x = "best"')
Traceback:

1. ci.coords(roc1, 5, input = "threshold")
2. ci.coords.roc(roc1, 5, input = "threshold")
3. stop("'threshold' output is only supported for best ROC point ('x = \"best\"')")

Expected behavior A confidence interval for sensitivity and specificity at the chosen threshold.

Additional context I can see why choosing a return threshold generates an error. But this is an input threshold.

[xrobin]

This is because you have an implied "threshold" in the default value of ret.

This will work right away, setting the return value without threshold:

> ci.coords(roc1, 5, input="threshold", ret=c("se", "sp"))
  |======================================================================| 100%
95% CI (2000 stratified bootstrap replicates):
                         2.5%    50% 97.5%
threshold 5: sensitivity  0.8 0.9333     1
threshold 5: specificity  0.2 0.6000     1 

The threshold itself won't vary.

However in this case it should indeed be possible to return a (constant) threshold. I will investigate why it isn't the case.

In addition the default value should probably be able to auto-detect whether 'threshold' can be computed.

[pgcudahy]

Thanks! Your solution works for me. I'm still a little confused, since a threshold is given by the user, what does it mean for the function to return a threshold, other than just show the input value? Shouldn't ret=c("se", "sp") be the default if the input is a threshold?

[xrobin]

I'm not sure if it should be the default. It's useful to ping it back in the case where many thresholds are given as input.

[xrobin]

Fixed. Threshold is kept by default whenever possible, and removed from the return values otherwise. I will attempt to push this to CRAN as 1.15.1 soon.