Comments (6)
Can you please provide a reproducible example and clarify what output you were expecting?
from proc.
Hi!
Thanks for the fast reply.
The data is attached. I am expecting to see that the AUROC of score_new is superior in terms of p-value than the score_old_2 and score_old_3. The variable status is the endpoint.
from proc.
Please clarify, what p-value were you expecting exactly? Or is this a request to handle ROC curves with different direction
arguments in delong.test?
from proc.
With score_new vs. score_old_3 I am expecting a p-value<0.05, but I receive the error message. So should I use another test or could I compute this with Delong somehow?
However, I do not thrust the results of the script below.
library(pROC)
auroc <- read.csv("a.csv", header=TRUE)
score_old_3 <- roc(response = auroc$endpoint, predictor = auroc$score_old_3)
score_new <- roc(response = auroc$endpoint, predictor = auroc$score_new)
roc.test(score_new, score_old_3, method = "delong")
from proc.
I cannot reproduce. Both score_old_3
and score_new
have the same direction (<
) and I get a p=0.02 and no warning.
What versions of R and pROC are you using? Please post the output of packageDescription("pROC")
and sessionInfo()
See the full transcript of what I am getting below. How does it differ from yours?
R version 3.4.1 (2017-06-30) -- "Single Candle"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(xlsx)
Loading required package: rJava
Loading required package: xlsxjars
> auroc <- read.xlsx("a.xlsx", 1)
>
> library(pROC)
Type 'citation("pROC")' for a citation.
Attaching package: ‘pROC’
The following objects are masked from ‘package:stats’:
cov, smooth, var
> score_old_3 <- roc(response = auroc$endpoint, predictor = auroc$score_old_3)
> print(score_old_3)
Call:
roc.default(response = auroc$endpoint, predictor = auroc$score_old_3)
Data: auroc$score_old_3 in 9 controls (auroc$endpoint 0) < 47 cases (auroc$endpoint 1).
Area under the curve: 0.5662
> score_new <- roc(response = auroc$endpoint, predictor = auroc$score_new)
> print(score_new)
Call:
roc.default(response = auroc$endpoint, predictor = auroc$score_new)
Data: auroc$score_new in 9 controls (auroc$endpoint 0) < 47 cases (auroc$endpoint 1).
Area under the curve: 0.8487
> roc.test(score_new, score_old_3, method = "delong")
DeLong's test for two correlated ROC curves
data: score_new and score_old_3
Z = 2.3215, p-value = 0.02026
alternative hypothesis: true difference in AUC is not equal to 0
sample estimates:
AUC of roc1 AUC of roc2
0.8486998 0.5661939
from proc.
In the absence of feedback I am closing this bug. Please feel free to reopen this issue if the problem still persists and you can provide additional information that could help reproduce it.
from proc.
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from proc.