[R] How to make a nomogam and Calibration plot

[sytangping]

Dear Harrell,

Many thanks for your quick response!
However, after try and try, I still have difficulty to solve my questions.
I post my questions again. I hope someone can help me run the data and draw
the nomogram and calibration plot for me. I know that is not good but indeed
I have no way to go. The problems almost drove me mad!

Best regards!

Ping Tang

Dear R users,

I am a new R user and something stops me when I try to write a academic
article. I want to make a nomogram to predict the risk of prostate cancer
(PCa) using several factors which have been selected from the Logistic
regression run under the SPSS. Always, a calibration plot is needed to
validate the prediction accuracy of the nomogram.
However, I tried many times and read a lot of posts with respect to this
topic but I still couldn't figure out how to draw the nomogram and the
calibration plot. Attached file is the dataset for the research. It will be
very grateful if someone can save his/her time to help for my questions.

Warmest regards!

Logistic Regression

Classification Tablea,b
	Observed	Predicted
		Pca-YN	Percentage Correct
		0	1	
Step 0	Pca-YN	0	295	0	100.0
		1	218	0	.0
	Overall Percentage			57.5


Variables in the Equation
		B	S.E.	Wald	df	Sig.	Exp(B)	95.0% C.I.for EXP(B)
								Lower	Upper
Step 1a	Age	.031	.015	4.491	1	.034	1.032	1.002	1.062
	DRE	1.173	.266	19.492	1	.000	3.233	1.920	5.443
	LogPV	-2.857	.509	31.532	1	.000	.057	.021	.156
	LogPSA	2.316	.246	88.416	1	.000	10.132	6.253	16.419
	Constant	-1.024	1.273	.648	1	.421	.359		
				

The equation:

Probability = 

 e-1.024+0.31age+1.173DRE+-2.857LogPV+2.316LogPSA
1+e-1.024+0.31age+1.173DRE+-2.857LogPV+2.316LogPSA

My questions are,

1.How to draw a nomogram (similar to the below figure 1) to predict the
probability of cancer using R?

2. How to make the Calibration plot (similar to the below figure 2) which
used to validate the prediction accuracy of the nomogram using R? And how to
calculate the concordance index (C-index) ?


http://r.789695.n4.nabble.com/file/n3714477/untitled.jpg 
http://r.789695.n4.nabble.com/file/n3714477/%E9%99%84%E4%BB%B62.jpg 
http://r.789695.n4.nabble.com/file/n3714477/Dataset.xls Dataset.xls 

--
View this message in context: http://r.789695.n4.nabble.com/How-to-make-a-nomogam-and-Calibration-plot-tp3710068p3714477.html
Sent from the R help mailing list archive at Nabble.com.