[R] How to make a nomogam and Calibration plot

[Frank Harrell]

The nomogram you included was produced by the Design package, the precursor
to the rms package.  You will have to take the time to intensively read the
rms package documentation.  Note that how you developed the model (e.g.,
allowing for non-linearity in log PSA, not using stepwise regression which
invalidates the results, making sure all clinically relevant predictors are
in the model, ...) is the most important step.  The process you are going
through generally requires an M.S. in biostatistics.
Frank

sytangping wrote:
> 
> 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 
> 


-----
Frank Harrell
Department of Biostatistics, Vanderbilt University
--
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