Utilizing Restricted Cubic Splines with PROC PHREG and Plotting the Results

fikel — Sat, 15 May 2021 06:36:10 GMT

I am doing survival analysis with proc phreg looking at a continuous nutrient exposure and colorectal cancer as the outcome. I have never performed restricted cubic splines analysis before and tried to find similar SAS posts and incorporate them into my model which I have listed here:

proc phreg data = want;
title "Colorectal-cancer incidence attempt";

effect resid_total_polys = spline(resid_total_poly / basis=tpf(noint) NATURALCUBIC details knotmethod=percentiles(4));

class categorical_covariate (ref="0");

model eof_age_CRC*Inc_CRC(0) =  resid_total_polys 
		categorical_covariate continuous_covariate
		/ entry=enrollment_agemonths rl=wald;
run;

First, I am not sure how to best compare the results of the spline models with the model I have done separately by quintiles. Should I compare the -2 Log L of the Global Fit Statistics or just use the P value (Pr >ChiSq) of testing the global null hypothesis output?

Second, I would like to be able to plot this data in a meaningful way, but am not sure how to appropriately plot this data or include 95% confidence bars if possible. I would hope it might look something like this:

Re: Utilizing Restricted Cubic Splines with PROC PHREG and Plotting the Results

fikel — Sat, 15 May 2021 19:54:31 GMT

I did some digging and was able to use this code:

proc phreg data = want; title "Colorectal-cancer incidence attempt"; effect resid_total_polys = spline(resid_total_poly / basis=tpf(noint) NATURALCUBIC details knotmethod=percentiles(4)); class categorical_covariate (ref="0"); model eof_age_CRC*Inc_CRC(0) = resid_total_polys categorical_covariate continuous_covariate / entry=enrollment_agemonths rl=wald; store work.coxr; run; %macro est(ref=212, start=0, end=3000, by=1); %Do i = 1 %To %eval(%SysFunc( Ceil( %SysEvalF( ( &End - &Start ) / &By ) ) ) +1) ; %Let value=%SysEvalF( ( &Start - &By ) + ( &By * &I ) ) ; estimate "&value." resid_total_polys [-1, &ref] [1, &value] / exp cl; %end; %mend est; ods exclude all; ods dataset Estimates=Estimates; proc plm restore=work.coxr; %est(ref=212, start=0, end=3000, by=1); run; ods exclude none; data estimates; set estimates; resid_total_poly=label*1; run; proc sgplot data=estimates NOAUTOLEGEND Noborder; Series y=ExpEstimate x=resid_total_poly / LINEATTRS=(color=black thickness=3px); Series y=LowerExp x=resid_total_poly / LINEATTRS=(pattern=ShortDash color=Black THICKNESS=1); Series y=UpperExp x=resid_total_poly / LINEATTRS=(pattern=ShortDash color=Black THICKNESS=1); band x=resid_total_poly upper=UpperExp lower=LowerExp / fillattrs=(color=graydd) transparency=.50; REFLINE 1 / axis=y; REFLINE 3000 / Axis=X LINEATTRS=(pattern=ThinDot color=Black THICKNESS=1);; yaxis Values=(0.5 0.8 1 1.2 1.5) Label="Hazard ratio" Type=LOG LABELATTRS=(weight=BOLD); xaxis min=0 VALUES=(0 to 3000 by 100) LABELATTRS=(weight=BOLD); run;

which created this graph:

My remaining question would be what output from proc PHREG I should use to compare this to the model by quintiles or the linear model to determine how much better the cubic splines model is. Do I then use this to decide how many knots to use?

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Utilizing Restricted Cubic Splines with PROC PHREG and Plotting the Results

Re: Utilizing Restricted Cubic Splines with PROC PHREG and Plotting the Results