topic Re: Generate a spline plot in PROC GLIMMIX in Statistical Procedures

Generate a spline plot in PROC GLIMMIX

Kabuto — Sat, 10 Mar 2018 07:18:23 GMT

I am using PROC GLIMMIX to fit a generalized linear mixed model with a spline function. The model looks like:

log(Y) = random intercept + fixed intercept + beta(X1) + f(X2) + offset

I know that the EFFECT statement can create a spline function in the model, which can be written by

proc glimmix;
	class subj
	effect spl = spline(X2);
	model Y =  X1 spl / dist=poisson link=log offset=offset;
	random intercept / subject=subj type=un;
run;

However, the main problem is that there is no other statement to draw the spline plot in PROC GLIMMIX. I googled the info for a while, and most info points to the following link:

http://support.sas.com/kb/57/975.html

Nonetheless, the spline drawn in the example looks like a predicted spline, which y-axis is not the spline f(x) itself:

I somewhat knew that the STORE statement and the PROC PLM can generate a plot for the fitted spline, but still haven't figured out how to write the program. Any suggestion is helpful.

Re: Generate a spline plot in PROC GLIMMIX

Rick_SAS — Mon, 12 Mar 2018 00:38:03 GMT

Do you mean that you want a plot of the basis functions for the spline? You can use the OUTDESIGN= option on the PROC GLMMIX statement to output the basis functions. See the example in the section "Write the spline basis functions to a SAS data set" of the article

"Regression with restricted cubic splines in SAS"

Re: Generate a spline plot in PROC GLIMMIX

Kabuto — Mon, 12 Mar 2018 18:27:15 GMT

Rick,

I am glad that you can reply my post in person. I did review your blog article before posting my question, but I still cannot figure out how to plot the spline function via the output data generated from OUTDESIGN option. Here is my initial program:

proc glimmix data=CVD outdesign(names)=SplineBasis;
	class IndCode Criteria;
	effect spl = spline(hour_total);
	model CVD_Sic =  Criteria spl time / dist=poisson link=log offset=log_hire s;
	random intercept / subject=IndCode s type=un;
run;

The output data set 'SplineBasis' contains several new columns named by _X1 .... _X11 and _Z1. From the X matrix column definitions table, I can know that _X4~_X10 are the values of basis from the spline. However, when opening the output data set, I still have no idea how to draw them in a spline plot because in my understanding each x has only a value of f(x). Here I provide two screenshots from my outputs:

I think I have almost reached the final step, but need a further guidance to generate the plot. I also need to draw a 95% CI of the spline. Hopefully you can advise me. Thank you.

Re: Generate a spline plot in PROC GLIMMIX

Rick_SAS — Mon, 12 Mar 2018 19:31:24 GMT

The "ColumnNames" table shows which of the _X variables are associated with the splines. In the example below, it is _X5--_X11, but your values might be different. To see the spline bases, you need to wort the design by the underlying variable (hour_total, in your example). Here's an example that you can copy:

proc glimmix data=sashelp.cars outdesign(names)=SplineBasis;
	class Origin;
	effect spl = spline(weight);
	model mpg_city =  origin spl;
   ods select ColumnNames;
run;

proc sort data=SplineBasis 
          out=SplinesOnly(keep=weight _X5--_X11);
by weight;
run;

proc sgplot data=SplinesOnly;
series x=weight y=_X5;
series x=weight y=_X6;
series x=weight y=_X7;
series x=weight y=_X8;
series x=weight y=_X9;
series x=weight y=_X10;
series x=weight y=_X11;
run;

If you don't want to use multiple SERIES statements, you can transpose the data from wide to long and use a single SERIES statement with the GROUP= option.

Re: Generate a spline plot in PROC GLIMMIX

Kabuto — Tue, 13 Mar 2018 20:18:44 GMT

Rick,

Thanks for your help, even the solution is not what I expect. Your example code generates multiple basis functions in a single plot, but what I need is just a single spline function in the plot. By using R, it looks like:

(I have transformed the estimated spline into relative risk)

I guess I can export the design matrix of the spline, and use a matrix multiplication to determine the estimated spline. However, because of the publication issue, I decide to generate this plot in R to complete my manuscript for a journal publication first. Thank you again.

Re: Generate a spline plot in PROC GLIMMIX

Rick_SAS — Tue, 13 Mar 2018 20:56:12 GMT

I explicitly asked if you wanted a plot of the basis functions or something else. If you had posted that picture with your initial question, it would have given us something concrete to discuss and work towards.

A spline consists of a set of basis functions and parameters (or parameter estimates), so I assume the graph you show is using the estimated parameters to form the spline. You can do something similar in SAS. I know that @WarrenKuhfeld has written a lot about how to evaluate splines from their basis functions. For example, see his 2013 SGF talk:

BTW, If you want a marginal effects plot, you can use the EFFECTPLOT statement as shown in the articles:

Use the EFFECTPLOT statement to visualize regression models in SAS

Visualize multivariate regression models by slicing continuous variables

Re: Generate a spline plot in PROC GLIMMIX

fifi75 — Sat, 27 Nov 2021 20:45:50 GMT

Hi,

I m also looking for a way to estimate RR from spline with proc Glimmix. Did you find a solution ?

Also, can you explain how did you do with R ?

Thanks in advance.

Re: Generate a spline plot in PROC GLIMMIX

Kabuto — Sun, 28 Nov 2021 00:31:28 GMT

I still haven't figured out how to do that in GLIMMIX in these years. In R, if you use the mgcv package, you need to use the predict function to save the estimates of a spline as a new R object, and exponentiate the R object to compute the relative risks. For the other R packages, I have no idea.

Re: Generate a spline plot in PROC GLIMMIX

April2211 — Fri, 03 Dec 2021 02:22:23 GMT

ep=exp(p);
elower=exp(lower);
eupper=exp(upper);

Does ep output "odds" or " odds ratio"?

Re: Generate a spline plot in PROC GLIMMIX

fifi75 — Fri, 03 Dec 2021 09:56:06 GMT

What's 'p' in your code ?
Thanks

Re: Generate a spline plot in PROC GLIMMIX

April2211 — Fri, 03 Dec 2021 17:21:24 GMT

proc glimmix data=simulation() method=laplace; class strata; effect myspline=spline(t/knotmethod=list(1,3,5,7,9) NATURALCUBIC); model y(event="1")= intercept*myspline gender*t gender*myspline/dist=binary link=logit noint ; random strata; store mystore; run; *generate with values for t - this will be used drawing the spline; data template; intercept=0; do gender=1; do t=0 to 10 by 0.01; output; end; end; run; *calculate the predicated values for each value of t; proc plm restore=mystore; score data=template out=plot predicted=predicted lclm=lclm uclm=uclm; run; data plot; set plot; by t; *transform to oddsratio scale; oddsratio=exp(predicted); upper=exp(uclm); lower=exp(lclm); 'p' means 'predicted' but how can I get odds ratio with more than one covariates

Re: Generate a spline plot in PROC GLIMMIX

April2211 — Fri, 03 Dec 2021 17:24:49 GMT

"p" is "predicted"

Re: Generate a spline plot in PROC GLIMMIX

fifi75 — Tue, 07 Dec 2021 16:43:35 GMT

you can't introduce in the same model the spline effect and the variable itself .

model y(event="1")= intercept*myspline gender*t gender*myspline

Re: Generate a spline plot in PROC GLIMMIX

Rick_SAS — Tue, 07 Dec 2021 18:08:56 GMT

Furthermore, the spline effect includes the identity function (t) as one of the basis elements, so it is already included in the model.

Re: Generate a spline plot in PROC GLIMMIX

Amber_G — Mon, 29 Apr 2024 07:54:03 GMT

Hi,

I'm facing the same question to generate the spline plot and I cannot draw it in SAS. I wondering if you are willing to share your R code to get this plot?

Many thanks!

Re: Generate a spline plot in PROC GLIMMIX

Rick_SAS — Mon, 29 Apr 2024 10:07:08 GMT

Please start a NEW thread that describes your problem and what you want to do. If you have example data or a sketch of the graph you want to produce, please include that information as well.

Re: Generate a spline plot in PROC GLIMMIX

Kabuto — Mon, 29 Apr 2024 16:15:30 GMT

Wow... I wish I could help. You replied to my question that I posted six years ago, and I have forgotten how I may (or may not) resolve this issue. It is better that you post a new thread and disclose details of your questions. Hopefully, someone else can assist you.

Re: Generate a spline plot in PROC GLIMMIX

Ksharp — Tue, 30 Apr 2024 02:40:19 GMT

I think you could use ESTIMATE to get RR and its CI ,after that polt it to get the graph you want.

http://support.sas.com/kb/24/188.html

Re: Generate a spline plot in PROC GLIMMIX

StatDave — Wed, 01 May 2024 21:57:56 GMT

I'm just now seeing this issue. See this note that I added recently that shows how you can estimate and plot odds ratios, risk differences, or relative risks (risk ratios), as they change over a continuous, spline-smoothed predictor.

Re: Generate a spline plot in PROC GLIMMIX

Season — Sun, 07 Jul 2024 10:46:21 GMT

Is there any way to plot spline effects in models built by the PHREG, SURVEYREG and SURVEYLOGISTIC procedure? These are questions troubling me for a long time. The EFFECTPLOT statement in the PLM procedure simply does not work for models built with the three procedures.