topic Re: First time Making Kaplan Meier Curve- not sure if done correctly in New SAS User

First time Making Kaplan Meier Curve- not sure if done correctly

hpatel3 — Mon, 01 Oct 2018 13:59:27 GMT

Hello,

I've received my first project at work to make a Kaplan Meier curve. The question is " 5 & 10 year survival" for EndStage Heart Failure.

The categories given to me are:

Name

MRN

Gender

DOB

Date EndStage

Death=1, Alive at last Follow Up=0 [I made this my status variable and labeled it "Status" in my dataset]

Date of Last Visit

FU ES

Date Death

Adverse events prior to ES

time to nonfatal adverse event

Time transplant to Death

Time of Follow-up or to death [I made this my time variable and labeled it "FU_ES" in my dataset]

Date of last visit, living

My code is as follows:

libname Hetal "\\tuftsmc\home\hpatel3\SAS Datasets";

run;

proc import out=hetal.ES_database datafile="\\tuftsmc\home\hpatel3\SAS Datasets\ES Database Edit.csv" dbms=csv replace; getnames=yes; datarow=2;

run;

ods graphics on;

proc lifetest data=hetal.es_database conftype=loglog plot=(s) plots=(survival(atrisk=0 to 10 by 5 test));

time FU_ES*Status(0);

survival out=survci;

Title " 5 & 10 year Survival for ES";

run;

I just have absolutely no idea if I've done this correctly. Is the atrisk correct? Does the Product Limit Survival Estimate look...ok? is there only a 25% Quartile for the 95% CI because of the censored variables? HELP. Also attaching my results.

Re: First time Making Kaplan Meier Curve- not sure if done correctly

BeverlyBrown — Tue, 02 Oct 2018 13:40:08 GMT

Hi @hpatel3, this article by @JeffMeyers, Kaplan-Meier Survival Plotting Macro %NEWSURV, and items in this user's guide may be useful. @WarrenKuhfeld, anything you'd add?

Re: First time Making Kaplan Meier Curve- not sure if done correctly

hpatel3 — Tue, 02 Oct 2018 13:45:11 GMT

Hi @BeverlyBrown, does that mean I've done my graph wrong? Thank you for the extra resources, I'll definitely be perusing them! 🙂

Re: First time Making Kaplan Meier Curve- not sure if done correctly

BeverlyBrown — Tue, 02 Oct 2018 13:50:39 GMT

Oh, you wouldn't want me critiquing your graph! I'm a resource finder/connector, which is why I replied with links to docs and tagged Jeff and Warren. Hoping one of them or another expert will reply shortly.

Re: First time Making Kaplan Meier Curve- not sure if done correctly

JeffMeyers — Tue, 02 Oct 2018 14:26:48 GMT

Hello,

I was tagged in this conversation so I thought I'd chip in here. Your code is mostly correct, but if you're trying to find the 5 and 10 year survival rates then I would change it to be this:

proc lifetest data=hetal.es_database conftype=loglog plot=(s) plots=(survival)

TIMELIST=5 10 outs=survival_rates reduceout;

time FU_ES*Status(0);

run;

This will give you a dataset (survival_rates) that has the 5 and 10 year (assuming your time variable is in years) estimates and confidence bounds. If your time scale is not in years you will have to convert it before using proc lifetest.

The reason the medians (or confidence bounds) might not be evaluable is that the curve needs to cross the 50% survival threshold to have a median. The curve's upper CI bound has to cross 50% survival for the median's upper ci and the curve's lower CI bound has to cross 50% survival for the median's lower ci. Your curve just barely clips through the 50% survival so it wouldn't be able to have the 75% quartile nor the upper ci for your median.

If you want to run NEWSURV to give you the curve with the estimates in the graph you would use the following macro call (after initializing the macro code):

%newsurv(data=hetal.es_database,time=FU_ES,cens=Status,cen_vl=0,summary=0, timelist=5 10, timedx=years);

The macro defaults to loglog for confidence interval type so you wouldn't have to worry about that. You could add in ylabel and xlabel options to change those.

Re: First time Making Kaplan Meier Curve- not sure if done correctly

WarrenKuhfeld — Tue, 02 Oct 2018 17:52:13 GMT

Every thing I know about the KM plot, I put in that chapter. On the road now without computer access.

Re: First time Making Kaplan Meier Curve- not sure if done correctly

hpatel3 — Tue, 02 Oct 2018 18:13:07 GMT

@JeffMeyers Alright, Timelist worked great and I got my rates. Thank you!

My other question is, if I want to format my graph (remove the tick marks completely, remove the x-axis label completely, label the y-axis, make it "journal" quality, etc) --is there a data step within proc lifetest that will do it?

I'm familiar with just using proc sgplot to define the characteristics of my graph, is there anything similar to it that isn't macro (it seems to be not reading correctly for me)

EXAMPLE

Thank you!

Re: First time Making Kaplan Meier Curve- not sure if done correctly

JeffMeyers — Tue, 02 Oct 2018 18:28:01 GMT

I think Warren has some macros to modify the template for the LIFETEST procedure, but in all honesty it'll probably be faster if you just output the plot dataset and make your own SGPLOT.

ODS OUTPUT SURVIVALPLOT=survplot;
PROC LIFETEST....
**Your code here**
run;

If you have ODS graphics on, then the dataset that LIFETEST uses to make the graph will be saved into the dataset survplot, which you can then feed into SGPLOT to make it look as you wish.

Re: First time Making Kaplan Meier Curve- not sure if done correctly

hpatel3 — Tue, 02 Oct 2018 20:22:45 GMT

I have my ODS graphics on, and my Looks like this:

and the results I'm getting are, unfortunately, what I've been getting all day. My SGPlot looks nothing like my survival plot, I feel like I'm missing some silly step in the middle that gives me the data. If I Can just get my data to show up on here like it does in my Proc Test, I think I'll be golden for moving forward on the rest of my similar projects.

Re: First time Making Kaplan Meier Curve- not sure if done correctly

JeffMeyers — Tue, 02 Oct 2018 20:41:39 GMT

Your SGPLOT is referring to your original data instead of the survplot dataset. Your original data doesn't have any survival calculations. You need to use the dataset that came from lifetest (survplot) with its variables to recreate the survival plot.

Re: First time Making Kaplan Meier Curve- not sure if done correctly

JeffMeyers — Tue, 02 Oct 2018 20:47:03 GMT

Here's an example using the sashelp.bmt dataset:


ods output survivalplot=survplot;
proc lifetest data=sashelp.bmt;
  time t*status(0);
run;

 ods graphics / reset;
proc sgplot data=survplot;
   step x=time y=survival / lineattrs=(color=black pattern=1);
   scatter x=time y=censored / markerattrs=(symbol=plus color=black);
   xaxis min=0 max=2000 values=(0 to 2000 by 200);
   yaxis min=0 max=1 values=(0 to 1 by 0.1);
run;