Hello everyone,
Upon learning that sascommunity.org is being decommissioned I decided to move my wiki page to this website as an article to help me continue to share the code. This macro has been around for years and has been constantly evolving to be my pocketknife of survival analysis whether it's graphing or generating tables. I have presented this macro at four separate conferences and have been freely sharing the macro with anyone who is interested.
The research areas of pharmaceuticals and oncology clinical trials greatly depend on time-to-event endpoints such as overall survival and progression-free survival. One of the best graphical displays of these analyses is the Kaplan-Meier curve, which can be simple to generate with the LIFETEST procedure but difficult to customize. Journal articles generally prefer that statistics such as median time-to-event, number of patients, and time-point event-free rate estimates be displayed within the graphic itself, and this was previously difficult to do without an external program such as Microsoft Excel. The macro NEWSURV takes advantage of the Graph Template Language (GTL) that was added with the SG graphics engine to create this level of customizability without the need for backend manipulation. Taking this one step further, the macro was improved to be able to generate a lattice of multiple unique Kaplan-Meier curves for side by side comparisons or condensing figures for publications. The following is a paper describing the functionality of the macro and a description of how the key elements of the macro work.
The original purpose of creating the macro was to make a journal quality Kaplan-Meier (KM) curve that included common survival statistics within the curve itself so that I did not have to manually add them to an image post-hoc. Below is an example using the dataset SASHELP.BMT:
The macro allows for a vast amount of optional customization to fit the user's needs, but also allows for simple macro calls to get the ball rolling.
I added the ability for the macro to take the survival statistics it was calculating and organize them into a clean summary table using the REPORT procedure.
The macro automatically computes many commonly used survival statistics including the following:
There are parameters for customizing the automated analysis, including:
There are multitudes of survival based macros out there in the wild. Why should you choose to try this one instead of one of those or an internal macro?
Nearly all parts of the graph are customizable with multiple options.
The macro was written in SAS 9.2 and most of the options and techniques are still compatible with the older versions (9.2/9.3) of SAS. These features include creating multiple graphs, calculating the concordance index, and running cumulative incidence models.
The beginning of a macro has extensive documentation on each parameter including valid values and how to properly use each one.
Below are the examples that were included in the sascommunity.org webpage.
Make the dataset with the following code (also in macro documentation)
proc format;
value grpLabel 1='ALL' 2='AML low risk' 3='AML high risk';
run;
data BMT;
input DIAGNOSIS Ftime Status Gender@@;
label Ftime="Days";
format Diagnosis grpLabel.;
datalines;
1 2081 0 1 1 1602 0 1
1 1496 0 1 1 1462 0 0
1 1433 0 1 1 1377 0 1
1 1330 0 1 1 996 0 1
1 226 0 0 1 1199 0 1
1 1111 0 1 1 530 0 1
1 1182 0 0 1 1167 0 0
1 418 2 1 1 383 1 1
1 276 2 0 1 104 1 1
1 609 1 1 1 172 2 0
1 487 2 1 1 662 1 1
1 194 2 0 1 230 1 0
1 526 2 1 1 122 2 1
1 129 1 0 1 74 1 1
1 122 1 0 1 86 2 1
1 466 2 1 1 192 1 1
1 109 1 1 1 55 1 0
1 1 2 1 1 107 2 1
1 110 1 0 1 332 2 1
2 2569 0 1 2 2506 0 1
2 2409 0 1 2 2218 0 1
2 1857 0 0 2 1829 0 1
2 1562 0 1 2 1470 0 1
2 1363 0 1 2 1030 0 0
2 860 0 0 2 1258 0 0
2 2246 0 0 2 1870 0 0
2 1799 0 1 2 1709 0 0
2 1674 0 1 2 1568 0 1
2 1527 0 0 2 1324 0 1
2 957 0 1 2 932 0 0
2 847 0 1 2 848 0 1
2 1850 0 0 2 1843 0 0
2 1535 0 0 2 1447 0 0
2 1384 0 0 2 414 2 1
2 2204 2 0 2 1063 2 1
2 481 2 1 2 105 2 1
2 641 2 1 2 390 2 1
2 288 2 1 2 421 1 1
2 79 2 0 2 748 1 1
2 486 1 0 2 48 2 0
2 272 1 0 2 1074 2 1
2 381 1 0 2 10 2 1
2 53 2 0 2 80 2 0
2 35 2 0 2 248 1 1
2 704 2 0 2 211 1 1
2 219 1 1 2 606 1 1
3 2640 0 1 3 2430 0 1
3 2252 0 1 3 2140 0 1
3 2133 0 0 3 1238 0 1
3 1631 0 1 3 2024 0 0
3 1345 0 1 3 1136 0 1
3 845 0 0 3 422 1 0
3 162 2 1 3 84 1 0
3 100 1 1 3 2 2 1
3 47 1 1 3 242 1 1
3 456 1 1 3 268 1 0
3 318 2 0 3 32 1 1
3 467 1 0 3 47 1 1
3 390 1 1 3 183 2 0
3 105 2 1 3 115 1 0
3 164 2 0 3 93 1 0
3 120 1 0 3 80 2 1
3 677 2 1 3 64 1 0
3 168 2 0 3 74 2 0
3 16 2 0 3 157 1 0
3 625 1 0 3 48 1 0
3 273 1 1 3 63 2 1
3 76 1 1 3 113 1 0
3 363 2 1
;
run;
Four Variables:
%newsurv(DATA=bmt, TIME=FTIME, CENS=STATUS, CEN_VL=0, SUMMARY=0);
This is basic macro call using almost only required parameters. The graph is plotted with censor markers and confidence bounds by default, and displays number of patients, number of events, and median time to event within the graph. The following parameters are introduced:
%newsurv(DATA=bmt, TIME=FTIME, CENS=STATUS, CEN_VL=0, SUMMARY=0, CLASS=DIAGNOSIS, CLASSREF=ALL,CLASSORDER=1 3 2);
This example shows how to add a CLASS parameter to produce grouped survival curves. Doing so also adds hazard ratios and a p-value to the plot statistical summary table. The example shows how to use other parameters related to the CLASS variable. The following new parameters are introduced:
%newsurv(DATA=bmt, TIME=FTIME, CENS=STATUS, CEN_VL=0, SUMMARY=0, CLASS=DIAGNOSIS, CLASSREF=ALL,CLASSORDER=1 3 2, COLOR=black red green, PATTERN=solid, LINESIZE=3pt, SYMBOLSIZE=10pt, XDIVISOR=30.44, XMAX=100, XINCREMENT=10, XLABEL=Months, YTYPE=PPT, YLABEL=Proportion Alive);
This example shows how to change the X and Y axis scale and labels as well as the attributes of the Kaplan-Meier curves. The x-axis is changed from days to months (this does not affect the original dataset) and the tick values are determined by XMAX and XINCREMENT. The y-axis is changed to proportion using the YTYPE parameter. The Kaplan-Meier curves can have their colors, patterns, thickness, and censor symbols modified. The following new parameters are all introduced:
%newsurv(DATA=bmt, TIME=FTIME, CENS=STATUS, CEN_VL=0, SUMMARY=0, CLASS=DIAGNOSIS, CLASSREF=ALL,CLASSORDER=1 3 2, COLOR=black red green, PATTERN=solid, LINESIZE=3pt, SYMBOLSIZE=10pt, XDIVISOR=30.44, XMAX=100, XINCREMENT=10, XLABEL=Months, YTYPE=PPT, YLABEL=Proportion Alive, TIMELIST=20 40,TIMEDX=months,DISPLAY=legend timelist);
This example demonstrates changing which statistics are shown within the plot table and how to display Kaplan-Meier time-point event-free rates. One or more event-free rates can be specified, and they will be displayed vertically. The column that shows the time-point can be disabled when displaying only one time-point. The following new parameters are all introduced:
%newsurv(DATA=bmt, TIME=FTIME, CENS=STATUS, CEN_VL=0, SUMMARY=0, CLASS=DIAGNOSIS, CLASSREF=ALL,CLASSORDER=1 3 2, COLOR=black red green, PATTERN=solid, LINESIZE=3pt, SYMBOLSIZE=10pt, XDIVISOR=30.44, XMAX=100, XINCREMENT=10, XLABEL=Months, YTYPE=PPT, YLABEL=Proportion Alive, RISKLIST=0 to 100 by 10,RISKLOCATION=BOTTOM,RISKCOLOR=1);
This example gives a basic demonstration of adding the patients-at-risk counts to the bottom of the plot. There are many options to customize the location of the labels, headers, where the table is printed, and even what type of numbers are shown. The following new parameters are all introduced:
Other useful options:
%newsurv(DATA=bmt, TIME=FTIME, CENS=STATUS, CEN_VL=0, SUMMARY=0, CLASS=DIAGNOSIS, CLASSREF=ALL,CLASSORDER=1 3 2, COLOR=black red green, PATTERN=solid, LINESIZE=3pt, SYMBOLSIZE=10pt, METHOD=CIF, EV_VL=1);
This example shows how to plot cumulative incidence instead of Kaplan-Meier curves. The following new parameters are all introduced:
%newsurv(DATA=bmt, TIME=FTIME, CENS=STATUS, CEN_VL=0, SUMMARY=0, CLASS=DIAGNOSIS, CLASSREF=ALL,CLASSORDER=1 3 2, COLOR=black red green, PATTERN=solid, LINESIZE=3pt, SYMBOLSIZE=10pt, METHOD=KM|CIF, EV_VL=1, SREVERSE=1|0, NMODELS=2, ROWS=2, AUTOALIGN=BOTTOMRIGHT|TOPRIGHT);
This example shows how to produce multiple plots in a lattice diagram. Any options that will be different between plots have the | (capital \) delimiter to designate different settings per option. Any options without a | delimiter will keep the same settings across all models. This example also demonstrates the difference when plotting CIF versus 1-Survival. The following new parameters are all introduced:
%newsurv(DATA=bmt, TIME=FTIME, CENS=STATUS, CEN_VL=0, SUMMARY=0, CLASS=DIAGNOSIS, CLASSREF=ALL,CLASSORDER=1 3 2, COLOR=black red green, PATTERN=solid, LINESIZE=3pt, SYMBOLSIZE=10pt, REFLINES=medians,REFLINEAXIS=both);
This example shows how to add reference lines. Reference lines can highlight two different items: medians and time-point estimates. The reference lines can be dropped to either axis. The following new parameters are all introduced:
Other options:
%newsurv(DATA=bmt, TIME=FTIME, CENS=STATUS, CEN_VL=0, SUMMARY=0, CLASS=DIAGNOSIS, CLASSREF=ALL,CLASSORDER=1 3 2, COLOR=black red green, PATTERN=solid, LINESIZE=3pt, SYMBOLSIZE=10pt, PLOTCI=1);
This example shows how to add confidence intervals. Confidence intervals are automatically added for graphs with no CLASS variable. Confidence intervals can be added as a filled background, as lines, or both. By default only a filled background is used similar to the LIFETEST procedure. The following new parameters are all introduced:
Multivariate models are often necessary in survival analysis in order to account for confounding factors. Adjusting for other factors can dramatically change outcomes such as hazard ratio. When outcomes are dramatically changed in a multivariate model it can be inappropriate to plot the unadjusted curves. There are numerous methods available for creating adjusted survival curves, and none are the correct method for all situations. Thus there was a need to have a series of macros that could create the high quality plots of NEWSURV, but with the appropriate methodologies for adjusted survival curves. These macros were designed to adjust survival curves using either the direct adjustment or inverse weights methodologies. A third macro, NEWSURV_DATA, allows the user to pre-calculate their own survival curves and then plot them with the customization of NEWSURV.
The NEWSURV_ADJ_DIRECT macro calculates the adjusted survival curves based off of the predicted survival curves created by the PHREG procedure. This is described in more detail in the PharmaSUG 2017 paper.
The NEWSURV_ADJ_INVWTS macro calculates weights from the LOGISTIC procedure that it then supplies to the LIFETEST procedure WEIGHTS statement.This is described in more detail in the PharmaSUG 2017 paper.
The NEWSURV_DATA macro allows the user to specify their own dataset with time and survival variables that have been previously calculated in order to produce a highly customizable journal quality image. This allows the user to use their own adjustment or calculation method not available in the NEWSURV macros.
%newsurv_adj_invwts(DATA=bmt, TIME=FTIME, CENS=STATUS, CEN_VL=0, SUMMARY=0, CLASS=DIAGNOSIS, CLASSREF=ALL,CLASSORDER=1 3 2, COLOR=black red green,LINESIZE=3pt, SYMBOLSIZE=10pt, CLASSCOV=gender);
This example shows how to make adjusted survival curves using the inverse weights methods. The macro parameters are mainly similar to NEWSURV. The following new parameters are all introduced:
Other options:
Editor's note: we added this mention of SAS-provided macros/options for completeness.
In addition to the thorough options provided here and documented in @JeffMeyers papers, SAS also provides guidance and code for customizing the Kaplan Meier survival plot.
Note that these options/macros work only with the more recent versions of SAS.
Hi Jeff,
I have been using your %newsurv macro for generating the cumulative incidence curves. Thank you so much for creating the macro! However I have two questions:
1. How do I accommodate "Patients at Risk" numbers cleanly without getting crowded or overlapped? My data have 6 millions subjects and 16 years follow-up, so patients at risk for each year are million to few hundred thousand, so when I generate the CIF curves with patients at risk at the bottom, my year 1 numbers are overlapping year 2, year 2 numbers are overlapping Year 3, etc. How do I space them out by the X-axis years of follow-up.
%newsurv(DATA=bmt, TIME=FTIME, CENS=STATUS, CEN_VL=0, SUMMARY=0, CLASS=DIAGNOSIS, CLASSREF=ALL,CLASSORDER=1 3 2,
COLOR=black red green, PATTERN=solid, LINESIZE=3pt, SYMBOLSIZE=10pt,
RISKLIST=0 to 15 by 1,RISKLOCATION=BOTTOM, METHOD=CIF, EV_VL=1);
2. I also want to generate survival curves (proportion alive) for the same data for 6 million patients and follow-up period of 16 years. I am getting errors saying max is 2 million. Using the code below.
%newsurv(DATA=bmt, TIME=FTIME, CENS=STATUS, CEN_VL=0, SUMMARY=0, CLASS=DIAGNOSIS, CLASSREF=ALL,CLASSORDER=1 3 2,
COLOR=black red green, PATTERN=solid, LINESIZE=3pt, SYMBOLSIZE=10pt,
XDIVISOR=30.44, XMAX=100, XINCREMENT=10, XLABEL=Months, YTYPE=PPT, YLABEL=Proportion Alive,
RISKLIST=0 to 100 by 10,RISKLOCATION=BOTTOM,RISKCOLOR=1);
Thank you
Hello @sms1891
For your first question there are a few options you can do for more space. You can either increase the width of your graph (WIDTH), increase the interval listed in your RISKLIST, or decrease the fontsize of the numbers with PTABSIZE (set to the font size that you want).
For the second question the largest data I ever interacted with was only in the 10's of thousands, so I'm not sure what options are out there for larger datasets. I don't have anything in the macro that I've set as far as I know to limit the size of the data. I'm sorry I can't be more help here.
@JeffMeyers What parameter in the macro controls the X-axis minor tick marks?
Hi @JeffMeyers
I want to plot the Cumulative Incidence curve but I do not want the Hazard ratios (95%CI) and Median (95%ci) for my class variable in the plot.
Is there a way to do this.
Thank you
Yuba
Hello @yubaraj ,
You can specify which statistics you want to show and their order with the DISPLAY option in the macro call. For example if all you want is the legend you can specify DISPLAY=legend. Look up the documentation in the program to see all the available options for statistics.
Great Thanks @JeffMeyers , it was an easy fix. I should have looked at the documentation more closely.
I was wondering if it is possible to show faint horizontal gridlines along the Y-axis in the plot.
Thanks
Hello Jeff,
Apologies but my knowledge in terms of your weighted macros for NEW surv is limited. I have done an inverse weight propensity score model and now want to generate publication quality survival curves incorporating the PS weight. I can generate this in Proc lifetest however I cannot get beautiful graphs or a p-value for a comparison at 3 years survival. I was wondering if this is the kind of situation where i can use your NEWSURV_ADJ_INVWTS or NEWSURV_ADJ_DIRECT macros?
My categorical variable for stratification does have 3 levels.
Thank you,
Hi @JeffMeyers
Thanks for this very useful macro.
I am trying to customize my x axis for the cumulative incidence curve. My cohort is a fixed cohort with a same start (Nov 24 2017) and end of follow up date (May 23 2018) for all participants.
Instead of showing "number of days of follow up " along x-axis we wanted to show end date and middle date of each month.
In other words, we wanted to have Nov 24 2017 (beginning), Nov 30 2017. Dec 15 2017, Dec 31 2017, Jan 15 2018 and so on in the x-axis time markers.
I was hoping TIMEDX option will be helpful. please let me know.
Hi @JeffMeyers
thanks for this very useful macro.
I am trying to customize 2 graphs in one graph. Example on BMT data :
%newsurv(DATA=bmt, TIME=FTIME, CENS=STATUS, CEN_VL=0, SUMMARY=0, CLASS=DIAGNOSIS, CLASSREF=ALL,CLASSORDER=1 3 2,
COLOR=black red green, PATTERN=solid, LINESIZE=3pt, SYMBOLSIZE=10pt,NMODELS=2, ROWS=2,WHERE=gender=0|gender=1,
XDIVISOR=30.44, XMAX=100, XINCREMENT=10, XLABEL=Months, YTYPE=PPT, YLABEL=Proportion Alive,
RISKLIST=0 to 100 by 10,RISKLOCATION=BOTTOM,RISKCOLOR=1);
I obtain one graph with twice the same curve and datas. Have you an idea of the problem ? I am using SAS 9.4 Level 1M7 (Windows).
thanks for your help.
Hello @BGuyomarch ,
Could you e-mail me at jpmeyers.spa@gmail.com with your question and send me a de-identified example of what you're experiencing? I think this will be easier to figure out that way.
Hello @yubaraj ,
At this time I don't have an option to add a format to the x-axis, but if you search through the macro for XAXISOPTS and you should be able to add a format that you want with the TICKVALUEFORMAT option in the LINEAROPTS parentheses. You could set it up where day 1 is Nov 24 2017 and the days correspond to the months you're looking for. You could also save a version that uses time axes instead of linear. I'm sorry I don't have an easier solution right now.
Hi @JeffMeyers,
Long-time fan of your macro. I am trying to create a figure with lines by groups with a patients-at-risk table. But, my patients-at-risk table is showing a decimal point and/or empty parentheses behind the first two groups' first number (pic attached for reference). This problem does not happen if I do not use the groups options and it happens for every version of the patients-at-risk table. I have not had this problem with other datasets and this current dataset does not appear to be any different than previous sets in terms of structure or having missing data. Am I missing something?
I really appreciate any input!
Using SAS 9.4 on windows.
%newsurv(DATA=a.set, TIME=time_published, CENS=published, CEN_VL=0, SUMMARY=0,
CLASS=design, CLASSORDER=1 2 3, COLOR=green blue red,
PATTERN=solid, LINESIZE=2pt, CENSORMARKERS=0, METHOD=CIF, EV_VL=1,
YLABEL=Probability of Publication, XLABEL=Months, DISPLAY=legend, AUTOALIGN=TOPLEFT,
XMAX=60, XINCREMENT=6, XTICKVALSIZE=12pt, YTICKVALSIZE=12pt, LSIZE=12pt, PTABSIZE=8pt, TABLEDATASIZE=8pt,
PARSIZE=12pt, RISKLIST=0 to 60 by 6, RISKLOCATION=BOTTOM, RISKCOLOR=1, PARDISPLAY=PAR_NEVENTS, PARHEADER=Number Eligible, PARALIGN=LABELS, riskrowweights=0.04,
WIDTH=10in, DPI=300, PLOTTYPE=jpeg, GPATH=&path, plotname=time_to_pub_design_ncumulative)
Hi @JeffMeyers,
Thank you so much for creating such a helpful macro! Is there a way to stratify the survival curves within one graph? I am trying to generate four curves with two hazard ratios (two SOC arms and two intervention arms, one per strata).
I would prefer to not recode into one four-level class variable since that would necessitate running HRs separately and it's very nice to have them automatically embedded in the figure, but if it can't be avoided I can definitely just do it this way.
Appreciate any advice you're able to give!
Hello @ColeG
I have a version that can do this. E mail me at jpmeyers.spa@gmail.com and I can send you the version.
Hello @alwestb
can you email me at jpmeyers.spa@gmail.com with this issue? It will be easier to test if we discuss more offline
Hi @JeffMeyers,
Thanks for this amazing Macro. I want to make a CIF graph using this Macro but when I ran the code a blank graph was created and I got this error in the log "'&' is not a valid unit or graphics option. It will be ignored." Can you please guide me on how to get past this error?
This is my code:
: %newsurv(DATA=source.bigdata, TIME=time, CENS=event, CEN_VL=0, SUMMARY=0, CLASS=class, CLASSREF=NN, CLASSORDER=4 2 3 1,
COLOR=black red green blue, PATTERN=solid, LINESIZE=3pt, SYMBOLSIZE=10pt,
XMAX=13, XINCREMENT=3, XLABEL=Years, YTYPE=PPT, YMAX=0.4, YLABEL=Cumulative Incidence;
METHOD=CIF, EV_VL=1);
I wanted to modify the maximum value on the Yaxis, so I changed YMAX to 0.4, because the maximum cumulative incidence was less the 0.3. If this is what's caused the error is there another way to shorten the Y axis?
Thanks for your help.
Hi @JeffMeyers,
Thank you for this wonderful macro, it has helped us to make beautiful KM curves.
Could you please guide us what does NE stands for in the median column ( top right hand side of the attached image; highlighted for your reference)
Thanks for your help!
Hi @Saba_Zaki
NE stands for "not estimable". As you can see, less that 50% of the participants in the AML low risk group had the event of interest, so you can not estimate the median and its 90% CI.
Hi @JeffMeyers
I really appreciate this great MACRO. It helps me a lot.
May I ask you for help:
1. Can I close the legend of the plot?
2. Can I change the symbol of censor?
I would like to have the plot like following. As you can see in the plot, it does not show the legend and the symbol of censor is half of |, not +.
Thanks
I made some update to change the symbol of censor, using symbolchar option.
I added symbolchar name=U007C char='007C'x/voffset=.35; in define statgraph _km; block. and change symbol=plus to symbol=U007C.
Here the '007C'x is the unicode of |. and U007C is the user defined name of the symbol.
Hello @3fatty , Sorry for the delayed response. I haven't had as much time lately to peruse the communities page. That's an interesting solution for the censor symbol. You can remove the legend by putting LEGEND=%str( ) I believe. You can remove just the legend of the censors by setting CENSORMARKERS=0.
Hi Jeff,
Thank you for this useful macro !
I have the following problems :
- When I do subgroup analyses, I can not change the labels for "GROUP" and "KRAS".
- the number at risk overlap.
- Is it possible to remove straight line from the legend (remove the column "GROUP")
Do you have a solution for this ?
Thank you.
@JeffMeyers Hi Jeff, can you please direct me as to where I can find the NEWSURV_ADJ_DIRECT macro?
Thank you!
@JeffMeyers Hi Jeff, Thanks for writing this wonderful macro. I am having difficulty in italicizing the P of "Logrank P-value" in the figure. Could you please guide me?
Hello @MJAIN . This would be a bit tricky. The p-value is written using an ENTRY statement in GTL. In order to italicize just the P in p-value you would need the entry statement to look something like:
ENTRY textattrs=(style=italic) "p" textattrs=(style=normal) "-value:" ....;
The parameter PVALHEADER is meant to be placed in directly as text in the ENTRY statement, but this can be used to our advantage to manipulate the ENTRY statement:
%newsurv(data=sashelp.bmt,time=t,cens=status,class=group,
pvalheader=Logrank" textattrs=(style=italic) " p" textattrs=(style=normal) "-value:)
By using the double quotes in the parameter it will close off the text part of the ENTRY statement allowing for the textattrs to be applied to different pieces leading to the desired result:
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