How to automate Survival tests in JMP?

Question

I have been doing survival tests almost 50 of those for different gene polymorphisms manually, which is comparatively more time consuming compared to the chi-square contingency tables that can be applied to multiple variables by one click under 'Fit X by Y'. I would like to know if there is a way to automate the process, similar to a macro command.

neontiger · Answer

Just note that my background on coding/programming is relatively weak, given that I only hold an MD degree. The script appears to have 2 problems

a) It doesn't provide the same results as the 'manual' way. For example:

and

b) As you can see the original genotypes (categorical variables) are converted into 1,2,3.

Other than that the script runs smoothly and returns 20 tests.

I wouldn't also mind if I had to copy a string with all the column header names that I want to run (comma-separated) since I can do this easily from my file and generally I would aprreciate having a universal tool that can be applied in cases other than gene**.

ian_jmp · Answer

Many thanks. The script below shows the idea. The Journal file currently contains all the output, but I think you only want some of it. Copy the code below, do 'File > New > New Script' and paste it in, then 'Edit Run' script. Obviously this code relies on the way you have named your columns, but it would be easy to add a user interface that allows you to select them. NamesDefaultToHere(1); // (1) Make some dummy data in table 'dt' ng = 20; // Number of grouping (gene) columns to use dt = New Table( "Gene Polymorphism Survival", New Column( "Overall Survival", Numeric, "Continuous", Format( "Best", 12 ), Formula( Random Weibull( 1 ) ) ), New Column( ":Overall survival status", Numeric, "Nominal", Format( "Best", 12 ), Formula( Random Integer( 0, 1 ) ) ), Add Rows( 100 ) ); for (c = 1, c <= ng, c++, dt << New Column( "gene"||Char(c), Numeric, "Nominal", Format( "Best", 12 ), Formula( Random Integer( 3 ) ))); // (2) START HERE - Build a list of all the grouping (gene) columns in the table (gCol) gCols = dt << getColumnNames("String"); for(c = Nitems(gCols), c >= 1, c--, If(!StartsWith(gCols, "gene"), RemoveFrom(gCols, c))); // (3) Launch the survival platform (invisibly) for each gene column . . . for(c = 1, c <= Nitems(gCols), c++, sur = dt << Survival( Y( :Overall survival ), Censor( :Overall survival status ), Grouping( gCols ), Failure Plot( 0 ), Censor Code( 0 ), Invisible ); // (4) 'Harvest' and consolidate the results in some way: // Here we just build a JRN, but you can take whatever pieces of the report you like. sur << Journal; Report(sur) << closeWindow; );

neontiger · Answer

I am using SAS's JMP eleventh (11th) version. This is the output of what you've asked for

Survival(

Y( :Overall survival ),

Censor( :Overall survival status ),

Grouping( :Name( "gene1" ) ),

Failure Plot( 0 ),

Censor Code( 0 )

);

Other than automating survival tests, a function on saving images would be optimal.