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scripting t-test: picking favorite features from several ANOVA/t-tests; 2-sample vs 3+-sample?

aliegner1

So curious how to make this happen. I've got a long list of charts, some with 2 chambers, some with 3+ chambers. I'd like to script a t-test kind of script to standardize the output. Any advice? There's parts and pieces I like from several different options.

Goal:

- output a chart w/ student's t Circle Plots

- output a 'summary report' with sample count, mean, stDev

- output a p-value for the whole chart (Means/Anova/Pooled t")

- (nice to have: pair-wise p-value and labeling, but not that important).

I've noticed that the options and outputs are quite different if I have a 2-sample chart vs a 3+sample chart.

Any advice how to script this?

examples

Accepted answers

txnelson

If you have an easy way to check the number of levels, you can use an IF() to check and bypass the statement. Or, you can use a TRY() function to keep it from ending when the statement fails

try(report(ow[i])["Oneway Anova"]["Pooled t Test"] << visibility("Collapse"));

All comments

aliegner1

Edit/Update.

So I setup some JSL and edited as much as I can figure, but still hitting a roadblock. I can't seem to collapse/hide Student t Test subwindows.

Is there a BKM for simply outputting the YbyX chart, circles, histogram on upper level and then "Analysis of Variance, Summary, and Ordered Difference Report on lower level?

obj = Oneway(
	Y( :MEAN ),
	X( :TOOL_PROCESS_CHAMBER ),
	By(, :CHART_ID),
	
	Means( 1 ), //means/anova/pooled t
	Each Pair( //student's t-Test
		1,
		Difference Matrix( 0 ),
		Confidence Quantile( 0 ),
		LSD Threshold Matrix( 0 ),
		Connecting Letters Report( 0 ),
		Ordered Differences Report( 1 ),
		Detailed Comparisons Report( 0 )
	),
	
	//t Test ( 1), //standard t-test, only works on 2chamber charts
	//Means and Std Dev( 1 ), //extra table for count, Mean, StDev
	//Histograms( 1 ), // move this to the end so control position? obj << histograms(1);

	//Formatting
		Points Jittered( 1 ),
		Box Plots( 1 ),
		Mean Diamonds( 0 ),
		Mean Error Bars( 0 ),
		Std Dev Lines( 0 ),
		Grand Mean( 0 ),

	SendToReport(
		//x-axis formatting
		Dispatch(
			{},
			"2",
			ScaleBox,
			{Label Row(
				{Label Orientation( "Angled" ), Lower Frame( 1 ),
				Show Major Grid( 1 ), Tick Mark Style( "Long Divider" )}
				)
			}
		),
		//row legend by chamber
		Dispatch(
			{},
			"Oneway Plot",
			FrameBox,
			{Marker Size( 6 ), Marker Drawing Mode( "Normal" ),
			Row Legend(
				:TOOL_PROCESS_CHAMBER,
				Color( 1 ),
				Color Theme( "JMP Default" ),
				Marker( 0 ),
				Marker Theme( "" ),
				Continuous Scale( 0 ),
				Reverse Scale( 0 ),
				Excluded Rows( 0 )
				)
			}
		),
		//formatting the Summary table
		Dispatch({"Means and Std Deviations"},"",
			TableBox,
				{Set Column Borders( 1 ), 
				Set Row Borders( 1 ),
				Set Underline Headings( 1 ), 
				Set Shade Headings( 1 )}
		),
			Dispatch({"Means and Std Deviations"},"Mean",NumberColBox,{Set Format( "Fixed Dec", 9, 2 )}),
			Dispatch({"Means and Std Deviations"},"Std Dev",NumberColBox,{Set Format( "Fixed Dec", 9, 2 )}),
			Dispatch({"Means and Std Deviations"},"Std Err Mean",NumberColBox,{Visibility( "Collapse" )}),
			Dispatch({"Means and Std Deviations"},"Lower 95%",NumberColBox,{Visibility( "Collapse" )}),
			Dispatch({"Means and Std Deviations"},"Upper 95%",NumberColBox,{Visibility( "Collapse" )}),
		
		//formatting the "t Test"" tables
		Dispatch({"t Test"},"",
			TableBox,
				{Set Column Borders( 1 ), 
				Set Row Borders( 1 )}
		),
			Dispatch( {"t Test"}, "", StringColBox, {Visibility( "Collapse" )} ),
			Dispatch( {"t Test"}, "", ColStackBox, {Visibility( "Collapse" )} ),
		
		//formatting the "Each Pair, Student's t" tables
		Dispatch({"Means Comparisons", "Comparisons for each pair using Student's t","Ordered Differences Report"},"",
			TableBox,
				{Set Column Borders( 1 ), 
				Set Row Borders( 1 ),
				Set Underline Headings( 1 )}
		),
		Dispatch({"Means Comparisons", "Comparisons for each pair using Student's t","Ordered Differences Report"},"Difference",NumberColBox,{Set Format( "Fixed Dec", 9, 2 )}		),
		Dispatch({"Means Comparisons", "Comparisons for each pair using Student's t","Ordered Differences Report"},"Std Err Dif",NumberColBox,{Set Format( "Fixed Dec", 9, 2 )}),
		Dispatch({"Means Comparisons", "Comparisons for each pair using Student's t","Ordered Differences Report"},"Lower CL",NumberColBox,{Visibility( "Collapse" )}),
		Dispatch({"Means Comparisons", "Comparisons for each pair using Student's t","Ordered Differences Report"},"Upper CL",NumberColBox,{Visibility( "Collapse" )}),
		Dispatch({"Means Comparisons", "Comparisons for each pair using Student's t","Ordered Differences Report"},"~Difference",PlotColBox,{Visibility( "Collapse" )}),
		
		//formatting the "Means/Anova/Pooled t Test" tables
		Dispatch({"Oneway Anova", "Summary of Fit"},"",
			TableBox,
				{Set Column Borders( 1 ), 
				Set Row Borders( 1 )}
		),
		Dispatch({"Oneway Anova", "Pooled t Test"},"",StringColBox,{Visibility( "Collapse" )}),
		Dispatch({"Oneway Anova", "Pooled t Test"},"",ColStackBox,{Visibility( "Collapse" )}),
		Dispatch({"Oneway Anova", "Analysis of Variance"},"",
			TableBox,
				{Set Column Borders( 1 ), 
				Set Row Borders( 1 ),
				Set Underline Headings( 1 )}
		),
		Dispatch({"Oneway Anova", "Analysis of Variance"},"DF",NumberColBox,{Visibility( "Collapse" )}),
		Dispatch({"Oneway Anova", "Analysis of Variance"},"Sum of Squares",NumberColBox,{Visibility( "Collapse" )}),
		Dispatch({"Oneway Anova", "Analysis of Variance"},"Mean Square",NumberColBox,{Visibility( "Collapse" )}),
		Dispatch({"Oneway Anova", "Analysis of Variance"},"F Ratio",NumberColBox,{Visibility( "Collapse" )}),
		Dispatch({"Oneway Anova", "Means for Oneway Anova"},"",
			TableBox,
				{Set Column Borders( 1 ), 
				Set Row Borders( 1 ),
				Set Underline Headings( 1 )}
		),
		Dispatch({"Oneway Anova", "Means for Oneway Anova"},"Mean",NumberColBox,{Set Format( "Fixed Dec", 8, 2 )}),
		Dispatch({"Oneway Anova", "Means for Oneway Anova"},"Std Error",NumberColBox,{Set Format( "Fixed Dec", 7, 2 )}),
		Dispatch({"Oneway Anova", "Means for Oneway Anova"},"Lower 95%",NumberColBox,{Visibility( "Collapse" )}),
		Dispatch({"Oneway Anova", "Means for Oneway Anova"},"Upper 95%",NumberColBox,{Visibility( "Collapse" )})
	)
);
obj << histograms(1);
(current report() << xpath("//BoxPlotSeg")) << set line color(black); //sets boxplot to BLACK lines

txnelson

Because you are using a By() clause, the output report is actually a separate report for each level of the By(). Here is how I handle what you are asking for. My example is probably not exactly what you want, but it should move you in the correct direction.

names default to here(1);
dt=open("$sample_data/big class.jmp");
//dt<<color by column(:sex);
ow = Oneway(
	Y( :height ),
	X( :sex ),
	by(:age),
	Box Plots( 1 ),Means( 1 ), //means/anova/pooled t
	Each Pair( //student's t-Test
		1,
		Difference Matrix( 0 ),
		Confidence Quantile( 0 ),
		LSD Threshold Matrix( 0 ),
		Connecting Letters Report( 0 ),
		Ordered Differences Report( 1 ),
		Detailed Comparisons Report( 0 )
	),
	Points Jittered( 1 ),
		Box Plots( 1 ),
		Mean Diamonds( 0 ),
		Mean Error Bars( 0 ),
		Std Dev Lines( 0 ),
		Grand Mean( 0 ),
		SendToReport(
		//x-axis formatting
		Dispatch(
			{},
			"2",
			ScaleBox,
			{Label Row(
				{Label Orientation( "Angled" ), Lower Frame( 1 ),
				Show Major Grid( 1 ), Tick Mark Style( "Long Divider" )}
				)
			}
		),
		//row legend by chamber
		Dispatch(
			{},
			"Oneway Plot",
			FrameBox,
			{Marker Size( 6 ), Marker Drawing Mode( "Normal" ),
			Row Legend(
				:TOOL_PROCESS_CHAMBER,
				Color( 1 ),
				Color Theme( "JMP Default" ),
				Marker( 0 ),
				Marker Theme( "" ),
				Continuous Scale( 0 ),
				Reverse Scale( 0 ),
				Excluded Rows( 0 )
				)
			}
		)
	));

ow << histograms(1);
For(i=1,i<=nitems(ow),i++,
	report(ow[i])["Oneway Anova"]["Summary of Fit"] << visibility("Collapse");
	report(ow[i])["Oneway Anova"]["Pooled t Test"] << visibility("Collapse");
	report(ow[i])["Oneway Anova"]["Means for Oneway Anova"] << visibility("Collapse");
	report(ow[i])["Means Comparisons"] << visibility("Collapse");
)

aliegner1

Thank you. This is kinda working. One problem is that a graph with 3+ chambers does not have a Pooled t Test section, then it errors out and stops.

How to move past to next row while still staying in its i iteration?

txnelson

If you have an easy way to check the number of levels, you can use an IF() to check and bypass the statement. Or, you can use a TRY() function to keep it from ending when the statement fails

try(report(ow[i])["Oneway Anova"]["Pooled t Test"] << visibility("Collapse"));