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RE: st: RE: yscale in anovaplot


From   "Nick Cox" <n.j.cox@durham.ac.uk>
To   <statalist@hsphsun2.harvard.edu>
Subject   RE: st: RE: yscale in anovaplot
Date   Mon, 27 Apr 2009 10:55:11 +0100

That's a very helpful reference to keep questions clear and specific. 

That web page gives two graphs, and (modulo cosmetic details) both are
obtainable directly via -anovaplot-. The only twist is that the -anova-
to precede it is simpler than the -anova- used as example. 

use http://www.ats.ucla.edu/stat/stata/examples/kirk/spf2-4, clear
anova y a b a*b 
anovaplot 
anovaplot, scatter(ms(none)) 
anovaplot b a
anovaplot b a, scatter(ms(none))

The moral that the plots you want may pertain to a simpler ANOVA than
that you fit is valuable, and I'll build this example into the next
revision of the help for -anovaplot-. 

Nick 
n.j.cox@durham.ac.uk 

David Airey

Typical plots in the context of a split plot design are here:

http://www.ats.ucla.edu/stat/stata/examples/kirk/kirkstata12.htm

On Apr 26, 2009, at 1:19 PM, David Airey wrote:

> In the simplest within subject design, the paired ttest, it makes  
> sense to plot the data by subject, a line per subject. Or if you  
> measure subjects repeatedly over time, it also makes sense to keep  
> the graphic by subject. Or if you measure two groups, pre and post,  
> it makes sense to plot either two groups of different colored lines  
> (one line per subject) or ignore subject and make a profile plot as  
> other software does. As far as I can tell, none of the permutations  
> of the factors does this, and that is why I said anovaplot is for  
> between subjects designs only, or as the help says with maybe one  
> covariate. My query was as much to Diego, who seemed satisfied with  
> his use of -anovaplot- in a repeated measures context. I was just  
> curious what his final plot looked like and from what model.

 On Apr 26, 2009, at 12:14 PM, Nick Cox wrote:

>> You use it the way you expect to be most fruitful.
>>
>> I'm not minded to go upstream and find out what the example is  
>> about, or
>> learn enough about the subject-matter to make a guess at what  
>> should be
>> most helpful.
>>
>> But the default -anovaplot- has no inbuilt intelligence. It's likely
>> that some permutation of the factors improves on the default plot,  
>> for
>> example
>>
>> anovaplot s a b
>>
>> A simple but important issue is that whenever identifiers are quite
>> arbitrary, putting them on one axis may not yield a clear picture. It
>> may be worth re-labelling identifiers to make structure clearer.

David Airey

>> I always use it for between subjects ANOVAs. Perfect for that.
>>
>> The key thing in my response is that _I_ have not been satisfied with
>> my use in within subject designs or mixed models.
>>
>> Maybe I was not using it correctly. Let's use an example from UCLA
>> ATS, so that I can get it as correctly intended.
>>
>> From
>>
>> http://www.ats.ucla.edu/stat/stata/faq/xtmixed.htm
>>
>> just focusing on the ANOVA aspects of the page, let's do:
>>
>> use http://www.ats.ucla.edu/stat/stata/examples/kirk/spf2-4, clear
>> anova y a / s|a b a*b /, repeated(b)
>>
>> How do you use -anovaplot- here?

On Apr 26, 2009, at 11:26 AM, Nick Cox wrote:

>>> 2.1.1 is the latest publicly available version.
>>>
>>> -anovaplot- plots observed and fitted values after -anova- in  
>>> terms of
>>> predictor levels.
>>>
>>> It's a bit surprising to hear that you never found that useful. What
>>> do
>>> you do instead?
>>>
>>> A while back I went carefully through various classic texts on ANOVA
>>> from the 1950s. As I recall none of them included any plots based on
>>> data.

David Airey

>>> I never found -anovaplot- useful for anything but between subject
>>> designs. I'd be curious to see the repeated measures plots using -
>>> anovaplot-.
>>>
>>> Is the version on SSC not the latest?
>>>
>>> I have
>>>
>>> . which anovaplot
>>> /Users/dairey/Library/Application Support/Stata/ado/plus/a/
>>> anovaplot.ado
>>> *! 2.1.1 NJC 6 November 2004

On Apr 26, 2009, at 10:52 AM, Nick Cox wrote:

>>>> Thanks to Diego for this interesting question and to Thomas for
>>>> answering it so fully.
>>>>
>>>> To fill in a gap and to fill out the implicitly needed discussion:
>>>>
>>>> -anovaplot- is a program in the -modeldiag- package written up in  
>>>> the
>>>> Stata Journal within
>>>>
>>>> SJ-4-4  gr0009  . . . . . . . . . . Speaking Stata: Graphing model
>>>> diagnostics
>>>>     . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .  N.
>>>> J. Cox
>>>>     (help anovaplot, indexplot, modeldiag, ofrtplot, ovfplot,
>>>>     qfrplot, racplot, rdplot, regplot, rhetplot, rvfplot2,
>>>>     rvlrplot, rvpplot2 if installed)
>>>>     Q4/04   SJ 4(4):449--475
>>>>     plotting diagnostic information calculated from residuals
>>>>     and fitted values from regression models with continuous
>>>>     responses
>>>>
>>>> There's also an equivalent package on SSC that includes older
>>>> versions
>>>> of these programs.
>>>>
>>>> The paper is accessible to all via
>>>>
>>>> http://www.stata-journal.com/sjpdf.html?articlenum=gr0009
>>>>
>>>> -anovaplot- is described on p.458. I add this comment, which is
>>>> relevant
>>>> to Diego's question:
>>>>
>>>> "It is curious that analysis-of-variance people typically draw
>>>> interaction plots but suppress the data, whereas regression people
>>>> prefer to draw scatterplots showing both observed and fitted  
>>>> values.
>>>> Admittedly, a complicated set of crossing lines showing  
>>>> interactions
>>>> may
>>>> seem to leave little scope for showing data effectively, while a
>>>> relatively
>>>> simple regression leaves plenty of scope, but the difference is
>>>> nevertheless intriguing."
>>>>
>>>> I still treasure a comment made by a senior Stata user, who might  
>>>> not
>>>> want to be named for this, to the effect that showing the data on  
>>>> the
>>>> graph typically confuses the issue.
>>>>
>>>> Nevertheless I'll think about adding a -nodata- option, possibly
>>>> with a
>>>> sting in the tail. (For example, it might -drop- all your data, or
>>>> some
>>>> such.)

>>>> Thomas Steichen
>>>> ===============
>>>>
>>>> Although you have suppressed printing a symbol for the data points
>>>> via
>>>> -scatter(msym(none))-, Stata still allows room for that invisible
>>>> data
>>>> in its y-axis range. Therefore you cannot reduce the range given  
>>>> the
>>>> way
>>>> the code is written. Editing the code to allow what you want is
>>>> pretty
>>>> straightforward.
>>>>
>>>> Change line:
>>>>             numlist "2/`= 1 + `: word count `fits'''"
>>>> To:
>>>>             numlist "1/`= 1 + `: word count `fits'''"
>>>>
>>>> And line:
>>>>         twoway scatter `y' `x1' if e(sample), `scatter' ///
>>>> To:
>>>>         twoway `scatter'  ///
>>>>
>>>> Then edit line:
>>>> program anovaplot, sort
>>>> To:
>>>> program anovaplot0, sort
>>>>
>>>> Save it with new name anovaplot0.ado and invoke it with command
>>>> -anovaplot0-
>>>>
>>>> Nick Cox's original will keep working and you'll have this one for
>>>> your
>>>> purpose.
>>>>
>>>> Of course, you could get fancy and add a -nodata- option that  
>>>> allows
>>>> both forms in a single program.
>>>>
>>>> Diego Bellavia
>>>> ==============
>>>>
>>>> I am trying to plot an ANOVA for repeated measures model using the
>>>> amazing anovaplot command.
>>>> Everything works fine except the yscale range. I need to reduce the
>>>> range and increase the scale
>>>> to make differences clear. So I tried:
>>>>
>>>> anovaplot level groups, scatter(msym(none)) yscale (range(-12 -24))
>>>> ylabel(-12 (2) -24)
>>>>
>>>> The problem is that I actually reduced the numbered range and the
>>>> labelling but now almost half of the graph
>>>> is empty. Is there any way to change the range so that I can take
>>>> advantage of all the graph extension ?

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