[R] RE: R-help Digest, Vol 24, Issue 22

[Andrew Kniss]

I used SAS to analyze the data initially, since the data set was made up of
several files when I received it, and I'm still not very good at
manipulating data in R.  

I have posted the data set from one location at the following address:
http://uwstudentweb.uwyo.edu/A/AKNISS/sxherb.txt
var=cultivar
trt=herbicide treatment
yield=response variable of interest
All plot# from 101 to 104 are rep 1, 201-204 rep 2, and 301 to 304 rep 3.

It was the only file that was in an easy format for R to read at the moment,
and was probably the most reliable trial of the two locations. I would like
to use power.anova.test() with this data set to plan next years study (to
get a sample size for each herb*var combination), but I'm not quite sure how
that is done for an interaction effect.  Do I just use the MS for herb*var
as the between group variance and the MSE as the within group variance?  Or
do I need to somehow include other variance parameters in the model?
   
The model for this location (split-block design):
 yield = rep + herb + var + herb*var ## all are fixed effects
        rep*herb = error term for herb
        rep*var = error term for cultivar
        residual = error term for herb*var

I hope this attempt at my question was a little more clear.  I appreciate
any help that is offered.

Andrew Kniss
Assistant Research Scientist
University of Wyoming
Department of Plant Sciences
1000 E. Univesity Ave
Laramie, WY  82071  USA
akniss at uwyo.edu



-----Original Message-----
From: John Maindonald [mailto:john.maindonald at anu.edu.au] 
Sent: Tuesday, February 22, 2005 3:37 PM
To: r-help at stat.math.ethz.ch
Cc: akniss at uwyo.edu
Subject: Re: R-help Digest, Vol 24, Issue 22

You need to give the model formula that gave your output.
There are two sources of variation (at least), within and
between locations; though it looks as though your analysis
may have tried to account for this (but if so, the terms are
not laid out in a way that makes for ready interpretation.
The design is such (two locations) that you do not have
much of a check that effects are consistent over locations.

You need to check whether results really are similar
for all cultivars and for all herbicides, so that it is
legitimate to pool as happens in the overall analysis.
If a herbicide:cultivar combination has little effect the
variability may be large, while if it has a dramatic effect
(kills everything!), there may be no variability to speak of.
John Maindonald.

On 22 Feb 2005, at 10:06 PM, r-help-request at stat.math.ethz.ch wrote:

> To: "'Bob Wheeler'" <bwheeler at echip.com>
> Cc: r-help at stat.math.ethz.ch
> Subject: RE: [R] power.anova.test for interaction effects
> Reply-To: akniss at uwyo.edu
>
>
> It's a rather complex model.  A 37*4 factorial (37 cultivars[var]; 4
> herbicide treatments[trt]) with three replications[rep] was carried 
> out at
> two locations[loc], with  different randomizations within each rep at 
> each
> location.
>
> Source           DF   Error Term      MS
> Loc               1   Trt*rep(loc)    12314
> Rep(loc)          4   Trt*rep(loc)    1230.5
> Trt               3   Trt*rep(loc)    64.72
> Trt*loc           3   Trt*rep(loc)    33.42
> Trt*rep(loc)     12   Residual        76.78
> Var              36   Var*trt*loc     93.91
> Var*trt         108   Var*trt*loc     12.06
> Var*trt*loc     144   Residual        43.09
> Residual        575   NA              21.23
>
>
> -----Original Message-----
> From: Bob Wheeler [mailto:bwheeler at echip.com]
> Sent: Monday, February 21, 2005 4:33 PM
> To: akniss at uwyo.edu
> Cc: r-help at stat.math.ethz.ch
> Subject: Re: [R] power.anova.test for interaction effects
>
> Your F value is so low as to make me suspect your model. Where did the
> 144 denominator degrees of freedom come from?
>
John Maindonald             email: john.maindonald at anu.edu.au
phone : +61 2 (6125)3473    fax  : +61 2(6125)5549
Centre for Bioinformation Science, Room 1194,
John Dedman Mathematical Sciences Building (Building 27)
Australian National University, Canberra ACT 0200.