[R-sig-eco] Balanced split plot analysis in R

[Dixon, Philip M [STAT]]

Markus,

The presence or absence of an interaction has no bearing on the choice of 
analysis.  If you're a design-based person, as I am, you have two sizes of 
experimental unit (main plot and split plot).  If you're a model-based person, 
the multiple measurements (the split plots) on each main plot induces a 
correlation between split plot observations that needs to be accounted for in 
the model.  Both facts are different way of saying the same thing.  The 
presence or absence of an interaction doesn't change either fact.  You're 
concerned about appropriate comparisons of the main plot marginal means.

You're lucky that your design is balanced (equal numbers of observations for 
each combination of main plot and split plot factors).  Otherwise, the 
appropriate R analysis gets very hard very quickly.  (and there is considerable 
disagreement about what that appropriate analysis should be).

My suggestion:
Leave the interaction in the model.  It is part of the treatment design.  Test 
and do multiple comparisons among the split plot levels using the model you 
have.  If you are comparing cell means, the only correct comparisons are those 
between disturbance treatments within a grazing treatment.  If there is no 
evidence of an interaction, you're probably not comparing cell means, so that 
limitation is not an issue.
To get comparisons among levels of the main plot treatment: compute the average 
Y for each main plot, i.e. average over the split plots in each main plot.  
There is now only one treatment factor (grazing regime) and one blocking factor 
in the analysis.  The error in this analysis is the variability among main 
plots, which is what you want for comparisons among grazing levels.  
Straightforward test and multiple comparisons.

Best wishes,
Philip Dixon

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Re: [R-sig-eco] Using partykit::ctree with observations that are spatially autocorrelated

[Manuel Spínola]

What you say makes sense to me Kay.

Best,

Manuel

2012/3/21 Kay Cichini kay.cich...@gmail.com

 manuel,

 the sites where sampled repeatedly, such that the detection probability is
 sufficiently high. some occurrences might be overseen, but as i am not
 interested in the abundances or occurrence-rate per se i can live with
 missing some.

 another problem of regression like models is that i would not be can't
 include too many interactions because I soon will have some
 over-parameterisation... ctree can deal with this quite well, as far as i
 can tell.

 another point is that the practitioner that will be presented the results
 won't be very happy with
 regression-cofficients, model-comparisons, AIC and friends. contrary,
 ctree would yield an intuitive and simple result which i would fancy for
 this purpose!

 yours,
 kay



 2012/3/21 Manuel Spínola mspinol...@gmail.com

 That is true, but it can deal with detectability, and I am afraid ctree
 cannot.

 Best,

 Manuel

 2012/3/21 Kay Cichini kay.cich...@gmail.com

 thanks manuel,

 i'm afraid unmarked can not deal with spatial autocorrelation -
 see this post:
 http://groups.google.com/group/unmarked/browse_thread/thread/f45bd5ab12aa127d/26446409f3e2a140?lnk=gstq=spatial%23#26446409f3e2a140

 best,
 kay


 2012/3/20 Manuel Spínola mspinol...@gmail.com

 You need to look in the unmarked package.

 Best,

 Manuel Spínola

 2012/3/20 Isidore AMAHOWE ogoudje.amah...@gmail.com

  This may be possible with an R packages but i don't know. What i've
 been
  told is that a kind of analysis can be done with accupancy analysis
 and
  this will give possibility to model the envioronmental factors that
 can
  determine the presence of animal species. But this need a probabilitic
  method.
  good luck
 




 --
 *Manuel Spínola, Ph.D.*
 Instituto Internacional en Conservación y Manejo de Vida Silvestre
 Universidad Nacional
 Apartado 1350-3000
 Heredia
 COSTA RICA
 mspin...@una.ac.cr
 mspinol...@gmail.com
 Teléfono: (506) 2277-3598
 Fax: (506) 2237-7036
 Personal website: Lobito de ríohttps://sites.google.com/site/lobitoderio/
 Institutional website: ICOMVIS http://www.icomvis.una.ac.cr/





-- 
*Manuel Spínola, Ph.D.*
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspin...@una.ac.cr
mspinol...@gmail.com
Teléfono: (506) 2277-3598
Fax: (506) 2237-7036
Personal website: Lobito de río https://sites.google.com/site/lobitoderio/
Institutional website: ICOMVIS http://www.icomvis.una.ac.cr/

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