[R-sig-eco] manova repeated measures + Error

[Steve Brewer]

Marina,

I'm a little confused by your description. What is "tempo"? Is it just the
Portuguese word for the time variable?

>From what I gather, "plot" should be nested within "nurse" and "target",
but not within time. So, I think your model should be manova(Y ~
nurse*target*time + Error(plot). Not sure why tempo (assuming it is the
same as time) would need to be in parentheses.

Make sure that the time and plot variables are not being treated as
numeric continuous variables. They should be categorical variables.

Finally, a comment about RII. I would be wary of using this index. I don't
think it is necessary, and, like proportions, it usually is NOT normally
distributed. Just because many people use it doesn't mean it is a good
idea. I think just log transforming the data and taking the difference
between the nurse-present and nurse-absent plot halves would provide you
what you want (it is equivalent to a log response ratio, LRR, which is
superior to RII).

Good luck,
Steve




J. Stephen Brewer 
Professor 
Department of Biology
PO Box 1848
 University of Mississippi
University, Mississippi 38677-1848
 Brewer web page - http://home.olemiss.edu/~jbrewer/
FAX - 662-915-5144
Phone - 662-202-5877




On 2/13/15 9:58 AM, "Marina Vergara Fagundes" <marvefa at gmail.com> wrote:

>Dear all,
>
>I conducted a interaction plant experiment, with 20 adult plant species (5
>individuals each) and 3 seedling species, and a 100 plots in total. Each
>plot consist of two 2m² quadrants, the first contains one adult individual
>as a potential “nurse” and 3 seedling species below their canopy, and the
>second  just with 3 seedling species with no canopy influence  (in an open
>area).
>I measured growth variables of the seedlings (leaves number and height)
>over 8 weaks (times).
>For each growth variable I calculated a index (rii) with the difference of
>growth below and far from canopy.
>
>I'm analyzing this data with MANOVA with repeated measures. Where Y axes
>are the index of growth measurements (for leafs and height), and the X
>axes
>are the 20 nurse species and interactions with seedlings species and time.
>
>This is how my data frame is organized:
>plot   nurse  target    time    height_rii      leaves_rii
>113 algodao  angico     1    0.03703704  0.00000000
>113 algodao  aroeira     2    0.05660377  0.09090909
>113 algodao  cating      3    0.03846154  0.00000000
>115 algodao  angico     1    0.01818182  0.11111111
>115 algodao  aroeira     2    0.05660377  0.50000000
>115 algodao  cating      3    0.03703704  0.00000000
>
>This is the code for the MANOVA:
>Y <- with(tabela3, cbind(altura_rii, folhas_rii))
>m1 <- manova( Y ~ nurse*target*time+Error(tempo/plot),data=tabela3)
>summary(m1)
>
>When i ask for anova table i got this specific message:
>
>
>
>
>
>
>
>*Error: timeNo error degrees of freedom      Dftempo  7*Error: time:plot
>               Df  Pillai approx F num Df den Df    Pr(>F)
>nurse        19 0.17070  3.14316     38   1280 8.633e-10 ***
>nurse:time 133 0.24253  0.66405    266   1280         1
>Residuals   640
>---
>Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>
>Error: Within
>                       Df   Pillai approx F num Df den Df    Pr(>F)
>target                2 0.013439   4.3297      4   2560  0.001715 **
>nurse:target         38 0.178898   3.3090     76   2560 < 2.2e-16 ***
>target:time         14 0.027914   1.2941     28   2560  0.138459
>nurse:target:time  266 0.174314   0.4594    532   2560  1.000000
>Residuals          1280
>---
>Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>
>Any idea what is it about?
>Thanks a lot for help!
>Marina
>
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>
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