[R-sig-eco] R-sig-ecology Digest, Vol 39, Issue 16

Kari Lintulaakso kari.lintulaakso at gmail.com
Mon Jun 27 02:32:11 CEST 2011


Hi Kay,

I also get significant values (both from adonis and anova) when
running your code. I'm currently running my own adonis analysis which
most have significant results (this has been worrying me for some
time).
I do recall some R discussion about general R setting/value which
might set all the values analysed to be logarithmic. If there is this
kind of setting, does anyone know what it is and how to set it off?
I'm using Revolution R Enterprise 4.3.0 (14.4.2011) Academic version,
R version 2.12.2 (2011-02-25)
-Kari

My results:
for (i in 1:4) {print(summary(aov(spdf[, i] ~ treat * imp)))}
            Df  Sum Sq Mean Sq   F value Pr(>F)
treat        2 166.017  83.008 1316.5029 <2e-16 ***
imp          1  15.978  15.978  253.4022 <2e-16 ***
treat:imp    2   0.021   0.011    0.1666  0.847
Residuals   54   3.405   0.063
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
            Df  Sum Sq Mean Sq   F value Pr(>F)
treat        2 155.836  77.918 1323.0303 <2e-16 ***
imp          1  13.185  13.185  223.8864 <2e-16 ***
treat:imp    2   0.237   0.119    2.0159 0.1431
Residuals   54   3.180   0.059
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
            Df  Sum Sq Mean Sq   F value  Pr(>F)
treat        2 158.672  79.336 1091.8367 < 2e-16 ***
imp          1  16.069  16.069  221.1473 < 2e-16 ***
treat:imp    2   0.363   0.182    2.4987 0.09165 .
Residuals   54   3.924   0.073
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
            Df  Sum Sq Mean Sq F value Pr(>F)
treat        2 159.194  79.597 943.528 <2e-16 ***
imp          1  14.289  14.289 169.383 <2e-16 ***
treat:imp    2   0.093   0.047   0.554 0.5779
Residuals   54   4.555   0.084
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
>
> RevoMods:::revoFix(x)adonis(spdf ~ treat * imp, dist = "euclidean")

Call:
adonis(formula = spdf ~ treat * imp, dist = "euclidean")

          Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)
treat      2    3.4133 1.70666  640.19 0.80850  0.001 ***
imp        1    0.3150 0.31504  118.18 0.07462  0.001 ***
treat:imp  2    0.3495 0.17473   65.54 0.08278  0.001 ***
Residuals 54    0.1440 0.00267         0.03410
Total     59    4.2218                 1.00000


On Sun, Jun 26, 2011 at 8:00 PM,  <r-sig-ecology-request at r-project.org> wrote:
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>   1. Re: adonis question (Kay Cecil Cichini)
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 25 Jun 2011 12:20:44 +0200
> From: Kay Cecil Cichini <Kay.Cichini at uibk.ac.at>
> To: Etienne Laliberte <etiennelaliberte at gmail.com>
> Cc: r-sig-ecology at r-project.org
> Subject: Re: [R-sig-eco] adonis question
> Message-ID: <20110625122044.68992dwaacyxu6ps at web-mail.uibk.ac.at>
> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
>        format="flowed"
>
> hello etienne,
>
> i tried many times and it's alway significant.
>
> i also added:
>
> par(mfrow = c(2, 2))
> for (i in 1:4) {print(interaction.plot(treat, imp, spdf[, i]))}
>
> ...that did not show an interaction for any set of random numbers i tried.
>
> yours,
> kay
>
> Zitat von Etienne Laliberte <etiennelaliberte at gmail.com>:
>
>> Dear Kay,
>>
>> I ran your code and found no significant interactions. You just got
>> "unlucky" with rnorm(), as can happen. Try it again.
>>
>> Cheers,
>>
>> Etienne
>>
>> -----Original Message-----
>> From: r-sig-ecology-bounces at r-project.org
>> [mailto:r-sig-ecology-bounces at r-project.org] On Behalf Of Kay Cecil Cichini
>> Sent: Friday, 24 June 2011 9:31 PM
>> To: r-sig-ecology
>> Subject: [R-sig-eco] adonis question
>>
>> hi all,
>>
>> i played around with adonis and came across a result that i can't
>> explain - more precisely i get a sign interaction-effect where i
>> suppose there should be none:
>>
>> library(vegan)
>>
>> # species matrix/df
>> spdf <- matrix(NA, 60, 4, dimnames = list(1:60, c("sp1", "sp2", "sp3",
>> "sp4")))
>> spdf <- as.data.frame(spdf)
>>
>> # 1st factor = treatment:
>> treat <- gl(3, 20, labels = paste(1:3, "t", sep=""))
>>
>> # 2nd factor = impact:
>> imp <- rep(gl(2, 10, labels = c("yes", "no")), 3)
>>
>> # simulating effect -
>> # simulation will add similar effect
>> # across level combinations, no interactions:
>> eff <- sort(rep(1:6, 10))
>>
>> # add random noise:
>> spdf$sp1 = eff + rnorm(60, 0, 0.25)
>> spdf$sp2 = eff + rnorm(60, 0, 0.25)
>> spdf$sp3 = eff + rnorm(60, 0, 0.25)
>> spdf$sp4 = eff + rnorm(60, 0, 0.25)
>>
>> # difference imp:yes vs imp:no is the same across all levels of treatment
>> aggregate(sp1 ~ imp * treat, data = spdf, FUN = mean)
>>
>> # univariate ANOVAs with no interactions, as expected:
>> for (i in 1:4) {print(summary(aov(spdf[, i] ~ treat * imp)))}
>>
>> # PERMANOVA - strangly gives sign. interaction (??)
>> adonis(spdf ~ treat * imp, dist = "euclidean")
>>
>> thanks in advance,
>> kay
>>
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-- 
Kari Lintulaakso, M.Sc.(Biosciences)

Doctoral student
Paleontology and Paleoecology
Department of Geosciences and Geography
University of Helsinki

* Mobile: +358 50 40 33391
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