[R-sig-eco] adonis question
Kay Cecil Cichini
Kay.Cichini at uibk.ac.at
Mon Jun 27 16:14:26 CEST 2011
sorry for double posting: in my first mail i forgot to change the subject
which wrongly said "Re: [R-sig-eco] R-sig-ecology Digest, Vol 39, Issue 16"
----------------------------------------------
hi,
sorry - i'm afraid this was only due to a trivial syntax error:
"...,dist = "euclidean",..." should say "...,method = "euclidean",..."
with the wrong argument adonis defaults to "bray" - and with
bray-curtis dissim. the difference between 1 and 2 is really not the
same as the one between 2 and 3 or 4 and 5, isn't it?
so the message to you, regarding your suspicious p-values, might be to
check for the dissimilarity-index you use, what its characteristics
are and if it's appropriate for the questions you ask..
yours,
kay
following up my example:
# distance matrix with bray-curtis dissimilarity:
# dissimilarities *are the same*
dm <- as.matrix(vegdist(spdf, method = "bray"))
# assign names
dimnames(dm) <- list(paste(treat, imp), paste(treat, imp))
# see average off-diagonal dissimilarities (within treatments, between
impact levels)
mean(dm[11:20,1:10])
mean(dm[31:40,21:30])
mean(dm[51:60,41:50])
# distance matrix with euclidean dissimilarity:
dm <- as.matrix(vegdist(spdf, method = "euclidean"))
# assign names
dimnames(dm) <- list(paste(treat, imp), paste(treat, imp))
# see average off-diagonal dissimilarities (within treatments, between
impact levels)
# dissimilarities *are not the same*
mean(dm[11:20,1:10])
mean(dm[31:40,21:30])
mean(dm[51:60,41:50])
Zitat von Kari Lintulaakso <kari.lintulaakso at gmail.com>:
> 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)
>>
>>
>> ----------------------------------------------------------------------
>>
>> 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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>>> R-sig-ecology at r-project.org
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>>>
>>
>>
>>
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>> End of R-sig-ecology Digest, Vol 39, Issue 16
>> *********************************************
>>
>
>
>
> --
> Kari Lintulaakso, M.Sc.(Biosciences)
>
> Doctoral student
> Paleontology and Paleoecology
> Department of Geosciences and Geography
> University of Helsinki
>
> * Mobile: +358 50 40 33391
> * Office: +358 9 191 50842
> * Email: kari.lintulaakso at helsinki.fi
> * Post: Department of Geology, Gustaf Hällströmin katu 2a (P.O Box
> 64), 00014 University of Helsinki
> * Web page: http://blogs.helsinki.fi/lintulaa/
>
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