R-sig-ecology Digest, Vol 39, Issue 16 - R-SIG-ecology

Sun, Jun 26, 2011 5:32 PM #

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

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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Today's Topics:

? 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

_______________________________________________
R-sig-ecology mailing list
R-sig-ecology at r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

_______________________________________________
R-sig-ecology mailing list
R-sig-ecology at r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology


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 H?llstr?min katu 2a (P.O Box
64), 00014 University of Helsinki
* Web page: http://blogs.helsinki.fi/lintulaa/

Kay Cichini

Mon, Jun 27, 2011 3:36 AM #

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:

Send R-sig-ecology mailing list submissions to
? ? ? ?r-sig-ecology at r-project.org

To subscribe or unsubscribe via the World Wide Web, visit
? ? ? ?https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
or, via email, send a message with subject or body 'help' to
? ? ? ?r-sig-ecology-request at r-project.org

You can reach the person managing the list at
? ? ? ?r-sig-ecology-owner at r-project.org

When replying, please edit your Subject line so it is more specific
than "Re: Contents of R-sig-ecology digest..."


Today's Topics:

? 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

_______________________________________________
R-sig-ecology mailing list
R-sig-ecology at r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

_______________________________________________
R-sig-ecology mailing list
R-sig-ecology at r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology


End of R-sig-ecology Digest, Vol 39, Issue 16
*********************************************

_______________________________________________
R-sig-ecology mailing list
R-sig-ecology at r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

Kay Cichini

Mon, Jun 27, 2011 7:14 AM #

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:

Send R-sig-ecology mailing list submissions to
? ? ? ?r-sig-ecology at r-project.org

To subscribe or unsubscribe via the World Wide Web, visit
? ? ? ?https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
or, via email, send a message with subject or body 'help' to
? ? ? ?r-sig-ecology-request at r-project.org

You can reach the person managing the list at
? ? ? ?r-sig-ecology-owner at r-project.org

When replying, please edit your Subject line so it is more specific
than "Re: Contents of R-sig-ecology digest..."


Today's Topics:

? 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

_______________________________________________
R-sig-ecology mailing list
R-sig-ecology at r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

_______________________________________________
R-sig-ecology mailing list
R-sig-ecology at r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology


End of R-sig-ecology Digest, Vol 39, Issue 16
*********************************************

_______________________________________________
R-sig-ecology mailing list
R-sig-ecology at r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

_______________________________________________
R-sig-ecology mailing list
R-sig-ecology at r-project.org
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