Hi all,

Im using adonis for some plant community analysis and have been following
theBioBucket example of how to posthoc tests (
http://thebiobucket.blogspot.ch/2011/08/two-way-permanova-adonis-with-custom.html
)



data(dune)
data(dune.env)
ad1 <- adonis(dune ~ Management, data=dune.env, permutations=99)
# Call:
# adonis(formula = dune ~ Management, data = dune.env, permutations = 99)
#
# Terms added sequentially (first to last)
#
# Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)
# Management  3    1.4686 0.48953  2.7672 0.34161   0.01 **
# Residuals  16    2.8304 0.17690         0.65839
# Total      19    4.2990                 1.00000
# ---
#      Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

man <- dune.env$Management
contmat <- cbind(c(1,-1,0,0), c(1,0,-1,0), # construct a new contrast matrix
                 c(1,0,0,-1), c(0,1,-1,0),
                 c(0,1,0,-1), c(0,0,1,-1))
contrasts(man) <- contmat[,1:4]
trt1.2 <- model.matrix(~ man)[,2]
trt1.3 <- model.matrix(~ man)[,3]
trt1.4 <- model.matrix(~ man)[,4]

ad2 <- adonis(dune ~ trt1.2 + trt1.3 + trt1.4 )
# Call:
#      adonis(formula = dune ~ trt1.2 + trt1.3 + trt1.4)
#
# Terms added sequentially (first to last)
#
# Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)
# trt1.2     1    0.1483 0.14827  0.8381 0.03449  0.545
# trt1.3     1    0.8371 0.83712  4.7321 0.19472  0.001 ***
# trt1.4     1    0.4832 0.48321  2.7315 0.11240  0.032 *
# Residuals 16    2.8304 0.17690         0.65839
# Total     19    4.2990                 1.00000
# ---
# Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1


I was just wondering whether it was fair to say that the species with high
coefficients (adonis(...)$coefficients) were the ones causing that
difference?

ad2$coefficients[3,abs(ad$coefficients[3,])>1]
# Elepal    Poapra    Salrep    Poatri    Elyrep    Lolper    Alogen
# -1.091667  1.975000 -1.375000  3.283333  1.333333  3.000000  1.650000

If so, would it be better to take the coefficients from the original model
or the model used for the contrast, as these yield different results:

ad1$coefficients[3,abs(ad1$coefficients[3,])>1]
# Rumace   Tripra   Poatri   Plalan
# 2.316667 1.350000 1.516667 1.541667


Cheers,

Alan


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Email: aghaynes@gmail.com
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Skype: aghaynes

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