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zhenlisha

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专业: 环境微生物学

[求助] VPA分析（Vegan包Varpart程序）已有1人参与

这是varpart自带example，求大神解读：三个因子，为什么跑完程序图中会出现四个圈？
data(mite)
data(mite.env)
data(mite.pcnm)

# two explanatory data frames -- hellinger-transform y
mod <- varpart(mite, mite.env, mite.pcnm, transfo="hel" )
mod

## use fill colours
showvarparts(2, bg = c("hotpink","skyblue" ))
plot(mod, bg = c("hotpink","skyblue" ))
## test fraction [a] using partial rda, '~ .' in formula tells to use
## all variables of data mite.env.
afrac <- rda(decostand(mite, "hel" ) , mite.env, mite.pcnm)
anova(afrac)
## rsquareadj gives the same result as component [a] of varpart
rsquareadj(afrac)

## partition bray-curtis dissimilarities
varpart(vegdist(mite), mite.env, mite.pcnm)
## three explanatory tables with formula interface
mod <- varpart(mite, ~ subsdens + watrcont, ~ substrate + shrub + topo,
mite.pcnm, data=mite.env, transfo="hel" )
mod
showvarparts(3, bg=2:4)
plot(mod, bg=2:4)

## use rda to test fraction [a]
## matrix can be an argument in formula
rda.result <- rda(decostand(mite, "hell" ) ~ subsdens + watrcont +
condition(substrate + shrub + topo) +
condition(as.matrix(mite.pcnm)), data = mite.env)
anova(rda.result)

## four explanatory tables
mod <- varpart(mite, ~ subsdens + watrcont, ~substrate + shrub + topo,
mite.pcnm[,1:11], mite.pcnm[,12:22], data=mite.env, transfo="hel" )
mod
plot(mod, bg=2:5)
## show values for all partitions by putting 'cutoff' low enough:
plot(mod, cutoff = -inf, cex = 0.7, bg=2:5)

[ last edited by jjdg on 2019-5-7 at 09:11 ]

[ Last edited by jjdg on 2019-5-7 at 09:11 ]

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