[R-sig-eco] scaling issues with vegan's envfit()

[Gavin Simpson]

If I understand correctly Arnaud, you just need `predict()`:

predict(pca1, newdata = varechem, type = "sp", scaling = 1)[, 1:2]

where you set newdata to be the data frame of new variables you want to
add. This will add so-called passive species to the plot base on the linear
combinations of the site scores produced from the ordination of the
original data. Hence the new data need to be measured on the same sites and
have the same row names as the data used to fit the PCA (as that is how
vegan identifies them).

Using the example you gave I get:

> scores(pca1, scaling = 1, choices = 1:2, display = "sp")
                PC1        PC2
N         0.4008477  0.5267927
P        -1.5075888 -0.8781843
K        -1.5384951 -0.6850869
Ca       -1.5239497 -0.3582552
Mg       -1.4922949 -0.4141239
S        -1.4083631 -1.2567985
Al        0.4893605 -2.0353607
Fe        0.8599106 -1.6224771
Mn       -1.2181461  0.8183585
Zn       -1.4658174 -0.6861639
Mo       -0.1759892 -0.9685048
Baresoil -0.6925869  1.3373455
Humdepth -0.9968279  1.4290890
pH        0.7037755 -1.3647204
attr(,"const")
[1] 4.236078
> predict(pca1, varechem, type = "sp", scaling = 1)[, 1:2]
                PC1        PC2
N         0.4008477  0.5267927
P        -1.5075888 -0.8781843
K        -1.5384951 -0.6850869
Ca       -1.5239497 -0.3582552
Mg       -1.4922949 -0.4141239
S        -1.4083631 -1.2567985
Al        0.4893605 -2.0353607
Fe        0.8599106 -1.6224771
Mn       -1.2181461  0.8183585
Zn       -1.4658174 -0.6861639
Mo       -0.1759892 -0.9685048
Baresoil -0.6925869  1.3373455
Humdepth -0.9968279  1.4290890
pH        0.7037755 -1.3647204

So we are able to recover exactly the correct scores - you just need to
draw arrows (perhaps using ordiArrow()) from (0,0) to those coordinates.

I don't think `evnfit()` is the right approach here, especially trying to
fake this via `ordiArrowMul()` as that is trying to fill the space and in
scaling 1 you need to scale variables independently.

HTH

Gavin

On 12 September 2014 12:06, ADuranel <arnaud.duranel.09 at ucl.ac.uk> wrote:

> Hello
>
> I am running a PCA of some environmental variables. I have a second set of
> environmental variables that I would like to project passively onto the
> ordination plot, but with the same arrow length scaling as that used for
> the
> first dataset. I used envfit() in vegan for that purpose. To check that I
> get the same arrow length scaling in plot.envfit() as in plot.cca(), I
> fitted the same dataset:
>
> require(vegan)
> data(varechem)
> pca1<-rda(varechem, scale=T)
>
> ef<-envfit(pca1, scale(varechem))
> plot(pca1, type="points")
> sp.sc<-scores(pca1, display="species")
> ef.sc<-scores(ef, display="vectors")
> plot(ef, arrow.mul=abs(sp.sc[1,1]/ef.sc[1,1]), col="red")
> # equivalent to:
> plot(ef, arrow.mul=vegan:::ordiArrowMul(ef.sc)/vegan:::ordiArrowMul(sp.sc
> ))
>
> The last two lines are the only two ways I managed to get the same length
> scaling for the plot.cca() "species" and plot.envfit() vectors.
> However if I want to use another scaling (scaling=1 or 3) for the PCA plot,
> I can't get similar coordinates for the plot.cca() "species" and
> plot.envfit() vectors:
>
> ef1<-envfit(pca1, scale(varechem), scaling=1)
> plot(pca1, scaling=1, type="points")
> sp.sc1<-scores(pca1, scaling=1, display="species")
> ef.sc1<-scores(ef1, scaling=1, display="vectors")
> plot(ef1, arrow.mul=abs(sp.sc1[1,1]/ef.sc1[1,1]), col="red") # wrong: the
> ratio sp.sc/ef.sc varies according to "species" in this case...
> plot(ef1,
> arrow.mul=vegan:::ordiArrowMul(ef.sc1)/vegan:::ordiArrowMul(sp.sc1)) # the
> arrow length scaling varies according to "species".
>
> Can somebody tell me what I am doing wrong here?
>
> I use R version 3.1.1 (2014-07-10) with vegan_2.0-10
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> Many thanks
>
> Arnaud
>
>
>
>
>
> --
> View this message in context:
> http://r-sig-ecology.471788.n2.nabble.com/scaling-issues-with-vegan-s-envfit-tp7579076.html
> Sent from the r-sig-ecology mailing list archive at Nabble.com.
>
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-- 
Gavin Simpson, PhD

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