Hi everybody,
I'm working on PCA approach, and comparing outputs from ade4 and vegan
packages.
I'm ok with the normalization of the variables coordinates coming from ade4
outputs.
(with $co : coordinates are scaled to eigen values ; with $c1 : coordinates
are scaled to 1).
But I have difficulties to understand how are computed the Species scores in
vegan's outputs with scaling 1 or 2 options, and what means the message
concerning scaling, especially about the 'General scaling constant of
scores'.
For example :
'Scaling 2 for species and site scores
* Species are scaled proportional to eigenvalues
* Sites are unscaled: weighted dispersion equal on all dimensions
* General scaling constant of scores: 4.226177 '
'
I've search on the archives of R-sig-ecology , cross validate and
stackoverflow, and found nothing that helped me. If somebody has some
information about it, I would greatly appreciate some help.
All the best.
Claire Della Vedova
Here some parts of my code :
library(ade4)
library(vegan)
doubs.env <- read.csv
('http://www.sci.muni.cz/botany/zeleny/wiki/anadat-r/data
-download/DoubsEnv.csv', row.names = 1)
###################### with ade4 ##########################################
pca.ad<-dudi.pca(doubs.env, scale = TRUE, center = TRUE, scann = FALSE,nf=3)
# eigen value of the fisrt eigen vector
pca.ad$eig[1]
[1] 5.968749
#variables coordinates in first eigen vector
pca.ad$co[,1]
[1] 0.85280863 -0.81918008 -0.45283333 0.75214647 -0.04996375 0.70722171
[7] 0.83048310 0.90260821 0.79011263 -0.76485397 0.76373149
#check the normalization of laodings
sum(pca.ad$co[,1]^2)
[1] 5.968749
#=> coordinatesscaled to eigen values
#variables normed scores in first eigen vector
pca.ad$c1[,1]
[1] 0.34906791 -0.33530322 -0.18535177 0.30786532 -0.02045094 0.28947691
[7] 0.33992972 0.36945166 0.32340546 -0.31306670 0.31260725
#check the normalization
sum(pca.ad$c1[,1]^2)
[1] 1
#=> coordinates scaled to 1
###################### with vegan ######################################
pca.veg<-rda(doubs.env, scale = TRUE)
# species scores for the fisrt eigen vector, with sacling 1
summary(pca.veg, scaling=1)
das alt pen deb pH dur pho
1.4752228 -1.4170507 -0.7833294 1.3010933 -0.0864293 1.2233806 1.4366031
nit amm oxy dbo
1.5613681 1.3667687 -1.3230752 1.3211335
'Scaling 1 for species and site scores
* Sites are scaled proportional to eigenvalues
* Species are unscaled: weighted dispersion equal on all dimensions
* General scaling constant of scores: 4.226177
'
summary(pca.veg, scaling=2)[1][[1]][,1]
das alt pen deb pH dur
1.08668311 -1.04383225 -0.57701847 0.95841533 -0.06366582 0.90117039
pho nit amm oxy dbo
1.05823501 1.15013974 1.00679334 -0.97460773 0.97317743
'Scaling 2 for species and site scores
* Species are scaled proportional to eigenvalues
* Sites are unscaled: weighted dispersion equal on all dimensions
* General scaling constant of scores: 4.226177 '
--
View this message in context:
http://r-sig-ecology.471788.n2.nabble.com/how-are-compuetd-the-species-scores-of-pca-from-vegan-package-tp7578918.html
Sent from the r-sig-ecology mailing list archive at Nabble.com.
_______________________________________________
R-sig-ecology mailing list
R-sig-ecology@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
