[R-sig-Geo] ENFA specialization values

[Aschim, Ruth]

Hello,

I am running an ENFA analysis and am having trouble interpreting the specialization values. Do the specialization values correspond to each ecogeographical variable? If so they don't make sense in terms of what I am seeing for the marginality values, i.e. marginality value for water is high and displays a long arrow on the biplot. Therefore, I would think that the specialization value for water would be high, but if the vector of specialization values corresponds to each ecogeographical variable then this is not the case. Am I missing a line of code? An explanation of how to interpret the specialization values from the code and output below would be much appreciated.


slot(maps,"data")[,1:9] <- sqrt(slot(maps,"data")[,1:9])
hist(maps, type = "l")

## Prepare the data for the ENFA
tab <- slot(maps, "data")
pr <- slot(count.points(pipl, maps), "data")[,1]


## Perform the PCA before the ENFA
pc <- dudi.pca(tab, scannf = FALSE)
pc

(enfa1 <- enfa(pc, pr,scannf = FALSE))

enfa1$s #gives specialization values
enfa1$mar#gives marginality values

##OUTPUT##

> (enfa1 <- enfa(pc, pr,scannf = FALSE))
ENFA
$call: enfa(dudi = pc, pr = pr, scannf = FALSE)

marginality: 1.731
eigen values of specialization: 6.61 2.583 1.924 1.49 1.153 ...
$nf: 1 axis of specialization saved

  vector length mode    content
1 $pr    385923 numeric vector of presence
2 $lw    385923 numeric row weights
3 $cw    10     numeric column weights
4 $mar   10     numeric coordinates of the marginality vector
5 $s     9      numeric eigen values of specialization

  data.frame nrow   ncol content
1 $tab       385923 10   modified array
2 $li        385923 2    row coordinates
3 $co        10     2    column coordinates

> enfa1$s  #gives specialization values
[1] 6.6101077 2.5830759 1.9242150 1.4895781 1.1533000 1.0651184 0.8456433 0.7114272 0.4710257

> enfa1$mar #gives marginality values
           Annual         Perennial         Grassland         Deciduous        Coniferous
       0.38442513        0.33468805        0.62931566       -0.31320996       -0.55314134
            Mixed             Water           Wetland             Shrub Distance_to_Roads
      -0.53532160        0.55172030       -0.25751795        0.02533396       -0.11602451

Thank you
~Ruth








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