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--></style></head><body lang=EN-US link=blue vlink="#954F72"><div class=WordSection1><p class=MsoNormal>Hi Ruth,</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I had some experience with ENFA 5 years ago. Based on what I wrote back then, I didn’t interpret the specialization values as is, but instead they were aggregated into the overall (global) specialization index and then converted into the tolerance value by simply inverted it (x becomes 1/x). However, the absolute values are the ones that matter in interpreting the specialization coefficient of each EGV: “the higher the absolute value, the more restricted is the range of the focal species on the corresponding variable” Hirzel’s original paper (2002) page 2031 right below the equation (10).</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Hope this helps a bit.</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Adrian</p><p class=MsoNormal><o:p> </o:p></p><div style='mso-element:para-border-div;border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='border:none;padding:0in'><b>From: </b><a href="mailto:ruth.kost@usask.ca">Aschim, Ruth</a><br><b>Sent: </b>Monday, March 23, 2020 8:36 AM<br><b>To: </b><a href="mailto:r-sig-geo@r-project.org">r-sig-geo@r-project.org</a><br><b>Subject: </b>[R-sig-Geo] ENFA specialization values</p></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Hello,</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>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.</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>slot(maps,"data")[,1:9] <- sqrt(slot(maps,"data")[,1:9])</p><p class=MsoNormal>hist(maps, type = "l")</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>## Prepare the data for the ENFA</p><p class=MsoNormal>tab <- slot(maps, "data")</p><p class=MsoNormal>pr <- slot(count.points(pipl, maps), "data")[,1]</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>## Perform the PCA before the ENFA</p><p class=MsoNormal>pc <- dudi.pca(tab, scannf = FALSE)</p><p class=MsoNormal>pc</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>(enfa1 <- enfa(pc, pr,scannf = FALSE))</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>enfa1$s #gives specialization values</p><p class=MsoNormal>enfa1$mar#gives marginality values</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>##OUTPUT##</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>> (enfa1 <- enfa(pc, pr,scannf = FALSE))</p><p class=MsoNormal>ENFA</p><p class=MsoNormal>$call: enfa(dudi = pc, pr = pr, scannf = FALSE)</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>marginality: 1.731</p><p class=MsoNormal>eigen values of specialization: 6.61 2.583 1.924 1.49 1.153 ...</p><p class=MsoNormal>$nf: 1 axis of specialization saved</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal> vector length mode content</p><p class=MsoNormal>1 $pr 385923 numeric vector of presence</p><p class=MsoNormal>2 $lw 385923 numeric row weights</p><p class=MsoNormal>3 $cw 10 numeric column weights</p><p class=MsoNormal>4 $mar 10 numeric coordinates of the marginality vector</p><p class=MsoNormal>5 $s 9 numeric eigen values of specialization</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal> data.frame nrow ncol content</p><p class=MsoNormal>1 $tab 385923 10 modified array</p><p class=MsoNormal>2 $li 385923 2 row coordinates</p><p class=MsoNormal>3 $co 10 2 column coordinates</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>> enfa1$s #gives specialization values</p><p class=MsoNormal>[1] 6.6101077 2.5830759 1.9242150 1.4895781 1.1533000 1.0651184 0.8456433 0.7114272 0.4710257</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>> enfa1$mar #gives marginality values</p><p class=MsoNormal> Annual Perennial Grassland Deciduous Coniferous</p><p class=MsoNormal> 0.38442513 0.33468805 0.62931566 -0.31320996 -0.55314134</p><p class=MsoNormal> Mixed Water Wetland Shrub Distance_to_Roads</p><p class=MsoNormal> -0.53532160 0.55172030 -0.25751795 0.02533396 -0.11602451</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Thank you</p><p class=MsoNormal>~Ruth</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal> [[alternative HTML version deleted]]</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>_______________________________________________</p><p class=MsoNormal>R-sig-Geo mailing list</p><p class=MsoNormal>R-sig-Geo@r-project.org</p><p class=MsoNormal>https://stat.ethz.ch/mailman/listinfo/r-sig-geo</p><p class=MsoNormal><o:p> </o:p></p></div></body></html>