Valerie and Sarah, Thank you for encouraging piracy by posting the URL of an illegal PDF of our book :-(
By the way, just look at ?vegemite and you'll find easily the solution to your problem: with the argument scale="log" your numeric data will be converted to 1-char symbols. François ------------------------------------------------------------------------------- Prof. *François Gillet* Université de Franche-Comté - CNRS UMR 6249 Chrono-environnement UFR Sciences et Techniques 16, Route de Gray F-25030 Besançon cedex France http://chrono-environnement.univ-fcomte.fr/ http://chrono-environnement.univ-fcomte.fr/spip.php?article530 Phone: +33 (0)3 81 66 62 81 iPhone: +33 (0)7 88 37 07 76 Location: La Bouloie, Bât. Propédeutique, *-114L* ------------------------------------------------------------------------------- Editor of* Plant Ecology and Evolution* http://www.plecevo.eu ------------------------------------------------------------------------------- * *** 2013/7/24 Sarah Goslee <sarah.gos...@gmail.com> > Hi Valerie, > > Did the suggestions given on the R-help list fail to work? > > You do need to provide you abundance data as one character, as specified in > ?vegemite which also gives suggestions for conversion. > > Sarah > > On Tuesday, July 23, 2013, Valerie Mucciarelli wrote: > > > Hello, > > > > I am relatively new to R and I am working through the code that is > > provided in the book Numerical Ecology with R: > > http://xa.yimg.com/kq/groups/19243105/1919134110/name/Numerical.pdf (pg > > 79) > > > > and I have run across an error message that I can't seem to figure out. > > > > I am using the vegan, ade4, gclus and cluster packages. The code is as > > follows: > > > > # Ordered community table > > # Species are ordered by their weighted averages on site scores > > > > or <- vegemite(spe, spe.chwo) > > > > spe is the dataframe, here is part of it: > > > > AGA ANT BON CAL1 CAL CER CRY DES EUTH FRY > > 1 0.420 0.092 0.051 0.000 0.975 0.000 0.111 0.000 0.127 0 > > 2 0.000 0.000 0.007 0.002 0.915 0.000 0.000 0.000 0.151 0 > > 4 0.000 0.008 0.000 0.009 0.124 0.003 0.000 0.000 0.095 0 > > 7 0.000 0.002 0.003 0.002 0.121 0.002 0.000 3.573 0.180 0 > > 12 0.000 0.020 0.000 0.002 0.444 0.001 0.000 0.000 0.242 0 > > 13 8.727 0.000 0.000 0.000 0.743 0.000 0.000 0.000 0.050 0 > > 14 2.163 0.009 0.000 0.003 1.121 0.000 0.000 0.000 0.051 0 > > 15 0.000 0.004 0.000 0.000 0.109 0.000 0.000 0.000 0.007 0 > > 18 9.021 0.018 0.002 0.000 0.286 0.000 0.000 0.000 0.028 0 > > 19 0.000 0.038 0.000 0.019 0.509 0.000 0.000 0.000 0.155 0 > > > > spe.chwo came from: > > > > spe.norm <- decostand(spe, "normalize") > > spe.ch <- vegdist(spe.norm, "euc") > > spe.ch.UPGMA <- hclust(spe.ch, method = "average") > > spe.chwo <- reorder.hclust(spe.ch.UPGMA, spe.ch) > > > > > > and the error is: > > > > Error in vegemite(spe, spe.chwo) : > > Cowardly refusing to use longer than 1 char symbols: > > Use scale > > > > The data in the dataframe is biomass data recorded to 4 digits. I'm > > wondering if this code is not working because my data is more than one > > digit long. > > > > Any suggestions or insight on how to get this code to work would be > > greatly appreciated. > > > > Thank you, > > > > Val > > > > > > -- > Sarah Goslee > http://www.stringpage.com > http://www.sarahgoslee.com > http://www.functionaldiversity.org > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > [[alternative HTML version deleted]]
_______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
