Hello everyone, I have a problem trying to use vegan's capscale() on a phylobetadiversity distance matrix, reproduced below using the example:
library(psych) # For the PCA test involved # Opens a full matrix of 245 x 245 phylobetadiversity distances bnti.ses = read.csv(file.choose(), header = T, row.names=1); dim(bnti.ses); # this gives the dimensions bnti.ses[1:5,1:5]; # this gives a look at the first 5 rows and columns # Test PCA scores test = data.frame(replicate(10,sample(0:100,245,rep=TRUE))) test pca = principal(teste, nfactors = 3, covar = FALSE, scores = TRUE) meta.pca.scores = pca$scores rownames(meta.pca.scores)=rownames(bnti.ses) ## dbRDA # betaNTI standard effect size bnti.ses = bnti.ses + abs(min(bnti.ses)); bnti.ses = bnti.ses/max(bnti.ses); range(bnti.ses); identical(rownames(bnti.ses),colnames(bnti.ses)); # must be TRUE to proceed identical(rownames(bnti.ses),rownames(meta.pca.scores)); # must be TRUE to proceed # Here is where the error occurs bnti.ses.dbrda.int = capscale(as.dist(bnti.ses) ~ 1,data=meta.pca.scores); bnti.ses.dbrda.full = capscale(as.dist(bnti.ses) ~ .,data=meta.pca.scores); bnti.ses.select.rsq = ordiR2step(bnti.ses.dbrda.int, scope = formula(bnti.ses.dbrda.full),direction = "both",pstep=10000, perm.max = 100000); bnti.ses.select.rsq; I get the message: Error in formula.default(object, env = baseenv()) : invalid formula I tried the same code using the varespec and varechem example files present in capscale's help and it worked. I checked the dimensions of the phylobetadiversity matrix and they are ok (245 x 245). I tried to omit the row names but the problem persists. For me the very last test that should have worked was bnti.ses = data.frame(replicate(245,sample(0:100,245,rep=TRUE))) rownames(bnti.ses)=rownames(meta.pca.scores)colnames(bnti.ses)=rownames(bnti.ses) and then working this artificial bnti.ses through the subsequent standardization and capscale steps. However, I got the same error mesage with this example. Am I missing something, or is there a workaround? Thanks, Alexandre -- Dr. Alexandre F. Souza Professor Ajunto II Universidade Federal do Rio Grande do Norte CB, Departamento de Ecologia Campus Universitário - Lagoa Nova 59072-970 - Natal, RN - Brasil lattes: lattes.cnpq.br/7844758818522706 http://www.docente.ufrn.br/alexsouza -- Dr. Alexandre F. Souza Professor Ajunto II Universidade Federal do Rio Grande do Norte CB, Departamento de Ecologia Campus Universitário - Lagoa Nova 59072-970 - Natal, RN - Brasil lattes: lattes.cnpq.br/7844758818522706 http://www.docente.ufrn.br/alexsouza [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology