Thanks Jim, I removed the corresponding cases and tried again. What I discovery now is if I run the function without paired = T (pairwise.t.test(x = data$tss,data$pa) is works. However, if I add the paired = T (pairwise.t.test(x = data$tss,data$pa,paired = T) is gives me the error ' Error in complete.cases(x, y) : not all arguments have the same length'. In fact it seems to do a paired test even without the paired = T argument. I really don't know why.
Regards, *Erica Csekö Nolasco* Mestranda em Modelagem em Ciências da Terra e do Ambiente http://lattes.cnpq.br/2117508819823917 Universidade Estadual de Feira de Santana Avenida Transnordestina s/n, Novo Horizonte Feira de Santana - BA, Brasil CEP 44.036-900. Graduate Student in Modeling of Environmental and Earth Sciences http://lattes.cnpq.br/2117508819823917 Universidade Estadual de Feira de Santana Transnordestina Ave, Novo Horizonte Feira de Santana - BA, Brazil 44.036-900. 2015-06-02 22:34 GMT-03:00 Jim Lemon <drjimle...@gmail.com>: > Hi Erica, > The problem may be that you are specifying a grouping factor (mdl) in > which the group sizes are unequal. If one case in group "tot" is > missing, is it possible to identify the corresponding cases in the > other factor levels and delete them? > > Jim > > > On Tue, Jun 2, 2015 at 11:59 PM, Erica Cseko Nolasco > <ecnola...@gmail.com> wrote: > > Dear listers, > > > > I'm performing a PERMANOVA (adonis{vegan}) to compare the results (ROC, > > TSS) of models based on two factors (model, algo). I was not able to > find a > > pairwise test for adonis, on PRIMER it would be a Tukey test. Though, I > > chose to perform a pairwise.t.test what would be quite simple. However, > no > > matter I rearrange my response and factor vectors (as a factor or > numeric) > > it gives me the following error (the code on the bottom - Error in > > complete.cases(x, y) : > > not all arguments have the same length). I also tried to make a list of > > the vectors, but it also gives me the error 'Error in sort.list(y) : 'x' > > must be atomic for 'sort.list' Have you called 'sort' on a list?' > > > > I would appreciate any suggestions to solve this issue. > > > > Best, > > > > Erica > > > >> setwd('D:\\Erica\\mestrado\\analises\\results') > >> library(vegan) > >> rest=read.table('results_permanova.txt',sep="\t",header=T) > >> rest$modelN=as.numeric(rest$model) > >> rest$algoN=as.numeric(rest$algo) > >> data=rest[complete.cases(rest),] > >> head(data) > > algo pa run model ROC TSS modelN algoN > > 1 ANN PA1 RUN1 alt 0.947 0.867 2 2 > > 2 ANN PA10 RUN1 alt 0.978 0.869 2 2 > > 3 ANN PA11 RUN1 alt 0.993 0.931 2 2 > > 4 ANN PA12 RUN1 alt 0.961 0.845 2 2 > > 5 ANN PA13 RUN1 alt 0.988 0.960 2 2 > > 6 ANN PA14 RUN1 alt 0.996 0.988 2 2 > >> summary(data) > > algo pa run model ROC > > TSS > > CTA :240 PA10 : 120 : 0 alt : 200 Min. :0.5290 > > Min. :0.0580 > > FDA :240 PA11 : 120 RUN1:2399 altPet : 200 1st Qu.:0.8780 > > 1st Qu.:0.7160 > > GAM :240 PA12 : 120 b1 : 200 Median :0.9350 > > Median :0.8270 > > GBM :240 PA13 : 120 b13 : 200 Mean :0.9184 > > Mean :0.7988 > > GLM :240 PA14 : 120 b13PETalt: 200 3rd Qu.:0.9790 > > 3rd Qu.:0.9110 > > MARS :240 PA15 : 120 b14 : 200 Max. :1.0000 > > Max. :1.0000 > > (Other):959 (Other):1679 (Other) :1199 > > > > modelN algoN > > Min. : 2.000 Min. : 2.000 > > 1st Qu.: 4.500 1st Qu.: 4.000 > > Median : 7.000 Median : 7.000 > > Mean : 7.498 Mean : 6.502 > > 3rd Qu.:10.000 3rd Qu.: 9.000 > > Max. :13.000 Max. :11.000 > > > >> tss=data$TSS > >> summary(tss) > > Min. 1st Qu. Median Mean 3rd Qu. Max. > > 0.0580 0.7160 0.8270 0.7988 0.9110 1.0000 > >> mdl=factor(data$model) > >> summary(mdl) > > alt altPet b1 b13 b13PETalt b14 b18 > > b7 pet pluv > > 200 200 200 200 200 200 200 > > 200 200 200 > > temp tot > > 200 199 > >> length(complete.cases(mdl,tss)) > > [1] 2399 > >> pairwise.t.test(tss,mdl,p.adj='bonf',paired=T,pool.sd = FALSE) > > Error in complete.cases(x, y) : > > not all arguments have the same length > >> > > > > *Erica Csekö Nolasco* > > Mestranda em Modelagem em Ciências da Terra e do Ambiente > > http://lattes.cnpq.br/2117508819823917 > > Universidade Estadual de Feira de Santana > > Avenida Transnordestina s/n, Novo Horizonte > > Feira de Santana - BA, Brasil CEP 44.036-900. > > > > Graduate Student in Modeling of Environmental and Earth Sciences > > http://lattes.cnpq.br/2117508819823917 > > Universidade Estadual de Feira de Santana > > Transnordestina Ave, Novo Horizonte > > Feira de Santana - BA, Brazil 44.036-900. > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
