> On 03 Jun 2015, at 19:14 , Erica Cseko Nolasco <ecnola...@gmail.com> wrote: > > 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.
What makes you say that? It would be a pretty bad error if it did paired tests and data aren't paired/matched. Are you sure that you actually want paired tests? -pd > > 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. -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd....@cbs.dk Priv: pda...@gmail.com ______________________________________________ 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.
