[R] pairwise.t.test non numeric factors error
Michael Dewey
lists at dewey.myzen.co.uk
Wed Jun 3 21:45:43 CEST 2015
Just to be on the safe side, what is T? It is recommended to use TRUE in
case you set T to something else. I think this is very unlikely to solve
the problem but it is worth trying.
On 03/06/2015 18:14, Erica Cseko Nolasco 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.
>
> 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 <drjimlemon at 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
>> <ecnolasco at 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]]
>>>
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>>> 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 at 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.
>
--
Michael
http://www.dewey.myzen.co.uk/home.html
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