[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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