[R] pairwise.t.test non numeric factors error

Jim Lemon
Wed, 03 Jun 2015 01:34:08 -0000

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 Csek? Nolasco*
> Mestranda em Modelagem em Ci?ncias 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.
>
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>
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