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

Erica Cseko Nolasco
Tue, 02 Jun 2015 13:59:53 -0000

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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