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.
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