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 <drjimle...@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
<ecnola...@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.
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