[R-sig-ME] [FORGED] Re: Export several lme outputs to a single excel file
Mario Garrido
g@@d|o @end|ng |rom po@t@bgu@@c@||
Tue Oct 29 18:55:34 CET 2019
Hi again,
after adding a column with the name using the command $Md to Anova models,
I tried to do the same, but for any reason is not working.
I create a series of model and make them compete:
> lmeGPBYPGAlowNULL <- lme(StdzDiff ~ 1, data = DataBM_GP_StdzDiffGAlow,
random = ~ 1|factor(ExpID),method="ML")
> lmeGPBYPGAlowOnlyT <- lme(StdzDiff ~ Trtmnt2, data =
DataBM_GP_StdzDiffGAlow, random = ~ 1|factor(ExpID),method="ML")
> (msAICc <- model.sel(lmeGPBYPGAlowNULL,lmeGPBYPGAlowOnlyT))
Model selection table
(Intrc) Trtm2 df logLik AICc delta weight
lmeGPBYPGAlowNULL 3.367 3 -73.434 154.4 0.00 0.83
lmeGPBYPGAlowOnlyT 3.367 + 4 -73.433 157.5 3.17 0.17
Models ranked by AICc(x)
Random terms (all models):
‘1 | factor(ExpID)’
Then I get the results of the Model selection, and a column with the name.
> BM_MuMIn_GP_ByP_GAlow<-(msAICc <-
model.sel(lmeGPBYPGAlowNULL,lmeGPBYPGAlowOnlyT))
> BM_MuMIn_GP_ByP_GAlow$Md<-"BM GP MuMIn By periods GAlow"
It seems that there is no problem. And t confirm I run it
> BM_MuMIn_GP_ByP_GAlow
Model selection table
(Intrc) Trtm2 df logLik AICc delta weight
Md
lmeGPBYPGAlowNULL 3.367 3 -73.434 154.4 0.00 0.83 BM GP MuMIn
By periods GAlow
lmeGPBYPGAlowOnlyT 3.367 + 4 -73.433 157.5 3.17 0.17 BM GP MuMIn
By periods GAlow
Models ranked by AICc(x)
Random terms (all models):
‘1 | factor(ExpID)’
*BUT*, when I do the same with other objects with the same amount of
columns, etc and bind them, the column Md doesnt appear
> BM_MuMIn_GP_AllP_results <-
rbind(BM_MuMIn_GP_AllP_peakAll,BM_MuMIn_GP_AllP_earlypeak,BM_MuMIn_GP_AllP_latepeak)
> BM_MuMIn_GP_AllP_results
Model selection table
(Int) Tr2 Prd Prd:Tr2 df logLik AICc delta weight
lmeGPAllPearlypNULL 1.547 3 -261.853 530.0 0.00 0.521
lmeGPAllPpAllNULL 1.441 3 -262.736 531.8 1.77 0.215
lmeGPAllPearlypOnlyT 1.547 + 4 -261.824 532.1 2.14 0.178
lmeGPAllPpAllOnlyT 1.441 + 4 -262.714 533.9 3.92 0.073
lmeGPAllPlatepNULL 1.229 3 -266.356 539.0 9.01 0.006
lmeGPAllPlatepOnlyT 1.229 + 4 -266.346 541.2 11.19 0.002
lmeGPAllPearlyp2wTP 1.587 + + + 10 -259.508 541.9 11.95 0.001
lmeGPAllPearlyp2wTP1 1.587 + + + 10 -259.508 541.9 11.95 0.001
lmeGPAllPpAll2wTP 1.484 + + + 10 -260.089 543.1 13.11 0.001
lmeGPAllPpAll2wTP1 1.484 + + + 10 -260.089 543.1 13.11 0.001
lmeGPAllPlatep2wTP 1.277 + + + 10 -262.725 548.4 18.39 0.000
lmeGPAllPlatep2wTP1 1.277 + + + 10 -262.725 548.4 18.39 0.000
But still each object have the Md column
> BM_MuMIn_GP_AllP_peakAll
Model selection table
(Int) Tr2 Prd Prd:Tr2 df logLik AICc delta weight
Md
lmeGPAllPpAllNULL 1.441 3 -262.736 531.8 0.00 0.742 BM
GP MuMIn All periods Interact peakAll
lmeGPAllPpAllOnlyT 1.441 + 4 -262.714 533.9 2.16 0.252 BM
GP MuMIn All periods Interact peakAll
lmeGPAllPpAll2wTP 1.484 + + + 10 -260.089 543.1 11.35 0.003 BM
GP MuMIn All periods Interact peakAll
lmeGPAllPpAll2wTP1 1.484 + + + 10 -260.089 543.1 11.35 0.003 BM
GP MuMIn All periods Interact peakAll
Models ranked by AICc(x)
Random terms (all models):
‘1 | factor(ExpID)’
> BM_MuMIn_GP_AllP_earlypeak
Model selection table
(Int) Tr2 Prd Prd:Tr2 df logLik AICc delta weight
Md
lmeGPAllPearlypNULL 1.547 3 -261.853 530.0 0.00 0.742
BM GP MuMIn All periods Interact earlypeak
lmeGPAllPearlypOnlyT 1.547 + 4 -261.824 532.1 2.14 0.254
BM GP MuMIn All periods Interact earlypeak
lmeGPAllPearlyp2wTP 1.587 + + + 10 -259.508 541.9 11.95 0.002
BM GP MuMIn All periods Interact earlypeak
lmeGPAllPearlyp2wTP1 1.587 + + + 10 -259.508 541.9 11.95 0.002
BM GP MuMIn All periods Interact earlypeak
Models ranked by AICc(x)
Random terms (all models):
‘1 | factor(ExpID)’
> BM_MuMIn_GP_AllP_latepeak
Model selection table
(Int) Tr2 Prd Prd:Tr2 df logLik AICc delta weight
Md
lmeGPAllPlatepNULL 1.229 3 -266.356 539.0 0.00 0.738 BM
GP MuMIn All periods Interact latepeak
lmeGPAllPlatepOnlyT 1.229 + 4 -266.346 541.2 2.18 0.248 BM
GP MuMIn All periods Interact latepeak
lmeGPAllPlatep2wTP 1.277 + + + 10 -262.725 548.4 9.38 0.007 BM
GP MuMIn All periods Interact latepeak
lmeGPAllPlatep2wTP1 1.277 + + + 10 -262.725 548.4 9.38 0.007 BM
GP MuMIn All periods Interact latepeak
Models ranked by AICc(x)
Random terms (all models):
‘1 | factor(ExpID)’
El mar., 8 oct. 2019 a las 11:08, Rolf Turner (<r.turner using auckland.ac.nz>)
escribió:
>
> On 8/10/19 9:28 PM, Mario Garrido wrote:
>
> > Dear Emmanuel Curis,
> > your approach was working perfectly, but at some point w gives me the
> > error. when introduced the new column
> > I have no problem in running model, the errors appears when introducing
> > extra $Md column. I wonder whether the problem is the * of the
> > significance, but is not, also is not due to character strings since my
> > variables are recognized as factors. I have no missing data in my
> > matrix,... And, as I said, problem only arise when I introduced the new
> > column
> >
> > Thanks in advanxe
> >> anova(TempLight_StdzDiff_3trt_earlypeak)-> r15
> >> r15
> > Analysis of Variance Table
> >
> > Response: StdzDiff
> > Df Sum Sq Mean Sq F value Pr(>F)
> > Trtmnt 2 0.991 0.4953 0.2382 0.78891
> > sp 2 13.781 6.8904 3.3134 0.04407 *
> > Trtmnt:sp 4 4.123 1.0306 0.4956 0.73898
> > Residuals 53 110.217 2.0796
> > ---
> > Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
> >> r15$Md<- "TempLight_StdzDiff_3trt_earlypeak"
> >> r15
> > Analysis of Variance Table
> >
> > Response: StdzDiff
> > Df Sum Sq Mean Sq F value Pr(>F) Md
> > Trtmnt 2 0.991 0.4953 0.2382 0.78891
> > sp 2 13.781 6.8904 3.3134 0.04407
> > Trtmnt:sp 4 4.123 1.0306 0.4956 0.73898
> > Residuals 53 110.217 2.0796
> > Warning message:
> > In data.matrix(x) : NAs introducidos por coerción
>
> This is a "generic" problem; it is not peculiar to your model nor to
> models fitted using lme, or other mixed modelling software.
>
> Consider the following example:
>
> set.seed(42)
> x <- 1:20
> y <- rnorm(20)
> fit <- lm(y ~ x)
> m <- anova(fit)
> m$newColumn <- "yeeeeks"
> m
>
> This produces:
>
> > Analysis of Variance Table
> >
> > Response: y
> > Df Sum Sq Mean Sq F value Pr(>F) newColumn
> > x 1 4.113 4.1130 2.5865 0.12518
> > Residuals 18 28.624 1.5902
> > Warning message:
> > In data.matrix(x) : NAs introduced by coercion
>
> The "reason" is that m is (in the first instance) of class "anova" and
> there are (not unreasonably) certain restrictions as to how you can
> treat an object of this class.
>
> A work-around to get something like what you appear to want could be:
>
> set.seed(42)
> x <- 1:20
> y <- rnorm(20)
> fit <- lm(y ~ x)
> m <- anova(fit)
> m <- cbind(m,newColumn=c("yeeeks",rep("",nrow(m)-1)))
> m
>
> However m is now of class "data.frame" whence it is printed by the
> method print.data.frame() rather than print.anova(). Consequently NAs
> show up in the output of the print method:
>
> Df Sum Sq Mean Sq F value Pr(>F) newColumn
> x 1 0.04176282 0.04176282 0.03784897 0.8479256 yeeeks
> Residuals 18 19.86132473 1.10340693 NA NA
>
> You could just live with those NAs, or you could convert the "F value"
> and "Pr(>F)" columns from numeric to character mode and replace the NAs
> by null strings "".
>
> HTH
>
> cheers,
>
> Rolf Turner
>
> --
> Honorary Research Fellow
> Department of Statistics
> University of Auckland
> Phone: +64-9-373-7599 ext. 88276
>
--
Mario Garrido Escudero, PhD
Dr. Hadas Hawlena Lab
Mitrani Department of Desert Ecology
Jacob Blaustein Institutes for Desert Research
Ben-Gurion University of the Negev
Midreshet Ben-Gurion 84990 ISRAEL
gaiarrido using gmail.com; gaadio using post.bgu.ac.il
phone: (+972) 08-659-6854
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