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Hola!=0D
=0D
plot( augPred(papas2.nlme.5), layout=3Dc(5,5,6) )=0D
Error in predict.nlme(object, value[1:(nrow(value)/nL), , drop =3D FALSE], :
=0D
Levels 1,2,3,4,5 not allowed for medio=0D
=0D
plot( augPred(papas2.nlme.2), layout=3Dc(5,5,6) )=0D
... succeeds=0D
plot( augPred(papas2.nlme.2,level=3D0:1), layout=3Dc(5,5,6) )=0D
... succeeds=0D> plot( augPred(papas2.nlme.3), layout=3Dc(5,5,6) )=0D
Error in predict.nlme(object, value[1:(nrow(value)/nL), , drop =3D FALSE], :
=0D
Levels 1,2,3,4,5 not allowed for medio=0D> plot( augPred(papas2.nlme.4), layout=3Dc(5,5,6) )=0D
Error in predict.nlme(object, value[1:(nrow(value)/nL), , drop =3D FALSE], :
=0D
Levels 1,2,3,4,5 not allowed for medio=0D
=0D
The difference between the object papas2.nlme.2 where it succeeds and =0D
papas2.nlme.3, papas2.nlme.4, papas2.nlme.5 where it not, is that in the
last =0D
objects the argument fixed to nlme models the parameters as regressions on =0D
covariables (factors), while in the first object the parametrs have only an
intercept. =0D
The covariables are constant in each group (plant), so the augPred plot =0D
seems to make sense, no averaging should be necessary. =0D
An excerpt from debug(predict.nlme) follows:=0D> plot( augPred(papas2.nlme.5), layout=3Dc(5,5,6) )=0D
debugging in: predict.nlme(object, value[1:(nrow(value)/nL), , drop =3D FALSE]
=0D
.=0D
.=0D
.=0D
debug: revOrder <- match(origOrder, row.names(dataMix))=0D
Browse[1]> n=0D
debug: contr <- object$contrasts=0D
Browse[1]> n=0D
debug: for (i in names(dataMix)) {=0D
if (inherits(dataMix[, i], "factor") &&
!is.null(contr[[i]])) {=0D
levs <- levels(dataMix[, i])=0D
levsC <- dimnames(contr[[i]])[[1]]=0D
if (any(wch <- is.na(match(levs, levsC)))) {=0D
stop(paste("Levels", paste(levs[wch], collapse =3D
","), =0D
"not allowed for", i))=0D
}=0D
attr(dataMix[, i], "contrasts") <- contr[[i]][levs, , =0D
drop =3D FALSE]=0D
}=0D
}=0D
Browse[1]> contr=0D
$medio=0D
[1] "contr.treatment"=0D
$variedad=0D
[1] "contr.treatment"=0D
# contr have names of functions supposed to construct contrast matrices.=0D
Browse[1]> dimnames(contr[["medio"]])=0D
NULL=0D
Browse[1]> n=0D
debug: i=0D
Browse[1]> n=0D
debug: if (inherits(dataMix[, i], "factor") &&
!is.null(contr[[i]])) {=0D
levs <- levels(dataMix[, i])=0D
levsC <- dimnames(contr[[i]])[[1]]=0D
if (any(wch <- is.na(match(levs, levsC)))) {=0D
# the code seems to assume that contr has the actual contrast matrix!=0D
stop(paste("Levels", paste(levs[wch], collapse =3D
","), =0D
"not allowed for", i))=0D
}=0D
attr(dataMix[, i], "contrasts") <- contr[[i]][levs, , drop =3D
FALSE]=0D
}=0D
=2E=0D
=2E=0D
=2E=0D
=2E=0D
debug: levs <- levels(dataMix[, i])=0D
Browse[1]> n=0D
debug: levsC <- dimnames(contr[[i]])[[1]]=0D
Browse[1]> levs=0D
[1] "1" "2" "3" "4" "5"=0D
Browse[1]> n=0D
debug: if (any(wch <- is.na(match(levs, levsC)))) {=0D
stop(paste("Levels", paste(levs[wch], collapse =3D ","),
"not allowed for"
=0D
i))=0D
}=0D
Browse[1]> n=0D
debug: stop(paste("Levels", paste(levs[wch], collapse =3D
","), "not allowed
for", =0D
i))=0D
Browse[1]> n=0D
Error in predict.nlme(object, value[1:(nrow(value)/nL), , drop =3D FALSE], :
=0D
Levels 1,2,3,4,5 not allowed for medio=0D
# because dimnames of "contr.treatment" is NULL!=0D
=0D
Kjetil Halvorsen
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<TR>
<TD id=3DINCREDITEXTREGION style=3D"PADDING-RIGHT: 7px; PADDING-LEFT:
7px; FONT-SIZE: 10pt; FONT-FAMILY: Comic Sans MS"=20
width=3D"100%">
<DIV>Hola!</DIV>
<DIV><BR>plot( augPred(papas2.nlme.5), layout=3Dc(5,5,6)
)<BR>Error in=20
predict.nlme(object, value[1:(nrow(value)/nL), , drop =3D
FALSE], :=20
<BR>
Levels 1,2,3,4,5 not=20
allowed for medio</DIV>
<DIV><BR> plot( augPred(papas2.nlme.2),
layout=3Dc(5,5,6)=20
)<BR> ... succeeds</DIV>
<DIV>plot( augPred(papas2.nlme.2,level=3D0:1), layout=3Dc(5,5,6)=20
)<BR> ... succeeds</DIV>
<DIV>> plot( augPred(papas2.nlme.3), layout=3Dc(5,5,6)
)<BR>Error in=20
predict.nlme(object, value[1:(nrow(value)/nL), , drop =3D
FALSE], :=20
<BR>
Levels 1,2,3,4,5 not=20
allowed for medio<BR>> plot( augPred(papas2.nlme.4),
layout=3Dc(5,5,6)=20
)<BR>Error in predict.nlme(object, value[1:(nrow(value)/nL), , drop
=3D=20
FALSE], :
<BR>
Levels=20
1,2,3,4,5 not allowed for medio</DIV>
<DIV><BR>The difference between the object papas2.nlme.2 where
it succeeds=20
and <BR>papas2.nlme.3, papas2.nlme.4, papas2.nlme.5 where it not, is
that=20
in the last <BR>objects the argument fixed to nlme models the
parameters=20
as regressions on <BR>covariables (factors), while in the first
object the=20
parametrs have only an intercept. <BR>The covariables are constant
in each=20
group (plant), so the augPred plot <BR>seems to make sense, no
averaging=20
should be necessary. </DIV>
<DIV>An excerpt from debug(predict.nlme) follows:</DIV>
<DIV>> plot( augPred(papas2.nlme.5), layout=3Dc(5,5,6)
)<BR>debugging in:=20
predict.nlme(object, value[1:(nrow(value)/nL), , drop =3D FALSE],=20
<BR> .<BR>
.<BR> .</DIV>
<DIV>debug: revOrder <- match(origOrder,=20
row.names(dataMix))<BR>Browse[1]> n<BR>debug: contr
<-=20
object$contrasts<BR>Browse[1]> n<BR>debug: for (i in
names(dataMix))=20
{<BR> if (inherits(dataMix[, i],
"factor") &&=20
!is.null(contr[[i]]))
{<BR>
levs=20
<- levels(dataMix[,
i])<BR> =20
levsC <-=20
dimnames(contr[[i]])[[1]]<BR>
if=20
(any(wch <- is.na(match(levs, levsC))))=20
{<BR> =20
stop(paste("Levels", paste(levs[wch], collapse =3D
","),=20
<BR> =20
"not allowed for",
i))<BR> =20
}<BR>
attr(dataMix[, i],=20
"contrasts") <- contr[[i]][levs, ,=20
<BR> =20
drop =3D FALSE]<BR>
}<BR>}<BR>Browse[1]>=20
contr<BR>$medio<BR>[1] "contr.treatment"</DIV>
<DIV>$variedad<BR>[1] "contr.treatment"</DIV>
<DIV># contr have names of functions supposed to construct
contrast=20
matrices.</DIV>
<DIV>Browse[1]>
dimnames(contr[["medio"]])<BR>NULL<BR>Browse[1]>=20
n<BR>debug: i<BR>Browse[1]> n<BR>debug: if
(inherits(dataMix[, i],=20
"factor") && !is.null(contr[[i]]))
{<BR> levs=20
<- levels(dataMix[, i])<BR>
levsC <-=20
dimnames(contr[[i]])[[1]]<BR> if
(any(wch <-=20
is.na(match(levs, levsC)))) {</DIV>
<DIV> # the code seems to assume that contr has the actual
contrast=20
matrix!</DIV>
<DIV>
stop(paste("Levels",=20
paste(levs[wch], collapse =3D ","),=20
<BR> =20
"not allowed for", i))<BR>
}<BR> =20
attr(dataMix[, i], "contrasts") <- contr[[i]][levs, ,
drop =3D=20
FALSE]<BR>}<BR>.<BR>.<BR>.<BR>.</DIV>
<DIV>debug: levs <- levels(dataMix[,
i])<BR>Browse[1]> n<BR>debug:=20
levsC <- dimnames(contr[[i]])[[1]]<BR>Browse[1]>
levs<BR>[1] "1" "2"=20
"3" "4" "5"<BR>Browse[1]>
n<BR>debug: if (any(wch <-=20
is.na(match(levs, levsC)))) {<BR>
stop(paste("Levels",=20
paste(levs[wch], collapse =3D ","), "not allowed
for",=20
<BR>
i))<BR>}<BR>Browse[1]>=20
n<BR>debug: stop(paste("Levels", paste(levs[wch], collapse
=3D ","), "not=20
allowed for", <BR>
i))<BR>Browse[1]> n<BR>Error in=20
predict.nlme(object, value[1:(nrow(value)/nL), , drop =3D
FALSE], :=20
<BR>
Levels 1,2,3,4,5 not=20
allowed for medio</DIV>
<DIV># because dimnames of "contr.treatment" is
NULL!</DIV>
<DIV> </DIV>
<DIV>Kjetil Halvorsen</DIV>
<DIV> </DIV></TD></TR>
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