Re: [R-sig-eco] error in layernames and RasterStack
Thanks Jim. names(r) <-- command worked...
I still get this error although I get the estimates and their standard
errors...
> fm2 <- maxlike(~x1 + x2 + x3, r, xy)
Warning message:
In layerNames(rasters) :
the layerNames function is obsolete. Use "names" instead
Coefficients:
EstSE z P(>|z|)
(Intercept) -0.817 0.221 -3.687 2.27e-04
x1 1.157 0.129 8.987 2.54e-19
x2 0.152 0.190 0.801 4.23e-01
x3 -0.102 0.109 -0.933 3.51e-01
Alok K. Bohara, Ph.D.
UNM
From: Baldwin, Jim -FS [jbald...@fs.fed.us]
Sent: Thursday, December 06, 2012 11:46 AM
To: Alok K. Bohara; r-sig-ecology@r-project.org
Subject: RE: error in layernames and RasterStack
I think you might want
names(r) <- c("x1", "x2", "x3")
rather than
r@layernames <- c("x1", "x2", "x3")
Jim
-Original Message-
From: r-sig-ecology-boun...@r-project.org
[mailto:r-sig-ecology-boun...@r-project.org] On Behalf Of Alok K. Bohara
Sent: Thursday, December 06, 2012 10:26 AM
To: r-sig-ecology@r-project.org
Subject: [R-sig-eco] error in layernames and RasterStack
Hi: I am trying to replicate some commands in maxlike.
#***
library(raster)
set.seed(131)
x1 <- sort(rnorm(100))
x1 <- raster(outer(x1, x1), xmn=0, xmx=100, ymn=0, ymx=100)
x2 <- raster(matrix(runif(1e4), 100, 100), 0, 100, 0, 100)
x3 <- raster(matrix(c(0,1), 100, 100), 0, 100, 0, 100) r <- stack(x1, x2, x3)
r@layernames <- c("x1", "x2", "x3")
#
Error #1: After the last line, I get an Error:
Error in checkSlotAssignment(object, name, value) :
'layernames' is not a slot in class "RasterStack"
>
Error # 2: Later, I also get an error:
In addition: Warning message:
> fm2 <- maxlike(~x1 + x2 + x3, r, xy)
Error in maxlike(~x1 + x2 + x3, r, xy) :
at least 1 covariate in the formula is not in rasters.
In layerNames(rasters) :
the layerNames function is obsolete. Use "names" instead
I am using R 2.15.2. I do not know if the error #2 is the result of the error
#1.Thanks.
Best,
Alok K. Bohara,
UNM
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Re: [R-sig-eco] error in layernames and RasterStack
That's because the function maxlike explicitly calls "layerNames(rasters)" in
cd.names <- layerNames(rasters)
By typing
maxlike()
you can see the code and find the statement mentioned above. The two fixes are
(1) make your own version of maxlike with the "names" fix and/or write the
developer of maxlike and let him or her know about this issue.
Jim
-Original Message-
From: Alok K. Bohara [mailto:boh...@unm.edu]
Sent: Friday, December 07, 2012 7:03 AM
To: Baldwin, Jim -FS; r-sig-ecology@r-project.org
Subject: RE: error in layernames and RasterStack
Thanks Jim. names(r) <-- command worked...
I still get this error although I get the estimates and their standard
errors...
> fm2 <- maxlike(~x1 + x2 + x3, r, xy)
Warning message:
In layerNames(rasters) :
the layerNames function is obsolete. Use "names" instead
Coefficients:
EstSE z P(>|z|)
(Intercept) -0.817 0.221 -3.687 2.27e-04
x1 1.157 0.129 8.987 2.54e-19
x2 0.152 0.190 0.801 4.23e-01
x3 -0.102 0.109 -0.933 3.51e-01
Alok K. Bohara, Ph.D.
UNM
From: Baldwin, Jim -FS [jbald...@fs.fed.us]
Sent: Thursday, December 06, 2012 11:46 AM
To: Alok K. Bohara; r-sig-ecology@r-project.org
Subject: RE: error in layernames and RasterStack
I think you might want
names(r) <- c("x1", "x2", "x3")
rather than
r@layernames <- c("x1", "x2", "x3")
Jim
-Original Message-
From: r-sig-ecology-boun...@r-project.org
[mailto:r-sig-ecology-boun...@r-project.org] On Behalf Of Alok K. Bohara
Sent: Thursday, December 06, 2012 10:26 AM
To: r-sig-ecology@r-project.org
Subject: [R-sig-eco] error in layernames and RasterStack
Hi: I am trying to replicate some commands in maxlike.
#***
library(raster)
set.seed(131)
x1 <- sort(rnorm(100))
x1 <- raster(outer(x1, x1), xmn=0, xmx=100, ymn=0, ymx=100)
x2 <- raster(matrix(runif(1e4), 100, 100), 0, 100, 0, 100)
x3 <- raster(matrix(c(0,1), 100, 100), 0, 100, 0, 100) r <- stack(x1, x2, x3)
r@layernames <- c("x1", "x2", "x3")
#
Error #1: After the last line, I get an Error:
Error in checkSlotAssignment(object, name, value) :
'layernames' is not a slot in class "RasterStack"
>
Error # 2: Later, I also get an error:
In addition: Warning message:
> fm2 <- maxlike(~x1 + x2 + x3, r, xy)
Error in maxlike(~x1 + x2 + x3, r, xy) :
at least 1 covariate in the formula is not in rasters.
In layerNames(rasters) :
the layerNames function is obsolete. Use "names" instead
I am using R 2.15.2. I do not know if the error #2 is the result of the error
#1.Thanks.
Best,
Alok K. Bohara,
UNM
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the intended recipients. Any unauthorized interception of this message or the
use or disclosure of the information it contains may violate the law and
subject the violator to civil or criminal penalties. If you believe you have
received this message in error, please notify the sender and delete the email
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[R-sig-eco] Conditional inference forest error: levels in factors do not match
#Conditional inference forest ("Party" package) error message states
that levels in factors of new data do not match original data, but they
do...
#create conditional inference forest
oc_listed.fit1 <- cforest(Listed~
HabMode,controls=cforest_unbiased(ntree=500), data=oc.complete)
#use predict function for subset of data
#this works correctly
predict(oc_listed.fit1,newdata=oc.complete[1:10,])
#use predict on new set of data
predict(oc_listed.fit1,newdata=DD_NOT)
#produces this error message
#Error in checkData(oldData, RET) :
#Levels in factors of new data do not match original data
#We can show that all of the levels match
table(DD_NOT$ORD %in% oc.complete$ORD)
#same check
sum(!levels(DD_NOT$ORD) %in% levels(oc.complete$ORD))
#equals 0, all levels are the same.
#Then why does it fail?
Thanks,
Ana
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