Re: [R] Getting an error calling MASS::boxcox in a function
Aha. Many thanks, John. Never would have gotten there on my own.
-- Bert
On Sat, Jul 8, 2023 at 2:01 PM John Fox wrote:
>
> Hi Bert,
>
> On 2023-07-08 3:42 p.m., Bert Gunter wrote:
> > Caution: This email may have originated from outside the organization.
> > Please exercise additional caution with any links and attachments.
> >
> >
> > Thanks John.
> >
> > ?boxcox says:
> >
> > *
> > Arguments
> >
> > object
> >
> > a formula or fitted model object. Currently only lm and aov objects are
> > handled.
> > *
> > I read that as saying that
> >
> > boxcox(lm(z+1 ~ 1),...)
> >
> > should run without error. But it didn't. And perhaps here's why:
> > BoxCoxLambda <- function(z){
> > b <- MASS:::boxcox.lm(lm(z+1 ~ 1), lambda = seq(-5, 5, length.out =
> > 61), plotit = FALSE)
> > b$x[which.max(b$y)]# best lambda
> > }
> >
> >> lambdas <- apply(dd,2 , BoxCoxLambda)
> > Error in NextMethod() : 'NextMethod' called from an anonymous function
> >
> > and, indeed, ?UseMethod says:
> > "NextMethod should not be called except in methods called by UseMethod
> > or from internal generics (see InternalGenerics). In particular it
> > will not work inside anonymous calling functions (e.g.,
> > get("print.ts")(AirPassengers))."
> >
> > BUT
> > BoxCoxLambda <- function(z){
> >b <- MASS:::boxcox(z+1 ~ 1, lambda = seq(-5, 5, length.out = 61),
> > plotit = FALSE)
> >b$x[which.max(b$y)]# best lambda
> > }
> >
> >> lambdas <- apply(dd,2 , BoxCoxLambda)
> >> lambdas
> > [1] 0.167 0.167
>
> As it turns out, it's the update() step in boxcox.lm() that fails, and
> the update takes place because $y is missing from the lm object, so the
> following works:
>
> BoxCoxLambda <- function(z){
> b <- boxcox(lm(z + 1 ~ 1, y=TRUE),
> lambda = seq(-5, 5, length.out = 101),
> plotit = FALSE)
> b$x[which.max(b$y)]
> }
>
> >
> > The identical lambdas do not seem right to me;
>
> I think that's just an accident of the example (using the BoxCoxLambda()
> above):
>
> > apply(dd, 2, BoxCoxLambda, simplify = TRUE)
> [1] 0.2 0.2
>
> > dd[, 2] <- dd[, 2]^3
> > apply(dd, 2, BoxCoxLambda, simplify = TRUE)
> [1] 0.2 0.1
>
> Best,
> John
>
> > nor do I understand why
> > boxcox.lm apparently throws the error while boxcox.formula does not
> > (it also calls NextMethod()) So I would welcome clarification to clear
> > my clogged (cerebral) sinuses. :-)
> >
> >
> > Best,
> > Bert
> >
> >
> > On Sat, Jul 8, 2023 at 11:25 AM John Fox wrote:
> >>
> >> Dear Ron and Bert,
> >>
> >> First (and without considering why one would want to do this, e.g.,
> >> adding a start of 1 to the data), the following works for me:
> >>
> >> -- snip --
> >>
> >> > library(MASS)
> >>
> >> > BoxCoxLambda <- function(z){
> >> + b <- boxcox(z + 1 ~ 1,
> >> + lambda = seq(-5, 5, length.out = 101),
> >> + plotit = FALSE)
> >> + b$x[which.max(b$y)]
> >> + }
> >>
> >> > mrow <- 500
> >> > mcol <- 2
> >> > set.seed(12345)
> >> > dd <- matrix(rgamma(mrow*mcol, shape = 2, scale = 5), nrow = mrow,
> >> ncol =
> >> +mcol)
> >>
> >> > dd1 <- dd[, 1] # 1st column of dd
> >> > res <- boxcox(lm(dd1 + 1 ~ 1), lambda = seq(-5, 5, length.out = 101),
> >> plotit
> >> + = FALSE)
> >> > res$x[which.max(res$y)]
> >> [1] 0.2
> >>
> >> > apply(dd, 2, BoxCoxLambda, simplify = TRUE)
> >> [1] 0.2 0.2
> >>
> >> -- snip --
> >>
> >> One could also use the powerTransform() function in the car package,
> >> which in this context transforms towards *multi*normality:
> >>
> >> -- snip --
> >>
> >> > library(car)
> >> Loading required package: carData
> >>
> >> > powerTransform(dd + 1)
> >> Estimated transformation parameters
> >> Y1Y2
> >> 0.1740200 0.2089925
> >>
> >> I hope this helps,
> >>John
> >>
> >> --
> >> John Fox, Professor Emeritus
> >> McMaster University
> >> Hamilton, Ontario, Canada
> >> web: https://www.john-fox.ca/
> >>
> >> On 2023-07-08 12:47 p.m., Bert Gunter wrote:
> >>> Caution: This email may have originated from outside the organization.
> >>> Please exercise additional caution with any links and attachments.
> >>>
> >>>
> >>> No, I'm afraid I'm wrong. Something went wrong with my R session and gave
> >>> me incorrect answers. After restarting, I continued to get the same error
> >>> as you did with my supposed "fix." So just ignore what I said and sorry
> >>> for
> >>> the noise.
> >>>
> >>> -- Bert
> >>>
> >>> On Sat, Jul 8, 2023 at 8:28 AM Bert Gunter wrote:
> >>>
> Try this for your function:
>
> BoxCoxLambda <- function(z){
> y <- z
> b <- boxcox(y + 1 ~ 1,lambda = seq(-5, 5, length.out = 61), plotit =
> FALSE)
> b$x[which.max(b$y)]# best lambda
> }
>
> ***I think*** (corrections and clarification strongly welcomed!) that `~`
> (the formula
Re: [R] Getting an error calling MASS::boxcox in a function
Hi Bert,
On 2023-07-08 3:42 p.m., Bert Gunter wrote:
Caution: This email may have originated from outside the organization. Please
exercise additional caution with any links and attachments.
Thanks John.
?boxcox says:
*
Arguments
object
a formula or fitted model object. Currently only lm and aov objects are handled.
*
I read that as saying that
boxcox(lm(z+1 ~ 1),...)
should run without error. But it didn't. And perhaps here's why:
BoxCoxLambda <- function(z){
b <- MASS:::boxcox.lm(lm(z+1 ~ 1), lambda = seq(-5, 5, length.out =
61), plotit = FALSE)
b$x[which.max(b$y)]# best lambda
}
lambdas <- apply(dd,2 , BoxCoxLambda)
Error in NextMethod() : 'NextMethod' called from an anonymous function
and, indeed, ?UseMethod says:
"NextMethod should not be called except in methods called by UseMethod
or from internal generics (see InternalGenerics). In particular it
will not work inside anonymous calling functions (e.g.,
get("print.ts")(AirPassengers))."
BUT
BoxCoxLambda <- function(z){
b <- MASS:::boxcox(z+1 ~ 1, lambda = seq(-5, 5, length.out = 61),
plotit = FALSE)
b$x[which.max(b$y)]# best lambda
}
lambdas <- apply(dd,2 , BoxCoxLambda)
lambdas
[1] 0.167 0.167
As it turns out, it's the update() step in boxcox.lm() that fails, and
the update takes place because $y is missing from the lm object, so the
following works:
BoxCoxLambda <- function(z){
b <- boxcox(lm(z + 1 ~ 1, y=TRUE),
lambda = seq(-5, 5, length.out = 101),
plotit = FALSE)
b$x[which.max(b$y)]
}
The identical lambdas do not seem right to me;
I think that's just an accident of the example (using the BoxCoxLambda()
above):
> apply(dd, 2, BoxCoxLambda, simplify = TRUE)
[1] 0.2 0.2
> dd[, 2] <- dd[, 2]^3
> apply(dd, 2, BoxCoxLambda, simplify = TRUE)
[1] 0.2 0.1
Best,
John
nor do I understand why
boxcox.lm apparently throws the error while boxcox.formula does not
(it also calls NextMethod()) So I would welcome clarification to clear
my clogged (cerebral) sinuses. :-)
Best,
Bert
On Sat, Jul 8, 2023 at 11:25 AM John Fox wrote:
Dear Ron and Bert,
First (and without considering why one would want to do this, e.g.,
adding a start of 1 to the data), the following works for me:
-- snip --
> library(MASS)
> BoxCoxLambda <- function(z){
+ b <- boxcox(z + 1 ~ 1,
+ lambda = seq(-5, 5, length.out = 101),
+ plotit = FALSE)
+ b$x[which.max(b$y)]
+ }
> mrow <- 500
> mcol <- 2
> set.seed(12345)
> dd <- matrix(rgamma(mrow*mcol, shape = 2, scale = 5), nrow = mrow, ncol =
+mcol)
> dd1 <- dd[, 1] # 1st column of dd
> res <- boxcox(lm(dd1 + 1 ~ 1), lambda = seq(-5, 5, length.out = 101),
plotit
+ = FALSE)
> res$x[which.max(res$y)]
[1] 0.2
> apply(dd, 2, BoxCoxLambda, simplify = TRUE)
[1] 0.2 0.2
-- snip --
One could also use the powerTransform() function in the car package,
which in this context transforms towards *multi*normality:
-- snip --
> library(car)
Loading required package: carData
> powerTransform(dd + 1)
Estimated transformation parameters
Y1Y2
0.1740200 0.2089925
I hope this helps,
John
--
John Fox, Professor Emeritus
McMaster University
Hamilton, Ontario, Canada
web: https://www.john-fox.ca/
On 2023-07-08 12:47 p.m., Bert Gunter wrote:
Caution: This email may have originated from outside the organization. Please
exercise additional caution with any links and attachments.
No, I'm afraid I'm wrong. Something went wrong with my R session and gave
me incorrect answers. After restarting, I continued to get the same error
as you did with my supposed "fix." So just ignore what I said and sorry for
the noise.
-- Bert
On Sat, Jul 8, 2023 at 8:28 AM Bert Gunter wrote:
Try this for your function:
BoxCoxLambda <- function(z){
y <- z
b <- boxcox(y + 1 ~ 1,lambda = seq(-5, 5, length.out = 61), plotit =
FALSE)
b$x[which.max(b$y)]# best lambda
}
***I think*** (corrections and clarification strongly welcomed!) that `~`
(the formula function) is looking for 'z' in the GlobalEnv, the caller of
apply(), and not finding it. It finds 'y' here explicitly in the
BoxCoxLambda environment.
Cheers,
Bert
On Sat, Jul 8, 2023 at 4:28 AM Ron Crump via R-help
wrote:
Hi,
Firstly, apologies as I have posted this on community.rstudio.com too.
I want to optimise a Box-Cox transformation on columns of a matrix (ie, a
unique lambda for each column). So I wrote a function that includes the
call to MASS::boxcox in order that it can be applied to each column easily.
Except that I'm getting an error when calling the function. If I just
extract a column of the matrix and run the code not in the function, it
works. If I call the function either with an extracted column (ie dd1 in
the reprex below) or in a call to apply I get an error (see the reprex
below).
I'm
Re: [R] Getting an error calling MASS::boxcox in a function
Thanks John.
?boxcox says:
*
Arguments
object
a formula or fitted model object. Currently only lm and aov objects are handled.
*
I read that as saying that
boxcox(lm(z+1 ~ 1),...)
should run without error. But it didn't. And perhaps here's why:
BoxCoxLambda <- function(z){
b <- MASS:::boxcox.lm(lm(z+1 ~ 1), lambda = seq(-5, 5, length.out =
61), plotit = FALSE)
b$x[which.max(b$y)]# best lambda
}
> lambdas <- apply(dd,2 , BoxCoxLambda)
Error in NextMethod() : 'NextMethod' called from an anonymous function
and, indeed, ?UseMethod says:
"NextMethod should not be called except in methods called by UseMethod
or from internal generics (see InternalGenerics). In particular it
will not work inside anonymous calling functions (e.g.,
get("print.ts")(AirPassengers))."
BUT
BoxCoxLambda <- function(z){
b <- MASS:::boxcox(z+1 ~ 1, lambda = seq(-5, 5, length.out = 61),
plotit = FALSE)
b$x[which.max(b$y)]# best lambda
}
> lambdas <- apply(dd,2 , BoxCoxLambda)
> lambdas
[1] 0.167 0.167
The identical lambdas do not seem right to me; nor do I understand why
boxcox.lm apparently throws the error while boxcox.formula does not
(it also calls NextMethod()) So I would welcome clarification to clear
my clogged (cerebral) sinuses. :-)
Best,
Bert
On Sat, Jul 8, 2023 at 11:25 AM John Fox wrote:
>
> Dear Ron and Bert,
>
> First (and without considering why one would want to do this, e.g.,
> adding a start of 1 to the data), the following works for me:
>
> -- snip --
>
> > library(MASS)
>
> > BoxCoxLambda <- function(z){
> + b <- boxcox(z + 1 ~ 1,
> + lambda = seq(-5, 5, length.out = 101),
> + plotit = FALSE)
> + b$x[which.max(b$y)]
> + }
>
> > mrow <- 500
> > mcol <- 2
> > set.seed(12345)
> > dd <- matrix(rgamma(mrow*mcol, shape = 2, scale = 5), nrow = mrow, ncol =
> +mcol)
>
> > dd1 <- dd[, 1] # 1st column of dd
> > res <- boxcox(lm(dd1 + 1 ~ 1), lambda = seq(-5, 5, length.out = 101),
> plotit
> + = FALSE)
> > res$x[which.max(res$y)]
> [1] 0.2
>
> > apply(dd, 2, BoxCoxLambda, simplify = TRUE)
> [1] 0.2 0.2
>
> -- snip --
>
> One could also use the powerTransform() function in the car package,
> which in this context transforms towards *multi*normality:
>
> -- snip --
>
> > library(car)
> Loading required package: carData
>
> > powerTransform(dd + 1)
> Estimated transformation parameters
> Y1Y2
> 0.1740200 0.2089925
>
> I hope this helps,
> John
>
> --
> John Fox, Professor Emeritus
> McMaster University
> Hamilton, Ontario, Canada
> web: https://www.john-fox.ca/
>
> On 2023-07-08 12:47 p.m., Bert Gunter wrote:
> > Caution: This email may have originated from outside the organization.
> > Please exercise additional caution with any links and attachments.
> >
> >
> > No, I'm afraid I'm wrong. Something went wrong with my R session and gave
> > me incorrect answers. After restarting, I continued to get the same error
> > as you did with my supposed "fix." So just ignore what I said and sorry for
> > the noise.
> >
> > -- Bert
> >
> > On Sat, Jul 8, 2023 at 8:28 AM Bert Gunter wrote:
> >
> >> Try this for your function:
> >>
> >> BoxCoxLambda <- function(z){
> >> y <- z
> >> b <- boxcox(y + 1 ~ 1,lambda = seq(-5, 5, length.out = 61), plotit =
> >> FALSE)
> >> b$x[which.max(b$y)]# best lambda
> >> }
> >>
> >> ***I think*** (corrections and clarification strongly welcomed!) that `~`
> >> (the formula function) is looking for 'z' in the GlobalEnv, the caller of
> >> apply(), and not finding it. It finds 'y' here explicitly in the
> >> BoxCoxLambda environment.
> >>
> >> Cheers,
> >> Bert
> >>
> >>
> >>
> >> On Sat, Jul 8, 2023 at 4:28 AM Ron Crump via R-help
> >> wrote:
> >>
> >>> Hi,
> >>>
> >>> Firstly, apologies as I have posted this on community.rstudio.com too.
> >>>
> >>> I want to optimise a Box-Cox transformation on columns of a matrix (ie, a
> >>> unique lambda for each column). So I wrote a function that includes the
> >>> call to MASS::boxcox in order that it can be applied to each column
> >>> easily.
> >>> Except that I'm getting an error when calling the function. If I just
> >>> extract a column of the matrix and run the code not in the function, it
> >>> works. If I call the function either with an extracted column (ie dd1 in
> >>> the reprex below) or in a call to apply I get an error (see the reprex
> >>> below).
> >>>
> >>> I'm sure I'm doing something silly, but I can't see what it is. Any help
> >>> appreciated.
> >>>
> >>> library(MASS)
> >>>
> >>> # Find optimised Lambda for Boc-Cox transformation
> >>> BoxCoxLambda <- function(z){
> >>> b <- boxcox(lm(z+1 ~ 1), lambda = seq(-5, 5, length.out = 61), plotit
> >>> = FALSE)
> >>> b$x[which.max(b$y)]# best lambda
> >>> }
> >>>
> >>> mrow <- 500
> >>> mcol <- 2
> >>> set.seed(12345)
> >>> dd <- matrix(rgamma(mrow*mcol, shape = 2,
Re: [R] Getting an error calling MASS::boxcox in a function
Dear Ron and Bert,
First (and without considering why one would want to do this, e.g.,
adding a start of 1 to the data), the following works for me:
-- snip --
> library(MASS)
> BoxCoxLambda <- function(z){
+ b <- boxcox(z + 1 ~ 1,
+ lambda = seq(-5, 5, length.out = 101),
+ plotit = FALSE)
+ b$x[which.max(b$y)]
+ }
> mrow <- 500
> mcol <- 2
> set.seed(12345)
> dd <- matrix(rgamma(mrow*mcol, shape = 2, scale = 5), nrow = mrow, ncol =
+mcol)
> dd1 <- dd[, 1] # 1st column of dd
> res <- boxcox(lm(dd1 + 1 ~ 1), lambda = seq(-5, 5, length.out = 101),
plotit
+ = FALSE)
> res$x[which.max(res$y)]
[1] 0.2
> apply(dd, 2, BoxCoxLambda, simplify = TRUE)
[1] 0.2 0.2
-- snip --
One could also use the powerTransform() function in the car package,
which in this context transforms towards *multi*normality:
-- snip --
> library(car)
Loading required package: carData
> powerTransform(dd + 1)
Estimated transformation parameters
Y1Y2
0.1740200 0.2089925
I hope this helps,
John
--
John Fox, Professor Emeritus
McMaster University
Hamilton, Ontario, Canada
web: https://www.john-fox.ca/
On 2023-07-08 12:47 p.m., Bert Gunter wrote:
Caution: This email may have originated from outside the organization. Please
exercise additional caution with any links and attachments.
No, I'm afraid I'm wrong. Something went wrong with my R session and gave
me incorrect answers. After restarting, I continued to get the same error
as you did with my supposed "fix." So just ignore what I said and sorry for
the noise.
-- Bert
On Sat, Jul 8, 2023 at 8:28 AM Bert Gunter wrote:
Try this for your function:
BoxCoxLambda <- function(z){
y <- z
b <- boxcox(y + 1 ~ 1,lambda = seq(-5, 5, length.out = 61), plotit =
FALSE)
b$x[which.max(b$y)]# best lambda
}
***I think*** (corrections and clarification strongly welcomed!) that `~`
(the formula function) is looking for 'z' in the GlobalEnv, the caller of
apply(), and not finding it. It finds 'y' here explicitly in the
BoxCoxLambda environment.
Cheers,
Bert
On Sat, Jul 8, 2023 at 4:28 AM Ron Crump via R-help
wrote:
Hi,
Firstly, apologies as I have posted this on community.rstudio.com too.
I want to optimise a Box-Cox transformation on columns of a matrix (ie, a
unique lambda for each column). So I wrote a function that includes the
call to MASS::boxcox in order that it can be applied to each column easily.
Except that I'm getting an error when calling the function. If I just
extract a column of the matrix and run the code not in the function, it
works. If I call the function either with an extracted column (ie dd1 in
the reprex below) or in a call to apply I get an error (see the reprex
below).
I'm sure I'm doing something silly, but I can't see what it is. Any help
appreciated.
library(MASS)
# Find optimised Lambda for Boc-Cox transformation
BoxCoxLambda <- function(z){
b <- boxcox(lm(z+1 ~ 1), lambda = seq(-5, 5, length.out = 61), plotit
= FALSE)
b$x[which.max(b$y)]# best lambda
}
mrow <- 500
mcol <- 2
set.seed(12345)
dd <- matrix(rgamma(mrow*mcol, shape = 2, scale = 5), nrow = mrow, ncol =
mcol)
# Try it not using the BoxCoxLambda function:
dd1 <- dd[,1] # 1st column of dd
bb <- boxcox(lm(dd1+1 ~ 1), lambda = seq(-5, 5, length.out = 101), plotit
= FALSE)
print(paste0("1st column's lambda is ", bb$x[which.max(bb$y)]))
#> [1] "1st column's lambda is 0.2"
# Calculate lambda for each column of dd
lambdas <- apply(dd, 2, BoxCoxLambda, simplify = TRUE)
#> Error in eval(predvars, data, env): object 'z' not found
Created on 2023-07-08 with reprex v2.0.2
Thanks for your time and help.
Ron
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Getting an error calling MASS::boxcox in a function
No, I'm afraid I'm wrong. Something went wrong with my R session and gave
me incorrect answers. After restarting, I continued to get the same error
as you did with my supposed "fix." So just ignore what I said and sorry for
the noise.
-- Bert
On Sat, Jul 8, 2023 at 8:28 AM Bert Gunter wrote:
> Try this for your function:
>
> BoxCoxLambda <- function(z){
>y <- z
>b <- boxcox(y + 1 ~ 1,lambda = seq(-5, 5, length.out = 61), plotit =
> FALSE)
>b$x[which.max(b$y)]# best lambda
> }
>
> ***I think*** (corrections and clarification strongly welcomed!) that `~`
> (the formula function) is looking for 'z' in the GlobalEnv, the caller of
> apply(), and not finding it. It finds 'y' here explicitly in the
> BoxCoxLambda environment.
>
> Cheers,
> Bert
>
>
>
> On Sat, Jul 8, 2023 at 4:28 AM Ron Crump via R-help
> wrote:
>
>> Hi,
>>
>> Firstly, apologies as I have posted this on community.rstudio.com too.
>>
>> I want to optimise a Box-Cox transformation on columns of a matrix (ie, a
>> unique lambda for each column). So I wrote a function that includes the
>> call to MASS::boxcox in order that it can be applied to each column easily.
>> Except that I'm getting an error when calling the function. If I just
>> extract a column of the matrix and run the code not in the function, it
>> works. If I call the function either with an extracted column (ie dd1 in
>> the reprex below) or in a call to apply I get an error (see the reprex
>> below).
>>
>> I'm sure I'm doing something silly, but I can't see what it is. Any help
>> appreciated.
>>
>> library(MASS)
>>
>> # Find optimised Lambda for Boc-Cox transformation
>> BoxCoxLambda <- function(z){
>> b <- boxcox(lm(z+1 ~ 1), lambda = seq(-5, 5, length.out = 61), plotit
>> = FALSE)
>> b$x[which.max(b$y)]# best lambda
>> }
>>
>> mrow <- 500
>> mcol <- 2
>> set.seed(12345)
>> dd <- matrix(rgamma(mrow*mcol, shape = 2, scale = 5), nrow = mrow, ncol =
>> mcol)
>>
>> # Try it not using the BoxCoxLambda function:
>> dd1 <- dd[,1] # 1st column of dd
>> bb <- boxcox(lm(dd1+1 ~ 1), lambda = seq(-5, 5, length.out = 101), plotit
>> = FALSE)
>> print(paste0("1st column's lambda is ", bb$x[which.max(bb$y)]))
>> #> [1] "1st column's lambda is 0.2"
>>
>> # Calculate lambda for each column of dd
>> lambdas <- apply(dd, 2, BoxCoxLambda, simplify = TRUE)
>> #> Error in eval(predvars, data, env): object 'z' not found
>>
>> Created on 2023-07-08 with reprex v2.0.2
>>
>> Thanks for your time and help.
>>
>> Ron
>> [[alternative HTML version deleted]]
>>
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Getting an error calling MASS::boxcox in a function
Try this for your function:
BoxCoxLambda <- function(z){
y <- z
b <- boxcox(y + 1 ~ 1,lambda = seq(-5, 5, length.out = 61), plotit =
FALSE)
b$x[which.max(b$y)]# best lambda
}
***I think*** (corrections and clarification strongly welcomed!) that `~`
(the formula function) is looking for 'z' in the GlobalEnv, the caller of
apply(), and not finding it. It finds 'y' here explicitly in the
BoxCoxLambda environment.
Cheers,
Bert
On Sat, Jul 8, 2023 at 4:28 AM Ron Crump via R-help
wrote:
> Hi,
>
> Firstly, apologies as I have posted this on community.rstudio.com too.
>
> I want to optimise a Box-Cox transformation on columns of a matrix (ie, a
> unique lambda for each column). So I wrote a function that includes the
> call to MASS::boxcox in order that it can be applied to each column easily.
> Except that I'm getting an error when calling the function. If I just
> extract a column of the matrix and run the code not in the function, it
> works. If I call the function either with an extracted column (ie dd1 in
> the reprex below) or in a call to apply I get an error (see the reprex
> below).
>
> I'm sure I'm doing something silly, but I can't see what it is. Any help
> appreciated.
>
> library(MASS)
>
> # Find optimised Lambda for Boc-Cox transformation
> BoxCoxLambda <- function(z){
> b <- boxcox(lm(z+1 ~ 1), lambda = seq(-5, 5, length.out = 61), plotit
> = FALSE)
> b$x[which.max(b$y)]# best lambda
> }
>
> mrow <- 500
> mcol <- 2
> set.seed(12345)
> dd <- matrix(rgamma(mrow*mcol, shape = 2, scale = 5), nrow = mrow, ncol =
> mcol)
>
> # Try it not using the BoxCoxLambda function:
> dd1 <- dd[,1] # 1st column of dd
> bb <- boxcox(lm(dd1+1 ~ 1), lambda = seq(-5, 5, length.out = 101), plotit
> = FALSE)
> print(paste0("1st column's lambda is ", bb$x[which.max(bb$y)]))
> #> [1] "1st column's lambda is 0.2"
>
> # Calculate lambda for each column of dd
> lambdas <- apply(dd, 2, BoxCoxLambda, simplify = TRUE)
> #> Error in eval(predvars, data, env): object 'z' not found
>
> Created on 2023-07-08 with reprex v2.0.2
>
> Thanks for your time and help.
>
> Ron
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Getting an error calling MASS::boxcox in a function
Hi,
Firstly, apologies as I have posted this on community.rstudio.com too.
I want to optimise a Box-Cox transformation on columns of a matrix (ie, a
unique lambda for each column). So I wrote a function that includes the call to
MASS::boxcox in order that it can be applied to each column easily. Except that
I'm getting an error when calling the function. If I just extract a column of
the matrix and run the code not in the function, it works. If I call the
function either with an extracted column (ie dd1 in the reprex below) or in a
call to apply I get an error (see the reprex below).
I'm sure I'm doing something silly, but I can't see what it is. Any help
appreciated.
library(MASS)
# Find optimised Lambda for Boc-Cox transformation
BoxCoxLambda <- function(z){
b <- boxcox(lm(z+1 ~ 1), lambda = seq(-5, 5, length.out = 61), plotit =
FALSE)
b$x[which.max(b$y)]# best lambda
}
mrow <- 500
mcol <- 2
set.seed(12345)
dd <- matrix(rgamma(mrow*mcol, shape = 2, scale = 5), nrow = mrow, ncol = mcol)
# Try it not using the BoxCoxLambda function:
dd1 <- dd[,1] # 1st column of dd
bb <- boxcox(lm(dd1+1 ~ 1), lambda = seq(-5, 5, length.out = 101), plotit =
FALSE)
print(paste0("1st column's lambda is ", bb$x[which.max(bb$y)]))
#> [1] "1st column's lambda is 0.2"
# Calculate lambda for each column of dd
lambdas <- apply(dd, 2, BoxCoxLambda, simplify = TRUE)
#> Error in eval(predvars, data, env): object 'z' not found
Created on 2023-07-08 with reprex v2.0.2
Thanks for your time and help.
Ron
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
