[R] Getting an error calling MASS::boxcox in a function

[Bert Gunter]

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 <bgunter.4567 using gmail.com> 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 <r-help using r-project.org>
> 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]]
>>
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>

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