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

[John Fox]

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
        Y1        Y2
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 <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]]
>>>
>>> ______________________________________________
>>> R-help using 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 using 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.