Dear Brittany, There is an essentially perfect linear dependency among the variables in your data (note the last eigenvalue, which is 0 within rounding error):
> eigen(cor(problem.data.boxcox[,-1]), only.values=TRUE) $values [1] 3.644257e+00 1.821582e+00 1.712152e+00 1.205091e+00 1.007231e+00 9.231163e-01 9.048724e-01 [8] 8.718398e-01 8.379187e-01 7.371353e-01 6.334100e-01 5.235629e-01 4.757997e-01 4.246831e-01 [15] 2.773471e-01 -2.802502e-16 In addition, some of your variables have many tied values at the bottom of their distributions, making them very poor candidates for normalizing power transformations; for example, > sum(problem.data.boxcox$variable2 == 1) [1] 626 I hope this helps, John ------------------------------------------------ John Fox, Professor McMaster University Hamilton, Ontario, Canada http://socserv.mcmaster.ca/jfox/ On Thu, 11 Jun 2015 09:37:57 -0600 Brittany Demmitt <[email protected]> wrote: > Hi John, > > Thank you so much for the info! I have attached the data in .csv format that > is giving me the warning along with the command that I am running. It i a > data frame with 1510 sample IDs and then their values for 16 variables. I am > trying to transform the 16 variables. I do not receive the warning when I > run each variable independently, just when I run the entire dataframe at > once. However, I have run this command with other larger data frames all at > once with no warnings, so I am not sure why it is not working now. > > Any help is appreciated! Thanks! :-) > > Britt > > Commands Run: > > #read in the data frame > problem.data.boxcox <- read.csv(“problem.data.boxcox.csv") > > #run a power transformation (I do not run that on the first column because > it is just sample ids) > > problem.data.boxcox.pT <- powerTransform(problem.data.boxcox[,-1]) > > Warning message: > In estimateTransform(x, y, NULL, ...) : > Convergence failure: return code = 1 > > > > > > > > > > > On Jun 10, 2015, at 2:15 PM, John Fox <[email protected]> wrote: > > > > Dear Brittany, > > > > As explained in ?powerTransform, this function uses optim() to optimize a > > generalized Box-Cox criterion. For explanation of return codes, see ?optim. > > > > In particular, code 1 indicates that the maximum number of iterations was > > exceeded. Although you might try increasing the permitted number of > > iterations or otherwise tweaking the arguments to optim(), your problem is > > probably ill-conditioned in some manner that is impossible to know without > > more information, such as your data. > > > > I hope this helps, > > John > > > > ------------------------------------------------ > > John Fox, Professor > > McMaster University > > Hamilton, Ontario, Canada > > http://socserv.mcmaster.ca/jfox/ > > > > > > On Wed, 10 Jun 2015 10:54:30 -0600 > > Brittany Demmitt <[email protected]> wrote: > >> Hello, > >> > >> I am trying to use the powerTransform function in the package car to > >> identify the lambda: transform my data. However, I receive the following > >> warning: > >> > >> Warning message: > >> In estimateTransform(x, y, NULL, ...) : > >> Convergence failure: return code = 1 > >> > >> I can not find a description of what return code =1 means for the car > >> package. How do I look that up, or does anyone know what the warning > >> means? > >> > >> Thank you so much! > >> > >> Brittany > >> [[alternative HTML version deleted]] > >> > >> ______________________________________________ > >> [email protected] 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. > > > > > > > > > ______________________________________________ [email protected] 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.
