Hi John, That does help, thanks!
Brittany > On Jun 11, 2015, at 4:02 PM, John Fox <[email protected]> wrote: > > 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.
