[R] NADA package/cenboxplot() method: maximum censored percentage

[William Dunlap]

You get this error if the factor given as the group argument
has any unused factor levels.  E.g.,

> library(NADA)
> data(Golden)
> with(Golden, cenboxplot(Blood, BloodCen, factor(DosageGroup,levels=c("Low","High","<unused>"))))
Error in if ((length(obs[censored])/length(obs)) > 0.8) { : 
  missing value where TRUE/FALSE needed

(0/0 is NaN, which triggers the 'missing value where TRUE/FALSE needed' message.)

You should complain to the maintainer of the NADA package - the test should be
more like 'length(obs)>0 && ...'.

To work around it use factor(group) instead of group when calling cenboxplot.

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com


> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf
> Of David Winsemius
> Sent: Monday, August 20, 2012 10:15 AM
> To: Rich Shepard
> Cc: r-help at r-project.org
> Subject: Re: [R] NADA package/cenboxplot() method: maximum censored percentage
> 
> 
> On Aug 20, 2012, at 9:22 AM, Rich Shepard wrote:
> 
> > On Thu, 16 Aug 2012, David L Lorenz wrote:
> >
> >> The cenboxplot function uses cenros to estimate the censored
> >> values. The
> >> cenros function requires at least 2 uncensored observations to be
> >> able to
> >> do the regression. The cenros function does issue a warning when
> >> there are
> >> more than 80% censored data, but that is suppressed in cenboxplot.
> >
> >  There must be something other than > 2 uncensored observations in
> > my data
> > that prevent cenboxplot from functioning. For example, dissolved
> > arsenic
> > concentrations have 578 total observations. Of these, 180 (31.14%) are
> > censored and 398 are uncensored. Both number of uncensored
> > observations and
> > the percentage of censored observations appear to be well within
> > plotable
> > limits, but cenboxplot() returns this error:
> >
> > cenboxplot(as.d$quant, as.d$ceneq1, as.d$era, range=1.5,
> > main='Dissolved
> > Arsenic', ylab='Concentration (mg/L)', xlab='Time Period')
> > Error in if ((length(obs[censored])/length(obs)) > 0.8) { :
> >  missing value where TRUE/FALSE needed
> >
> >  I would like to understand how the function obtains a censored
> > ratio > 0.8
> > when it is actually 0.3114.
> 
> I see no evidence from what you have posted that the function "obtains
> a censored ratio > 0.8". The error messages says there were missing
> values. You might consider looking at :
> 
> table(Q=is.na(as.d$quant), CE=is.na(as.d$ceneq1), ERA=as.d$era)
> 
> My guess is that this test is failing for one or more categories of
> as.d$era.
> 
> >  Displaying the data frame, as.d, has a logical TRUE or FALSE for
> > each row;
> > it can be provided if needed.
> 
> You could use dput() and post through Nabble, which would let people
> download if they were interested. Seems on the large size to be
> considered "minimal" .
> 
> --
> 
> David Winsemius, MD
> Alameda, CA, USA
> 
> ______________________________________________
> R-help at r-project.org mailing list
> 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.