plot observed vs fitted with model with NAs in data
I don't see 'na.action' in your code anywhere.
This works for me:
mymodel = lmer(hp ~ (1| disp) + (1|cyl), data=mydata,
na.action=na.exclude)
plot(mymodel, hp ~ fitted(.))
**However**, the real answer is this item from
https://github.com/lme4/lme4/blob/master/inst/NEWS.Rd, under BUG FIXES
for version 1.1-3:
\item \code{fitted} now respects \code{na.action} settings (Github
issue #149)
We are hoping to release a new version to CRAN very soon, but in the
meantime version 1.1-4 is available at
http://lme4.r-forge.r-project.org/repos , or from github ...
Ben Bolker
On 14-03-05 10:40 AM, Paul Tanger wrote:
Thanks for that tip but it didn't seem to help. I get the same error. Is
there a way to tell it not to predict a value for an NA? Here is a
reproducible example:
data(mtcars)
mydata = mtcars[2:8]
# insert some NAs
mydata$hp = apply(mydata[2], 2, function(x) {x[sample(c(1:length(x)),
floor(length(x)/10)) ] = NA; x} )
# run model
mymodel = lmer(hp ~ (1| disp) + (1|cyl), data=mydata)
# try to plot obs vs fitted
plot(mymodel, hp ~ fitted(.))
Note that whatever na.action I attempt, the error remains.
Maybe there is a simple solution that I'm missing?
Thanks!
On Wed, Mar 5, 2014 at 1:24 AM, ONKELINX, Thierry
<Thierry.ONKELINX at inbo.be>wrote:
You probably need to fit your model with the na.action = na.exclude argument. A more detailed answer requires more information. Have a look at
http://www.r-project.org/posting-guide.html ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance Kliniekstraat 25 1070 Anderlecht Belgium + 32 2 525 02 51 + 32 54 43 61 85 Thierry.Onkelinx at inbo.be www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -----Oorspronkelijk bericht----- Van: r-sig-mixed-models-bounces at r-project.org [mailto: r-sig-mixed-models-bounces at r-project.org] Namens Paul Tanger Verzonden: woensdag 5 maart 2014 8:24 Aan: r-sig-mixed-models at r-project.org Onderwerp: [R-sig-ME] plot observed vs fitted with model with NAs in data Hi, I have a model that I fit from data with some NAs in it.. everything is going well until I try to plot observed vs fitted.. and I can figure out how to fix this.. any ideas? I can see that there are 1049 observed and 1050 fitted.. but can I resolve this without fitting new models after discarding NAs? I would really rather not do that. plot(model, resp~ fitted(.)) Error in `[<-.data.frame`(`*tmp*`, , ".y", value = c(130.983333333333, : replacement has 1050 rows, data has 1049 [[alternative HTML version deleted]] _______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models * * * * * * * * * * * * * D I S C L A I M E R * * * * * * * * * * * * * Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document.