Thanks - a previous response resolved the issue and I'm off and running with the analyses.
-----Original Message----- From: David Winsemius [mailto:dwinsem...@comcast.net] Sent: Thursday, June 4, 2020 5:02 PM To: Ted Stankowich <theodore.stankow...@csulb.edu> Cc: Rui Barradas <ruipbarra...@sapo.pt>; William Dunlap <wdun...@tibco.com>; r-help@r-project.org Subject: Re: [R] na.omit not omitting rows CAUTION: This email was sent from an external source. Use caution when replying, opening links or attachments. Perhaps indexing with rowSums(is.na(dfrm))? — David Sent from my iPhone > On Jun 4, 2020, at 4:58 PM, Ted Stankowich <theodore.stankow...@csulb.edu> > wrote: > > This worked! Thank you! > > -----Original Message----- > From: Rui Barradas [mailto:ruipbarra...@sapo.pt] > Sent: Thursday, June 4, 2020 2:49 PM > To: Ted Stankowich <theodore.stankow...@csulb.edu>; William Dunlap > <wdun...@tibco.com> > Cc: r-help@r-project.org > Subject: Re: [R] na.omit not omitting rows > > CAUTION: This email was sent from an external source. Use caution when > replying, opening links or attachments. > > > Hello, > > If the problem is the "na.action" attribute, here are two ways of solving it. > > First, an example data set. > > set.seed(2020) # Make the example reproducible > phamComplBinomial <- sprintf("f%003d", 1:356) > is.na(UphamComplBinomial) <- sample(356, 37) DarkEum <- > factor(sample(1:2, 356, TRUE)) > Protect1 <- data.frame(UphamComplBinomial = > factor(UphamComplBinomial), > DarkEum) > > > 1. Setting the attribute "na.action" to NULL removes it > > Protect2 <- na.omit(Protect1) > attributes(Protect2) > attr(Protect2, "na.action") <- NULL > attributes(Protect2) > > > 2. Use an index vector to subset the data > > na <- is.na(Protect1$UphamComplBinomial) > Protect3 <- Protect1[!na, ] > > > The results are identical. But if you have more than one column with NA's, > this second way will be more complicated. > > identical(Protect2, Protect3) > #[1] TRUE > > > Hope this helps, > > Rui Barradas > > Às 22:27 de 04/06/20, Ted Stankowich escreveu: >> Thanks, but no that doesn’t work. The na.omit attributes are still in >> the dataframe, which you can see in the str outputs from the post. >> The problem line is likely: - attr(*, "na.action")= 'omit' Named int >> [1:2] 2 3 >> >> From: William Dunlap [mailto:wdun...@tibco.com] >> Sent: Thursday, June 4, 2020 12:39 PM >> To: Ted Stankowich <theodore.stankow...@csulb.edu> >> Cc: r-help@r-project.org >> Subject: Re: [R] na.omit not omitting rows >> >> CAUTION: This email was sent from an external source. Use caution when >> replying, opening links or attachments. >> >> Does droplevels() help? >> >>> d <- data.frame(size = factor(c("S","M","M","L","L"), >>> levels=c("S","M","L")), id=c(101,NA,NA,104,105)) >>> str(d) >> 'data.frame': 5 obs. of 2 variables: >> $ size: Factor w/ 3 levels "S","M","L": 1 2 2 3 3 $ id : num 101 >> NA NA 104 105 >>> str(na.omit(d)) >> 'data.frame': 3 obs. of 2 variables: >> $ size: Factor w/ 3 levels "S","M","L": 1 3 3 $ id : num 101 104 >> 105 >> - attr(*, "na.action")= 'omit' Named int [1:2] 2 3 >> ..- attr(*, "names")= chr [1:2] "2" "3" >>> str(droplevels(na.omit(d))) >> 'data.frame': 3 obs. of 2 variables: >> $ size: Factor w/ 2 levels "S","L": 1 2 2 $ id : num 101 104 105 >> - attr(*, "na.action")= 'omit' Named int [1:2] 2 3 >> ..- attr(*, "names")= chr [1:2] "2" "3" >> >> Bill Dunlap >> TIBCO Software >> wdunlap tibco.com<http://tibco.com> >> >> >> On Thu, Jun 4, 2020 at 12:18 PM Ted Stankowich >> <theodore.stankow...@csulb.edu<mailto:theodore.stankow...@csulb.edu>> wrote: >> Hello! I'm trying to create a subset of a dataset and then remove all rows >> with NAs in them. Ultimately, I am running phylogenetic analyses with trees >> that require the tree tiplabels to match exactly with the rows in the >> dataframe. But when I use na.omit to delete the rows with NAs, there is >> still a trace of those omitted rows in the data.frame, which then causes an >> error in the phylogenetic analyses. Is there any way to completely scrub >> those omitted rows from the dataframe? The code is below. As you can see >> from the result of the final str(Protect1) line, there are attributes with >> the omitted features still in the dataframe (356 species names in the >> UphamComplBinomial factor, but only 319 observations). These traces are >> causing errors with the phylo analyses. >> >>> Protect1=as.data.frame(cbind(UphamComplBinomial, DarkEum, NoctCrep, >>> Shade)) #Create the dataframe with variables of interest from an >>> attached dataset row.names(Protect1)=Protect1$UphamComplBinomial >>> #assign species names as rownames >>> Protect1=as.data.frame(na.omit(Protect1)) #drop rows with missing >>> data >>> str(Protect1) >> 'data.frame': 319 obs. of 4 variables: >> $ UphamComplBinomial: Factor w/ 356 levels >> "Allenopithecus_nigroviridis_CERCOPITHECIDAE_PRIMATES",..: 1 2 3 4 5 8 9 10 >> 11 12 ... >> $ DarkEum : Factor w/ 2 levels "0","1": 2 1 2 2 2 2 2 2 2 2 ... >> $ NoctCrep : Factor w/ 2 levels "0","1": 1 2 1 1 1 1 1 1 1 1 ... >> $ Shade : Factor w/ 59 levels "0.1","0.2","0.25",..: 10 58 53 >> 17 49 52 52 39 39 41 ... >> - attr(*, "na.action")= 'omit' Named int 6 7 23 36 37 40 42 50 51 60 ... >> ..- attr(*, "names")= chr "Alouatta_macconnelli_ATELIDAE_PRIMATES" >> "Alouatta_nigerrima_ATELIDAE_PRIMATES" "Ateles_fusciceps_ATELIDAE_PRIMATES" >> "Callicebus_baptista_PITHECIIDAE_PRIMATES" ... >> >> Dr. Ted Stankowich >> Associate Professor >> Department of Biological Sciences >> California State University Long Beach Long Beach, CA 90840 >> theodore.stankow...@csulb.edu<mailto:theodore.stankow...@csulb.edu><m >> a >> ilto:theodore.stankow...@csulb.edu<mailto:theodore.stankowich@csulb.e >> d >> u>> >> 562-985-4826 >> http://www.csulb.edu/mammal-lab/ >> @CSULBMammalLab >> >> >> >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-help@r-project.org<mailto:R-help@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@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. >> > ______________________________________________ > R-help@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. ______________________________________________ R-help@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.
