[R] na.omit not omitting rows

[Ted Stankowich]

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:wdunlap using tibco.com]
Sent: Thursday, June 4, 2020 12:39 PM
To: Ted Stankowich <Theodore.Stankowich using csulb.edu>
Cc: r-help using r-project.org
Subject: Re: [R] na.omit not omitting rows

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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.Stankowich using csulb.edu<mailto:Theodore.Stankowich using 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.stankowich using csulb.edu<mailto:theodore.stankowich using csulb.edu><mailto:theodore.stankowich using csulb.edu<mailto:theodore.stankowich using csulb.edu>>
562-985-4826
http://www.csulb.edu/mammal-lab/
@CSULBMammalLab




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