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><mailto:theodore.stankow...@csulb.edu<mailto:theodore.stankow...@csulb.edu>>
562-985-4826
http://www.csulb.edu/mammal-lab/
@CSULBMammalLab
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