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Ted Stankowich

2020-Jun-04 21:27 UTC

[R] na.omit not omitting rows

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 at tibco.com]
Sent: Thursday, June 4, 2020 12:39 PM
To: Ted Stankowich <Theodore.Stankowich at csulb.edu>
Cc: r-help at 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.Stankowich at
csulb.edu<mailto:Theodore.Stankowich at 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 at csulb.edu<mailto:theodore.stankowich at
csulb.edu><mailto:theodore.stankowich at
csulb.edu<mailto:theodore.stankowich at csulb.edu>>
562-985-4826
http://www.csulb.edu/mammal-lab/
@CSULBMammalLab




        [[alternative HTML version deleted]]

______________________________________________
R-help at r-project.org<mailto:R-help at 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]]

Rui Barradas

2020-Jun-04 21:49 UTC

head link

[R] na.omit not omitting rows

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

?s 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:wdunlap at tibco.com]
> Sent: Thursday, June 4, 2020 12:39 PM
> To: Ted Stankowich <Theodore.Stankowich at csulb.edu>
> Cc: r-help at 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.Stankowich at
csulb.edu<mailto:Theodore.Stankowich at 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 at csulb.edu<mailto:theodore.stankowich at
csulb.edu><mailto:theodore.stankowich at
csulb.edu<mailto:theodore.stankowich at csulb.edu>>
> 562-985-4826
> http://www.csulb.edu/mammal-lab/
> @CSULBMammalLab
> 
> 
> 
> 
>          [[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at r-project.org<mailto:R-help at 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 at 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.
>

Ted Stankowich

2020-Jun-04 22:35 UTC

head link

[R] na.omit not omitting rows

This worked! Thank you!

-----Original Message-----
From: Rui Barradas [mailto:ruipbarradas at sapo.pt] 
Sent: Thursday, June 4, 2020 2:49 PM
To: Ted Stankowich <Theodore.Stankowich at csulb.edu>; William Dunlap
<wdunlap at tibco.com>
Cc: r-help at 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

?s 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:wdunlap at tibco.com]
> Sent: Thursday, June 4, 2020 12:39 PM
> To: Ted Stankowich <Theodore.Stankowich at csulb.edu>
> Cc: r-help at 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.Stankowich at
csulb.edu<mailto:Theodore.Stankowich at 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 at csulb.edu<mailto:theodore.stankowich at
csulb.edu><ma
> ilto:theodore.stankowich at csulb.edu<mailto:theodore.stankowich at
csulb.ed
> u>>
> 562-985-4826
> http://www.csulb.edu/mammal-lab/
> @CSULBMammalLab
>
>
>
>
>          [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org<mailto:R-help at 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 at 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 - Jun 2020 - na.omit not omitting rows

[R] na.omit not omitting rows

[R] na.omit not omitting rows

[R] na.omit not omitting rows