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Muhuri, Pradip (SAMHSA/CBHSQ)

2012-Nov-22 14:11 UTC

[R] Data Extraction

Hello,

I would appreciate if someone could help me resolve the following:

1. df1[!is.na( X1 | X2 | X3 | X4 | X5),][,1:5] # This does not work

2. Is these message harmful?  The following object(s) are masked from 'df1
(position 3)':
    X1, X2, X3, X4, X5

Thanks,

Pradip Muhuri


#Reproducible Example
set.seed(5)
df1<-data.frame(matrix(sample(c(1:10,NA),100,replace=TRUE),ncol=5))
attach (df1)
#delete rows if any of them NA for X1
df1[!is.na( X1),][,1:5] # This works

#delete rows if any of them NA for X1, X2, X3, X4 or X5
df1[!is.na( X1 | X2 | X3 | X4 | X5),][,1:5] # This does not work

Sarah Goslee

2012-Nov-22 14:21 UTC

head link

[R] Data Extraction

Hi,

is.na( X1 | X2 | X3 | X4 | X5)
isn't a valid construct.

You'd need
!(is.na(X1) | is.na(X2) etc )

Or more elegantly
df1[apply(df1, 1, function(x)all(!is.na(x))), ]

Sarah

On Thursday, November 22, 2012, Muhuri, Pradip (SAMHSA/CBHSQ) wrote:
> Hello,
>
> I would appreciate if someone could help me resolve the following:
>
> 1. df1[!is.na( X1 | X2 | X3 | X4 | X5),][,1:5] # This does not work
>
> 2. Is these message harmful?  The following object(s) are masked from
'df1
> (position 3)':
>     X1, X2, X3, X4, X5
>
> Thanks,
>
> Pradip Muhuri
>
>
> #Reproducible Example
> set.seed(5)
> df1<-data.frame(matrix(sample(c(1:10,NA),100,replace=TRUE),ncol=5))
> attach (df1)
> #delete rows if any of them NA for X1
> df1[!is.na( X1),][,1:5] # This works
>
> #delete rows if any of them NA for X1, X2, X3, X4 or X5
> df1[!is.na( X1 | X2 | X3 | X4 | X5),][,1:5] # This does not work
>
> ______________________________________________
> R-help@r-project.org <javascript:;> mailing list
> 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.
>

-- 
Sarah Goslee
http://www.stringpage.com
http://www.sarahgoslee.com
http://www.functionaldiversity.org

	[[alternative HTML version deleted]]

PIKAL Petr

2012-Nov-22 14:33 UTC

head link

[R] Data Extraction

Hi

do you want this?
> df1[complete.cases(df1),]   X1 X2 X3 X4 X5
2   8  8  3  2 10
6   8  6  7 10  1
11  4  5  5 10  8
12  6  1  7  8  4
17  5  7  3  1  3
18 10  7  3  8  7
19  7  5  3  5  6
20 10  5  2  4  6

Regards
Petr
> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
> project.org] On Behalf Of Muhuri, Pradip (SAMHSA/CBHSQ)
> Sent: Thursday, November 22, 2012 3:11 PM
> To: Muhuri, Pradip (SAMHSA/CBHSQ); r-help at r-project.org
> Subject: [R] Data Extraction
> 
> Hello,
> 
> I would appreciate if someone could help me resolve the following:
> 
> 1. df1[!is.na( X1 | X2 | X3 | X4 | X5),][,1:5] # This does not work
> 
> 2. Is these message harmful?  The following object(s) are masked from
> 'df1 (position 3)':
>     X1, X2, X3, X4, X5
> 
> Thanks,
> 
> Pradip Muhuri
> 
> 
> #Reproducible Example
> set.seed(5)
> df1<-data.frame(matrix(sample(c(1:10,NA),100,replace=TRUE),ncol=5))
> attach (df1)
> #delete rows if any of them NA for X1
> df1[!is.na( X1),][,1:5] # This works
> 
> #delete rows if any of them NA for X1, X2, X3, X4 or X5 df1[!is.na( X1
> | X2 | X3 | X4 | X5),][,1:5] # This does not work
> 
> ______________________________________________
> R-help at r-project.org mailing list
> 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.

Berend Hasselman

2012-Nov-22 14:49 UTC

head link

[R] Data Extraction

On 22-11-2012, at 15:11, Muhuri, Pradip (SAMHSA/CBHSQ) wrote:
> Hello,
> 
> I would appreciate if someone could help me resolve the following:
> 
> 1. df1[!is.na( X1 | X2 | X3 | X4 | X5),][,1:5] # This does not work
> 
> 2. Is these message harmful?  The following object(s) are masked from
'df1 (position 3)':
>    X1, X2, X3, X4, X5
> 
> Thanks,
> 
> Pradip Muhuri
> 
> 
> #Reproducible Example
> set.seed(5)
> df1<-data.frame(matrix(sample(c(1:10,NA),100,replace=TRUE),ncol=5))
> attach (df1)
> #delete rows if any of them NA for X1
> df1[!is.na( X1),][,1:5] # This works
> 
> #delete rows if any of them NA for X1, X2, X3, X4 or X5
> df1[!is.na( X1 | X2 | X3 | X4 | X5),][,1:5] # This does not work
Yet another way of doing this is 

df1[!is.na(rowSums(df1)),][1:5]

But Petr's solution appears to be quickest.
See this:
> N <- 100000
> set.seed(13)
> df <- data.frame(matrix(sample(c(1:10,NA),N,replace=TRUE),ncol=50))  
> library(rbenchmark)
>
> f1 <- function(df) {df[apply(df, 1,
function(x)all(!is.na(x))),][,1:ncol(df)]}
> f2 <- function(df) {df[!is.na(rowSums(df)),][1:ncol(df)]}
> f3 <- function(df) {df[complete.cases(df),][1:ncol(df)]}
>
> benchmark(d1 <- f1(df), d2 <- f2(df), d3 <- f3(df),
columns=c("test","elapsed", "relative",
"replications"))          test elapsed relative replications
1 d1 <- f1(df)   3.675   13.172          100
2 d2 <- f2(df)   0.401    1.437          100
3 d3 <- f3(df)   0.279    1.000          100
> identical(d1,d2)
[1] TRUE> identical(d1,d3)[1] TRUE


Berend

Muhuri, Pradip (SAMHSA/CBHSQ)

2012-Nov-22 15:56 UTC

head link

[R] Data Extraction

Hi Sarah,

I am glad you have precisely caught where I made the mistake.  Thank you so
much.

regards,

Pradip Muhuri

________________________________________
From: Sarah Goslee [sarah.goslee at gmail.com]
Sent: Thursday, November 22, 2012 9:21 AM
To: Muhuri, Pradip (SAMHSA/CBHSQ)
Cc: r-help at r-project.org
Subject: Re: [R] Data Extraction

Hi,

is.na<http://is.na/>( X1 | X2 | X3 | X4 | X5)
isn't a valid construct.

You'd need
!(is.na<http://is.na>(X1) | is.na<http://is.na>(X2) etc )

Or more elegantly
df1[apply(df1, 1, function(x)all(!is.na<http://is.na>(x))), ]

Sarah

On Thursday, November 22, 2012, Muhuri, Pradip (SAMHSA/CBHSQ) wrote:
Hello,

I would appreciate if someone could help me resolve the following:

1. df1[!is.na<http://is.na>( X1 | X2 | X3 | X4 | X5),][,1:5] # This does
not work

2. Is these message harmful?  The following object(s) are masked from 'df1
(position 3)':
    X1, X2, X3, X4, X5

Thanks,

Pradip Muhuri


#Reproducible Example
set.seed(5)
df1<-data.frame(matrix(sample(c(1:10,NA),100,replace=TRUE),ncol=5))
attach (df1)
#delete rows if any of them NA for X1
df1[!is.na<http://is.na>( X1),][,1:5] # This works

#delete rows if any of them NA for X1, X2, X3, X4 or X5
df1[!is.na<http://is.na>( X1 | X2 | X3 | X4 | X5),][,1:5] # This does not
work

______________________________________________
R-help at r-project.org<javascript:;> mailing list
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.


--
Sarah Goslee
http://www.stringpage.com
http://www.sarahgoslee.com
http://www.functionaldiversity.org

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