Re: [R] include

[Jim Lemon]

Hi Val,
Try this:

preval<-data.frame(Col1=unique(unlist(mydat[,c("Col2","col3")]))[-1],
 Col2=NA,col3=NA)
rbind(preval,mydat)

Jim

On Sat, Feb 24, 2018 at 3:34 PM, Val  wrote:
> Hi All,
>
> I am reading a file as follow,
>
> mydat <- read.table(textConnection("Col1 Col2 col3
> Z2 NA NA
> Z3 X1 NA
> Z4 Y1 W1"),header = TRUE)
>
> 1. "NA" are   missing  should be replace by 0
> 2.  value that are in COl2 and Col3  should be included  in col1 before
> they appear
> in col2 and col3. So the output data looks like as follow,
>
> X1  0  0
> Y1  0  0
> W1  0  0
> Z2  0  0
> Z3 X1  0
> Z4 Y1 W1
>
> Thank you in advance
>
> [[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.

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[R] include

[Val]

Hi All,

I am reading a file as follow,

mydat <- read.table(textConnection("Col1 Col2 col3
Z2 NA NA
Z3 X1 NA
Z4 Y1 W1"),header = TRUE)

1. "NA" are   missing  should be replace by 0
2.  value that are in COl2 and Col3  should be included  in col1 before
they appear
in col2 and col3. So the output data looks like as follow,

X1  0  0
Y1  0  0
W1  0  0
Z2  0  0
Z3 X1  0
Z4 Y1 W1

Thank you in advance

[[alternative HTML version deleted]]

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Re: [R] change location of temporary files

[Sariya, Sanjeev]

You can set this in script as:

library("unixtools ")
set.tempdir("/home/path_to_dir/temp_dir/")

--
Sanjeev 

-Original Message-
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Kumar Mainali
Sent: Friday, February 23, 2018 1:53 PM
To: R Help 
Subject: [R] change location of temporary files

I would like to change where R stores the temporary files to my external hard 
drive in my iMac. This is important because the temporary files R creates are 
huge and I do not have enough available space in my internal HD. Again, this is 
for macOS.

This change has to be temporary. Later I need to use the usual location for 
temp files in the internal HD.

Thanks in advance,
Kumar Mainali

--
Postdoctoral Associate
Department of Biology
University of Maryland, College Park
ᐧ

[[alternative HTML version deleted]]

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Re: [R] change location of temporary files

[Henrik Bengtsson]

On Fri, Feb 23, 2018 at 1:55 PM, William Dunlap via R-help
 wrote:
> Does setting the environment variable TMPDIR, before starting R,
> to a directory on a bigger file system help?  On Linux I get
>
>   % mkdir /tmp/RTMP-BILL
>   % env TMPDIR=/tmp/RTMP-BILL R --quiet --vanilla
>   > tempdir()
>   [1] "/tmp/RTMP-BILL/Rtmppgowz4"
>   > tempfile()
>   [1] "/tmp/RTMP-BILL/Rtmppgowz4/file7ce36ec5cb1e"
>
> I don't know if there is an R-specific environment variable or startup
> flag for this.

Yes, TMPDIR needs to be set *prior* to launching R in order for R to
acknowledge it.  Although most environment variables can be set in
platform-independent Renviron files which are processed early during
the R startup, TMPDIR is one of the exception - it is simply too late
to set it there because R =needs it very very early on.  So, it needs
to be set as in Bill's example above, or similarly:

export TMPDIR=/tmp/RTMP-BILL

/Henrik

>
>
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
> On Fri, Feb 23, 2018 at 10:52 AM, Kumar Mainali  wrote:
>
>> I would like to change where R stores the temporary files to my external
>> hard drive in my iMac. This is important because the temporary files R
>> creates are huge and I do not have enough available space in my internal
>> HD. Again, this is for macOS.
>>
>> This change has to be temporary. Later I need to use the usual location for
>> temp files in the internal HD.
>>
>> Thanks in advance,
>> Kumar Mainali
>>
>> --
>> Postdoctoral Associate
>> Department of Biology
>> University of Maryland, College Park
>> ᐧ
>>
>> [[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.
>>
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
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> and provide commented, minimal, self-contained, reproducible code.

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Re: [R] change location of temporary files

[William Dunlap via R-help]

Does setting the environment variable TMPDIR, before starting R,
to a directory on a bigger file system help?  On Linux I get

  % mkdir /tmp/RTMP-BILL
  % env TMPDIR=/tmp/RTMP-BILL R --quiet --vanilla
  > tempdir()
  [1] "/tmp/RTMP-BILL/Rtmppgowz4"
  > tempfile()
  [1] "/tmp/RTMP-BILL/Rtmppgowz4/file7ce36ec5cb1e"

I don't know if there is an R-specific environment variable or startup
flag for this.



Bill Dunlap
TIBCO Software
wdunlap tibco.com

On Fri, Feb 23, 2018 at 10:52 AM, Kumar Mainali  wrote:

> I would like to change where R stores the temporary files to my external
> hard drive in my iMac. This is important because the temporary files R
> creates are huge and I do not have enough available space in my internal
> HD. Again, this is for macOS.
>
> This change has to be temporary. Later I need to use the usual location for
> temp files in the internal HD.
>
> Thanks in advance,
> Kumar Mainali
>
> --
> Postdoctoral Associate
> Department of Biology
> University of Maryland, College Park
> ᐧ
>
> [[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.
>

[[alternative HTML version deleted]]

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Re: [R] change location of temporary files

[Hasan Diwan]

Kumar,
tempfile has a dir parameter that you can use to designate the directory
the file will be created in.-- H

On 23 February 2018 at 10:52, Kumar Mainali  wrote:

> I would like to change where R stores the temporary files to my external
> hard drive in my iMac. This is important because the temporary files R
> creates are huge and I do not have enough available space in my internal
> HD. Again, this is for macOS.
>
> This change has to be temporary. Later I need to use the usual location for
> temp files in the internal HD.
>
> Thanks in advance,
> Kumar Mainali
>
> --
> Postdoctoral Associate
> Department of Biology
> University of Maryland, College Park
> ᐧ
>
> [[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.
>



-- 
OpenPGP:
https://sks-keyservers.net/pks/lookup?op=get=0xFEBAD7FFD041BBA1
If you wish to request my time, please do so using
http://bit.ly/hd1ScheduleRequest.
Si vous voudrais faire connnaisance, allez a
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[R] change location of temporary files

[Kumar Mainali]

I would like to change where R stores the temporary files to my external
hard drive in my iMac. This is important because the temporary files R
creates are huge and I do not have enough available space in my internal
HD. Again, this is for macOS.

This change has to be temporary. Later I need to use the usual location for
temp files in the internal HD.

Thanks in advance,
Kumar Mainali

-- 
Postdoctoral Associate
Department of Biology
University of Maryland, College Park
ᐧ

[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] Aggregate over multiple and unequal column length data frames

[PIKAL Petr]

Hi

Your example is rather confusing - partly because HTML formating, partly 
because weird coding.

You probably could concatenate your data frames e.g. by rbind or merge and 
after that you could try to aggregate them somehow.

I could construct example data.frames myself but most probably they would be 
different from yours and also the result would not be necessary the same as you 
expect.

You should post those data frames as output from dput(data) and show us real 
desired result from those example data frames.

Cheers
Petr

> -Original Message-
> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Ek Esawi
> Sent: Wednesday, February 21, 2018 3:34 AM
> To: r-help@r-project.org
> Subject: [R] Aggregate over multiple and unequal column length data frames
>
>  Hi All--
>
> I have generated several 2 column data frames with variable length. The data
> frames have the same column names and variable types. I was trying to
> aggregate over the 2nd column for all the date frames, but could not figure 
> out
> how.
>
> I thought i could make them all of equal length then combine them in 1 data
> frame where i can use aggregate, the formula version Or to put them in a list
> and loop use lapply but did not know how to do that and thought there might
> be a simpler way.
>
> Below is an example of 3 data frames and the desired result; note that some
> levels don't appear in all and may be null over all variable, like the case 
> of dd
> on the desired result which i would like to list all levels even if some are 
> all null.
>
> Thanks in advance,
>
> EK
>
>df1   df2  df3
>
> c1 c2 c1 c2 c1 c2
> 1 aa 1 bb 1 aa
> 2 aa 2 bb 2 aa
> 3 bb 3 cc
> 4 cc 4 bb
> 5 bb
>
> desired result
>
> c1 c2 c2 c2
> aa 2 2
> bb 1 2 2
> cc 1 1
> dd
>
> [[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.


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[R] Quantile regression with some parameters fixed across tau..

[Mark R Payne]

Hi,

I would like to fit the following model with quantile regression:

y ~ alpha + beta

where both alpha and beta are factors. The conceptual model I have in my
head is that alpha is a constant set of values, that should be independent
of the quantile, tau and that all of the variability arises due to beta. If
I just fit the model using the quantreg package like so:

mdl <- rq( y ~ alpha +beta, data, tau=c(0.25,0.5,0.75))

..the values of alpha that I get vary according to the tau. Is there anyway
to force alpha to be the same across all taus?

Best wishes,

Mark

[[alternative HTML version deleted]]

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Re: [R] How to Save the residuals of an LM object greater or less than a certin value to an R object?

[Peter Dalgaard]

Also,

which( abs( stdresiduals ) > 2.5 )

will tell you which of the standardized residuals are bigger than 2.5 in 
absolute value. It returns a vector of indices, as in

> set.seed(1234)
> x <- rnorm(100)
> which (abs(x) > 2.5)
[1] 62
> x[62]
[1] 2.548991


-pd

> On 23 Feb 2018, at 05:56 , Jeff Newmiller  wrote:
> 
> Residuals are stored as a numeric vector. The R software comes with a 
> document "Introduction to R" that discusses basic math functions and logical 
> operators that can create logical vectors:
> 
> abs( stdresiduals ) > 2.5
> 
> It also discusses indexing using logical vectors:
> 
> stdresiduals[ abs( stdresiduals ) > 2.5 ]
> 
> Note that in most cases it is worth going  the extra step of making your 
> example reproducible [1][2][3] because many problems arise from issues in the 
> data or in code that you don't think is broken. 
> 
> [1] 
> http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
> 
> [2] http://adv-r.had.co.nz/Reproducibility.html
> 
> [3] https://cran.r-project.org/web/packages/reprex/index.html (read the 
> vignette)
> -- 
> Sent from my phone. Please excuse my brevity.
> 
> On February 22, 2018 8:09:49 PM PST, faiz rasool  wrote:
>> Dear list members,
>> 
>> I want to  save residuals above or less than a certain value to an R
>> object. I have performed a multiple linear regression, and now I want
>> to find out which cases have a residual of above + 2.5 and – 2.5.
>> 
>> Below I provide the R  commands I have used.
>> 
>> Reg<-lm(a~b+c+d+e+f) # perform multiple regression with a as the
>> dependent variable.
>> 
>> Residuals<-residuals(reg) # store residuals to an R object.
>> stdresiduals<-rstandard(reg) #save the standardized residuals.
>> #now I want to type a  command that will save the residuals  of
>> certain range to an object.
>> 
>> I realize that by plotting  the data I can quickly  see the  residuals
>> outside a certain boundtry, however, I am totally blind, so visually
>> inspecting the plot is not possible for me.
>> 
>> Thank you for any help.
>> 
>> Regards,
>> Faiz.
>> 
>> __
>> 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.
> 
> __
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> and provide commented, minimal, self-contained, reproducible code.

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk  Priv: pda...@gmail.com

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Re: [R] Problem with geterrmessage()

[Martin Maechler]

> Dennis Fisher 
> on Thu, 22 Feb 2018 13:01:37 -0800 writes:

> Luke
> Thanks — I revised the code to:
> ERRORMESSAGE <- try(source(USERSCRIPTFILE, local=T), silent=T) 

> print(ERRORMESSAGE) now returns:
> $value
> [1] 0

> $visible
> [1] FALSE

> Not clear what to make of that.
> Dennis

The help page   ?try   has

contained for a long time

 ‘try’ is implemented using ‘tryCatch’; for programming, instead of
 ‘try(expr, silent = TRUE)’, something like ‘tryCatch(expr, error =
 function(e) e)’ (or other simple error handler functions) may be
 more efficient and flexible.

and you do use 'silent=T' (which is "unsafe" (*) !)

I'd strongly advocate you use the 2nd proposition by given by
Luke Tierney (cited below):
 Learn to use tryCatch() instead of try() and then such things
 can be done considerably less obscurely. 

Best,
Martin Maechler, ETH Zurich

--
*) Using 'T' instead of 'TRUE'  (of 'F' instead of 'FALSE' *is* unsafe):
   a previous  'T <- 0'  will change what you really wanted.
   TRUE and FALSE are  "constants" in R, whereas  T and F are variables


> Dennis Fisher MD
> P < (The "P Less Than" Company)
> Phone / Fax: 1-866-PLessThan (1-866-753-7784)
> www.PLessThan.com




>> On Feb 22, 2018, at 12:45 PM, luke-tier...@uiowa.edu wrote:
>> 
>> Only the default error handler puts the error message in a buffer
>> where it can be retrieved with geterrmessage. try() replaces the
>> default error handler. Either look at the value returned by try() or
>> use tryCatch with conditionMessage.
>> 
>> Best,
>> 
>> luke
>> 
>> On Thu, 22 Feb 2018, Dennis Fisher wrote:
>> 
>>> R 3.4.3
>>> OS X
>>> 
>>> Colleagues
>>> 
>>> I have a 20K line script in which I encounter an unexpected problem.
>>> 
>>> If the script detects presence of a particular file USERCODE.txt, it 
executes:
>>> source(“USERCODE.txt”)
>>> If that file is not present, the script executes without a problem.
>>> 
>>> There might be syntax errors in USERCODE.txt; therefore, the code above 
is embedded in a try command:
>>> try(source(“USERCODE.txt", local=T), silent=T)
>>> followed by:
>>> ERRORMESSAGE <- geterrmessage()
>>> 
>>> For unclear reasons, an earlier command is yielding an error message:
>>> unused argument (\"\\n\")
>>> Despite identifying the exact source of that error, I can’t fix it (and 
it is of no consequence).
>>> 
>>> Ideally, I would like to clear out the pre-existing error message 
immediately before the “try” command (or perhaps at that particular location 
where it is being created) — but I can’t figure out how to do so.
>>> 
>>> Any suggestions would be welcome.
>>> 
>>> Dennis
>>> 
>>> Dennis Fisher MD
>>> P < (The "P Less Than" Company)
>>> Phone / Fax: 1-866-PLessThan (1-866-753-7784)
>>> www.PLessThan.com
>>> 
>>> __
>>> 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.
>>> 
>> 
>> -- 
>> Luke Tierney
>> Ralph E. Wareham Professor of Mathematical Sciences
>> University of Iowa  Phone: 319-335-3386
>> Department of Statistics andFax:   319-335-3017
>> Actuarial Science
>> 241 Schaeffer Hall  email:   luke-tier...@uiowa.edu
>> Iowa City, IA 52242 WWW:  http://www.stat.uiowa.edu

> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
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http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

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[R-es] Falta de datos en R

[Juan Bautista]

Hola a todos:
Cuando en un experimento hay datos perdidos, cuando trabajaba en SAS en lugar 
de anova usaba GLM.
En R ... también puedo usar el proc GLM ??  También estima los datos perdidos y 
te permite hacer el análisis de varianza ??
Y la segunda opción ... ¿Hay algún procedimiento en "R" para estimar los datos 
perdidos y luego poder hacer los análisis estadísticos pertinentes???

Un saludo.

Juan Bautista Relloso Barrio


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