Re: [R] R Sig-Geo group - loop for creating spatial matrix

[Giorgio Garziano]

You may handle that as a list of "nb" objects.

library(spdep)
example(columbus)
coord <- coordinates(columbus)

z <- c(1,2,3,4,5,6,7,8,9)
neighbors.knn <- list()

for (val in z) {
  neighbors.knn <- c(neighbors.knn, list(knn2nb(knearneigh(coord, val, 
longlat=F), sym=F)))
}

class(neighbours.knn)

class(neighbors.knn[[1]])
plot(neighbors.knn[[1]], coord)

class(neighbors.knn[[2]])
plot(neighbors.knn[[2]], coord)

and so on.

Best,

--
GG


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Re: [R] Plotting Dates Time Series Data

[Giorgio Garziano]

This tutorial may help:

http://faculty.washington.edu/ezivot/econ424/Working%20with%20Time%20Series%20Data%20in%20R.pdf

See pages 20 and 27 for your specific issue.


Best,

--
GG




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Re: [R] Modelling non-Negative Time Series

[Giorgio Garziano]

https://cran.r-project.org/web/packages/tsintermittent/tsintermittent.pdf


Best,

--
GG



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[R] R Sig-Geo group - loop for creating spatial matrix

[Francesco Perugini]

Dear all,I want to create a routine to generate an object for different value 
of val: 

z <- c(1,2,3,4,5,6,7,8,9)
for (val in z) {
 neighbors.knn <- knn2nb(knearneigh(coord, val, longlat=F),
 row.names=cod_pro,sym=F)
 }
 
However, it seems it does not work. 
How to store the neighbors.knn created matrix befoire being overwritten.
In other words, I want to create multiple spatial matrix, say, for different k 
neighbours.
Thanks a lot for any help. 
francper


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Re: [R] Efficient way to create new column based on comparison with another dataframe

[Hervé Pagès]

Hi Gaius,

On 01/29/2016 10:52 AM, Gaius Augustus wrote:

I have two dataframes. One has chromosome arm information, and the other
has SNP position information. I am trying to assign each SNP an arm
identity.  I'd like to create this new column based on comparing it to the
reference file.

*1) Mapfile (has millions of rows)*

NameChr   Position
S1  1  3000
S2  1  6000
S3  1  1000

*2) Chr.Arms   file (has 39 rows)*

ChrArmStart   End
1  p  0   5000
1  q  50011


*R Script that works, but slow:*
Arms  <- c()
for (line in 1:nrow(Mapfile)){
   Arms[line] <- Chr.Arms$Arm[ Mapfile$Chr[line] == Chr.Arms$Chr &
  Mapfile$Position[line] > Chr.Arms$Start &  Mapfile$Position[line] <
Chr.Arms$End]}
}
Mapfile$Arm <- Arms


*Output Table:*

Name   Chr   Position   Arm
S1  1 3000  p
S2  1 6000  q
S3  1 1000  p


In words: I want each line to look up the location ( 1) find the right Chr,
2) find the line where the START < POSITION < END), then get the ARM
information and place it in a new column.

This R script works, but surely there is a more time/processing efficient
way to do it.


You could use the GenomicRanges package for this:

1) Turn 'Mapfile' and 'Chr.Arms' into GRanges objects:

  library(GenomicRanges)
  query <- makeGRangesFromDataFrame(Mapfile, start.field="Position",
 end.field="Position")
  subject <- makeGRangesFromDataFrame(Chr.Arms)

2) Call findOverlaps() on them:

  Mapfile2Chr.Arms <- findOverlaps(query, subject, select="arbitrary")

3) Use the result of findOverlaps() to create the column to add to
  'Mapfile':

  Mapfile$Arm <- Chr.Arms$Arm[Mapfile2Chr.Arms]
  Mapfile
  #   Name Chr Position Arm
  # 1   S1   1 3000   p
  # 2   S2   1 6000   q
  # 3   S3   1 1000   p

Should be very fast.

Note that GenomicRanges is a Bioconductor package:

  http://bioconductor.org/packages/GenomicRanges

Make sure you follow the Installation instructions on that page.

Cheers,
H.



Thanks in advance for any help,
Gaius

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--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

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Re: [R] as(, "numeric") vs as.numeric()

[Hervé Pagès]

On 02/01/2016 07:33 AM, Duncan Murdoch wrote:

On 01/02/2016 10:00 AM, Erik Wright wrote:

Dear Frank,

Thank you for the quick response.

I am familiar with the tradeoffs between integers and doubles.
However, I do not believe this answers my question.

If you look at the help information for the as() function it says:
"as(x, "numeric") uses the existing as.numeric function."  But clearly
the result is different in each case.


Since is.numeric(1:10) and is(1:10, "numeric") are both true, the as()
function eventually bails out and does nothing.


But it should. Because as() has an extra argument 'strict' that is TRUE
by default. From the man page for as():

  strict: logical flag.  If ‘TRUE’, the returned object must be
  strictly from the target class (unless that class is a
  virtual class, in which case the object will be from the
  closest actual class, in particular the original object, if
  that class extends the virtual class directly).

  If ‘strict = FALSE’, any simple extension of the target class
  will be returned, without further change.  A simple extension
  is, roughly, one that just adds slots to an existing class.

So the current behavior is clearly a bug, has been reported several
times, and is known from the R-core folks:

  https://stat.ethz.ch/pipermail/r-devel/2015-December/072079.html

FWIW this bug is actually related to this other bug:

  x <- 1:10
  class(x)
  # [1] "integer"

  class(x) <- "numeric"
  class(x)
  # [1] "integer"

Cheers,
H.



 So yes, as(x,
"numeric") uses as.numeric() when it needs to coerce, but not when no
coercion is necessary.   The docs could perhaps add this condition.

Duncan Murdovh


If the help for as() is correct, then as(1:10, "numeric") should also
return doubles, and the second argument is not ignored.

Erik


> On Feb 1, 2016, at 8:16 AM, Franklin Bretschneider
 wrote:
>
> Dear Erik Wright,
>
>
> Re:
>
>> Could someone please explain this R behavior to me:
>>
>>> typeof(as.numeric(1:10))
>> [1] "double"
>>> typeof(as(1:10, "numeric"))
>> [1] "integer"
>>
>> I expected "double" in both cases.  In the help for the "as"
function it says:
>>
>> "Methods are pre-defined for coercing any object to one of the
basic datatypes. For example, as(x, "numeric") uses the existing
as.numeric function."
>
>
> This happens because 1:10 yields only integers, and so can be stored
cheap,
> whereas as.numeric() actually means: as.double.
> The "numeric" in the second line is an unused argument.
>
> Best regards,
>
> Frank
> ---
>
>
>
>
> Franklin Bretschneider
> Dept of Biology
> Utrecht University
> brets...@xs4all.nl
>
>
>

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--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

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[R] How to read ./configure messages

[p_connolly]

I've installed R from the tgz file since about R-0.9.x following the
INSTALL instructions and have always succeeded using rpm-based OSes.
With each new OS, that involved installing various additional packages
before the configure script would complete.  Figuring out which
packages were required usually involved searching for rpms that
supplied missing .so or .h files, dev packages or something else I
could figure out.

I'm now trying to do the same with LinuxMint 17.2 but I got stuck when
this message came up:

   checking for main in -ltermlib... no
   checking for rl_callback_read_char in -lreadline... no
   checking for history_truncate_file... no
   configure: error: --with-readline=yes (default) and headers/libs are 
not available


Near the bottom of the log file it shows this:

   configure:6747: gcc -E -I/usr/local/include conftest.c
   configure:6747: $? = 0
   configure:6761: gcc -E -I/usr/local/include conftest.c
   conftest.c:17:28: fatal error: ac_nonexistent.h: No such file or 
directory

#include 
   ^
   compilation terminated.
   configure:6761: $? = 1
   configure: failed program was:
   | /* confdefs.h */
   | #define PACKAGE_NAME "R"

So I'm assuming that's behind the failure.  Searching shows the same
problem shows up in all sorts of places for decades, notably cygwin
users.  But I didn't see anything that would help to work out what is
missing.

Ideas greatly appreciated.


best
Patrick

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Re: [R] String Matching

[Berend Hasselman]

> On 1 Feb 2016, at 08:03, PIKAL Petr  wrote:
> 
> Hi
> 
> Maybe I am completely wrong but do you really need regular expressions?
> 
> You say you want to compare first nine characters of id?
> 
>> substr(id, 1,9)==cusip
> [1] TRUE
>> 
> 
> or the last six?
> 
>> substr(id, nchar(id)-6, nchar(id))=="432.rds"
> [1] TRUE
>> 
> 
> Cheers
> Petr
> 
> 
>> -Original Message-
>> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Glenn
>> Schultz
>> Sent: Friday, January 29, 2016 6:02 PM
>> To: R Help R
>> Subject: [R] String Matching
>> 
>> All,
>> 
>> I have a file named as so 313929BL4FNMA2432.rds  the user may pass
>> either the first 9 character or the last six characters.  I need to
>> match the remainder of the file name using either the first nine or
>> last six.  I have read the help files for Regular Expression as used in
>> R and I think what I want to use is glob2rx.
>> 
>> I have worked a minimal example to test my code:
>> 
>> id <- "313929BL4FNMA2432.rds"
>> cusip <- "313929BL4"
>> poolnumm <- "FNMA2432"
>> paste(cusip, ".*", ".rds")
>> glob2rx(paste(cusip, ".*", ".rds"), trim.head = TRUE, trim.tail = TRUE)
>> 
>> This returns false which leads me to believe that it is not working
>> glob2rx(paste(cusip, ".*", ".rds"), trim.head = TRUE, trim.tail = TRUE)
>> == id
>> 
>> I am going to use as follows in the function below - which returns the
>> error file not found
>> 
>> MBS_Test <- function(MBS.id = "character"){ MBS <-
>> glob2rx(paste(MBS.id, ".*", "//.rds", sep = ""), trim.tail = TRUE)
>> MBS.Conn <- gzfile(description = paste(system.file(package =
>> "BondLab"), "/BondData/", MBS, sep = ""), open = "rb") MBS <-
>> readRDS(MBS.Conn)
>> on.exit(close.connection(MBS.Conn))
>> return(MBS)
>> }
>> 


I don't think you are using (glob) wild characters correctly; where you write 
.* you likely need *?
In addition why not use paste0, which does not use  as separator,  
instead of paste?
Finally your poolnumm variable consists of 8 characters and not 6.

If you change your minimal example to this:

paste0(cusip, "*", ".rds")
glob2rx(paste0(cusip, "*", ".rds"))
grepl(glob2rx(paste0(cusip, "*", ".rds")), id)
grepl(glob2rx(paste0("*", poolnumm, ".rds")), id)

you get TRUE twice.

But Petr's solution for the first 9 characters is much simpler.
And for matching the last 6 (8) you'll have to remove the extension first and 
then use substr (if I understand your problem correctly).

Berend

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Re: [R] String Matching

[PIKAL Petr]

Hi

Maybe I am completely wrong but do you really need regular expressions?

You say you want to compare first nine characters of id?

> substr(id, 1,9)==cusip
[1] TRUE
>

or the last six?

> substr(id, nchar(id)-6, nchar(id))=="432.rds"
[1] TRUE
>

Cheers
Petr


> -Original Message-
> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Glenn
> Schultz
> Sent: Friday, January 29, 2016 6:02 PM
> To: R Help R
> Subject: [R] String Matching
>
> All,
>
> I have a file named as so 313929BL4FNMA2432.rds  the user may pass
> either the first 9 character or the last six characters.  I need to
> match the remainder of the file name using either the first nine or
> last six.  I have read the help files for Regular Expression as used in
> R and I think what I want to use is glob2rx.
>
> I have worked a minimal example to test my code:
>
> id <- "313929BL4FNMA2432.rds"
> cusip <- "313929BL4"
> poolnumm <- "FNMA2432"
> paste(cusip, ".*", ".rds")
> glob2rx(paste(cusip, ".*", ".rds"), trim.head = TRUE, trim.tail = TRUE)
>
> This returns false which leads me to believe that it is not working
> glob2rx(paste(cusip, ".*", ".rds"), trim.head = TRUE, trim.tail = TRUE)
> == id
>
> I am going to use as follows in the function below - which returns the
> error file not found
>
> MBS_Test <- function(MBS.id = "character"){ MBS <-
> glob2rx(paste(MBS.id, ".*", "//.rds", sep = ""), trim.tail = TRUE)
> MBS.Conn <- gzfile(description = paste(system.file(package =
> "BondLab"), "/BondData/", MBS, sep = ""), open = "rb") MBS <-
> readRDS(MBS.Conn)
> on.exit(close.connection(MBS.Conn))
> return(MBS)
> }
>
> Any help to get me in the right direction is appreciated - Glenn
> __
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> https://stat.ethz.ch/mailman/listinfo/r-help
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> guide.html
> and provide commented, minimal, self-contained, reproducible code.


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Re: [R] Multilevel Modeling in R

[Thierry Onkelinx]

Dear David,

R-sig-mixedmodels is a better mailing list for this kind of question.

1) yes
2) use  (Treatment | Random_Assignment_Block) instead of  (1 |
Random_Assignment_Block)

Best regards,

ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey

2016-01-29 7:10 GMT+01:00 David Roy :

> I am conducting a multilevel regression analysis on the effect of an
> intervention on student test results, and am not sure how to implement the
> necessary R code to correctly capture the nested structure.
>
>
>
> The outcome measure for the study is whether a student passed or failed a
> final exam.  The structure of the data is students nested within schools,
> and then schools nested within random assignment blocks.  Treatment (i.e.,
> the intervention) was implemented at the school-level.  The covariates that
> I am planning to use are prior year test scores (this is also a binary
> variable for pass or fail), race, and gender.
>
>
>
> My ideal output would show the impact of the treatment for each of the
> random assignment blocks, and then the weighted average of the impact
> across all of the random assignment blocks.
>
>
>
> Based on my research thus far, it seems like the **lmer** function from the
> **lme4** package would be the best route to go.
>
>
>
> This is the code that I have tried:
>
>
>
> # Fit multilevel regression with random assignment blocks
>
> glmer2 <- glmer(Post_Test_Score ~ Treatment +
>
>   Pre_Test_Score +
>
>   (1 | School) +
>
>   (1 | Random_Assignment_Block),
>
> data = StudyData,
>
> family = binomial("logit"))
>
>
>
> My two questions are the following:
>
>
>
> 1.) Given the nested structure of my data, would the above regression
> output the correct coefficient for the impact of treatment across all
> random assignment blocks?
>
>
>
> 2.) How would I code the interaction effect between Treatment and
> Random_Assignment_Block in order to generate separate impact estimates for
> each of the random assignment blocks?
>
> [[alternative HTML version deleted]]
>
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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] as(, "numeric") vs as.numeric()

[Erik Wright]

Hi everyone,

Could someone please explain this R behavior to me:

> typeof(as.numeric(1:10))
[1] "double"
> typeof(as(1:10, "numeric"))
[1] "integer"

I expected "double" in both cases.  In the help for the "as" function it says:

"Methods are pre-defined for coercing any object to one of the basic datatypes. 
For example, as(x, "numeric") uses the existing as.numeric function."

Thanks,
Erik

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[R] [R-pkgs] New Package: backblazer

[phill]

 

Dear R users, 

I'm pleased to announce that my first package has been accepted in CRAN.


https://cran.r-project.org/web/packages/backblazer/ 

backblazer provides bindings to Backblaze's B2 cloud storage API. 

As it is my first package on CRAN, I would certainly appreciate feedback
and suggestions from more experienced packagers. 

Regards, 

Phill 

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

Re: [R] updating elements of a list of matrixes without 'for' cycles

[Bert Gunter]

A perhaps faster approach takes advantage of the column major ordering
of arrays and the expand.grid() function. I say "perhaps" faster,
because "apply" family functions are still actually loops at the R
level.

Anyway, try this (using your little example):

## create a data frame (which is also a list) of i,j,k,index combinations:
z <- expand.grid(i=1:2, j= 1:2, k = 1:2)

## Use do.call() to feed the columns of z to mapply
yourarray <- array(do.call(mapply,c(prod,z)),dim=c(2,2,2))


Cheers,
Bert
Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Mon, Feb 1, 2016 at 6:29 AM, Jue Lin-Ye  wrote:
>>
>> Date: Sat, 30 Jan 2016 01:03:30 +
>> From: Matteo Richiardi <
>>
>> matteo.richia...@maths.ox.ac.uk>
>> To: r-help@r-project.org
>> Subject: [R] updating elements of a list of matrixes without 'for'
>> cycles
>> Message-ID:
>> <
>> cabsru1lkohuz8m9jw1ju+nemksprirrtd_0wzotrlwi3z6d...@mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Hi, following an earlier suggestion from the list, I am storing my
>> data in a "cube", i.e. an array of matrixes.
>> Is there any smarter way of updating the elements of the cube through
>> a function, other than the three 'for' cycles in the example below?
>> (please note that the example is simplistic; in particular, my
>> function is more complicated).
>>
>> # parameters
>> I <- 2L
>> J <- 2L
>> H <- 2L
>>
>> # data container: an array of matrixes
>> mycube <- array(dim=c(I,J,H))
>>
>> # initialisation
>> for (h in 1:H) {
>>   init <- matrix(c(rep(0,J)),nrow=I,ncol=J)
>>   mycube[,,h] <- init
>> }
>>
>> # function
>> foo = function(i,j,h){
>>   mycube[i,j,h] <<- i*j*h
>> }
>>
>> # update
>>
>> for(h in 1:H){
>>   # males:
>>   for(i in 1:I)
>> for(j in 1:J)
>>   foo(i,j,h)
>> }
>>
>> Thanks a lot for your help. Matteo
>>
>>
>>
> Greetings! Have you tried sapply() on this script?
>
> --
> Jue
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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> 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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Re: [R] open script from web

[Uwe Ligges]

Well, two steps: download.file() and then file.edit().

Best,
Uwe Ligges



On 02.02.2016 06:16, Benn Fine wrote:

Hello

In R, is it possible to load a script file into the editor via a web
address?

That is, I have a script file I want people to grab located at
http://www.foo.com/bar.R
and want to do something like file.edit("http://www.foo.com/bar.R;). But
that doesn't seem to work.

thanks

[[alternative HTML version deleted]]

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

[R] open script from web

[Benn Fine]

Hello

In R, is it possible to load a script file into the editor via a web
address?

That is, I have a script file I want people to grab located at
http://www.foo.com/bar.R
and want to do something like file.edit("http://www.foo.com/bar.R;). But
that doesn't seem to work.

thanks

[[alternative HTML version deleted]]

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Re: [R] amending R+dependencies

[Uwe Ligges]

Install a recent version of R such as R-3.2.3.

R-3.0.2 is unsupported.


Best,
Uwe Ligges




On 02.02.2016 01:00, kle...@sxmail.de wrote:

Dear all,[a] after I have virtually given up on gearing up my R (v. 3.0.2; GUI: 
rkward; on last Linux Kubuntu LTS) for properly installing useful packages 
containing functions that were not delivered with base R, amendment of R 
through getting packages from CRAN became the only viable way to obtain 
functionality in R for me so far.[b] By the time I used my GUI for 
supplementary packages' installation, dependencies were treated by that GUI's 
updater and it occurred that packages were uninstallable due to packages not 
suitable for that very R version.[c] Now I wonder whether there were any 
(massive?) impending problems when one would eventually proceed to extract 
corresponding package archives upon download into the corresponding file folder 
subsequently using R, say in its interactive mode via the GUI of choice. I am 
referring to that kind of problem(s) which the R console (interactive mode) 
could throw after me, I have to be sufficiently precise...Best regards,Markus 
Hofst!

et!

  ter


[[alternative HTML version deleted]]

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Re: [R] open script from web

[Jeff Newmiller]

In almost all cases the answer is No.

Some Web servers support WebDAV, but standard HTTP does not work that way. Has 
nothing to do with R.
-- 
Sent from my phone. Please excuse my brevity.

On February 1, 2016 9:16:59 PM PST, Benn Fine  wrote:
>Hello
>
>In R, is it possible to load a script file into the editor via a web
>address?
>
>That is, I have a script file I want people to grab located at
>http://www.foo.com/bar.R
>and want to do something like file.edit("http://www.foo.com/bar.R;).
>But
>that doesn't seem to work.
>
>thanks
>
>   [[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] How to read ./configure messages

[Peter Langfelder]

I am not overly familar with Mint, but you need the "development
version" of the readline library. If you have a GUI package manager
installed, open it and search for readline. You should see a version
that ends with -dev or -devel; you need to install that.

HTH,

Peter

On Mon, Feb 1, 2016 at 3:06 PM, p_connolly  wrote:
>
> I've installed R from the tgz file since about R-0.9.x following the
> INSTALL instructions and have always succeeded using rpm-based OSes.
> With each new OS, that involved installing various additional packages
> before the configure script would complete.  Figuring out which
> packages were required usually involved searching for rpms that
> supplied missing .so or .h files, dev packages or something else I
> could figure out.
>
> I'm now trying to do the same with LinuxMint 17.2 but I got stuck when
> this message came up:
>
>checking for main in -ltermlib... no
>checking for rl_callback_read_char in -lreadline... no
>checking for history_truncate_file... no
>configure: error: --with-readline=yes (default) and headers/libs are not
> available
>
> Near the bottom of the log file it shows this:
>
>configure:6747: gcc -E -I/usr/local/include conftest.c
>configure:6747: $? = 0
>configure:6761: gcc -E -I/usr/local/include conftest.c
>conftest.c:17:28: fatal error: ac_nonexistent.h: No such file or
> directory
> #include 
>^
>compilation terminated.
>configure:6761: $? = 1
>configure: failed program was:
>| /* confdefs.h */
>| #define PACKAGE_NAME "R"
>
> So I'm assuming that's behind the failure.  Searching shows the same
> problem shows up in all sorts of places for decades, notably cygwin
> users.  But I didn't see anything that would help to work out what is
> missing.
>
> Ideas greatly appreciated.
>
>
> best
> Patrick
>
> __
> 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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Re: [R] Panel Data Help

[Jeff Newmiller]

I am going to go out on a limb and say that the answer to your question is 
"Yes".

However,  I cannot decipher specifics from your description.  If you want a 
more useful answer you need to follow the advice in the Posting Guide mentioned 
in the footer  (including posting in plain text rather than HTML, and providing 
some sample data). You will also benefit from reading [1], with particular 
attention to using the dput function. 

[1] 
http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
-- 
Sent from my phone. Please excuse my brevity.

On February 1, 2016 12:36:36 PM PST, Daniel Dorchuck  
wrote:
>Hi,
>
>I'm currently working on an econometrics project on banking and looking
>to
>merge a dataframe of bank specific data with dataframes of macro
>variables.
>I am then going to transform the data set into a plm dataframe using
>the plm
>package. The bank specific observations are indexed across time while
>the
>macro ones are indexed only across time. Is there a way to merge the
>two so
>I can use both in my panel regression?
>
>Best,
>Dan
>
>   [[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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and provide commented, minimal, self-contained, reproducible code.

[R] Panel Data Help

[Daniel Dorchuck]

Hi,

I'm currently working on an econometrics project on banking and looking to
merge a dataframe of bank specific data with dataframes of macro variables.
I am then going to transform the data set into a plm dataframe using the plm
package. The bank specific observations are indexed across time while the
macro ones are indexed only across time. Is there a way to merge the two so
I can use both in my panel regression?

Best,
Dan

[[alternative HTML version deleted]]

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

Re: [R] on specifying an encoding for plot's main-argument

[Daniel Bastos]

Duncan Murdoch  writes:

> On 29/01/2016 10:35 AM, Daniel Bastos wrote:
>> Here's how I plot a graph.
>>
>>plot(c(1,2,3), main = "graph ç")
>>
>> The main-string has a UTF-8 character "ç".  I believe I'm using the
>> windows device.  It opens up on my screen.  (The window says ``R
>> Graphics: Device 2 (ACTIVE)''.)  How can I tell it to use my encoding of
>> choice?
>
> As far as I know that's impossible.  R uses the system encoding, and I
> don't think any Windows versions use UTF-8 code pages.  They use
> UTF-16 for wide characters, and some 8 bit encoding for byte-sized
> characters. R will use whatever 8 bit code page Windows chooses.

You seem to be correct.  Here's what Microsoft has to say.  ``[...]
UTF-16 [...] is the most common encoding of Unicode and the one used for
native Unicode encoding on Windows operating systems.''[1] 

They also claim that ``[w]hile Unicode-enabled functions in Windows use
UTF-16, it is also possible to work with data encoded in UTF-8 or UTF-7,
which are supported in Windows as multibyte character set code
pages.''[1]

But I couldn't verify the claim.

The documentation of setlocale[2] says the ``set of available locale
names, languages, country/region codes, and code pages includes all
those supported by the Windows NLS API except code pages that require
more than two bytes per character, such as UTF-7 and UTF-8. If you
provide a code page value of UTF-7 or UTF-8, setlocale will fail,
returning NULL.''[2]

That seems to be correct as per the following C code.

  printf("locale: %s\n", setlocale(LC_ALL, "UTF-8"));

And [3] makes me think that _wsetlocale behaves the same way:
``_wsetlocale [...] is a wide-character version of setlocale; the
arguments and return values of _wsetlocale are wide-character strings.''
The following program seems to confirm it.

int main(int argc, char *argv[]) {
  printf("locale: %s\n", _wsetlocale(LC_ALL, (const wchar_t *) "UTF-8"));
  return 0;
}

[...]

(*) A workaround

Since R comes with iconv(), the following might be a safe way to
translate UTF-8 into the current system locale, displaying correctly
plot's titles on Windows systems.

  iconv("utf8-string", from="UTF-8", 
 to=localeToCharset(Sys.getlocale("LC_CTYPE")))

(*) References

[1] MSDN Unicode
https://msdn.microsoft.com/en-us/library/windows/desktop/dd374081(v=vs.85).aspx

[2] MSDN setlocale
https://msdn.microsoft.com/en-us/library/x99tb11d.aspx

[3] MSDN Locales and Code Pages
https://msdn.microsoft.com/en-us/library/8w60z792.aspx

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[R] amending R+dependencies

[klerer]

Dear all,[a] after I have virtually given up on gearing up my R (v. 3.0.2; GUI: 
rkward; on last Linux Kubuntu LTS) for properly installing useful packages 
containing functions that were not delivered with base R, amendment of R 
through getting packages from CRAN became the only viable way to obtain 
functionality in R for me so far.[b] By the time I used my GUI for 
supplementary packages' installation, dependencies were treated by that GUI's 
updater and it occurred that packages were uninstallable due to packages not 
suitable for that very R version.[c] Now I wonder whether there were any 
(massive?) impending problems when one would eventually proceed to extract 
corresponding package archives upon download into the corresponding file folder 
subsequently using R, say in its interactive mode via the GUI of choice. I am 
referring to that kind of problem(s) which the R console (interactive mode) 
could throw after me, I have to be sufficiently precise...Best regards,Markus 
Hofstet!
 ter


[[alternative HTML version deleted]]

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

Re: [R] as(, "numeric") vs as.numeric()

[Franklin Bretschneider]

Dear Erik Wright,


Re:

> Could someone please explain this R behavior to me:
> 
>> typeof(as.numeric(1:10))
> [1] "double"
>> typeof(as(1:10, "numeric"))
> [1] "integer"
> 
> I expected "double" in both cases.  In the help for the "as" function it says:
> 
> "Methods are pre-defined for coercing any object to one of the basic 
> datatypes. For example, as(x, "numeric") uses the existing as.numeric 
> function."


This happens because 1:10 yields only integers, and so can be stored cheap,
whereas as.numeric() actually means: as.double.
The "numeric" in the second line is an unused argument.

Best regards,

Frank
---




Franklin Bretschneider
Dept of Biology
Utrecht University
brets...@xs4all.nl

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Re: [R] updating elements of a list of matrixes without 'for' cycles

[Jue Lin-Ye]

>
> Date: Sat, 30 Jan 2016 01:03:30 +
> From: Matteo Richiardi <
> ​​
> matteo.richia...@maths.ox.ac.uk>
> To: r-help@r-project.org
> Subject: [R] updating elements of a list of matrixes without 'for'
> cycles
> Message-ID:
> <
> cabsru1lkohuz8m9jw1ju+nemksprirrtd_0wzotrlwi3z6d...@mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi, following an earlier suggestion from the list, I am storing my
> data in a "cube", i.e. an array of matrixes.
> Is there any smarter way of updating the elements of the cube through
> a function, other than the three 'for' cycles in the example below?
> (please note that the example is simplistic; in particular, my
> function is more complicated).
>
> # parameters
> I <- 2L
> J <- 2L
> H <- 2L
>
> # data container: an array of matrixes
> mycube <- array(dim=c(I,J,H))
>
> # initialisation
> for (h in 1:H) {
>   init <- matrix(c(rep(0,J)),nrow=I,ncol=J)
>   mycube[,,h] <- init
> }
>
> # function
> foo = function(i,j,h){
>   mycube[i,j,h] <<- i*j*h
> }
>
> # update
>
> for(h in 1:H){
>   # males:
>   for(i in 1:I)
> for(j in 1:J)
>   foo(i,j,h)
> }
>
> Thanks a lot for your help. Matteo
>
>
>
​Greetings! Have you tried sapply() on this script?​

-- 
​Jue

[[alternative HTML version deleted]]

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Re: [R] as(, "numeric") vs as.numeric()

[Duncan Murdoch]

On 01/02/2016 10:00 AM, Erik Wright wrote:

Dear Frank,

Thank you for the quick response.

I am familiar with the tradeoffs between integers and doubles.  However, I do 
not believe this answers my question.

If you look at the help information for the as() function it says:  "as(x, 
"numeric") uses the existing as.numeric function."  But clearly the result is 
different in each case.


Since is.numeric(1:10) and is(1:10, "numeric") are both true, the as() 
function eventually bails out and does nothing.  So yes, as(x, 
"numeric") uses as.numeric() when it needs to coerce, but not when no 
coercion is necessary.   The docs could perhaps add this condition.


Duncan Murdovh


If the help for as() is correct, then as(1:10, "numeric") should also return 
doubles, and the second argument is not ignored.

Erik


> On Feb 1, 2016, at 8:16 AM, Franklin Bretschneider  wrote:
>
> Dear Erik Wright,
>
>
> Re:
>
>> Could someone please explain this R behavior to me:
>>
>>> typeof(as.numeric(1:10))
>> [1] "double"
>>> typeof(as(1:10, "numeric"))
>> [1] "integer"
>>
>> I expected "double" in both cases.  In the help for the "as" function it 
says:
>>
>> "Methods are pre-defined for coercing any object to one of the basic datatypes. For 
example, as(x, "numeric") uses the existing as.numeric function."
>
>
> This happens because 1:10 yields only integers, and so can be stored cheap,
> whereas as.numeric() actually means: as.double.
> The "numeric" in the second line is an unused argument.
>
> Best regards,
>
> Frank
> ---
>
>
>
>
> Franklin Bretschneider
> Dept of Biology
> Utrecht University
> brets...@xs4all.nl
>
>
>

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Re: [R] as(, "numeric") vs as.numeric()

[Erik Wright]

Dear Frank,

Thank you for the quick response.

I am familiar with the tradeoffs between integers and doubles.  However, I do 
not believe this answers my question.

If you look at the help information for the as() function it says:  "as(x, 
"numeric") uses the existing as.numeric function."  But clearly the result is 
different in each case.

If the help for as() is correct, then as(1:10, "numeric") should also return 
doubles, and the second argument is not ignored.

Erik


> On Feb 1, 2016, at 8:16 AM, Franklin Bretschneider  wrote:
> 
> Dear Erik Wright,
> 
> 
> Re:
> 
>> Could someone please explain this R behavior to me:
>> 
>>> typeof(as.numeric(1:10))
>> [1] "double"
>>> typeof(as(1:10, "numeric"))
>> [1] "integer"
>> 
>> I expected "double" in both cases.  In the help for the "as" function it 
>> says:
>> 
>> "Methods are pre-defined for coercing any object to one of the basic 
>> datatypes. For example, as(x, "numeric") uses the existing as.numeric 
>> function."
> 
> 
> This happens because 1:10 yields only integers, and so can be stored cheap,
> whereas as.numeric() actually means: as.double.
> The "numeric" in the second line is an unused argument.
> 
> Best regards,
> 
> Frank
> ---
> 
> 
> 
> 
> Franklin Bretschneider
> Dept of Biology
> Utrecht University
> brets...@xs4all.nl
> 
> 
>

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