Re: [R] Depends and Imports in DESCRIPTION file

[Henrik Bengtsson]

On Tue, Oct 22, 2013 at 8:03 PM, Marc Girondot  wrote:
> Dear list members:
>
> I try to check my updated package to include a new version in CRAN
> (phenology) but a new error is indicated and I don't find the logic.
> First my system:
> * using R version 3.0.2 Patched (2013-09-27 r64011)
> * using platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> Here is the message:
>
> * checking dependencies in R code ... NOTE
> Packages in Depends field not imported from:
> ‘fields’ ‘zoo’
> These packages needs to imported from for the case when
> this namespace is loaded but not attached.
> See the information on DESCRIPTION files in the chapter ‘Creating R
> packages’ of the ‘Writing R Extensions’ manual.

Just as packages under 'Imports:' in your DESCRIPTION file need to
have corresponding import()/importFrom() statements in the NAMESPACE
file, so do packages under 'Depends:'.  That is what this 'R CMD
check' NOTE is trying to say.  If you don't do this, those package's
functions/variables will only be available if you *attach* your
package, but not if you only *load* it.  That's also what the NOTE
tries to say.

When you do library()/require(), you *attach* a package and it appear
in the search() path and all functions/variables in the search() path
will be found by the user and from all packages attached/loaded.

When a package is *loaded* - explicitly via
loadNamespace()/requireNamespace(), but more commonly via Imports:
statements in DESCRIPTION, it is *not* attached to the search() path
and therefore none of its functions/variables are found.  Such
functions/variables are only found if they are explicitly imported via
import()/importFrom() in the NAMESPACE file.

Most people will *attach* your package, i.e. library("YourPackage"),
and currently the functions/variables of the packages under "Depends:"
will be on the search() and therefore found by the functions of your
package.  To see what packages are attached (=on the search() path)
and which are only loaded, look as sessionInfo().

So far so, good.  However, if someone else decides to use one of your
package's functions in their package and put it under 'Imports:", e.g.

Package: AnotherPackage
Depends: SomePackage
Imports: YourPackage  <= your package

you will be in trouble.  Because, library("AnotherPackage") will
*attach* AnotherPackage and SomePackage to the search() path and
*load* YourPackage.  In turn, you have specified in your DESCRIPTION
will *load* all packages under its "Imports:" as well as "Depends:".
However, since your NAMESPACE file does not import()/importFrom() any
of the packages under "Depends:", none of those functions will be
found.  Your functions will give errors like 'could not find function
"foo".

Basically, "Depends:" could be though of as "AttachOrLoad:" and
"Imports:" as "LoadOnly:".

To learn more about how all this works and why/why not, I strongly
recommend Suraj Gupta's nice write up 'How R Searches and Finds Stuff'
(Mar 2012):  http://obeautifulcode.com/R/How-R-Searches-And-Finds-Stuff/

/Henrik

>
> It is based on this line in DESCRIPTION file:
> Depends: fields, zoo, coda, R (>= 2.14.0)
>
> I use indeed functions from fields and zoo packages.
>
> If I create a new line:
> Imports: fields, zoo
> and remove these two packages from depends, I have still a problem in
> Imports and errors because functions from fields and zoo are not available.
> * checking dependencies in R code ... NOTE
> Namespaces in Imports field not imported from:
> ‘fields’ ‘zoo’
> All declared Imports should be used.
> See the information on DESCRIPTION files in the chapter ‘Creating R
> packages’ of the ‘Writing R Extensions’ manual.
> * checking R code for possible problems ... NOTE
> .read_phenology: no visible global function definition for ‘na.locf’
> plot.phenologymap: no visible global function definition for
> ‘image.plot’
>
>
> If I add the packages fields, zoo packages in both Depends and Imports, I
> have also error because packages fields, zoo are indicated twice and I have
> the same errors as previously indicated.
> * checking DESCRIPTION meta-information ... NOTE
> Packages listed in more than one of Depends, Imports, Suggests, Enhances:
> ‘fields’ ‘zoo’
> A package should be listed in only one of these fields.
>
> Of course I read ‘Creating R packages’ of the ‘Writing R Extensions’ manual,
> but I can't find solution to this problem.
>
> Thanks a lot,
>
> Marc Girondot
>
> --
> __
> Marc Girondot, Pr
>
> Laboratoire Ecologie, Systématique et Evolution
> Equipe de Conservation des Populations et des Communautés
> CNRS, AgroParisTech et Université Paris-Sud 11 , UMR 8079
> Bâtiment 362
> 91405 Orsay Cedex, France
>
> Tel:  33 1 (0)1.69.15.72.30   Fax: 33 1 (0)1.69.15.73.53
> e-mail: marc.giron...@u-psud.fr
> Web: http://www.ese.u-psud.fr/epc/conservation/Marc.html
> Skype: girondot
>
> __
> R-help@r-project.org mailing list
> https://sta

Re: [R] Depends and Imports in DESCRIPTION file

[Marc Girondot]

Le 23/10/13 05:03, Marc Girondot a écrit :

Dear list members:

I try to check my updated package to include a new version in CRAN 
(phenology) but a new error is indicated and I don't find the logic.

First my system:
* using R version 3.0.2 Patched (2013-09-27 r64011)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)

Here is the message:

* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘fields’ ‘zoo’
These packages needs to imported from for the case when
this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.


I begin to find the origin of the problem... but not still the solution.
When the NAMESPACE file is created by package.skeleton(), it includes:
import(coda)
but not
import(fields)
import(zoo)

If I add these manually, the check is ok.

Now the question becomes: why package.skeleton() does not add them and 
how to force package.skeleton() to add them ?


Sincerely,

Marc Girondot



--
__
Marc Girondot, Pr

Laboratoire Ecologie, Systématique et Evolution
Equipe de Conservation des Populations et des Communautés
CNRS, AgroParisTech et Université Paris-Sud 11 , UMR 8079
Bâtiment 362
91405 Orsay Cedex, France

Tel:  33 1 (0)1.69.15.72.30   Fax: 33 1 (0)1.69.15.73.53
e-mail: marc.giron...@u-psud.fr
Web: http://www.ese.u-psud.fr/epc/conservation/Marc.html
Skype: girondot

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Re: [R] cbind() function : Not able to display columns

[Richard M. Heiberger]

In addition to what the others have told you, it looks like you might
be confusing
matrices with data.frames.  Please see
?data.frame

I think what you are looking for is

> b <- c('a','b','c')
> c <- c("ee","tt","rr")
> k <- cbind(a,b,c)
> K <- data.frame(a, b, c)
> K
  a b  c
1 1 a ee
2 2 b tt
3 3 c rr

I recommend using " <- " for assignment (not the spaces on both sides), not "=".

On Wed, Oct 23, 2013 at 12:01 AM, Jeff Newmiller
 wrote:
> Hard to say, not sure what you want to do. But the columns are not denoted by 
> [a], [b] or [c]. You should learn to use the str function to understand what 
> various expressions really are, and return to the "Introduction to R" 
> document that comes with the software. There is a distinct difference between 
> a and "a" in R, and square brackets are not at all like quotes. See help("[") 
> and the ItoR section on indexing.
>
> You might get what you want by k[,"b"] for example.
> ---
> Jeff NewmillerThe .   .  Go Live...
> DCN:Basics: ##.#.   ##.#.  Live Go...
>   Live:   OO#.. Dead: OO#..  Playing
> Research Engineer (Solar/BatteriesO.O#.   #.O#.  with
> /Software/Embedded Controllers)   .OO#.   .OO#.  rocks...1k
> ---
> Sent from my phone. Please excuse my brevity.
>
> Vivek Singh  wrote:
>>Hi All,
>>
>>
>>I have create a matrix using cbind() function as follows:
>>
>>
>>> a=c(1,2,3)
>>
>>> b=c('a','b','c')
>>
>>> c=c("ee","tt","rr")
>>
>>
>>> k=cbind(a,b,c)
>>
>>
>>Problem: when we print the matrix k,
>>
>>> k
>>
>>a   b   c
>>
>>[1,] "1" "a" "ee"
>>
>>[2,] "2" "b" "tt"
>>
>>[3,] "3" "c" "rr"
>>
>>we can see that rows are represented by [1,] , [2,] and [3,].
>>Similarly,
>>the columns are denoted by [a], [b] and [c]. When we try to print the
>>corresponding columns, we are able to print for k[a], i.e., the first
>>column but not able to correctly print the second and third columns.
>>
>>> k[a]
>>
>>[1] "1" "2" "3"
>>
>>> k[b]
>>
>>[1] NA NA NA
>>
>>> k[c]
>>
>>[1] NA NA NA
>>
>>Please let me know what am I doing wrong.
>
> __
> R-help@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.

__
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Re: [R] How do I use simple calls to java methods?

[Jeff Newmiller]

Or use the literal form 4L.
---
Jeff NewmillerThe .   .  Go Live...
DCN:Basics: ##.#.   ##.#.  Live Go...
  Live:   OO#.. Dead: OO#..  Playing
Research Engineer (Solar/BatteriesO.O#.   #.O#.  with
/Software/Embedded Controllers)   .OO#.   .OO#.  rocks...1k
--- 
Sent from my phone. Please excuse my brevity.

Hurr  wrote:
>What I was missing was that I had to put as.integer(-4) to make it an
>integer.
>
>
>
>
>--
>View this message in context:
>http://r.789695.n4.nabble.com/How-do-I-use-simple-calls-to-java-methods-tp4678753p4678844.html
>Sent from the R help mailing list archive at Nabble.com.
>
>__
>R-help@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.

__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] cbind() function : Not able to display columns

[Jeff Newmiller]

Hard to say, not sure what you want to do. But the columns are not denoted by 
[a], [b] or [c]. You should learn to use the str function to understand what 
various expressions really are, and return to the "Introduction to R" document 
that comes with the software. There is a distinct difference between a and "a" 
in R, and square brackets are not at all like quotes. See help("[") and the 
ItoR section on indexing.

You might get what you want by k[,"b"] for example.
---
Jeff NewmillerThe .   .  Go Live...
DCN:Basics: ##.#.   ##.#.  Live Go...
  Live:   OO#.. Dead: OO#..  Playing
Research Engineer (Solar/BatteriesO.O#.   #.O#.  with
/Software/Embedded Controllers)   .OO#.   .OO#.  rocks...1k
--- 
Sent from my phone. Please excuse my brevity.

Vivek Singh  wrote:
>Hi All,
>
>
>I have create a matrix using cbind() function as follows:
>
>
>> a=c(1,2,3)
>
>> b=c('a','b','c')
>
>> c=c("ee","tt","rr")
>
>
>> k=cbind(a,b,c)
>
>
>Problem: when we print the matrix k,
>
>> k
>
>a   b   c
>
>[1,] "1" "a" "ee"
>
>[2,] "2" "b" "tt"
>
>[3,] "3" "c" "rr"
>
>we can see that rows are represented by [1,] , [2,] and [3,].
>Similarly,
>the columns are denoted by [a], [b] and [c]. When we try to print the
>corresponding columns, we are able to print for k[a], i.e., the first
>column but not able to correctly print the second and third columns.
>
>> k[a]
>
>[1] "1" "2" "3"
>
>> k[b]
>
>[1] NA NA NA
>
>> k[c]
>
>[1] NA NA NA
>
>Please let me know what am I doing wrong.

__
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Re: [R] cbind() function : Not able to display columns

[arun]

Hi,

Try:

  k[,"a"]
#[1] "1" "2" "3"
 k[,"b"]
#[1] "a" "b" "c"
 k[,"c"]
#[1] "ee" "tt" "rr"
A.K.






On Tuesday, October 22, 2013 11:37 PM, Vivek Singh  
wrote:
Hi All,


I have create a matrix using cbind() function as follows:


> a=c(1,2,3)

> b=c('a','b','c')

> c=c("ee","tt","rr")


> k=cbind(a,b,c)


Problem: when we print the matrix k,

> k

    a   b   c

[1,] "1" "a" "ee"

[2,] "2" "b" "tt"

[3,] "3" "c" "rr"

we can see that rows are represented by [1,] , [2,] and [3,]. Similarly,
the columns are denoted by [a], [b] and [c]. When we try to print the
corresponding columns, we are able to print for k[a], i.e., the first
column but not able to correctly print the second and third columns.

> k[a]

[1] "1" "2" "3"

> k[b]

[1] NA NA NA

> k[c]

[1] NA NA NA

Please let me know what am I doing wrong.

-- 
Thanks and Regards,

Vivek Kumar Singh

Research Assistant,
School of Computing,
National University of Singapore
Mobile:(0065) 82721535

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


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Re: [R] How do I use simple calls to java methods?

[Hurr]

What I was missing was that I had to put as.integer(-4) to make it an
integer.




--
View this message in context: 
http://r.789695.n4.nabble.com/How-do-I-use-simple-calls-to-java-methods-tp4678753p4678844.html
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[R] cbind() function : Not able to display columns

[Vivek Singh]

Hi All,


I have create a matrix using cbind() function as follows:


> a=c(1,2,3)

> b=c('a','b','c')

> c=c("ee","tt","rr")


> k=cbind(a,b,c)


Problem: when we print the matrix k,

> k

a   b   c

[1,] "1" "a" "ee"

[2,] "2" "b" "tt"

[3,] "3" "c" "rr"

we can see that rows are represented by [1,] , [2,] and [3,]. Similarly,
the columns are denoted by [a], [b] and [c]. When we try to print the
corresponding columns, we are able to print for k[a], i.e., the first
column but not able to correctly print the second and third columns.

> k[a]

[1] "1" "2" "3"

> k[b]

[1] NA NA NA

> k[c]

[1] NA NA NA

Please let me know what am I doing wrong.

-- 
Thanks and Regards,

Vivek Kumar Singh

Research Assistant,
School of Computing,
National University of Singapore
Mobile:(0065) 82721535

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[R] Depends and Imports in DESCRIPTION file

[Marc Girondot]

Dear list members:

I try to check my updated package to include a new version in CRAN 
(phenology) but a new error is indicated and I don't find the logic.

First my system:
* using R version 3.0.2 Patched (2013-09-27 r64011)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)

Here is the message:

* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘fields’ ‘zoo’
These packages needs to imported from for the case when
this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.

It is based on this line in DESCRIPTION file:
Depends: fields, zoo, coda, R (>= 2.14.0)

I use indeed functions from fields and zoo packages.

If I create a new line:
Imports: fields, zoo
and remove these two packages from depends, I have still a problem in 
Imports and errors because functions from fields and zoo are not available.

* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘fields’ ‘zoo’
All declared Imports should be used.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking R code for possible problems ... NOTE
.read_phenology: no visible global function definition for ‘na.locf’
plot.phenologymap: no visible global function definition for
‘image.plot’


If I add the packages fields, zoo packages in both Depends and Imports, 
I have also error because packages fields, zoo are indicated twice and I 
have the same errors as previously indicated.

* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘fields’ ‘zoo’
A package should be listed in only one of these fields.

Of course I read ‘Creating R packages’ of the ‘Writing R Extensions’ 
manual, but I can't find solution to this problem.


Thanks a lot,

Marc Girondot

--
__
Marc Girondot, Pr

Laboratoire Ecologie, Systématique et Evolution
Equipe de Conservation des Populations et des Communautés
CNRS, AgroParisTech et Université Paris-Sud 11 , UMR 8079
Bâtiment 362
91405 Orsay Cedex, France

Tel:  33 1 (0)1.69.15.72.30   Fax: 33 1 (0)1.69.15.73.53
e-mail: marc.giron...@u-psud.fr
Web: http://www.ese.u-psud.fr/epc/conservation/Marc.html
Skype: girondot

__
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Re: [R] How do I use simple calls to java methods?

[Hurr]

Thanks so much for the reply.
I did the search for "rJava examples" and found the Scott 
Hoover instructions which seemed like exactly what I needed.
I compiled the java code and copied myExchange.java and 
myExchange.class to the directory where I started R where 
I did and the calls suggested inside worked.
But there are no parameters passed in the examples.
I need to do something like this:
dateStg <- "201310221439591234"
dateStg
doubleLin <- .jcall(CalqsLin, "D", "linTimOfCalqsStgIsLev",dateStg,-4)
or
doubleLin <- .jcall(CalqsLin, "D",
"linTimOfCalqsStgIsLev","201310221439591234",-4)
where the latter two parameters are passed to linTimOfCalqsStgIsLev.
Neither way works and I cannot understand the .jcall() instructions in
rJava.pdf well enough.
I'll keep trying, but would like help.




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View this message in context: 
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[R] warning messages

[Ms khulood aljehani]

Hi,
i made a loop , then i got more than 50 warning messages, and i know what these 
messages and why they appears
 
my question here
is the warning message affecting in the accuracy of the results
 
this is my loop
 
nrep= 1000
n1=25
set.seed(123)
nw1<-c() 
for (i in 1:nrep) {
e<- rnorm(n1,0,0.1)
x<- runif(n1,0,1)   
mx<- 1-x+exp(-200*(x-0.5)^2)   
y<- mx+e   
h<- bw.ucv(x,nb = 1000)
est1 <- ksmooth(x, y, kernel = "normal", bandwidth = h, x.points = x)$y  
nw1 <- cbind(nw1,est1)   
}
There were 50 or more warnings (use warnings() to see the first 50)

RegardsKhulood H.  
-
áäÓÃá Çááå ÇáÌäÉ æãÇ íÞÑøÈ ÅáíåÇ ãä Þæá æÚãá
  
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Re: [R] 'XML' package cannot be un-zipped or un-tar'd"

[Paul Bivand]

R FAQ 5.1.2: Some CRAN packages that do not build out of the box on
Windows, require additional software, or are shipping third party libraries
for Windows cannot be made available on CRAN in form of a Windows binary
package. Nevertheless, some of these packages are available at the
“CRAN extras”
repository at http://www.stats.ox.ac.uk/pub/RWin/ kindly provided by Brian
D. Ripley. Note that this repository is a default repository for recent
versions of R for Windows.

This applies to the 'XML' package. install.packages("XML") should work.

This is a regular issue coming up on the mailing list, so a quick search
should have found the issue. The XML readme file points out that building
on windows is not as simple as on other platforms.

Paul Bivand


On 19 October 2013 20:51, Steven Dwayne Randolph <
randolph_steve...@lilly.com> wrote:

> Even when I attempt to unzip the file on windows, I get an error that says
> its not a compressed file.
>
>
>
> From: Rolf Turner [mailto:rolf.tur...@xtra.co.nz]
> Sent: Tuesday, October 01, 2013 4:23 PM
> To: Steven Dwayne Randolph
> Cc: r-help@r-project.org
> Subject: Re: [R] 'XML' package cannot be un-zipped or un-tar'd"
>
> On 10/02/13 00:22, Steven Dwayne Randolph wrote:
>
>
>
> R-help,
>
>
>
> There are several packages that have package 'XML' as a  dependency.  I
> cannot get this package (XML) to extract or  install.  I have tried
> manually downloaded to local machines (client PC and Linux), unsuccessful
> extraction.  How can this be compiled manually?  How can a new version be
> on CRAN and this problem still exist?   See the thread for specific errors
> and screen shots.
>
> What do you mean by "cannot get this package (XML) to extract or install"?
>
> Did you download the tarball "XML_3.98-1.1.tar.gz"?  If so, what happens
> when you do "tar xvf XML_3.98-1.1.tar.gz"?
>
> Do you have the requisite R development tools (appropriate compilers etc.)
> installed?
>
> What happens if you do the install from within R, as in
>
> > install.packages("XML",lib= permission>)   ???
>
> When I tried that I got a whinge about a lack of "xml2-config".  After sum
> yumming around
> (I use Fedora Linux) I found that
>
> sudo yum install libxml2.x86_64 libxml2-devel.x86_64
>
> did the trick, and I was then able to install XML using install.packages().
>
> cheers,
>
> Rolf Turner
>
> [[alternative HTML version deleted]]
>
> __
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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] Help with loop ;(

[arun]

Hi, 

The conditions are not very clear. For example, it is not mentioned whether 
vectors are of same length or not.  Assuming the former case:
fun1 <- function(x,y){
 if(length(x)==length(y) & length(x)%%2==0){
 res <- x+y
 }
 else if(length(x)==length(y) & length(x)%%2==1){
 res <- abs(x-y)
}
else print("Lengths are not same")
res
}
 vec1 <- 1:10
 vec2 <- 11:20
 vec3 <- 1:9
 vec4 <- 10:18
 fun1(vec3,vec4)
 fun1(vec1,vec2)
fun1(vec1,vec3)

A.K.





Hi, I'm new on this forum, and I need some help with for loop. I have to write 
loop that will add two vectors, if they are even. Even if they 
are odd, it must subtract the two vectors.

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Re: [R] Graphing complex functions

[Hans W Borchers]

John Van Praag  jvp247.com> writes:
> 
> Does R have any facilities, or packages, for graphing complex functions?

Package 'elliptic' has function view() for

"Visualization of complex functions using colourmaps and contours"

Hans Werner

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Re: [R] How to draw figures in a graph?

[Greg Snow]

You will want to be very careful in adding things to a plot that are
not conveying information.  One term for these things is "chartjunk"
which should give you a feel for the general opinion about doing this.

If you still feel the need to add to a graph (and promise to think
hard about it and be careful in the implementation that the added
figures do not distort the data) then you can start by looking at the
rasterImage function (and grid.raster for grid based graphics).  The
grImport package could also be useful if your images are in a vector
format, see the import vignette from that package.  Possibly also the
my.symbols function in the TeachingDemos package.

On Tue, Oct 22, 2013 at 9:08 AM, halim10-fes  wrote:
> Hi All,
>
> Hope you guys are doing well. I am thinking of drawing some figures within a
> graph to make it more interesting. To make a graph more storytelling, like the
> attached one.
>
> I am looking for a couple of days but couldn't come up with any solution on 
> how
> to do it with R. Any ideas will be greatly appreciated.
>
> Thanks,
>
> ---
> Md. Abdul Halim
> Assistant Professor
> Department of Forestry and Environmental Science
> Shahjalal University of Science and Technology,Sylhet-3114,
> Bangladesh.
> Cell: +8801714078386.
> alt. e-mail: xo...@yahoo.com
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
>
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> and provide commented, minimal, self-contained, reproducible code.
>



-- 
Gregory (Greg) L. Snow Ph.D.
538...@gmail.com

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Re: [R] Graphing complex functions

[Duncan Murdoch]

On 22/10/2013 1:07 PM, John Van Praag wrote:

Does R have any facilities, or packages, for graphing complex functions?


I don't think base R does, but if you have a complex-valued function of 
a real variable, it wouldn't be hard to write one.

For your example:

library(rgl)
xvals <- seq(0, 2*pi, len=256)
f <- function(x) cos(x) + 1i * sin(x)
zvals <- f(xvals)
plot3d(xvals, Re(zvals), Im(zvals), type="l")

For the case of a real-valued function of a complex variable, you could 
use persp() or persp3d().  For both argument and value being complex, 
you'll need 4 dimensions, and that's hard to do nicely, though I suppose 
you could overlay contour or perspective plots of the real and imaginary 
parts of the value.  For example:


x <- y <- seq(0, 2*pi, len=50)
z <- outer(x, y, function(x,y) x + 1i*y)
zvals <- f(z)
persp3d(x, y, Re(zvals), col="red", alpha=0.5, xlab="Re(z)", 
ylab="Im(z)", zlab="f(z)")

surface3d(x, y, Im(zvals), col="blue", alpha=0.5)

Duncan Murdoch



I find that 'curve' does not do the trick. Example:

> f = function(x) cos(x) + 1i * sin(x)
> curve(f, -pi, pi)
Error in xy.coords(x, y, xlabel, ylabel, log) :
   (converted from warning) imaginary parts discarded in coercion

Enter a frame number, or 0 to exit

1: curve(f, -pi, pi)
2: plot(x = x, y = y, type = type, xlab = xlab, ylab = ylab, xlim = xlim,
log = lg, ...)
3: plot.default(x = x, y = y, type = type, xlab = xlab, ylab = ylab, xlim =
xlim, log = lg, ...)
4: xy.coords(x, y, xlabel, ylabel, log)
5: .signalSimpleWarning("imaginary parts discarded in coercion",
quote(xy.coords(x, y, xlabel, ylabel, log)))
6: withRestarts({
 .Internal(.signalCondition(simpleWarning(msg, call), msg, call))
 .Internal(.dfltWarn(msg, call))
}, muffleWarning = function() NULL)
7: withOneRestart(expr, restarts[[1]])
8: doWithOneRestart(return(expr), restart)
9: (function ()
{
 error()
 utils::recover()
})()

Selection:

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Re: [R] Hdf files Download

[David Winsemius]

On Oct 22, 2013, at 11:34 AM, Roy Mendelssohn - NOAA Federal wrote:

> Your script didn't make it.  There are restrictions on the mail list for 
> attached files.  You might try putting the script directly into the email.

Thinking that the rejection might have be due to a Nabble posting I located it 
there and here include it. I'm hoping to use the method as well.

#

# title : MODIS_download_HTTP.R
# purpose   : Download of MODIS EVI images for the British Colombia;
# reference : 
http://spatial-analyst.net/wiki/index.php?title=Download_and_resampling_of_MODIS_images
# producer  : Prepared by T. Hengl (addapted by T. Smejkalova)
# last update   : Southampton, UK, 18 October 2013.
# inputs: Coordinates of the area of interest; proj4 parameters; ftp 
addresses etc.;
# outputs   : a series of EVI images (geoTIFF) projected in the local 
coordinate system;
# remarks 1 : To run this script, you need to obtain and install the MODIS 
resampling tool from 
[https://lpdaac.usgs.gov/lpdaac/tools/modis_reprojection_tool];
# remarks 2 : You should also obtain the WGET from 
[http://users.ugent.be/~bpuype/wget/]  --- simply copy the wget exe to windows 
system folder;
# remarks 3 : make sure you disable your antivirus tools such as Norton or 
McAfee otherwise it might block wget from running!

library(rgdal)
library(RCurl)
setInternet2(use = TRUE)
# Obtain the MODIS tool from: 
http://lpdaac.usgs.gov/landdaac/tools/modis/index.asp
# setwd("E:/PineBeetleBC/MODIS")
# location of the MODIS 1 km monthly blocks:
MOD09GQ <- "http://e4ftl01.cr.usgs.gov/MOLT/MOD09GQ.005/";
MOD09GQa <- "http://anonymous:t...@e4ftl01.cr.usgs.gov/MOLT/MOD09GQ.005/";
product = "MOD09GQ"
year = 2000
# location of the mosaicing tool:
MRT <- 'D:\\MRT\\MRT_Win\\bin\\'
workd <- 'D:\\R_Modis\\'
setwd('D:\\R_Modis\\')
options(download.file.method="auto")

# get the list of directories (thanks to Barry Rowlingson):
items1 <- strsplit(getURL(MOD09GQ), "\n")[[1]]

# get the directory names and create a new data frame:
dates=data.frame(dirname=substr(items1[20:length(items1)],52,62))

# get the list of *.hdf files:
dates$BLOCK1 <- rep(NA, length(dates))
dates$BLOCK2 <- rep(NA, length(dates))
#dates$BLOCK3 <- rep(NA, length(dates))
#dates$BLOCK4 <- rep(NA, length(dates))

for (i in 1:1)#length(dates))# for each date per year
{
  getlist <- strsplit(getURL(paste(MOD09GQ, dates$dirname[i], sep="")), 
">")[[1]]
  getlist=getlist[grep(product,getlist)]
  getlist=getlist[grep(".hdf<",getlist)]
  filenames=substr(getlist,1,nchar(getlist[1])-3)
  BLOCK1 <- filenames[grep(filenames,pattern="MOD09GQ.*.h18v02.*.hdf")[1]]
  BLOCK2 <- filenames[grep(filenames,pattern="MOD09GQ.*.h19v02.*.hdf")[1]]
  
  # write up the file names back to the dates.txt:
  for(j in 2:3){
dates[i,j] <- get(paste("BLOCK", j-1, sep=""))
  }
  
  # Download all blocks from the list to a local drive:
  # 
while(!is.na(dates[i,2])&!is.na(dates[i,3])&!is.na(dates[i,4])&!is.na(dates[i,5])&!is.na(dates[i,6])&!is.na(dates[i,7])&!is.na(dates[i,8])&!is.na(dates[i,9])&!is.na(dates[i,10])){
  download.file(paste(MOD09GQa,  dates$dirname[i], 
dates$BLOCK1[i],sep=""),destfile=paste(getwd(), "/", BLOCK1, sep=""))
  download.file(paste(MOD09GQ,  dates$dirname[i], 
dates$BLOCK2[i],sep=""),destfile=paste(getwd(), "/", BLOCK2, sep=""), 
cacheOK=FALSE, )
  
  # remove "." from the file name:
  dirname1 <- sub(sub(pattern="\\.", replacement="_", dates$dirname[[i]]), 
pattern="\\.", replacement="_", dates$dirname[[i]])
  # mosaic the blocks:
  mosaicname = file(paste(MRT, "TmpMosaic.prm", sep=""), open="wt")
  write(paste(workd, BLOCK1, sep=""), mosaicname)
  write(paste(workd, BLOCK2, sep=""), mosaicname, append=T)
  #write(paste(workd, BLOCK3, sep=""), mosaicname, append=T)
  #write(paste(workd, BLOCK4, sep=""), mosaicname, append=T)
  close(mosaicname)

  # generate temporary mosaic:
  shell(cmd=paste(MRT, 'mrtmosaic -i ', MRT, 'TmpMosaic.prm -s "0 1 0 0 0 0 0 0 
0 0 0" -o ', workd, 'TmpMosaic.hdf', sep=""))
  
  # resample to epsg=3005:
  filename = file(paste(MRT, "mrt", dirname1, ".prm", sep=""), open="wt")
  write(paste('INPUT_FILENAME = ', workd, 'TmpMosaic.hdf', sep=""), filename) 
  # write(paste('INPUT_FILENAMES = ( ', workd, BLOCK1, ' ', workd, BLOCK2, ' ', 
workd, BLOCK3, ' ', workd, BLOCK4, ' ', workd, BLOCK5, ' ', workd, BLOCK6, ' ', 
workd, BLOCK7, ' ', workd, BLOCK8, ' ', workd, BLOCK9, ' )', sep=""), filename) 
 # unfortunatelly does not work via command line  :(
  write('  ', filename, append=TRUE) 
  # write('SPECTRAL_SUBSET = ( 0 1 0 0 0 0 0 0 0 0 0 )', filename, append=TRUE)
  write('SPECTRAL_SUBSET = ( 1 )', filename, append=TRUE)
  write('  ', filename, append=TRUE)
  write('SPATIAL_SUBSET_TYPE = OUTPUT_PROJ_COORDS', filename, append=TRUE)
  write('  ', filename, append=TRUE)
  write('SPATIAL_SUBSET_UL_CORNER = ( 50.0 -180.0 )', filename, 
append=TRUE)
  write('SPATIAL_SUBSET_LR_CORNER = ( 160.0 -270.0 )', file

Re: [R] More Columns than column names Error

[arun]

Hi,

The "Garbage.txt" file you showed in the original post is slighly different (in 
spacing) from the one you are showing now.

lines1 <- readLines("Garbage.txt",warn=FALSE)

lines2 <- readLines("GarbageNew.txt",warn=FALSE) #saved the new as 
"GarbageNew.txt"

lines1
 [1] "Material\tWeight(Million Tons)\tPercent"
 [2] "Food Scraps\t25.9\t\t\t11.2"    
 [3] "Glass\t\t12.8\t\t\t5.5" 
 [4] "Metals\t\t18.0\t\t\t7.8"    
 [5] "Paper\t\t86.7\t\t\t37.4"    
 [6] "Plastics\t24.7\t\t\t10.7"   
 [7] "Textiles\t15.8\t\t\t6.8"    
 [8] "Wood\t\t12.7\t\t\t5.5"  
 [9] "Yard trimmings\t27.7\t\t\t11.9" 
[10] "Other\t\t7.5\t\t\t3.2"  
[11] "Total\t\t231.9\t\t\t100.0"  
 lines2
 [1] "Material\tWeight(Million Tons)\tPercent"
 [2] "Food Scraps\t25.9\t11.2"    
 [3] "Glass\t12.8\t5.5"   
 [4] "Metals\t18.0\t7.8"  
 [5] "Paper\t86.7\t37.4"  
 [6] "Plastics\t24.7\t10.7"   
 [7] "Textiles\t15.8\t6.8"    
 [8] "Wood\t12.7\t5.5"    
 [9] "Yard trimmings\t27.7 11.9"   #here there are two delimiters "\t" and 
"space"    
[10] "Other\t7.5\t3.2"    
[11] "Total\t231.9\t100.0"  


Looks like you changed the tab spaces.
dat1 <- 
read.table(text=gsub("\t+","\t",lines1),stringsAsFactors=FALSE,sep="\t",check.names=FALSE,header=TRUE)
 #no errors

#able to reproduce the error mentioned

dat2 <- 
read.table(text=gsub("\t+","\t",lines2),stringsAsFactors=FALSE,sep="\t",check.names=FALSE,header=TRUE)
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  : 
  line 8 did not have 3 elements

#Try this
 dat2 <- read.table(text=gsub("(.*\\d+) 
(\\d+)","\\1\t\\2",lines2),stringsAsFactors=FALSE,sep="\t",check.names=FALSE,header=TRUE)
 identical(dat1,dat2)
#[1] TRUE

jpeg("garbageweight.jpg",width=800)
 
barplot(dat2[-10,2],names.arg=dat2[-10,1],ylab=colnames(dat2)[2],col=rainbow(9),main="American
 garbage")
 dev.off()


Attached is the pdf of the figure
A.K.



Garbage.txt

The error I get now is "Line 8 did not have 3 elements" 





On Tuesday, October 22, 2013 9:41 AM, arun  wrote:
Hi,
Try:
 lines1 <- readLines("Garbage.txt",warn=FALSE)
dat1 <- 
read.table(text=gsub("\t+","\t",lines1),stringsAsFactors=FALSE,sep="\t",check.names=FALSE,header=TRUE)
 str(dat1)
#'data.frame':    10 obs. of  3 variables:
# $ Material    : chr  "Food Scraps" "Glass" "Metals" "Paper" ...
# $ Weight(Million Tons): num  25.9 12.8 18 86.7 24.7 ...
# $ Percent : num  11.2 5.5 7.8 37.4 10.7 6.8 5.5 11.9 3.2 100
jpeg("garbageweight.jpg",width=800)
 
barplot(dat1[-10,2],names.arg=dat1[-10,1],ylab=colnames(dat1)[2],col=rainbow(9),main="American
 garbage")
 dev.off()


A.K.


Hello guys, I'm having this weird problem with my assignment. I can't seem to 
import the data that I have created. 

I keep getting an error that says "Error: More Columns than Column names" 

This is my data file. 
Garbage.txt

Was also wondering if you guys could send me into the right direction on how to 
do this. 

1. Create a data frame with the data given above. 
2. Create the bar plot for weight variable with appropriate labels. Resize the 
graphics 
panel/ window so that all labels are visible. 
3. Add colors. Suppose n is the number of bars. 
> barplot(..., col = rainbow(n)) 
4. Save the plot to garbageweight.jpg 

This is how it's supposed to look like at the end.

garbage.weight.pdf
Description: Adobe PDF document
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Re: [R] Replace NA values with previous valid value in array

[arun]

Hi,

c1 = (1,2,3,4,5,6,NA,7,8,NA,9,10,NA)
library(zoo)

na.locf(c1)
# [1]  1  2  3  4  5  6  6  7  8  8  9 10 10

A.K.

Hi, I want to "fix" an array that contains several NA elements. And I 
would like to replace them with the previous valid element. 

So my array c = (1,2,3,4,5,6,NA,7,8,NA,9,10,NA) become cfixed= 
(1,2,3,4,5,6,6,7,8,8,9,10,10) 

(that's an example the actual array has thousands of elements) 

Thanks!

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Re: [R] Hdf files Download

[Roy Mendelssohn - NOAA Federal]

Your script didn't make it.  There are restrictions on the mail list for 
attached files.  You might try putting the script directly into the email.

-Roy

On Oct 22, 2013, at 9:40 AM, "Tereza Smejkalova"  wrote:

> I am triing one more time since my first message was rejected by the filter:
> 
> 
> 
> Dear all, 
> I need to download and process large amounts of MODIS surface reflectance
> imagery. I have adapted a script written by T. Hengl (
>  _images>
> http://www.spatial-analyst.net/wiki/?title=Download_and_resampling_of_MODIS_
> images) for download from the new HTTP (since FTP is no longer available).
> The downloaded .HDF files however have no headers and it is impossible to
> work with them. If I download directly from the webpage everything is fine.
> Does anyone know what the problem might be, please? 
> 
> I am attaching my code
> 
> 
> 
> Please it is urgent. 
> 
> Thanks a lot.
> 
> 
> 
> 
> 
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> and provide commented, minimal, self-contained, reproducible code.

**
"The contents of this message do not reflect any position of the U.S. 
Government or NOAA."
**
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
1352 Lighthouse Avenue
Pacific Grove, CA 93950-2097

e-mail: roy.mendelss...@noaa.gov (Note new e-mail address)
voice: (831)-648-9029
fax: (831)-648-8440
www: http://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected" 
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

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[R] reference class error

[Filippo Monari]

hi,
I'm new to reference classes but as I have experience with python I 
decided to port some of my code in this frame work.

I have the following two reference classes in separate files:

#1#
uvRndVar = setRefClass(
Class = 'uvRndVar',
fields = list(
desc = 'character',
type = 'character',
pars = 'list',
MAP = c('numeric'),
post = c('numeric')
),
methods = list(
initialize = function (desc, type, pars) {
types = c('norm', 'lnorm', 'beta', 'gamma')
parameters = list(norm = c('mean', 'sd'), lnorm = c('mean', 
'sd'),

beta = c('shape1', 'shape2'), gamma = c('shape', 'rate'))
if (!any(types == type)) {
stop('not correct type provided')
} else {
if (length(names(pars)) == length(parameters[[type]])) {
for (i in 1:length(names(pars))) {
a = which(parameters[[type]] == names(pars)[i])
if (length(a)) {
parameters[[type]] = parameters[[type]][-a]
} else {
stop(paste('parameter', names(pars)[i], 
'not compatible with provided type'))

}
}
.self$desc = desc
.self$type = type
.self$pars = pars
.self$MAP = NaN
.self$post = NaN
} else {
stop('parameter list provided has wrong length')
}
}
}
)
)


#2#
NG = setRefClass(
Class = 'NG',
fields = list(
Y = 'matrix',
X = 'matrix',
CvFun = 'Cf',
CfHp = 'list',
lam = 'uvRndVar',
lam.upd = 'logical',
A = 'array',
basis = 'matrix',
Y.star = 'matrix',
X.star = 'matrix',
lam.star = 'numeric',
lam.star.upd = 'logical',
A.star = 'matrix'
),
methods = list(
initialize = function (Y, X, Cf, CfHp, lam, A, basis) {
if (nrow(Y) != nrow(X)) {
stop('X and Y have different numbers of rows')
} else if (dim(A)[1] != dim(A)[2]) {
stop('A is not a square matrix')
} else if (dim(A)[1] != nrow(basis)) {
stop('basis matrix and precision matrix A have 
different number of rows')

} else if (dim(A)[3] != nrow(X)) {
stop('dim(A)[3] != nrow(X)')
} else if (ncol(basis) != ncol(Y)) {
stop('basis matrix and Y have different number of columns')
} else {
CvFun$checkModel(Y, X, CfHp)
}
.self$q = ncol(Y)
.self$m = nrow(X)
.self$p = ncol(X)
.self$n = nrow(basis)
.self$Y = Y
.self$X = X
.self$CvFun = CvFun
.self$CfHp = CfHp
.self$lam = lam
.self$A = A
.self$basis = basis
}
)
)


the second takes an object of the first class in two of its fields. I 
load the first class and then the second with the 'source' command, but 
then I got this error which i don't understand:


Error in match(x, table, nomatch = 0L) :
  argument "type" is missing, with no default

I'm working with Ubuntu 12.04 and R 3.0.2.
Any suggestions about what is going wrong?
Thanks in advance,
Filippo

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[R] nls model definition help

[Wayne.W.Jones]

Hi fellow R users,

I'm trying to fit a model using nls with the following model definition:

y(t+1)=(th1*x1 + R1*x2) * exp(a1*x3) + (1-th1*x1 + R1*x2)*y(t)

y is the dependent variable (note on both sides of eq) and the x's represent 
the regressors.
th1, R1 and a1 are parameters to be estimated. The problem is non- linear and 
hence why I'm trying to fit using the well used "nls" function.

To fit the model I would like to be able to use the formula interface rather 
than build my own ugly function definition.
Any ideas if this is achievable and if not any ideas on how to fit this model?


Many thanks,

Wayne





Wayne Jones
Statistics & Chemometrics
Shell Global Solutions (UK)
Shell Technology Centre Thornton
P.O. Box 1, Chester CH1 3SH, United Kingdom
Tel: +44 (0) 151 373 5977 Mobile: +44 (0) 7896 536026
Email: wayne.w.jo...@shell.com
Intranet: Statistics and Chemometrics - Shell 
Wiki
Internet: Shell Global Solutions

Shell Global Solutions (UK) is a division of Shell Research Limited which has 
its Registered Office at Shell Centre, London SE1 7NA and is registered in 
England & Wales with No.539964.


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[R] Graphing complex functions

[John Van Praag]

Does R have any facilities, or packages, for graphing complex functions?

I find that 'curve' does not do the trick. Example:

> f = function(x) cos(x) + 1i * sin(x)
> curve(f, -pi, pi)
Error in xy.coords(x, y, xlabel, ylabel, log) :
  (converted from warning) imaginary parts discarded in coercion

Enter a frame number, or 0 to exit

1: curve(f, -pi, pi)
2: plot(x = x, y = y, type = type, xlab = xlab, ylab = ylab, xlim = xlim,
log = lg, ...)
3: plot.default(x = x, y = y, type = type, xlab = xlab, ylab = ylab, xlim =
xlim, log = lg, ...)
4: xy.coords(x, y, xlabel, ylabel, log)
5: .signalSimpleWarning("imaginary parts discarded in coercion",
quote(xy.coords(x, y, xlabel, ylabel, log)))
6: withRestarts({
.Internal(.signalCondition(simpleWarning(msg, call), msg, call))
.Internal(.dfltWarn(msg, call))
}, muffleWarning = function() NULL)
7: withOneRestart(expr, restarts[[1]])
8: doWithOneRestart(return(expr), restart)
9: (function ()
{
error()
utils::recover()
})()

Selection:

[[alternative HTML version deleted]]

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[R] How to draw figures in a graph?

[halim10-fes]

Hi All,

Hope you guys are doing well. I am thinking of drawing some figures within a 
graph to make it more interesting. To make a graph more storytelling, like the 
attached one.

I am looking for a couple of days but couldn't come up with any solution on how 
to do it with R. Any ideas will be greatly appreciated.

Thanks,

---
Md. Abdul Halim
Assistant Professor
Department of Forestry and Environmental Science
Shahjalal University of Science and Technology,Sylhet-3114,
Bangladesh.
Cell: +8801714078386.
alt. e-mail: xo...@yahoo.com

-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

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[R] [R-pkgs] scholar 0.1.0 on CRAN

[James Keirstead]

Dear R users,

A new package 'scholar' (version 0.1.0) is now available on CRAN: 
http://cran.r-project.org/web/packages/scholar/index.html.


The scholar package provides functions to extract citation data from 
Google Scholar.  In addition to retrieving basic information about a 
single scholar, the package also allows you to compare multiple scholars 
and predict future h-index values based on the method of Acuna et al.  
For example, we can compare the careers of Richard Feynman and Stephen 
Hawking as follows:


   ids <- c('B7vSqZsJ', 'qj74uXkJ')
   df <- compare_scholar_careers(ids)
   ggplot(df, aes(x=career_year, y=cites)) + geom_line(aes(linetype=name))

For more information and examples of how to use the package, please see 
https://github.com/jkeirstead/scholar.


Your comments and suggestions would be appreciated.

Best wishes,
James

--
Dr James Keirstead
Lecturer
Dept of Civil and Environmental Engineering
Imperial College
South Kensington, London
SW7 2AZ

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[R] Hdf files Download

[Tereza Smejkalova]

I am triing one more time since my first message was rejected by the filter:

 

Dear all, 
I need to download and process large amounts of MODIS surface reflectance
imagery. I have adapted a script written by T. Hengl (

http://www.spatial-analyst.net/wiki/?title=Download_and_resampling_of_MODIS_
images) for download from the new HTTP (since FTP is no longer available).
The downloaded .HDF files however have no headers and it is impossible to
work with them. If I download directly from the webpage everything is fine.
Does anyone know what the problem might be, please? 

I am attaching my code

 

Please it is urgent. 

Thanks a lot.

 

 

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Re: [R] XML package not working

[Berend Hasselman]

On 22-10-2013, at 15:19, Steven Dwayne Randolph  
wrote:

> Ista,... Thank you for your response.   Here is what is occurring when I 
> attempt to command-line install.
> --
>> install.packages('XML')
> Installing package into ‘C:/Users/xxx/Documents/R/win-library/3.0’
> (as ‘lib’ is unspecified)
> trying URL 'http://cran.rstudio.com/bin/windows/contrib/3.0/XML_3.98-1.1.zip'
> Content type 'application/zip' length 4287270 bytes (4.1 Mb)
> opened URL
> downloaded 4.1 Mb
> 
> Warning in install.packages :
>  downloaded length 4276224 != reported length 4287270


Look at what is reported here. The downloaded length is not equal to the 
reported (i.e. actual) length of  the zip.
What is the length if you download the .zip file manually?
So something has gone wrong with the download.
Can you open a .zip file in another program? If so see what happens if you open 
it in that program.
You have to do detective work.

Berend


> Warning in install.packages :
>  error 1 in extracting from zip file
> Warning in install.packages :
>  cannot open compressed file 'XML/DESCRIPTION', probable reason 'No such file 
> or directory'
> Error in install.packages : cannot open the connection
> 
> --
> 
> STeven
> -Original Message-
> From: Ista Zahn [mailto:istaz...@gmail.com] 
> Sent: Tuesday, October 22, 2013 8:09 AM
> To: Steven Dwayne Randolph
> Cc: Duncan Murdoch; r-help@r-project.org; stevendrando...@aol.com; Piyush 
> Singh - Network
> Subject: Re: [R] XML package not working
> 
> Hi Steven,
> 
> I still don't understand why you are downloading it manually. What happens 
> when you
> 
> install.packages("XML")
> 
> ?
> 
> Best,
> Ista
> 
> On Tue, Oct 22, 2013 at 8:03 AM, Steven Dwayne Randolph 
>  wrote:
>> Duncan... Thank you.
>> 
>>1.   I am able to download the XML file via my corporate network, 
>> other packages without this same issue, even rcurl and bitops which are 
>> pre-requisites on the same page as XML.
>>2.   I  have attempted to download this from my own wifi at home 
>> using xfinity/Comcast to my personal pc and still get the same error on this 
>> package alone.
>>3.   I am genuinely baffled by this package download and 
>> install experience.
>> 4.  I would gladly build this from source, If indeed I could 
>> find the source and then use RTools to compile it.  That has been 
>> unsuccessful as well.   Nightmare? Slightly.
>> 
>> Thanks for your response.
>> Steven
>> 
>> -Original Message-
>> From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
>> Sent: Sunday, October 20, 2013 12:13 PM
>> To: Steven Dwayne Randolph; r-help@r-project.org; Ista Zahn
>> Cc: stevendrando...@aol.com
>> Subject: Re: [R] XML package not working
>> 
>> On 13-10-20 9:23 AM, Steven Dwayne Randolph wrote:
>>> My apologies for not conforming to the posting guideline.
>>> 
>>> 
>>> Sys.info()
>>>  sysname  release   
>>>version
>>>"Windows"  "7 x64" "build 7601, 
>>> Service Pack 1"
>>> nodename  machine   
>>>  login
>>>"xxNU247BZ1S" "x86-64"   
>>>  "XX"
>>> user   effective_user
>>>"xxx""xxx"
>>> 
>>> When I attempt to install a local copy of the xml.zip file:
>>> 
>>> in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
>>>   cannot open the connection
>>> In addition: Warning messages:
>>> 1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip 
>>> file
>>> 2: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
>>>   cannot open compressed file 'XML/DESCRIPTION', probable reason 'No such 
>>> file or directory'
>> 
>> I think it is pretty clear that the problem is at your end:  you aren't 
>> downloading the file properly, even though everyone else is.  Perhaps you 
>> are behind a firewall, or something else is interfering with your downloads?
>> 
>> Duncan Murdoch
>> 
>>> 
>>> 
>>> -Original Message-
>>> From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
>>> Sent: Saturday, October 19, 2013 8:23 PM
>>> To: Steven Dwayne Randolph; r-help@r-project.org
>>> Cc: stevendrando...@aol.com
>>> Subject: Re: [R] XML package not working
>>> 
>>> On 13-10-19 3:47 PM, Steven Dwayne Randolph wrote:
 I know I  cannot be the only one who is not able to install the XML 
 package from CRAN (zip or tar file)  Many packages depend on this XML 
 package.  Can someone help me either access the source for a good binary?  
 I have received no 

Re: [R] speeding up "sum of squared differences" calculation

[William Dunlap]

outer() and dist() are good for speed on smaller problems but they
require O(length(X)^2) memory.  This can slow things down or even
stop the calculations for large problems.  You can gain a lot of speed
without the memory problem by summing things up in chunks.
E.g., On a Linux box I compared
fChunk <- function(x) {
ans <- 0
for(i in seq_along(x)[-1]) {
ans <- ans + sum( (x[i] - x[seq_len(i-1)])^2)
}
2*ans
}
with the original algorithm (slightly cleaned up)
fOrig <-function (x) {
ans <- 0
for (i in seq_along(x)[-1]) {
for (j in seq_len(i)) {
ans <- ans + (x[i] - x[j])^2
}
}
2 * ans
}
and the ones based on outer() and dist().
   fOuter <- function(x) sum(outer(x, x, FUN=`-`)^2)
   fDist <- function(x) 2 * sum(dist(x)^2)
for a vector of length 1.

   > z <- rnorm(10^4)
   > t(sapply(list(fOrig=fOrig, fChunk=fChunk, fDist=fDist, fOuter=fOuter),
function(f)tryCatch(system.time(f(z)), error=function(e)NA)[1:3]))
  user.self sys.self elapsed
   fOrig 90.2620.000  90.378
   fChunk 0.7760.004   0.779
   fDist  1.0920.276   1.370
   fOuter 0.7401.068   1.855

They all give slightly different answers because the round-off error depends on
the order in which sums and squares are done.

Of course, the Rcpp version has no memory penalty and is faster than any of 
them.

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com


> -Original Message-
> From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On 
> Behalf
> Of S Ellison
> Sent: Tuesday, October 22, 2013 6:08 AM
> To: r-help@r-project.org
> Cc: Ken Knoblauch
> Subject: Re: [R] speeding up "sum of squared differences" calculation
> 
> > Conclusion: hard to beat outer() for this purpose in R
> ... unless you use Ken Knoblauch's suggestion of dist() or Rccp.
> 
> Nice indeed.
> 
> 
> S Ellison
> 
> 
> ***
> This email and any attachments are confidential. Any use...{{dropped:8}}
> 
> __
> R-help@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.

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Re: [R] list and <<-

[Greg Snow]

Look carefully at your output (and I don't think that you are showing
us the output of what you actually ran in the order that you ran it).
After running `x %=% 1` you should see that x has the value `1`, but
your output shows `2`, this is the result of the next command `y$a %=%
2`, see the `<<-` assignment will always assign to `x`, not to the
variable named in the local variable x.

An operator like %=% should be used to somehow combine its 2 arguments
and return the result, not ever change a variable value.  The job of
assigning the result should go to the user/caller.  You could possibly
create a new class and an assignment method for that class that would
work like the assignment.

If you can give us more of an idea of what your ultimate goal is then
we may be able to help you find a better approach.

On Tue, Oct 22, 2013 at 2:04 AM, Taiyun Wei  wrote:
> Many thanks:)
>
> I have a list(), eg. named opt, I want to check and assign values to it:
>
> if(is.null(opt$a)) opt$a = 'x'
> if(is.null(opt$b)) opt$a = 'y'
> ...
>
> I need to do a lot of these jobs, so I write a function to simplify it:
>
> '%=%' = function(x, y){
> if(is.null(x)) {
> x <<- y
> }
> }
>
> x=NULL
> y=list()
>
>> is.null(x)
> [1] TRUE
>> is.null(y$a)
> [1] TRUE
>
>> x %=% 1;
>> x
> [1] 2
>> y$a %=% 2; ## Can't assign 2 to y$a, still NULL
>> y$a
> NULL
>
>
>
>
>
>
> On Mon, Oct 21, 2013 at 11:38 PM, Greg Snow <538...@gmail.com> wrote:
>>
>> See fortune(174).
>>
>> It is best to avoid using '<<-', if you tell us what you are trying to
>> accomplish then we may be able to provide a better means to accomplish
>> it.
>>
>> On Sat, Oct 19, 2013 at 10:28 PM, Taiyun Wei  wrote:
>> > Dear All,
>> >
>> >> opt = list()
>> >> opt$aa <<- TRUE
>> > Error in opt$aa <<- TRUE : object 'opt' not found
>> >
>> > Why?
>> >
>> > --
>> > Regards,
>> > Taiyun
>> > --
>> > Taiyun Wei 
>> > Homepage: http://blog.cos.name/taiyun/
>> > Phone: +86-15201142716
>> > Renmin University of China
>> >
>> > __
>> > R-help@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.
>>
>>
>>
>> --
>> Gregory (Greg) L. Snow Ph.D.
>> 538...@gmail.com
>
>
>
>
> --
> Regards,
> Taiyun
> --
> Taiyun Wei 
> Homepage: http://blog.cos.name/taiyun/
> Phone: +86-15201142716
> Renmin University of China



-- 
Gregory (Greg) L. Snow Ph.D.
538...@gmail.com

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Re: [R] Am I working with regularly spaced time series?

[Gabor Grothendieck]

On Tue, Oct 22, 2013 at 11:37 AM, Paul Gilbert  wrote:
>
>
> On 13-10-22 06:00 AM, Weiwu Zhang  wrote:
>>
>> My data is sampled once per minute.
>
>
> At the same second each minute or not? Regularly spaced would mean exactly
> one minute between observations.
>
>
> There are invalid samples, leaving
>>
>> a lot of holes in the samples, successful sample is around 80% of all
>> minutes in a day. and during the last 4 months sampling, one month's
>> data was stored on a harddisk that failed, leaving a month's gap in
>> between.
>
>
> This is called "missing observations". With regular spacing you need to fill
> in the holes with NA. With irregular spacing you can either drop the missing
> observations or, if you know the time at which they were missed, you could
> fill in with NA.
>
>
>>
>> So am I working with regularly spaced time series or not? Should I
>> padd all missing data with NAs, and start with ts(), and followed by
>> forecast package (which seems to have all the functions I need in the
>> begining) or should I start with a library with irregular time series
>> in mind?
>>
>> Also, ts() manual didn't say how to create time-series with one minute
>> as daltat. Its seems to assume time-series is about dates. So the data
>> I have with me, is it really time series at all?
>
>
> ts() representations works best with regularly spaced monthly, quarterly, or
> annual data. You can use it for other things if they fit nicely into the
> regular spaced observations with a frequency of observation, such as 12
> times per year or 60 times per hour. This usually only makes sense if the
> frequency has something to do with your problem, like seasonality questions.
> You can also use frequency 1 for one observation per period, like annual
> data, which in your case would be once per minute. I'm inclined to think
> that a zoo (see package zoo) represenation would fit your problem better.
>

Also note that the zoo package has two classes:

1. zoo for irregularly spaced series
2. zooreg for series with an underlying regularity but for which some
of the points are missing (which seems to be the situation under
discussion)

The two classes are nearly the same but zooreg series have a frequency
and some methods act differently -- most notably lag and diff.

-- 
Statistics & Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com

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Re: [R] Am I working with regularly spaced time series?

[Paul Gilbert]

On 13-10-22 06:00 AM, Weiwu Zhang  wrote:

My data is sampled once per minute.


At the same second each minute or not? Regularly spaced would mean 
exactly one minute between observations.


There are invalid samples, leaving

a lot of holes in the samples, successful sample is around 80% of all
minutes in a day. and during the last 4 months sampling, one month's
data was stored on a harddisk that failed, leaving a month's gap in
between.


This is called "missing observations". With regular spacing you need to 
fill in the holes with NA. With irregular spacing you can either drop 
the missing observations or, if you know the time at which they were 
missed, you could fill in with NA.




So am I working with regularly spaced time series or not? Should I
padd all missing data with NAs, and start with ts(), and followed by
forecast package (which seems to have all the functions I need in the
begining) or should I start with a library with irregular time series
in mind?

Also, ts() manual didn't say how to create time-series with one minute
as daltat. Its seems to assume time-series is about dates. So the data
I have with me, is it really time series at all?


ts() representations works best with regularly spaced monthly, 
quarterly, or annual data. You can use it for other things if they fit 
nicely into the regular spaced observations with a frequency of 
observation, such as 12 times per year or 60 times per hour. This 
usually only makes sense if the frequency has something to do with your 
problem, like seasonality questions. You can also use frequency 1 for 
one observation per period, like annual data, which in your case would 
be once per minute. I'm inclined to think that a zoo (see package zoo) 
represenation would fit your problem better.


HTH,
Paul


Newbie question indeed. Thanks.



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Re: [R] integer -> factor

[Bert Gunter]

... and ?ordered for bmi.

And if the OP has not already done so, read An Introduction to R or
other web tutorial and stop posting such basic questions here.

Cheers,
Bert

On Tue, Oct 22, 2013 at 8:21 AM, Sarah Goslee  wrote:
> Hi,
>
> You should probably start by reading
>
> ?factor
>
> Sarah
>
> On Tue, Oct 22, 2013 at 5:50 AM, luana  wrote:
>> Hi!
>> I have a dataset composed by bmi, sex, age, and race.
>> I have to convert bmi, sex and race in factor and they have still to be in
>> the same dataset with their names.
>> That's because I need to do an Ordered Logistic Regression.
>> Can you help me?
>> really tnx!
>>
>>
>
> --
> Sarah Goslee
> http://www.functionaldiversity.org
>
> __
> R-help@r-project.org mailing list
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-- 

Bert Gunter
Genentech Nonclinical Biostatistics

(650) 467-7374

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Re: [R] cor matrix in multivariate regression

[Martin Maechler]

> Suyan Tian 
> on Tue, 22 Oct 2013 01:18:10 + writes:

> Sorry to bother, I want to construct a correlation matrix
> in multivariate regression (several dependent variables
> and they are correlated in some ways) like the followings,

> 1   0.8   0  0 … 0 0 
> 0.8 1 0  0  …0 0 
> 00 1  0.8 …  0 0 
> 0   0  0.8 1  … 0 0 
> . .   . . ….

> . ..   .  

> 0  0  1  0.8 
> 0  0   0.8 1 

> Does anyone know how to do it? 

Of course, with many such problems in R, there are *many* ways.

I believe one of the nicest ways here is to use  toeplitz() :

  n <- 12  ## or whatever your  n is
  toeplitz(c(1,0.8, rep(0, n-2)))

Note that for larger n, under some circumstances it may be
beneficial to use the Matrix package and its *sparse* matrices,
e.g.,

> require(Matrix)
> n <- 12; toeplitz(as(c(1,0.8, rep(0, n-2)), "sparseVector"))
12 x 12 sparse Matrix of class "dsCMatrix"
 
 [1,] 1.0 0.8 .   .   .   .   .   .   .   .   .   .  
 [2,] 0.8 1.0 0.8 .   .   .   .   .   .   .   .   .  
 [3,] .   0.8 1.0 0.8 .   .   .   .   .   .   .   .  
 [4,] .   .   0.8 1.0 0.8 .   .   .   .   .   .   .  
 [5,] .   .   .   0.8 1.0 0.8 .   .   .   .   .   .  
 [6,] .   .   .   .   0.8 1.0 0.8 .   .   .   .   .  
 [7,] .   .   .   .   .   0.8 1.0 0.8 .   .   .   .  
 [8,] .   .   .   .   .   .   0.8 1.0 0.8 .   .   .  
 [9,] .   .   .   .   .   .   .   0.8 1.0 0.8 .   .  
[10,] .   .   .   .   .   .   .   .   0.8 1.0 0.8 .  
[11,] .   .   .   .   .   .   .   .   .   0.8 1.0 0.8
[12,] .   .   .   .   .   .   .   .   .   .   0.8 1.0
> 

Best regards,
Martin Maechler, ETH Zurich

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Re: [R] integer -> factor

[Sarah Goslee]

Hi,

You should probably start by reading

?factor

Sarah

On Tue, Oct 22, 2013 at 5:50 AM, luana  wrote:
> Hi!
> I have a dataset composed by bmi, sex, age, and race.
> I have to convert bmi, sex and race in factor and they have still to be in
> the same dataset with their names.
> That's because I need to do an Ordered Logistic Regression.
> Can you help me?
> really tnx!
>
>

-- 
Sarah Goslee
http://www.functionaldiversity.org

__
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Re: [R] XML package not working

[Steven Dwayne Randolph]

Ista,... Thank you for your response.   Here is what is occurring when I 
attempt to command-line install.
 
--
> install.packages('XML')
Installing package into ‘C:/Users/xxx/Documents/R/win-library/3.0’
(as ‘lib’ is unspecified)
trying URL 'http://cran.rstudio.com/bin/windows/contrib/3.0/XML_3.98-1.1.zip'
Content type 'application/zip' length 4287270 bytes (4.1 Mb)
opened URL
downloaded 4.1 Mb

Warning in install.packages :
  downloaded length 4276224 != reported length 4287270
Warning in install.packages :
  error 1 in extracting from zip file
Warning in install.packages :
  cannot open compressed file 'XML/DESCRIPTION', probable reason 'No such file 
or directory'
Error in install.packages : cannot open the connection

--

STeven
-Original Message-
From: Ista Zahn [mailto:istaz...@gmail.com] 
Sent: Tuesday, October 22, 2013 8:09 AM
To: Steven Dwayne Randolph
Cc: Duncan Murdoch; r-help@r-project.org; stevendrando...@aol.com; Piyush Singh 
- Network
Subject: Re: [R] XML package not working

Hi Steven,

I still don't understand why you are downloading it manually. What happens when 
you

install.packages("XML")

?

Best,
Ista

On Tue, Oct 22, 2013 at 8:03 AM, Steven Dwayne Randolph 
 wrote:
> Duncan... Thank you.
>
> 1.   I am able to download the XML file via my corporate network, 
> other packages without this same issue, even rcurl and bitops which are 
> pre-requisites on the same page as XML.
> 2.   I  have attempted to download this from my own wifi at home 
> using xfinity/Comcast to my personal pc and still get the same error on this 
> package alone.
> 3.   I am genuinely baffled by this package download and 
> install experience.
>  4.  I would gladly build this from source, If indeed I could 
> find the source and then use RTools to compile it.  That has been 
> unsuccessful as well.   Nightmare? Slightly.
>
> Thanks for your response.
> Steven
>
> -Original Message-
> From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
> Sent: Sunday, October 20, 2013 12:13 PM
> To: Steven Dwayne Randolph; r-help@r-project.org; Ista Zahn
> Cc: stevendrando...@aol.com
> Subject: Re: [R] XML package not working
>
> On 13-10-20 9:23 AM, Steven Dwayne Randolph wrote:
>> My apologies for not conforming to the posting guideline.
>>
>>
>> Sys.info()
>>   sysname  release   
>>version
>> "Windows"  "7 x64" "build 7601, 
>> Service Pack 1"
>>  nodename  machine   
>>  login
>> "xxNU247BZ1S" "x86-64"   
>>  "XX"
>>  user   effective_user
>> "xxx""xxx"
>>
>> When I attempt to install a local copy of the xml.zip file:
>>
>> in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
>>cannot open the connection
>> In addition: Warning messages:
>> 1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip 
>> file
>> 2: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
>>cannot open compressed file 'XML/DESCRIPTION', probable reason 'No such 
>> file or directory'
>
> I think it is pretty clear that the problem is at your end:  you aren't 
> downloading the file properly, even though everyone else is.  Perhaps you are 
> behind a firewall, or something else is interfering with your downloads?
>
> Duncan Murdoch
>
>>
>>
>> -Original Message-
>> From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
>> Sent: Saturday, October 19, 2013 8:23 PM
>> To: Steven Dwayne Randolph; r-help@r-project.org
>> Cc: stevendrando...@aol.com
>> Subject: Re: [R] XML package not working
>>
>> On 13-10-19 3:47 PM, Steven Dwayne Randolph wrote:
>>> I know I  cannot be the only one who is not able to install the XML package 
>>> from CRAN (zip or tar file)  Many packages depend on this XML package.  Can 
>>> someone help me either access the source for a good binary?  I have 
>>> received no assistance from the author/developer of the package.
>>
>> It installs fine for me.
>>
>> Duncan Murdoch
>>
>
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] integer -> factor

[luana]

Hi!
I have a dataset composed by bmi, sex, age, and race.
I have to convert bmi, sex and race in factor and they have still to be in
the same dataset with their names.
That's because I need to do an Ordered Logistic Regression.
Can you help me?
really tnx!



--
View this message in context: 
http://r.789695.n4.nabble.com/integer-factor-tp4678778.html
Sent from the R help mailing list archive at Nabble.com.

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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.

Re: [R] list and <<-

[Taiyun Wei]

Many thanks:)

I have a list(), eg. named opt, I want to check and assign values to it:

if(is.null(opt$a)) opt$a = 'x'
if(is.null(opt$b)) opt$a = 'y'
...

I need to do a lot of these jobs, so I write a function to simplify it:

'%=%' = function(x, y){
if(is.null(x)) {
x <<- y
}
}

x=NULL
y=list()

> is.null(x)
[1] TRUE
> is.null(y$a)
[1] TRUE

> x %=% 1;
> x
[1] 2
> y$a %=% 2; ## Can't assign 2 to y$a, still NULL
> y$a
NULL






On Mon, Oct 21, 2013 at 11:38 PM, Greg Snow <538...@gmail.com> wrote:

> See fortune(174).
>
> It is best to avoid using '<<-', if you tell us what you are trying to
> accomplish then we may be able to provide a better means to accomplish
> it.
>
> On Sat, Oct 19, 2013 at 10:28 PM, Taiyun Wei  wrote:
> > Dear All,
> >
> >> opt = list()
> >> opt$aa <<- TRUE
> > Error in opt$aa <<- TRUE : object 'opt' not found
> >
> > Why?
> >
> > --
> > Regards,
> > Taiyun
> > --
> > Taiyun Wei 
> > Homepage: http://blog.cos.name/taiyun/
> > Phone: +86-15201142716
> > Renmin University of China
> >
> > __
> > R-help@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.
>
>
>
> --
> Gregory (Greg) L. Snow Ph.D.
> 538...@gmail.com
>



-- 
Regards,
Taiyun
--
Taiyun Wei 
Homepage: http://blog.cos.name/taiyun/
Phone: +86-15201142716
Renmin University of China

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Re: [R] colour code areas of a plot

[Olivier Crouzet]

On Tue, 22 Oct 2013 16:43:18 +0200
Martin Batholdy  wrote:

Hi,

you should replace your "color names" by calls to the rgb() function in
order to generate the adequate colors, something like:

bg_colors <- c(rep (rgb (0,1,0),20), rep (rgb (0,1,1),10), rep (rgb
(0,1,0),20), rep(rgb (1,0,0),5), rep(rgb (1,1,0),45)) 

(though it should obviously be automatically extracted from your data I
suppose).

Then it is possible to use the color vector as an option to
any plotting command e.g.:

plot(color_scheme$t, color_scheme$t,col=bg_colors)

or (something like):

rect(xleft = color_scheme$t[1:99], ybottom = -1, xright = color_scheme$t
[2:100], ytop = 1, col=bg_colors, lwd=0) 

Olivier.


> Hi,
> 
> I would like to colour different areas of a plot.
> But I don't know how to do this efficiently.
> 
> As an example;
> 
> lets say three stimuli were presented in an experiment, alternating,
> one at a time. Now I want to plot time on the x-axis and the
> plot-area should colour code the stimulus that was presented at that
> time interval (green for stimulus 1, yellow for stimulus 2 etc.)
> 
> 
> here an example:
> (t = time)
> 
> 
> t <- 1:100
> bg_colors <- c(rep('green',20), rep('yellow',10), rep('green',20), rep
> ('red',5), rep('yellow',45)) 
> 
> color_scheme <- data.frame(t, bg_colors)
> 
> plot(c(), c(), xlim = c(1,100), ylim=c(-1,1))
> 
> 
> rect(xleft = 1, ybottom = -1, xright = 20, ytop = 1, col = 'green',
> lwd=0) rect(xleft = 20, ybottom = -1, xright = 30, ytop = 1, col =
> 'yellow', lwd=0) …
> 
> 
> now how can I do this efficiently based on the color_scheme
> data-frame and without having to manually draw all the rectangles as
> in the example above?
> 
> 
> 
> thanks for any suggestions!
> __
> R-help@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.


-- 
  Olivier Crouzet, PhD
  Laboratoire de Linguistique -- EA3827
  Université de Nantes
  Chemin de la Censive du Tertre - BP 81227
  44312 Nantes cedex 3
  France

 phone:(+33) 02 40 14 14 05 (lab.)
   (+33) 02 40 14 14 36 (office)
 fax:  (+33) 02 40 14 13 27
 e-mail:   olivier.crou...@univ-nantes.fr

  http://www.lling.univ-nantes.fr/

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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.

Re: [R] [ADMB Users] R2admb compile problem

[Allan Clark]

Hello guys

Arni, you were correct. The R search path contained 'C:/MinGW/bin;' which
contains a g++ compiler. I removed it and now it works fine!
Thank you for the help.


Just for completeness sake: (the R code and output is included below)

#


> require(R2admb)
> setup_admb()
[1] "c:\\ADMB\\admb101-gcc452-win64"
> fn="Function1"
> compile_admb(fn, verbose=T)
compiling with args: ' ' ...
compile output:
*** tpl2cpp Function1 xxglobal.tmp xxhtop.tmp header.tmp xxalloc.tmp
xxtopm.tmp 1 file(s) copied. *** adcomp Function1 g++ -c -O3
-Wno-deprecated -D__GNUDOS__ -Dlinux -DOPT_LIB -DUSE_LAPLACE -fpermissive
-I. -I"c:\ADMB\admb101-gcc452-win64\include" -o Function1.obj Function1.cpp
*** adlink Function1 g++ -s -static -L"c:\ADMB\admb101-gcc452-win64\lib"
Function1.obj -ldf1b2o -ladmod -ladt -lado -ldf1b2o -ladmod -ladt -lado -o
Function1 Done
compile log:

> run_admb(fn)

> results <- read_admb(fn)

> results
Model file: Function1
Negative log-likelihood: 0
Coefficients:
x
5

> clean_admb(fn)
#=


I am not sure why 'C:/MinGW/bin;' is in the R search path since it it
not in any of the environment variables?

regards








On 21 October 2013 15:56, Ben Bolker  wrote:

> On 13-10-21 09:53 AM, Arni Magnusson wrote:
> > I've seen similar linking errors when there's more than one compiler in
> > the PATH, causing a version conflict. In this case, the solution is to
> > remove all but one compiler from the PATH.
> >
> > Arni
> >
>
>  So in this respect, to see what's going on in the within-R2admb/R
> context, you should run
>
> Sys.getenv("PATH")
>
> and compare it with whatever the equivalent command for examining the
> PATH environment variable is in Windows (I don't know, my Windows skills
> are really rusty)
>
> >
> >
> >> On 13-10-21 05:48 AM, Ben Stevenson wrote:
> >>
> >>> Hi Allan,
> >>>
> >>> Given that ADMB seems to be working fine on its own, you're probably
> >>> better off asking this question to an R2admb package maintainer as
> >>> only a few people here use R2admb.
> >>>
> >>> R2admb uses the system() R function to in order to compile the .tpl
> >>> file. My guess is that it is not finding the admb command, and this
> >>> will be something to do with environment variables. What happens when
> >>> you run system("admb") in R? Do you get an error saying about the
> >>> admb command not being found? This would confirm my suspicion.
> >>>
> >>> If this is the case, find where the admb binary is on your system.
> >>> From the output of setup_admb, my guess is that it's in
> >>> c:\\ADMB\\admb101-gcc452-win64\\bin. If you call Sys.getenv("PATH"),
> >>> does this directory appear?
> >>>
> >>> Cheers,
> >>>
> >>> Ben
> >>
> >>
> >>
> >> On Mon, 21 Oct 2013, Ben Bolker wrote:
> >>
> >> I am the R2admb package maintainer -- I saw this message go by on the
> >> R mailing list as well.
> >>
> >> The only clue I have here is that something is going wrong with the
> >> linking -- that's what's indicated by the last line you included in
> >> your R-help message,
> >>
> >> 'collect2: ld returned 1 exit status'
> >>
> >> Can you provide more of the 'verbose' output?  I wonder if there is an
> >> environment variable related to linking that's set in your external
> >> environment but not within R.  (Do you have spaces in any of your path
> >> names ... ?)
> >>
> >> You can respond to the list or e-mail me off-list (my e-mail is
> >> available via maintainer("R2admb") ...
> >>
> > ___
> > Users mailing list
> > us...@admb-project.org
> > http://lists.admb-project.org/mailman/listinfo/users
>
> ___
> Users mailing list
> us...@admb-project.org
> http://lists.admb-project.org/mailman/listinfo/users
>

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

Re: [R] XML package not working

[Steven Dwayne Randolph]

Duncan... Thank you.  
 
1.   I am able to download the XML file via my corporate network, other 
packages without this same issue, even rcurl and bitops which are 
pre-requisites on the same page as XML.
2.   I  have attempted to download this from my own wifi at home using 
xfinity/Comcast to my personal pc and still get the same error on this package 
alone.  
3.   I am genuinely baffled by this package download and 
install experience.
 4.  I would gladly build this from source, If indeed I could 
find the source and then use RTools to compile it.  That has been unsuccessful 
as well.   Nightmare? Slightly. 

Thanks for your response.
Steven

-Original Message-
From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com] 
Sent: Sunday, October 20, 2013 12:13 PM
To: Steven Dwayne Randolph; r-help@r-project.org; Ista Zahn
Cc: stevendrando...@aol.com
Subject: Re: [R] XML package not working

On 13-10-20 9:23 AM, Steven Dwayne Randolph wrote:
> My apologies for not conforming to the posting guideline.
>
>
> Sys.info()
>   sysname  release
>   version
> "Windows"  "7 x64" "build 7601, 
> Service Pack 1"
>  nodename  machine
> login
> "xxNU247BZ1S" "x86-64"
> "XX"
>  user   effective_user
> "xxx""xxx"
>
> When I attempt to install a local copy of the xml.zip file:
>
> in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
>cannot open the connection
> In addition: Warning messages:
> 1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip 
> file
> 2: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
>cannot open compressed file 'XML/DESCRIPTION', probable reason 'No such 
> file or directory'

I think it is pretty clear that the problem is at your end:  you aren't 
downloading the file properly, even though everyone else is.  Perhaps you are 
behind a firewall, or something else is interfering with your downloads?

Duncan Murdoch

>
>
> -Original Message-
> From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
> Sent: Saturday, October 19, 2013 8:23 PM
> To: Steven Dwayne Randolph; r-help@r-project.org
> Cc: stevendrando...@aol.com
> Subject: Re: [R] XML package not working
>
> On 13-10-19 3:47 PM, Steven Dwayne Randolph wrote:
>> I know I  cannot be the only one who is not able to install the XML package 
>> from CRAN (zip or tar file)  Many packages depend on this XML package.  Can 
>> someone help me either access the source for a good binary?  I have received 
>> no assistance from the author/developer of the package.
>
> It installs fine for me.
>
> Duncan Murdoch
>

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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.

Re: [R] colour code areas of a plot

[Ken Knoblauch]

Martin Batholdy  googlemail.com> writes:
> I would like to colour different areas of a plot.
> But I don't know how to do this efficiently.
> 
> here an example:
> (t = time)
> 
> t <- 1:100
> bg_colors <- c(rep('green',20), rep('yellow',10), 
rep('green',20), rep('red',5),
> rep('yellow',45)) 
> 
> color_scheme <- data.frame(t, bg_colors)
> 
> plot(c(), c(), xlim = c(1,100), ylim=c(-1,1))
> 
> rect(xleft = 1, ybottom = -1, xright = 20, ytop = 1, 
col = 'green', lwd=0) 
> rect(xleft = 20, ybottom = -1, xright = 30, ytop = 1, 
col = 'yellow', lwd=0) 
> …
> 
> now how can I do this efficiently based on the c
olor_scheme data-frame
 and without having to manually draw
> all the rectangles as in the example above?

The first 4 arguments of rect can be vectors 
as can be the col argument.  So you might be able to
draw all of the regions with a single call to rect.
I've done this to create alternating light and dark
regions to highlight condition changes.
See ?rect, of course.

> 
> thanks for any suggestions!
> 

-- 
Kenneth Knoblauch
Inserm U846
Stem-cell and Brain Research Institute
Department of Integrative Neurosciences
18 avenue du Doyen Lépine
69500 Bron
France
tel: +33 (0)4 72 91 34 77
fax: +33 (0)4 72 91 34 61
portable: +33 (0)6 84 10 64 10
http://www.sbri.fr/members/kenneth-knoblauch.html

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

[R] colour code areas of a plot

[Martin Batholdy]

Hi,

I would like to colour different areas of a plot.
But I don't know how to do this efficiently.

As an example;

lets say three stimuli were presented in an experiment, alternating, one at a 
time.
Now I want to plot time on the x-axis and the plot-area should colour code the 
stimulus that was presented at that time interval
(green for stimulus 1, yellow for stimulus 2 etc.)


here an example:
(t = time)


t <- 1:100
bg_colors <- c(rep('green',20), rep('yellow',10), rep('green',20), 
rep('red',5), rep('yellow',45)) 

color_scheme <- data.frame(t, bg_colors)

plot(c(), c(), xlim = c(1,100), ylim=c(-1,1))


rect(xleft = 1, ybottom = -1, xright = 20, ytop = 1, col = 'green', lwd=0) 
rect(xleft = 20, ybottom = -1, xright = 30, ytop = 1, col = 'yellow', lwd=0) 
…


now how can I do this efficiently based on the color_scheme data-frame and 
without having to manually draw all the rectangles as in the example above?



thanks for any suggestions!
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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.

Re: [R] How do I use simple calls to java methods?

[Jeff Newmiller]

I don't use rJava, but numerous examples came up when I Googled for "rjava 
examples". The fact that you have not referenced any of that material may be 
leaving a bad taste in the mouths of those few people who do use both R and 
Java. Or, they may just not spend time wading through emails on this list.

Also, note that Nabble has a poor reputation on this list, because it 
encourages you to look at Nabble for message history rather than including it 
in the email. Please re-read the Posting Guide for this list.
---
Jeff NewmillerThe .   .  Go Live...
DCN:Basics: ##.#.   ##.#.  Live Go...
  Live:   OO#.. Dead: OO#..  Playing
Research Engineer (Solar/BatteriesO.O#.   #.O#.  with
/Software/Embedded Controllers)   .OO#.   .OO#.  rocks...1k
--- 
Sent from my phone. Please excuse my brevity.

Hurr  wrote:
>I am surprised to not get a reply. 
>I suppose this means that extremely few, if any, use rJava.
>
>rJava.pdf says this, but I am too stupid to interpret it:
>Description
>.jcall calls a Java method with the supplied arguments.
>Usage
>.jcall(obj, returnSig = "V", method, ..., evalArray = TRUE,
>evalString = TRUE, check = TRUE, interface = "RcallMethod",
>simplify = FALSE, use.true.class = FALSE)
>
>Perhaps it means that to replace:
>  calCk <- calStgOfLinTim(linTm,tlev) 
>and use something like:
>  calCk <- .jcall(CalqsLin.class,returnSig = "S",
>  calStgOfLinTim(linTm,tlev),evalArray=FALSE, 
>  evalString = TRUE, check = TRUE, interface = "RcallMethod",
>  simplify = FALSE, use.true.class = TRUE)
>
>I suppose there are other setup things to do, 
>like start the JVM (java Virtual machine)
>and I don't know what obj means.
>
>Anyway, if I am able to do these simple java method calls, 
>it will be a big plus to our data analysis lab to use R conveniently.
>
>Please help
>
>
>
>
>--
>View this message in context:
>http://r.789695.n4.nabble.com/How-do-I-use-simple-calls-to-java-methods-tp4678753p4678786.html
>Sent from the R help mailing list archive at Nabble.com.
>
>__
>R-help@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.

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Re: [R] R - How to "physically" Increase Speed

[Prof J C Nash (U30A)]

The advice given is sensible. For a timing study see

http://rwiki.sciviews.org/doku.php?id=tips:rqcasestudy

We found that for optimization calculations, putting the objective
function calculation or parts thereof in Fortran was helpful. But we
kept those routines pretty small -- less than a page -- and we just
called them to evaluate things, avoiding passing around information back
and forth to R.

JN




On 13-10-22 06:00 AM, r-help-requ...@r-project.org wrote:
> Message: 58
> Date: Tue, 22 Oct 2013 05:47:15 -0400
> From: Jim Holtman 
> To: Alexandre Khelifa 
> Cc: "r-help@r-project.org" 
> Subject: Re: [R] R - How to "physically" Increase Speed
> Message-ID: <73d989da-b6b3-421d-838c-903da3435...@gmail.com>
> Content-Type: text/plain; charset=us-ascii
> 
> I would start with taking a subset of the data (definitely some that would 
> run in less than 10 minutes) and use the profiler "Rprof" to see where time 
> is being spent.  you can use the the task monitor (if on windows) to see how 
> much memory you are using; it sounds like you did not need the extra memory.
> 
> You might see if you can partition your data so you can run multiple versions 
> of R and then merge the results.
> 
> Anything that takes more than a half hour, for me, is looked into to see 
> where the problems are.  For example dataframes arevexpensive to access and 
> conversion to matrices is one way to speed it up.  the is where the profiler 
> helps.
>

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

Re: [R] speeding up "sum of squared differences" calculation

[Hadley Wickham]

> There's little practical difference; both hover from 0.00 to 0.03 s system 
> time. I could barely tell the difference even averaged over 100 runs; I was 
> getting an average around 0.007 (system time) and 2.5s user time for both 
> methods.

It's almost always better to use a high precision timer, as
implemented in the microbenchmark package:

library(microbenchmark)

ssqdif <- function(X, Y=X) {
  #From 'outer' without modification
  Y <- rep(Y, rep.int(length(X), length(Y)))
  X <- rep(X, times = ceiling(length(Y)/length(X)))
  #For this case:
  sum((X-Y)^2) #SLIGHTLY quicker than d<-X-Y; sum(d*d)
}

outerdif <- function(X, Y = X) {
  gg <- outer(X, Y, FUN="-")
  sum(gg*gg)
}

X <- runif(1000)

microbenchmark(
  ssqdif(X),
  outerdif(X)
)

Unit: milliseconds
expr  min   lq   median   uq  max neval
   ssqdif(X) 9.035473 9.912253 14.65940 16.34044 68.30620   100
 outerdif(X) 8.962955 9.647820 14.85338 17.00048 66.89351   100

Looking at the range of values you can see indeed that the performance
is indeed almost identical.

Hadley

-- 
Chief Scientist, RStudio
http://had.co.nz/

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Re: [R] More Columns than column names Error

[arun]

Hi,
Try:
 lines1 <- readLines("Garbage.txt",warn=FALSE)
dat1 <- 
read.table(text=gsub("\t+","\t",lines1),stringsAsFactors=FALSE,sep="\t",check.names=FALSE,header=TRUE)
 str(dat1)
#'data.frame':    10 obs. of  3 variables:
# $ Material    : chr  "Food Scraps" "Glass" "Metals" "Paper" ...
# $ Weight(Million Tons): num  25.9 12.8 18 86.7 24.7 ...
# $ Percent : num  11.2 5.5 7.8 37.4 10.7 6.8 5.5 11.9 3.2 100
jpeg("garbageweight.jpg",width=800)
 
barplot(dat1[-10,2],names.arg=dat1[-10,1],ylab=colnames(dat1)[2],col=rainbow(9),main="American
 garbage")
 dev.off()


A.K.


Hello guys, I'm having this weird problem with my assignment. I can't seem to 
import the data that I have created. 

I keep getting an error that says "Error: More Columns than Column names" 

This is my data file. 
Garbage.txt

Was also wondering if you guys could send me into the right direction on how to 
do this. 

1. Create a data frame with the data given above. 
2. Create the bar plot for weight variable with appropriate labels. Resize the 
graphics 
panel/ window so that all labels are visible. 
3. Add colors. Suppose n is the number of bars. 
> barplot(..., col = rainbow(n)) 
4. Save the plot to garbageweight.jpg 

This is how it's supposed to look like at the end.

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Re: [R] More Columns than column names Error

[Keith Jewell]

Carl is right.

Going to the nabble post and looking in the source data file 
 I see the 
headings row has 'Material' tab 'Weight...' tab 'Percent'.
Each of the data rows has 1 tab character between the 'Material' and 
'Weight' columns and 3 tab characters between the 'Weight...' and 
'Percent' columns.


On 22/10/2013 14:15, Carl Witthoft wrote:

What is the exact code you are using to try to load this file?
I strongly suspect the problem is a mixture of spaces and multiple tabs in
your text file.



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Re: [R] XML package not working

[Duncan Murdoch]

On 13-10-22 9:19 AM, Steven Dwayne Randolph wrote:

Ista,... Thank you for your response.   Here is what is occurring when I 
attempt to command-line install.
  
--

install.packages('XML')

Installing package into ‘C:/Users/xxx/Documents/R/win-library/3.0’
(as ‘lib’ is unspecified)
trying URL 'http://cran.rstudio.com/bin/windows/contrib/3.0/XML_3.98-1.1.zip'
Content type 'application/zip' length 4287270 bytes (4.1 Mb)
opened URL
downloaded 4.1 Mb

Warning in install.packages :
   downloaded length 4276224 != reported length 4287270
Warning in install.packages :
   error 1 in extracting from zip file
Warning in install.packages :
   cannot open compressed file 'XML/DESCRIPTION', probable reason 'No such file 
or directory'
Error in install.packages : cannot open the connection


Read the message:  your download is failing.  The file is being mangled 
during the download.


I just tried from the same mirror, and it was fine.

As I said before, there is something wrong on your system that is 
messing up file transfers.


You could try downloading the file some other way, and confirming that 
the length comes out to 4287270.


Duncan Murdoch



--

STeven
-Original Message-
From: Ista Zahn [mailto:istaz...@gmail.com]
Sent: Tuesday, October 22, 2013 8:09 AM
To: Steven Dwayne Randolph
Cc: Duncan Murdoch; r-help@r-project.org; stevendrando...@aol.com; Piyush Singh 
- Network
Subject: Re: [R] XML package not working

Hi Steven,

I still don't understand why you are downloading it manually. What happens when 
you

install.packages("XML")

?

Best,
Ista

On Tue, Oct 22, 2013 at 8:03 AM, Steven Dwayne Randolph 
 wrote:

Duncan... Thank you.

 1.   I am able to download the XML file via my corporate network, 
other packages without this same issue, even rcurl and bitops which are 
pre-requisites on the same page as XML.
 2.   I  have attempted to download this from my own wifi at home using 
xfinity/Comcast to my personal pc and still get the same error on this package 
alone.
 3.   I am genuinely baffled by this package download and 
install experience.
  4.  I would gladly build this from source, If indeed I could 
find the source and then use RTools to compile it.  That has been unsuccessful 
as well.   Nightmare? Slightly.

Thanks for your response.
Steven

-Original Message-
From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
Sent: Sunday, October 20, 2013 12:13 PM
To: Steven Dwayne Randolph; r-help@r-project.org; Ista Zahn
Cc: stevendrando...@aol.com
Subject: Re: [R] XML package not working

On 13-10-20 9:23 AM, Steven Dwayne Randolph wrote:

My apologies for not conforming to the posting guideline.


Sys.info()
   sysname  release 
 version
 "Windows"  "7 x64" "build 7601, Service 
Pack 1"
  nodename  machine 
   login
 "xxNU247BZ1S" "x86-64"
"XX"
  user   effective_user
 "xxx""xxx"

When I attempt to install a local copy of the xml.zip file:

in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
cannot open the connection
In addition: Warning messages:
1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip
file
2: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
cannot open compressed file 'XML/DESCRIPTION', probable reason 'No such 
file or directory'


I think it is pretty clear that the problem is at your end:  you aren't 
downloading the file properly, even though everyone else is.  Perhaps you are 
behind a firewall, or something else is interfering with your downloads?

Duncan Murdoch




-Original Message-
From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
Sent: Saturday, October 19, 2013 8:23 PM
To: Steven Dwayne Randolph; r-help@r-project.org
Cc: stevendrando...@aol.com
Subject: Re: [R] XML package not working

On 13-10-19 3:47 PM, Steven Dwayne Randolph wrote:

I know I  cannot be the only one who is not able to install the XML package 
from CRAN (zip or tar file)  Many packages depend on this XML package.  Can 
someone help me either access the source for a good binary?  I have received no 
assistance from the author/developer of the package.


It installs fine for me.

Duncan Murdoch





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Re: [R] speeding up "sum of squared differences" calculation

[Bos, Roger]

Thanks for the Rccp example Ken!  I vaguely knew about Rccp, but I didn't 
realize how easy it was to use it.

-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On 
Behalf Of Kenneth Knoblauch
Sent: Tuesday, October 22, 2013 9:13 AM
To: S Ellison
Cc: r-help@r-project.org
Subject: Re: [R] speeding up "sum of squared differences" calculation

Actually, you don't need to use c() in the dist example, either, which should 
shave off a few microseconds for a function call.  It was late last night ...

Ken

On 22-10-2013 15:08, S Ellison wrote:
>> Conclusion: hard to beat outer() for this purpose in R
> ... unless you use Ken Knoblauch's suggestion of dist() or Rccp.
> 
> Nice indeed.
> 
> 
> S Ellison
> 
> 
> ***
> This email and any attachments are confidential. Any use, copying or 
> disclosure other than by the intended recipient is unauthorised. If 
> you have received this message in error, please notify the sender 
> immediately via +44(0)20 8943 7000 or notify postmas...@lgcgroup.com 
> and delete this message and any copies from your computer and network.
> LGC Limited. Registered in England 2991879.
> Registered office: Queens Road, Teddington, Middlesex, TW11 0LY, UK

--
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Inserm U846
Stem-cell and Brain Research Institute
Department of Integrative Neurosciences
18 avenue du Doyen Lépine
69500 Bron
France
tel: +33 (0)4 72 91 34 77
fax: +33 (0)4 72 91 34 61
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Re: [R] More Columns than column names Error

[Carl Witthoft]

What is the exact code you are using to try to load this file?
I strongly suspect the problem is a mixture of spaces and multiple tabs in
your text file.



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Re: [R] How do I use simple calls to java methods?

[Hurr]

I am surprised to not get a reply. 
I suppose this means that extremely few, if any, use rJava.

rJava.pdf says this, but I am too stupid to interpret it:
Description
.jcall calls a Java method with the supplied arguments.
Usage
.jcall(obj, returnSig = "V", method, ..., evalArray = TRUE,
evalString = TRUE, check = TRUE, interface = "RcallMethod",
simplify = FALSE, use.true.class = FALSE)

Perhaps it means that to replace:
  calCk <- calStgOfLinTim(linTm,tlev) 
and use something like:
  calCk <- .jcall(CalqsLin.class,returnSig = "S",
  calStgOfLinTim(linTm,tlev),evalArray=FALSE, 
  evalString = TRUE, check = TRUE, interface = "RcallMethod",
  simplify = FALSE, use.true.class = TRUE)

I suppose there are other setup things to do, 
like start the JVM (java Virtual machine)
and I don't know what obj means.

Anyway, if I am able to do these simple java method calls, 
it will be a big plus to our data analysis lab to use R conveniently.

Please help




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Re: [R] speeding up "sum of squared differences" calculation

[Kenneth Knoblauch]

Actually, you don't need to use c() in the dist example, either, which 
should shave off a few microseconds for a function call.  It was late 
last night ...


Ken

On 22-10-2013 15:08, S Ellison wrote:

Conclusion: hard to beat outer() for this purpose in R

... unless you use Ken Knoblauch's suggestion of dist() or Rccp.

Nice indeed.


S Ellison


***
This email and any attachments are confidential. Any use, copying or
disclosure other than by the intended recipient is unauthorised. If
you have received this message in error, please notify the sender
immediately via +44(0)20 8943 7000 or notify postmas...@lgcgroup.com
and delete this message and any copies from your computer and network.
LGC Limited. Registered in England 2991879.
Registered office: Queens Road, Teddington, Middlesex, TW11 0LY, UK


--
Kenneth Knoblauch
Inserm U846
Stem-cell and Brain Research Institute
Department of Integrative Neurosciences
18 avenue du Doyen Lépine
69500 Bron
France
tel: +33 (0)4 72 91 34 77
fax: +33 (0)4 72 91 34 61
portable: +33 (0)6 84 10 64 10
http://www.sbri.fr/members/kenneth-knoblauch.html

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Re: [R] speeding up "sum of squared differences" calculation

[S Ellison]

> Conclusion: hard to beat outer() for this purpose in R
... unless you use Ken Knoblauch's suggestion of dist() or Rccp.

Nice indeed.

 
S Ellison


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Re: [R] speeding up "sum of squared differences" calculation

[S Ellison]

> I am using a sum of squared differences in the objective function of an
> optimization problem I am doing and I have managed to speed it up using
> the outer function versus the nested for loops, but my suspicion is
> that the calculation could be done even quicker.  Please see the code
> below for a simple example.  If anyone can point out a faster way I
> would appreciate it greatly.

First, look at ?system.time ; it's intended for finding out how much compute 
time a command takes. You're also calculating elapsed time which is dependent 
on (among other things) other processes running so maybe not the most reliable 
thing for benchmarking. 

Second, outer() is fast because it avoids loops and uses the fastest vector 
routines R can (essentially, replicating the vector and then relying on simple 
subtraction of vectors). In principle calling outer() loses a little time in 
internal checks on what object types and function you've provided etc.; in 
practice that doesn't add up to much. You can check by using just the core code 
from outer with an added multiplication instead of the dimensioning statement:

ssqdif <- function(X, Y=X) {
  #From 'outer' without modification
Y <- rep(Y, rep.int(length(X), length(Y)))
X <- rep(X, times = ceiling(length(Y)/length(X)))
#For this case:
sum((X-Y)^2) #SLIGHTLY quicker than d<-X-Y; sum(d*d)
}

system.time(ssqdif(X))

#Comparing outer() method:
system.time({gg <- outer(X, X, FUN="-"); sum(gg*gg)})

There's little practical difference; both hover from 0.00 to 0.03 s system 
time. I could barely tell the difference even averaged over 100 runs; I was 
getting an average around 0.007 (system time) and 2.5s user time for both 
methods.

Conclusion: hard to beat outer() for this purpose in R

S Ellison




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Re: [R] XML package not working

[Ista Zahn]

Hi Steven,

I still don't understand why you are downloading it manually. What
happens when you

install.packages("XML")

?

Best,
Ista

On Tue, Oct 22, 2013 at 8:03 AM, Steven Dwayne Randolph
 wrote:
> Duncan... Thank you.
>
> 1.   I am able to download the XML file via my corporate network, 
> other packages without this same issue, even rcurl and bitops which are 
> pre-requisites on the same page as XML.
> 2.   I  have attempted to download this from my own wifi at home 
> using xfinity/Comcast to my personal pc and still get the same error on this 
> package alone.
> 3.   I am genuinely baffled by this package download and 
> install experience.
>  4.  I would gladly build this from source, If indeed I could 
> find the source and then use RTools to compile it.  That has been 
> unsuccessful as well.   Nightmare? Slightly.
>
> Thanks for your response.
> Steven
>
> -Original Message-
> From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
> Sent: Sunday, October 20, 2013 12:13 PM
> To: Steven Dwayne Randolph; r-help@r-project.org; Ista Zahn
> Cc: stevendrando...@aol.com
> Subject: Re: [R] XML package not working
>
> On 13-10-20 9:23 AM, Steven Dwayne Randolph wrote:
>> My apologies for not conforming to the posting guideline.
>>
>>
>> Sys.info()
>>   sysname  release   
>>version
>> "Windows"  "7 x64" "build 7601, 
>> Service Pack 1"
>>  nodename  machine   
>>  login
>> "xxNU247BZ1S" "x86-64"   
>>  "XX"
>>  user   effective_user
>> "xxx""xxx"
>>
>> When I attempt to install a local copy of the xml.zip file:
>>
>> in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
>>cannot open the connection
>> In addition: Warning messages:
>> 1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip
>> file
>> 2: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
>>cannot open compressed file 'XML/DESCRIPTION', probable reason 'No such 
>> file or directory'
>
> I think it is pretty clear that the problem is at your end:  you aren't 
> downloading the file properly, even though everyone else is.  Perhaps you are 
> behind a firewall, or something else is interfering with your downloads?
>
> Duncan Murdoch
>
>>
>>
>> -Original Message-
>> From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
>> Sent: Saturday, October 19, 2013 8:23 PM
>> To: Steven Dwayne Randolph; r-help@r-project.org
>> Cc: stevendrando...@aol.com
>> Subject: Re: [R] XML package not working
>>
>> On 13-10-19 3:47 PM, Steven Dwayne Randolph wrote:
>>> I know I  cannot be the only one who is not able to install the XML package 
>>> from CRAN (zip or tar file)  Many packages depend on this XML package.  Can 
>>> someone help me either access the source for a good binary?  I have 
>>> received no assistance from the author/developer of the package.
>>
>> It installs fine for me.
>>
>> Duncan Murdoch
>>
>

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Re: [R] Error in heatmap

[Adams, Jean]

Do you have a row or column that is all missing?
 sum(apply(is.na(as.matrix(SPIV2)), 1, all)) > 0
 sum(apply(is.na(as.matrix(SPIV2)), 2, all)) > 0

For example, this code
 m <- as.matrix(mtcars)
 m[8, ] <- NA
 heatmap(m, na.rm=TRUE)
throws this error
 Error in hclustfun(distfun(x)) :
   NA/NaN/Inf in foreign function call (arg 11)

Jean



On Mon, Oct 21, 2013 at 1:04 PM, David Romero wrote:

> Hi,
>
>
>
> Could you please help?
>
>
>
> Heatmap  doesn't work with:
>
>
>
> > heatmap(as.matrix(SPIV2),na.rm = T)
>
> Error in hclustfun(distfun(x)) :
>
>   NA/NaN/Inf in foreign function call (arg 11)
>
>
>
> There are no 0 data rows or column
>
>
>
> Thanks a lot
>
>
>
> Regards
>
> ---
>
> David
>
>
>
>
> __
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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.
>
>

[[alternative HTML version deleted]]

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Re: [R] May I send a zip attachment to a post?

[Carl Witthoft]

Barry Rowlingson wrote
> On Mon, Oct 21, 2013 at 10:51 PM, David Winsemius
> <

> dwinsemius@

> > wrote:
>>
>> On Oct 21, 2013, at 2:15 PM, Hurr wrote:
>>
>>> May I send a .zip file attached to a post?
>>
>> No.
> 
>  That's not explicit from the posting guide:
> 
> "No binary attachments except for PS, PDF, and some image and archive
> formats "
> 
>  you have to click through to the General Instructions to see:
> 
> "Furthermore, most binary e-mail attachments are not accepted, i.e.,
> they are removed from the posting completely. As an exception, we
> allow application/pdf, application/postscript, and image/png (and
> x-tar and gzip on R-devel)."
> 
> Maybe the posting guide should be more explicit - not that anyone reads
> it...
> 
> Barry
> 
> __

> R-help@

>  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.

There's really no justification for attaching *any* file to a post.  Posts
should be clear and concise.  If there's really some value to providing an
image, a hyperlink should be provided.   I'd argue against any attempt to
work around the intent of the posting guide, regardless of the alleged
format of the attachment (remember, folks, if posting a "file.pdf" is
allowed, you could rename your "junk.zip" to "junk.pdf")





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Re: [R] Where is element 30?

[Gerrit Eichner]

Hi, Alaios,

check out

?which

and in particular its "Examples" and "See Also" section.

 Hth -- Gerrit

On Tue, 22 Oct 2013, Alaios wrote:


Hi I have a vector like that

readCsvFile$V1
 [1]  30  31  32  33  34  35  36  37  38  39 310 311 312 313 314 315 316 317 318
[20] 319 320 321  20  21  22  23  24  25  26  27  28  29 210 211 212 213 214 215
[39] 216 217 218 219 220 221 222 223  40  41  42  43  44  45  46  47  48  49 410
[58] 411 412 413 414 415 416 417 418 419 420 421


and I am looking to find where the number 31 is located. So I need one function 
to return me the index of where the number 31 is.
Is there a function for that in R?

Regards
Alex__
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[R] Where is element 30?

[Alaios]

Hi I have a vector like that

readCsvFile$V1
 [1]  30  31  32  33  34  35  36  37  38  39 310 311 312 313 314 315 316 317 318
[20] 319 320 321  20  21  22  23  24  25  26  27  28  29 210 211 212 213 214 215
[39] 216 217 218 219 220 221 222 223  40  41  42  43  44  45  46  47  48  49 410
[58] 411 412 413 414 415 416 417 418 419 420 421


and I am looking to find where the number 31 is located. So I need one function 
to return me the index of where the number 31 is.
Is there a function for that in R?

Regards
Alex
[[alternative HTML version deleted]]

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Re: [R] May I send a zip attachment to a post?

[Barry Rowlingson]

On Mon, Oct 21, 2013 at 10:51 PM, David Winsemius
 wrote:
>
> On Oct 21, 2013, at 2:15 PM, Hurr wrote:
>
>> May I send a .zip file attached to a post?
>
> No.

 That's not explicit from the posting guide:

"No binary attachments except for PS, PDF, and some image and archive formats "

 you have to click through to the General Instructions to see:

"Furthermore, most binary e-mail attachments are not accepted, i.e.,
they are removed from the posting completely. As an exception, we
allow application/pdf, application/postscript, and image/png (and
x-tar and gzip on R-devel)."

Maybe the posting guide should be more explicit - not that anyone reads it...

Barry

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Re: [R] R - How to "physically" Increase Speed

[Jim Holtman]

I would start with taking a subset of the data (definitely some that would run 
in less than 10 minutes) and use the profiler "Rprof" to see where time is 
being spent.  you can use the the task monitor (if on windows) to see how much 
memory you are using; it sounds like you did not need the extra memory.

You might see if you can partition your data so you can run multiple versions 
of R and then merge the results.

Anything that takes more than a half hour, for me, is looked into to see where 
the problems are.  For example dataframes arevexpensive to access and 
conversion to matrices is one way to speed it up.  the is where the profiler 
helps.

Sent from my iPad

On Oct 21, 2013, at 19:12, Alexandre Khelifa  wrote:

> Hi,
> 
> My name is Alexandre Khelifa and I have been using R at my work for about 2
> years. I have been working on a project when we do Monte Carlo Simulation
> and it involves a lot of calculations.
> 
> I am currently using R x64.3.0.1 and used to work on a 4GB machine.
> However, the calculation time was very long (about 2 weeks), and the IT
> team and I decided to add more memory and to make it a 8GB virtual machine.
> I also added the following line in my code:
> *
> *
> 
>   - *options(java.parameters = "-Xmx8192m") *
> 
> 
> I re-did the same calculations (4GB vs. 8GB) but did not see a significant
> increase in the calculation time, so I was wondering if I did anything
> wrong and/or what would be the best solution to increase this time.
> 
> Thanks a lot for your help and more generally for building such an amazing
> (and free) tool.
> Let me know if you have any questions.
> 
> Regards,
> 
> Alexandre Khelifa
> 
>[[alternative HTML version deleted]]
> 
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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] RWeka and multicore package

[Patrick Connolly]

On Thu, 17-Oct-2013 at 02:21PM -0300, Luís Paulo F. Garcia wrote:

|> I work very mutch with the packages RWeka and multicore. If you try to run
|> J48 or any tree of RWeka with multicore we hava some errors.
|> 
|> Example I:
|> 
|> library(RWeka);
|> library(multicore);
|> 
|> mclapply(1:100, function(i) {
|> J48(Species ~., iris);
|> });
|> 
|> 
|> Output:  "Error in .jcall(o, \"Ljava/lang/Class;\", \"getClass\") : \n
|> java.lang.ClassFormatError: Incompatible magic value 1347093252 in class
|> file java/lang/ProcessEnvironment$StringEnvironment\n"
|> 
|> 
|> Example II:
|> 
|> library(multicore);
|> 
|> mclapply(1:100, function(i) {
|> RWeka::J48(Species ~., iris);
|> });
|> 
|> Output: Erro em .jcall(x$classifier, "S", "toString") :
|>   RcallMethod: attempt to call a method of a NULL object.
|> 
|> 
|> Do you know some way to work with parallel processing and RWeka? I tried
|> MPI and SNOW without success.

Not much help, but I too have not been able to get parallelling RWeka
to work.  OTOH, what RWeka can do is very fast compared with, say, gbm
(which does work well with mclapply).  

I suspect that it has something to do with how Java is set up, but I
know nothing about setting up Java.




|> 
|> R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
|> Ubuntu 12.04 x64
|> 
|> 
|> -- 
|> Lu?s Paulo Faina Garcia
|> Engenheiro de Computa??o - Universidade de S?o Paulo
|> S?o Carlos - SP - Brasil
|> 
|>  [[alternative HTML version deleted]]
|> 

|> __
|> R-help@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.


-- 
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.   
   ___Patrick Connolly   
 {~._.~}   Great minds discuss ideas
 _( Y )_ Average minds discuss events 
(:_~*~_:)  Small minds discuss people  
 (_)-(_)  . Eleanor Roosevelt
  
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.

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Re: [R] Quick advice on loading packages

[jwd]

On Mon, 21 Oct 2013 19:32:17 -0400
"Data Analytics Corp."  wrote:

> Hi,
> 
> I need some quick advice/help on loading packages.  I want to write a 
> simple function to load a number of packages I intend to use at a 
> conference presentation.  I'm thinking of something like:
> 
>  fn.install <- function(){install.packages(c("ggplot2", 
> "scales"),  repos = "c:\\temp")}
> 
> There will be many more than just the two I listed.  All the zip
> files are in a Windows directory c:\temp.  Will this work?
> 
> Thanks,
> 
> Walt
> 
Just use a short script.  Install R, install the packages.  To load
them, write a short script, e.g.

#Sets working directory and loads essential libraries.
setwd([working directory here])
library(MASS, aplpack, cclust, ggplot, ...)

Call that from R and provided you have everything where you've R it
was, you're set.

JWDougherty

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Re: [R] Merging data.frames with overlapping intervals

[PIKAL Petr]

Hi

Your HTML formated message was scrammbled so it is impossible to say what 
result you expected.

Regards
Petr

> -Original Message-
> From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
> project.org] On Behalf Of Julius Tesoro
> Sent: Tuesday, October 22, 2013 9:35 AM
> To: r-help@r-project.org
> Subject: [R] Merging data.frames with overlapping intervals
> 
> How do I merge two data.frames with overlapping intervals?
> Data Frame 1
> read.table(textConnection("   from to Lith Form
> 1   0   1.2 GRN   BCM
> 2   1.2 5.0 GDI   BDI
> "),header=TRUE)
> Data Frame 2
> read.table(textConnection("   from to Weath Str
> 1   0  1.1  HW ES
> 2   1.1 2.9 SW VS
> 3   2.9 5.0 HW ST
> "),header=TRUE)
> Resulting Data Frame
> fromto WeathStrLithForm10.01.1HW ES GRN  BCM 21.11.2SW VS GRN  BCM
> 31.22.9SW VS GDI  BDI 42.95.0HW ST GDI  BDI
>   [[alternative HTML version deleted]]
> 
> __
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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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[R] Merging data.frames with overlapping intervals

[Julius Tesoro]

How do I merge two data.frames with overlapping intervals?
Data Frame 1
read.table(textConnection("   from to Lith Form 
1   0   1.2 GRN   BCM
2   1.2 5.0 GDI   BDI
"),header=TRUE)
Data Frame 2
read.table(textConnection("   from to Weath Str
1   0  1.1  HW ES
2   1.1 2.9 SW VS
3   2.9 5.0 HW ST 
"),header=TRUE)
Resulting Data Frame
fromto WeathStrLithForm10.01.1HW ES GRN  BCM 21.11.2SW VS GRN  BCM 31.22.9SW VS 
GDI  BDI 42.95.0HW ST GDI  BDI
[[alternative HTML version deleted]]

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