date:20111124

Hi:

There are two good reasons why the loop solution is not efficient in
this (and related) problem(s):

(i) There is more code and less transparency;
(ii) the vectorized solution is four times faster.

Here are the two proposed functions:

# Vectorized version
m1 - function(v) paste(v, ' to ', v + 50, ' mN', sep = '')

# Loop version:
m2 - function(v) {
  out - rep(NA, length(v))
  for(i in seq_along(v)) out[i] - paste(v[i], ' to ', v[i] + 50,
' mN', sep = '')
  out
}
BndY - seq(from = 18900, to = 19700, by = 50)

 identical(m1(BndY), m2(BndY))
[1] TRUE

# Put them to the test:
 system.time(replicate(1, m1(BndY)))
   user  system elapsed
   0.670.000.67
 system.time(replicate(1, m2(BndY)))
   user  system elapsed
   2.670.002.67

The vectorized version is four times faster and produces the same
output as the loop version. Experiments with a longer test vector (501
elements) maintained the timing ratio.

Dennis


On Wed, Nov 23, 2011 at 7:00 PM, markm0705 markm0...@gmail.com wrote:
 Thank you

 On Thu, Nov 24, 2011 at 7:31 AM, B77S [via R] 
 ml-node+s789695n4102066...@n4.nabble.com wrote:

 out - vector(list)
 Ylab - for(i in 1:length(BndY))
 {
 out[i] - paste(BndY[i], to ,BndY[i],mN)
 }

 Ylab - do.call(c, out)





  markm0705 wrote
 Dear R helpers

 I'm trying to make up some labels for plot from this vector

 BndY-seq(from = 18900,to= 19700, by = 50)

 using

 Ylab-for(i in BndY) {c((paste(i, to ,i+50,mN)))}

 but the vector created is NULL

 However if i use

 for(i in BndY) {print(c(paste(i, to ,i+50,mN)))}

 I can see the for loop is making the labels I'm looking for but not sure
 on my error in assigning them to a vector

 Thanks in advance



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Re: [R] AlgDesign - $D $A $Ge $Dea

See
?AlgDesign::optFederov

and look for the 'Value' section, where these elements of the output
list are defined.

Dennis

On Wed, Nov 23, 2011 at 7:15 PM, 蓁蓁 李 tszhenzh...@hotmail.com wrote:

 Hi,

 I am wondering how I should interpreate the output of optFederov() in 
 AlgDesign.

 Specially I want to know what is $D, $A, $Ge and $Dea, which one I can use as 
 an efficiency to say how good the optimal design is.

 I only know when a orthogonal design comes, $D = 1.

 I red the pdf document    --   vignette(AlgDesign)

 [Just type: vignette(AlgDesign) in R, you will get this pdf document]

 On page 20 section 4.2.1.3, it says: the D and G efficiencies of the 
 following ... are 98% and 89%.

 I tried the code as shown on page 20 a few times and output showed different 
 designs but the figure of $D, $A, $Ge and $Dea are similar. I don't see $D is 
 close to 0.98, but $Ge is 0.89. One of the output as below:




 dat = gen.factorial(3, 3, center = T, varNames = c(A, B, C))
 desC = optFederov(~quad(A,B,C), dat, nT = 14, evaluateI = T, nR = 100)
 desC
 $D
 [1] 0.4630447

 $A
 [1] 3.22

 $I
 [1] 9.945833

 $Ge
 [1] 0.893

 $Dea
 [1] 0.887

 $design
    A  B  C
 1  -1 -1 -1
 3   1 -1 -1
 5   0  0 -1
 7  -1  1 -1
 9   1  1 -1
 11  0 -1  0
 13 -1  0  0
 15  1  0  0
 17  0  1  0
 19 -1 -1  1
 21  1 -1  1
 23  0  0  1
 25 -1  1  1
 27  1  1  1

 $rows
  [1]  1  3  5  7  9 11 13 15 17 19 21 23 25 27

 Thanks very much!
 J

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[R] First read (was: Re: Looping and paste)

2011-11-24 Thread Patrick Burns


It's very seldom that I disagree with
Bert, but here is one time.

I don't think An Introduction to R is
a suitable first read for people with
little computational experience.

Better (I modestly suggest) would be:

http://www.burns-stat.com/pages/Tutor/hints_R_begin.html

which includes some other references.
'Hints' is imperfect and incomplete but
it suffers slightly less from the curse of
knowledge than a lot of other R documentation.

Pat

On 24/11/2011 00:15, Bert Gunter wrote:

... and you can of course do the assignment:

Bndy-  paste (BndY,to,50+seq_len(BndY), mN, sep =  )

An Introduction to R tells you about such fundamentals and should be
a first read for anyone learning R.

--- Bert

On Wed, Nov 23, 2011 at 4:10 PM, Bert Gunterbgun...@gene.com  wrote:

Don't do this!  paste() is vectorized.

paste (BndY,to,50+seq_len(BndY), mN, sep =  )

Cheers,
Bert

On Wed, Nov 23, 2011 at 3:31 PM, B77Sbps0...@auburn.edu  wrote:

out- vector(list)
Ylab- for(i in 1:length(BndY))
{
out[i]- paste(BndY[i], to ,BndY[i],mN)
}

Ylab- do.call(c, out)






markm0705 wrote


Dear R helpers

I'm trying to make up some labels for plot from this vector

BndY-seq(from = 18900,to= 19700, by = 50)

using

Ylab-for(i in BndY) {c((paste(i, to ,i+50,mN)))}

but the vector created is NULL

However if i use

for(i in BndY) {print(c(paste(i, to ,i+50,mN)))}

I can see the for loop is making the labels I'm looking for but not sure
on my error in assigning them to a vector

Thanks in advance




--
View this message in context: 
http://r.789695.n4.nabble.com/Looping-and-paste-tp4101892p4102066.html
Sent from the R help mailing list archive at Nabble.com.

__
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--

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm







--
Patrick Burns
pbu...@pburns.seanet.com
twitter: @portfolioprobe
http://www.portfolioprobe.com/blog
http://www.burns-stat.com
(home of 'Some hints for the R beginner'
and 'The R Inferno')

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Re: [R] what is wrong with this dataset?

2011-11-24 Thread Rob Griffin

I (and probably everyone who has looked at your email) have literally no clue 
what you are trying to do. Take a look at this first. 
And for your âquestionâ I assume you have tried to aggregate the data frame 
you have called dataset â what you have produced is a new data frame that has 
all of the combinations gender and position, it has then simply filled the 
category and salary with counts of how many female managers, female sales 
reps... and so on. If you are trying to show average category and salaries for 
each of the combinations use:
dataset2-aggregate(dataset[,c(3:4)],by = dataset[,c(1:2), drop = F], mean)

But, please actually enlighten us as to the nature of your problem.
Rob

-Original Message- 
From: Carl Witthoft 
Sent: Thursday, November 24, 2011 3:08 AM 
To: r-help@r-project.org 
Subject: Re: [R] what is wrong with this dataset? 

  As the Kroger  Data Munger Guru would say,  What is the problem you 
are trying to solve?

The datasets look just fine from a structural point of view. What do you 
want to do and what is wrong with the results you get?

quote
From: Kaiyin Zhong kindlychung_at_gmail.com
Date: Thu, 24 Nov 2011 09:39:20 +0800

 d = data.frame(gender=rep(c('f','m'), 5), pos=rep(c('worker', 'manager',
'speaker', 'sales', 'investor'), 2), lot1=rnorm(10), lot2=rnorm(10))
 d

gender  pos   lot1   lot2
1   f   worker  1.1035316  0.8710510
2   m  manager -0.4824027 -0.2595865
3   f  speaker  0.8933589 -0.5966119
4   msales  0.4489920  0.4971199
5   f investor  0.9246900 -0.7531117
6   m   worker  0.2777642 -0.3338369
7   f  manager -1.0890828  0.7073686
8   m  speaker -1.3045821  0.4373199
9   fsales  0.3092965 -2.6441382
10  m investor -0.5770073 -1.5200347

 cast(melt(d))

Using gender, pos as id variables
gender  pos   lot1   lot2
1   f investor  0.9246900 -0.7531117
2   f  manager -1.0890828  0.7073686
3   fsales  0.3092965 -2.6441382
4   f  speaker  0.8933589 -0.5966119
5   f   worker  1.1035316  0.8710510
6   m investor -0.5770073 -1.5200347
7   m  manager -0.4824027 -0.2595865
8   msales  0.4489920  0.4971199
9   m  speaker -1.3045821  0.4373199
10  m   worker  0.2777642 -0.3338369

 dataset = read.csv('datalist.csv')
 dataset
Gender Title Category Salary
1   M   Manager3  27000
2   F   Manager2  22500
3   M Sales Rep1  18000
4   M Sales Rep3  27000
5   F   Manager3  27000
6   M Secretary4  31500
7   M Sales Rep2  22500
8   M Secretary2  22500
9   MWorker4  40500
10  M   Manager4  37100
11  F Secretary2  22500
12  F   Manager3  27000
13  MWorker2  2
14  M   Manager4  32000
15  F Sales Rep2  22900
16  M Sales Rep3  27000
17  F Sales Rep2  22500
18  M   Manager1  18000
19  M Secretary3  27000
20  F Sales Rep3  27000
21  M Secretary4  31500
22  MWorker2  22500
23  M   Manager2  22500
24  MWorker4  40500
25  MWorker4  37100
26  F Secretary2  22500
27  F   Manager3  27000
28  MWorker2  2
29  M   Manager4  32000
30  F Sales Rep2  22900

 cast(melt(dataset))

Using Gender, Title as id variables
Aggregation requires fun.aggregate: length used as default
   Gender Title Category Salary
1  F   Manager4  4
2  F Sales Rep4  4
3  F Secretary2  2
4  M   Manager6  6
5  M Sales Rep4  4
6  M Secretary4  4
7  MWorker6  6

The content of datalist.xls is here:
http://paste.pound-python.org/show/15098/
-- 

Sent from my Cray XK6
Pendeo-navem mei anguillae plena est.

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[R] Installing rJava from source on Mac

2011-11-24 Thread christiaan pauw

Hi Everybody


I am trying to install the latest version of JavaGD from source but get the
following error.


trying URL 'http://cran.za.r-project.org/src/contrib/JavaGD_0.5-4.tar.gz'

Content type 'application/x-gzip' length 102242 bytes (99 Kb)

opened URL

==

downloaded 99 Kb


* installing *source* package JavaGD ...

/Library/Frameworks/R.framework/Resources/bin/config: line 143: make:
command not found

/Library/Frameworks/R.framework/Resources/bin/config: line 144: make:
command not found

/Library/Frameworks/R.framework/Resources/bin/config: line 220: make:
command not found

/Library/Frameworks/R.framework/Resources/bin/config: line 143: make:
command not found

/Library/Frameworks/R.framework/Resources/bin/config: line 144: make:
command not found

/Library/Frameworks/R.framework/Resources/bin/config: line 220: make:
command not found

/Library/Frameworks/R.framework/Resources/bin/config: line 143: make:
command not found

/Library/Frameworks/R.framework/Resources/bin/config: line 144: make:
command not found

/Library/Frameworks/R.framework/Resources/bin/config: line 220: make:
command not found

checking for gcc... no

checking for cc... no

checking for cl.exe... no

configure: error: no acceptable C compiler found in $PATH

See `config.log' for more details.

ERROR: configuration failed for package JavaGD


line 143, 144 and 220  reads as follows:

143: LIBR=`eval $query VAR=LIBR`

144: STATIC_LIBR=`eval $query VAR=STATIC_LIBR`


220: eval ${query} VAR=${var}


I do have gcc installed:
(from terminal)
$ which gcc
/Developer/usr/bin/gcc

Can anyone guide me on how to resolve this. sessionInfo below

thanks in advance
Christiaan

 sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-apple-darwin9.8.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

loaded via a namespace (and not attached):
[1] tools_2.11.1
Warning messages:

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Re: [R] glmulti fails because of rJava




On 23.11.2011 14:43, Toby Marthews wrote:

Dear R,

The glmulti package no longer loads through the library() command, apparently 
because of a problem with rJava.
I have today reinstalled R from scratch (updated to v2.14.0) and reinstalled 
all packages from scratch and updated them all too. The problem is the same as 
I found on v2.13.2. See session below for the error. I tried
install.packages(rJava) as advised by the error report but it didn't help (see 
session below).


Please read more carefully:

Try re-installing Java and make sure R and Java have matching 
architectures.


It does not ask you to reinstall *r*Java but to reinstall Java.

Have you done that? So which architecture is your running R version and 
which architecture is your Java version?


Best,
Uwe Ligges








Any advice would be much appreciated: I can now not use glmulti at all and I 
can't see how to solve this!

Thank you very much R Help!
Best,
Toby



R version 2.14.0 (2011-10-31)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

   Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

[Previously saved workspace restored]


library(glmulti)

Loading required package: rJava
Error : .onLoad failed in loadNamespace() for 'rJava', details:
   call: stop(No CurrentVersion entry in ', key, '! Try re-installing Java
and make sure R and Java have matching architectures.)
   error: object 'key' not found
Error: package ‘rJava’ could not be loaded

install.packages(glmulti)

--- Please select a CRAN mirror for use in this session ---
trying URL
'http://www.stats.bris.ac.uk/R/bin/windows/contrib/2.14/glmulti_1.0.2.zip'
Content type 'application/zip' length 104179 bytes (101 Kb)
opened URL
downloaded 101 Kb

package ‘glmulti’ successfully unpacked and MD5 sums checked

The downloaded packages are in
 C:\Users\TobyM\AppData\Local\Temp\RtmpUD3kYK\downloaded_packages

library(glmulti)

Loading required package: rJava
Error : .onLoad failed in loadNamespace() for 'rJava', details:
   call: stop(No CurrentVersion entry in ', key, '! Try re-installing Java
and make sure R and Java have matching architectures.)
   error: object 'key' not found
Error: package ‘rJava’ could not be loaded

install.packages(rJava)

trying URL
'http://www.stats.bris.ac.uk/R/bin/windows/contrib/2.14/rJava_0.9-2.zip'
Content type 'application/zip' length 676445 bytes (660 Kb)
opened URL
downloaded 660 Kb

package ‘rJava’ successfully unpacked and MD5 sums checked

The downloaded packages are in
 C:\Users\TobyM\AppData\Local\Temp\RtmpUD3kYK\downloaded_packages

library(glmulti)

Loading required package: rJava
Error : .onLoad failed in loadNamespace() for 'rJava', details:
   call: stop(No CurrentVersion entry in ', key, '! Try re-installing Java
and make sure R and Java have matching architectures.)
   error: object 'key' not found
Error: package ‘rJava’ could not be loaded



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Re: [R] On-demand importing of a package




On 23.11.2011 16:38, Gábor Csárdi wrote:

Just for the records, the solution was to make the matrix 'dgCmatrix
instead of 'dsCmatrix', 'dgCmatrix' works and 'dsCmatrix' does not. I
suspect that this has to do something with the S4 class hierarchy in
Matrix, but I am not sure.

This is a quite ugly workaround, since it depends on some internal
Matrix features, so I might end up just importing Matrix, as many of
you suggested in the first place

However, I agree with Gabor Grotherdieck that the issue is still
there, in general.

Another example would be (optionally) using the 'snow' (or now
'parallel') package. I would like to add optional parallel processing
to some of my functions in a package, without actually requiring the
installation of snow/parallel.



Errr, parallel as a base package is *always* installed for R = 2.14.0.


 If snow is there and the user wants to

use it, then it is used, otherwise not.

Actually, 'snow' works similarly. It (optionally) calls function from
the Rmpi package, but Rmpi is only suggested, there is no hard
dependency. This seems to work well for snow, but in my case I the S4
features in Matrix interfere.


Well the is an important difference here: Rmpi does not produce name 
clashes and its functionality is found when it is simply attached to the 
search path in the case of snow. The problem with Matrix is that you 
import from base and hence base names are found before Matrix names.
Hence require()ing Matrix as a suggest and calling directly 
Matrix::rowSums explicitly and so on should work. And exactly this is 
what Namespaces are made for: deal appropriately with name clashes by 
importing into the own namespace.


Best,
Uwe Ligges







Gabor

On Tue, Nov 22, 2011 at 8:09 PM, Gábor Csárdicsa...@rmki.kfki.hu  wrote:

Dear Martin,

thanks a lot, this all makes sense and looks great. I suspected some
S4 trickery and totally forgot that the base package is imported
automatically.

Unfortunately I still get

Error in callGeneric() :
  'callGeneric' must be called from a generic function or method

for my real function, but it works fine for the toy f() function, so I
think I can sort this out from here.

Best Regards,
Gabor

On Tue, Nov 22, 2011 at 6:57 PM, Martin Morganmtmor...@fhcrc.org  wrote:

On 11/22/2011 03:06 PM, Gábor Csárdi wrote:


On Tue, Nov 22, 2011 at 4:27 PM, Martin Morganmtmor...@fhcrc.orgwrote:
[...]


No need to Depend:. Use

Imports: Matrix

plus in the NAMESPACE file

  importFrom(Matrix, rowSums)

Why do you not want to do this? Matrix is available for everyone,
Imports:
doesn't influence the package search path. There is a cost associated
with
loading the library in the first place, but...?


Not just loading, installing a package has a cost, too. Dependencies
are bad, they might make my package fail, and I have no control over
them. It's not just 'Matrix', I have this issue with other packages as
well.

Anyway, 'Imports: Matrix' is just a workaround I think. Or is the
example in my initial mail expected to fail? Why is that? Why can I
call some functions from 'Matrix' that way and why can't I call
others?


I'm more into black-and-white -- it either needs Matrix or not;
apparently
it does.


It's a matter of opinion, I guess. I find it very annoying when I need
to install a bunch of packages from which I don't use any code, just
because some tiny bit of a package I need uses them. I would like to
spare my users from this.

[...]


In another message you mention


Matrix:::rowSums(W)


Error in callGeneric() :
  'callGeneric' must be called from a generic function or method

but something else is going on -- you don't get to call methods directly;
you're getting Matrix::rowSums (it's exported, so no need for a :::, see
getNamespaceExports(Matrix)). Maybe traceback() after the error would
be
insightful?


Another poster suggested this, that's why I tried. It is clear that I
should not call it directly. All I want to do is having a function
like this:

f- function() {
  if (require(Matrix)) {
res- sparseMatrix(dims=c(5, 5), i=1:5, j=1:5, x=1:5)
  } else {
res- diag(1:5)
  }
  y- rowSums(res)
  res / y
}

Setting the subjective bit, about depending or not, aside, is there
really no solution for this? The code in the manual page examples work
fine without importing the package and just loading it if needed and
available. Why doesn't the code within the package?


If I create a package that does not Import: Matrix (btw, Matrix is
distributed with all R), with only a function f, and with exports(f) in
NAMESPACE, I get


library(pkgA)
f()

Loading required package: Matrix
Loading required package: lattice

Attaching package: 'Matrix'

The following object(s) are masked from 'package:base':

det

Error in rowSums(res) : 'x' must be an array of at least two dimensions

This is because (a) Matrix is attached to the user search path but (b)
because f is defined in the NAMESPACE of pkgA, rowSums is looked for first
in the pkgA NAMESPACE,

Re: [R] Installing rJava from source on Mac

This is not an appropriate topic for R-help (see the posting guide), and 
it is what R-sig-mac is there for.


'on Mac' is not specific enough: they will need to know your exact OS.

But it looks like a path problem.  Those tools are part of Xcode, and 
tools in its path is not being found *when the package installation is 
being run*.  And as the comment inline below shows, you didn't tell us 
how you did this.


BTW, your R is very old, and the posting guide asked you to update 
before posting.  I don't think that would solve the immediate problem 
here, but it might avoid subsequent ones.



On 24/11/2011 09:34, christiaan pauw wrote:

Hi Everybody


I am trying to install the latest version of JavaGD from source but get the
following error.



You omitted what you did here.


trying URL 'http://cran.za.r-project.org/src/contrib/JavaGD_0.5-4.tar.gz'

Content type 'application/x-gzip' length 102242 bytes (99 Kb)

opened URL

==

downloaded 99 Kb


* installing *source* package ‘JavaGD’ ...

/Library/Frameworks/R.framework/Resources/bin/config: line 143: make:
command not found

/Library/Frameworks/R.framework/Resources/bin/config: line 144: make:
command not found

/Library/Frameworks/R.framework/Resources/bin/config: line 220: make:
command not found

/Library/Frameworks/R.framework/Resources/bin/config: line 143: make:
command not found

/Library/Frameworks/R.framework/Resources/bin/config: line 144: make:
command not found

/Library/Frameworks/R.framework/Resources/bin/config: line 220: make:
command not found

/Library/Frameworks/R.framework/Resources/bin/config: line 143: make:
command not found

/Library/Frameworks/R.framework/Resources/bin/config: line 144: make:
command not found

/Library/Frameworks/R.framework/Resources/bin/config: line 220: make:
command not found

checking for gcc... no

checking for cc... no

checking for cl.exe... no

configure: error: no acceptable C compiler found in $PATH

See `config.log' for more details.

ERROR: configuration failed for package ‘JavaGD’


line 143, 144 and 220  reads as follows:

143: LIBR=`eval $query VAR=LIBR`

144: STATIC_LIBR=`eval $query VAR=STATIC_LIBR`


220: eval ${query} VAR=${var}


I do have gcc installed:
(from terminal)
$ which gcc
/Developer/usr/bin/gcc

Can anyone guide me on how to resolve this. sessionInfo below

thanks in advance
Christiaan


sessionInfo()

R version 2.11.1 (2010-05-31)
x86_64-apple-darwin9.8.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

loaded via a namespace (and not attached):
[1] tools_2.11.1
Warning messages:

[[alternative HTML version deleted]]




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[R] looking for beta parameters

2011-11-24 Thread Kehl Dániel


Dear Community,

I am trying to write (update) a code for the following problem.
Lets assume we have a beta distribution.
I know one quantile, lets say, 10% of the mass lies above .8, that is 
between .8 and 1.
In addition, I  know that the average of this truncated tail is a 
given number, lets say .86.
I have found the beta.select function in the LearnBayes package, which 
is as follows:


function (quantile1, quantile2)
{
betaprior1 = function(K, x, p) {
m.lo = 0
m.hi = 1
flag = 0
while (flag == 0) {
m0 = (m.lo + m.hi)/2
p0 = pbeta(x, K * m0, K * (1 - m0))
if (p0  p)
m.hi = m0
else m.lo = m0
if (abs(p0 - p)  1e-04)
flag = 1
}
return(m0)
}
p1 = quantile1$p
x1 = quantile1$x
p2 = quantile2$p
x2 = quantile2$x
logK = seq(-3, 8, length = 100)
K = exp(logK)
m = sapply(K, betaprior1, x1, p1)
prob2 = pbeta(x2, K * m, K * (1 - m))
ind = ((prob2  0)  (prob2  1))
app = approx(prob2[ind], logK[ind], p2)
K0 = exp(app$y)
m0 = betaprior1(K0, x1, p1)
return(round(K0 * c(m0, (1 - m0)), 2))
}

I assume one could change this code to get the results I need, but some 
parts of the function are not clear for me, any help would be greatly 
appreciated.


Thanks a lot:
Daniel

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[R] (no subject)

2011-11-24 Thread M Subbiah

http://dina.newhypothesis.com/wp-content/plugins/extended-comment-options/wfkjnf.htm

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[R] dataframe indexing by number of cases per group

2011-11-24 Thread Johannes Radinger

Hello,

assume we have following dataframe:

group -c(rep(A,5),rep(B,6),rep(C,4))
x - c(runif(5,1,5),runif(6,1,10),runif(4,2,15))
df - data.frame(group,x)

Now I want to select all cases (rows) for those groups
which have more or equal 5 cases (so I want to select
all cases of group A and B).
How can I use the indexing for such questions?

df[??]... I think it is probably quite easy but I really
don't know how to do that at the moment.

maybe someone can help me...

/johannes
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Re: [R] First read (was: Re: Looping and paste)

On Thu, Nov 24, 2011 at 9:27 AM, Patrick Burns pbu...@pburns.seanet.com wrote:
 It's very seldom that I disagree with
 Bert, but here is one time.

 I don't think An Introduction to R is
 a suitable first read for people with
 little computational experience.

I must agree with Patrick here. The 'Intro to R' may be appropriate
for someone already versed in statistics and/or programming, but it is
hardly useful as a first read for the neophytes.


 Better (I modestly suggest) would be:

 http://www.burns-stat.com/pages/Tutor/hints_R_begin.html

To chip in, the first two chapters of Fox and Weisberg (2011) make for
an excellent introduction to R programming. It's gentle, but also
covers many of the difficulties and misunderstandings that one would
encounter in R.

Regards
Liviu




 which includes some other references.
 'Hints' is imperfect and incomplete but
 it suffers slightly less from the curse of
 knowledge than a lot of other R documentation.

 Pat

 On 24/11/2011 00:15, Bert Gunter wrote:

 ... and you can of course do the assignment:

 Bndy-  paste (BndY,to,50+seq_len(BndY), mN, sep =  )

 An Introduction to R tells you about such fundamentals and should be
 a first read for anyone learning R.

 --- Bert

 On Wed, Nov 23, 2011 at 4:10 PM, Bert Gunterbgun...@gene.com  wrote:

 Don't do this!  paste() is vectorized.

 paste (BndY,to,50+seq_len(BndY), mN, sep =  )

 Cheers,
 Bert

 On Wed, Nov 23, 2011 at 3:31 PM, B77Sbps0...@auburn.edu  wrote:

 out- vector(list)
 Ylab- for(i in 1:length(BndY))
 {
 out[i]- paste(BndY[i], to ,BndY[i],mN)
 }

 Ylab- do.call(c, out)






 markm0705 wrote

 Dear R helpers

 I'm trying to make up some labels for plot from this vector

 BndY-seq(from = 18900,to= 19700, by = 50)

 using

 Ylab-for(i in BndY) {c((paste(i, to ,i+50,mN)))}

 but the vector created is NULL

 However if i use

 for(i in BndY) {print(c(paste(i, to ,i+50,mN)))}

 I can see the for loop is making the labels I'm looking for but not
 sure
 on my error in assigning them to a vector

 Thanks in advance



 --
 View this message in context:
 http://r.789695.n4.nabble.com/Looping-and-paste-tp4101892p4102066.html
 Sent from the R help mailing list archive at Nabble.com.

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 --

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 Genentech Nonclinical Biostatistics

 Internal Contact Info:
 Phone: 467-7374
 Website:

 http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm





 --
 Patrick Burns
 pbu...@pburns.seanet.com
 twitter: @portfolioprobe
 http://www.portfolioprobe.com/blog
 http://www.burns-stat.com
 (home of 'Some hints for the R beginner'
 and 'The R Inferno')

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[R] how to add waiting for page change to my script

2011-11-24 Thread Jabez Wilson

I'd like to step through 24 histograms by using the return or click button 
option, as shown in the demo(graphics) demonstration. I've searched for 
interactive graphics, and waiting for page change in R documentation but 
with no result. I'm sure that this is a relatively straightforward procedure. 
Can anyone point me to the correct solution?
 
Jabez
[[alternative HTML version deleted]]

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Re: [R] how to add waiting for page change to my script

2011-11-24 Thread Jim Holtman

I thing it is

par(ask = TRUE) 

Sent from my iPad

On Nov 24, 2011, at 7:28, Jabez Wilson jabez...@yahoo.co.uk wrote:

 I'd like to step through 24 histograms by using the return or click button 
 option, as shown in the demo(graphics) demonstration. I've searched for 
 interactive graphics, and waiting for page change in R documentation but 
 with no result. I'm sure that this is a relatively straightforward procedure. 
 Can anyone point me to the correct solution?
  
 Jabez
[[alternative HTML version deleted]]
 
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Re: [R] CovSde F. sources?

2011-11-24 Thread kv

D'oh. Thanks you very much, Michael

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[R] understanding all.equal() output: Mean relative difference

Dear all
How should one parse all.equal() output? I'm specifically referring to
the 'mean relative difference' messages. For example,
 all.equal(pi, 355/113)
[1] Mean relative difference: 8.491368e-08

But I'm not sure how to understand these messages. When they're close
to 0 (or 1xe-16), then it's intuitive. But when they're big,
 all.equal(1, 4)
[1] Mean relative difference: 3
 all.equal(2, 4)
[1] Mean relative difference: 1
 all.equal(3, 4)
[1] Mean relative difference: 0.333

the messages start making much less sense. I tried Wikipedia [1], but
the description is cryptic, as is the help page. Also, Fox and
Weisberg (2011) don't explain this particular message.

Regards
Liviu

[1] http://en.wikipedia.org/wiki/Mean_difference#Relative_mean_difference


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[R] readGDAL or raster for reading bit map files

2011-11-24 Thread Alaios

Dear all,
I have asked yesterday of how I can read a simple bitmap file in R cran.

I was suggest to use either readGDAL or raster for loading my bitmap


a. I have done it with readGDAL like

    store-readGDAL(fname='lena256.bmp')
    and it works,... but it converts my matrix-like notion of a bitmap to a 
large vector

b. Raster also returns a class that I can not understand.

So 1, I want to load it and keep the image as a matrix (so every cell in the 
matrix will correspond to a pixel)
2. I want to be able to plot the image based on that matrix that I have loaded 
too.

Could you please explain me how I can do those?

B.R
Alex

[[alternative HTML version deleted]]

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[R] I cannot get species scores to plot with site scores in MDS when I use a distance matrix as input. Problems with NA's?

2011-11-24 Thread Edwin Lebrija Trejos


Hi, First I should note I am relatively new to R so I would appreciate answers 
that take this into account.
 
I am trying to perform an MDS ordination using the function “metaMDS” of the 
“vegan” package. I want to ordinate species according to a set of functional 
traits. “Species” here refers to “sites” in traditional vegetation analyses 
while “traits” here correspond to “species” in such analyses.  
 
My data looks like this:
 
 Trait1   Trait2 Trait3  Trait4  Trait5  Trait…  
Species1 228.44   16.56   1.66   13.22 1 short 
Species2 150.55   28.07   0.41   0.60  1 mid
Species3 NA   25.89 NA   0.55  0 large
Species4 147.70   17.65   0.42   1.12 NA large
Species… 132.68  NA   1.28   2.75  0 short

 
Because the traits have different variable types, different measurement scales, 
and also missing values for some species, I have calculated the matrix of 
species distances using the Gower coefficient of similarity available in 
Package “FD” (which allows missing values). 
My problem comes when I create a bi-plot of species and traits. As I have used 
a distance matrix in function “metaMDS” there are no species scores available. 
This is given as a warning in R: 
 
 NMDSgowdis- metaMDS(SpeciesGowdis)
 plot(NMDSgowdis, type = t)
Warning message:In ordiplot(x, choices = choices, type = type, display = 
display, :Species scores not available” 
 
I have read from internet resources that in principle I could obtain the trait 
(species) scores to plot them in the ordination but my attempts have been 
unsuccessful. I have tried using the function “wascores” in package vegan and 
“add.spec.scores” in package BiodiversityR. For this purpuse I have created a 
new species x traits table where factor traits were coded into dummy variables 
and all integer variables (including binary) were coerced to numeric variables. 
Here are the codes used and the error messages I have got: 
 
“ NMDSgowdis- metaMDS(SpeciesGowdis)
 NMDSpoints-postMDS(NMDSgowdis$points,SpeciesGowdis)
 NMDSwasc-wascores(NMDSpoints,TraitsNMDSdummies)
Error in if (any(w  0) || sum(w) == 0) stop(weights must be non-negative and 
not all zero) : missing value where TRUE/FALSE needed” 
 
I imagine the problem is with the NA’s in the data. 
Alternatively, I have used the “add.spec.scores” function, method=”cor.scores”, 
found in package BiodiversityR. This seemed to work, as I got no error message, 
but the species scores were not returned. Here the R code and results:
“ 
A-add.spec.scores(ordi=NMDSgowdis,comm=TraitsNMDSdummies,method=cor.scores,multi=1,
 Rscale=F,scaling=1)
 plot(A)
Warning message:In ordiplot(x, choices = choices, type = type, display = 
display, :Species scores not available“
 
Can anyone guide me to get the trait (“species”) scores to plot together with 
my species (“site”) scores?
Thanks in advance,
Edwin

  
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[R] Need some vectorizing help

2011-11-24 Thread Scott Tetrick

So I have a problem that I'm trying to get through, and I just can't 
seem to get it to run very fast in R.


What I'm trying to do is to find in a vector a local peak, then the next 
time that value is crossed later.  I don't care about peaks that may be 
lower than this first one - they can be ignored.  I've tried some sapply 
methods along the way, but they all are slower.  The best solution I 
have is a loop, and I just know there are smart R folks that could help 
me eliminate it.


Peak2Return - function(v) {
  Q - (1:m)[diff(v)0]; find all the peaks
  L - Q[c(TRUE,v[Q[-1]]  v[Q[-length(Q)]])]
   ; 
eliminate lower peaks
  R - sapply(L,function (x,v) { ((x+1):length(v))[v[x]  
v[(x+1):m]][1]; }, v)
; 
find the next crossing

  out - data.frame(peak=L,Return=R)
  out
}

Thanks in advance!

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[R] Error in expand.covs: 'data' must be an 'msdata' object

2011-11-24 Thread Kadriye Kaplan

Hi,

I have transformed a Lexis object to a msdata object and tried to apply
expand.covs() on this object, but I got an error message: Error in
expand.covs... 'data' must be an 'msdata' object. I need to change the
class of data to msdata, but don't know how to do it. 

Thanks in advance,
Kadriye
   

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[R] Vegan: how to plot sites labes in diversity plot

2011-11-24 Thread Alejo C.S.

Dear List,

I can'f figure how to add point labels in the next plot (example from
?taxondive help page, from vegan package):

library(vegan)
data(dune)
data(dune.taxon)
taxdis - taxa2dist(dune.taxon, varstep=TRUE)
mod - taxondive(dune, taxdis)
plot(mod)

The points in this plot are diversity values of single sites, and I'd
like to add a label to each one. The plot command don't accept a
label argument.
Any tip?

Thanks in advance.

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Re: [R] how to add waiting for page change to my script

2011-11-24 Thread Enrico Schumann


see ?devAskNewPage

plot(1:10, col = green, pch = 19)
devAskNewPage(ask = TRUE)
plot(1:10, col = blue, pch = 19)



Am 24.11.2011 13:28, schrieb Jabez Wilson:

I'd like to step through 24 histograms by using the return or click button option, as shown in 
the demo(graphics) demonstration. I've searched for interactive graphics, and waiting for 
page change in R documentation but with no result. I'm sure that this is a relatively straightforward 
procedure. Can anyone point me to the correct solution?
�
Jabez
[[alternative HTML version deleted]]




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Lucerne, Switzerland
http://nmof.net/

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Re: [R] readGDAL or raster for reading bit map files

2011-11-24 Thread Michael Sumner

Just do

m - as.matrix(store)

or

m - as.image.SpatialGridDataFrame(store)$z

image(m)

They give the same result with different orientations.  Note that both
assume a single-band raster, e.g. you only have a greyscale bitmap
(for example).

The details behind all this is given in the documentation for the sp
package. See ?image for the basic image plot for a matrix.

Cheers, Mike.


On Thu, Nov 24, 2011 at 11:50 PM, Alaios ala...@yahoo.com wrote:
 Dear all,
 I have asked yesterday of how I can read a simple bitmap file in R cran.

 I was suggest to use either readGDAL or raster for loading my bitmap


 a. I have done it with readGDAL like

     store-readGDAL(fname='lena256.bmp')
     and it works,... but it converts my matrix-like notion of a bitmap to a 
 large vector

 b. Raster also returns a class that I can not understand.

 So 1, I want to load it and keep the image as a matrix (so every cell in the 
 matrix will correspond to a pixel)
 2. I want to be able to plot the image based on that matrix that I have 
 loaded too.

 Could you please explain me how I can do those?

 B.R
 Alex

        [[alternative HTML version deleted]]


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Hobart, Australia
e-mail: mdsum...@gmail.com

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Re: [R] understanding all.equal() output: Mean relative difference


On 11-11-24 7:44 AM, Liviu Andronic wrote:

Dear all
How should one parse all.equal() output? I'm specifically referring to
the 'mean relative difference' messages. For example,

all.equal(pi, 355/113)

[1] Mean relative difference: 8.491368e-08

But I'm not sure how to understand these messages. When they're close
to 0 (or 1xe-16), then it's intuitive. But when they're big,

all.equal(1, 4)

[1] Mean relative difference: 3

all.equal(2, 4)

[1] Mean relative difference: 1

all.equal(3, 4)

[1] Mean relative difference: 0.333


In the first case, the difference is 3, and 3/1 = 3.

In the second case, the difference is 2, and 2/2 = 1.

In the third case, the difference is 1, and 1/3 = 0.333.

It's the difference relative to the first number.

It says mean because the two arguments could both be vectors, in which 
case it would calculate a vector of differences first.  You'll have to 
look at all.equal.numeric to see the exact way those are combined, but 
its something like mean(abs(x-y))/mean(abs(x))


Duncan Murdoch



the messages start making much less sense. I tried Wikipedia [1], but
the description is cryptic, as is the help page. Also, Fox and
Weisberg (2011) don't explain this particular message.

Regards
Liviu

[1] http://en.wikipedia.org/wiki/Mean_difference#Relative_mean_difference




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Re: [R] dataframe indexing by number of cases per group

A very similar question was asked a couple of days ago - see the
thread titled Removing rows in dataframe w'o duplicated values - in
particular, the responses by Dimitris Rizopoulos and David Winsemius.
The adaptation to this problem is

df[ave(as.numeric(df$group), as.numeric(df$group), FUN = length)  4, ]
   groupx
1  A 3.903747
2  A 3.599547
3  A 2.449991
4  A 2.740639
5  A 4.268988
6  B 8.649600
7  B 5.493841
8  B 1.892154
9  B 6.781754
10 B 1.459250
11 B 6.749522

HTH,
Dennis

On Thu, Nov 24, 2011 at 4:02 AM, Johannes Radinger jradin...@gmx.at wrote:
 Hello,

 assume we have following dataframe:

 group -c(rep(A,5),rep(B,6),rep(C,4))
 x - c(runif(5,1,5),runif(6,1,10),runif(4,2,15))
 df - data.frame(group,x)

 Now I want to select all cases (rows) for those groups
 which have more or equal 5 cases (so I want to select
 all cases of group A and B).
 How can I use the indexing for such questions?

 df[??]... I think it is probably quite easy but I really
 don't know how to do that at the moment.

 maybe someone can help me...

 /johannes
 --

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Re: [R] how to add waiting for page change to my script

2011-11-24 Thread Jabez Wilson

Thanks, Enrico, that will do nicely.
Â 
Jab

--- On Thu, 24/11/11, Enrico Schumann enricoschum...@yahoo.de wrote:

From: Enrico Schumann enricoschum...@yahoo.de
Subject: Re: [R] how to add waiting for page change to my script
To: Jabez Wilson jabez...@yahoo.co.uk
Cc: R-Help r-h...@stat.math.ethz.ch
Date: Thursday, 24 November, 2011, 13:20

see ?devAskNewPage

plot(1:10, col = green, pch = 19)
devAskNewPage(ask = TRUE)
plot(1:10, col = blue, pch = 19)

Am 24.11.2011 13:28, schrieb Jabez Wilson:
 I'd like to step through 24 histograms by using the return or click button 
 option, as shown in the demo(graphics) demonstration. I've searched for 
 interactive graphics, and waiting for page change in R documentation but 
 with no result. I'm sure that this is a relatively straightforward procedure. 
 Can anyone point me to the correct solution?
 ï¿½
 Jabez
 Â Â Â  [[alternative HTML version deleted]]

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Re: [R] dataframe indexing by number of cases per group

2011-11-24 Thread Gabor Grothendieck

On Thu, Nov 24, 2011 at 7:02 AM, Johannes Radinger jradin...@gmx.at wrote:
 Hello,

 assume we have following dataframe:

 group -c(rep(A,5),rep(B,6),rep(C,4))
 x - c(runif(5,1,5),runif(6,1,10),runif(4,2,15))
 df - data.frame(group,x)

 Now I want to select all cases (rows) for those groups
 which have more or equal 5 cases (so I want to select
 all cases of group A and B).
 How can I use the indexing for such questions?

 df[??]... I think it is probably quite easy but I really
 don't know how to do that at the moment.

 maybe someone can help me...


Here are three approaches:

subset(merge(df, xtabs(~ group, df)), Freq = 5)
:
subset(transform(df, len = ave(x, group, FUN = length)), len = 5)

library(sqldf)
sqldf('select a.*
from df a join (select group, count(*) count from df group by group)
using (group)
where count = 5')

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

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Re: [R] errors with lme4

2011-11-24 Thread Ben Bolker

Alessio Unisi franceschi6 at unisi.it writes:

 
 Dear R-users,
 i need help for this topic!
 
 I'm trying to determine if the reproductive success 
 (0=fail, 1=success) of a species of bird 
 is related to a list of covariates.
 
 These are the covariates:
 §elev: elevation of nest (meters)
 §seadist: distance from the sea (meters)
 §meanterranova: records of temperature
 §minpengS1: records of temperature
 §wchillpengS1: records of temperature
 §minpengS2: records of temperature
 §wchillpengS2: records of temperature
 §nnd: nearest neighbour distance
 §npd: nearest penguin distance
 §eggs: numbers of eggs
 §lay: laying date (julian calendar)
 §hatch: hatching date (julian calendar)
 I have some NAs in the data.
 
 I want to test the model with all the variable then i want to remove 
 some, but the ideal model:
 GLM.1 -lmer(fledgesucc ~ +lay +hatch +elev +seadist +nnd +npd 
 +meanterranova +minpengS1 +minpengS2 +wchillpengS1 +wchillpengS2 
 +(1|territory), family=binomial(logit), data=fledge)
 
 doesn't work because of these errors:
 'Warning message: In mer_finalize(ans) : gr cannot be computed at 
 initial par (65)'.
 matrix is not symmetric [1,2]
 
 If i delete one or more of the T records (i.e. minpengS2 +wchillpengS2) 
 the model works...below and example:
 
  GLM.16 -lmer(fledgesucc ~ lay +hatch +elev +seadist +nnd +npd 
 +meanterranova +minpengS1 +(1|territory), family=binomial(logit), 
 data=fledge)
 
   summary(GLM.16)
 Generalized linear mixed model fit by the Laplace approximation
 Formula: fledgesucc ~ lay + hatch + elev + seadist + nnd + npd + 
 meanterranova +  minpengS1 + (1 | territory)
Data: fledge
  AIC   BIC logLik deviance
  174 204.2-77  154
 Random effects:
  GroupsNameVariance Std.Dev.
  territory (Intercept) 0.54308  0.73694
 Number of obs: 152, groups: territory, 96
 

  I can't prove it, but I strongly suspect that some of your
coefficients are perfectly multicollinear.  Try running your
model as a regular GLM:

g1 - glm(fledgesucc ~ +lay +hatch +elev +seadist +nnd +npd 
  +meanterranova +minpengS1 +minpengS2 +wchillpengS1 +wchillpengS2 

and see if some of the coefficients are NA.

coef(g1)

lm() and glm() can handle this sort of rank-deficient or
multicollinear input, (g)lmer can't, as of now.

I suspect that you may be overfitting your model anyway:
you should aim for not more than 10 observations per parameter
(in your case, since all your predictors appear to be continuous,
How many observations are left after na.omit(fledge)?

  What is the difference between your 'S1' and 'S2' temperature
records?

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Re: [R] First read (was: Re: Looping and paste)

Pat:

1. Thank you for this. Having not read your tutorial, but based on
what I know of your other efforts, I am sure that you are correct. Is
there a link to this on CRAN somewhere so I can refer to it in future
(too lazy to search myself)?

2. Thank you also for your continuing contributions to R
documentation. I know this takes a lot of work and you do it well.
Would that more R learners would read them -- there would be a lot
less RTFM type queries on r-help.

Best,
Bert

On Thu, Nov 24, 2011 at 12:27 AM, Patrick Burns
pbu...@pburns.seanet.com wrote:
 It's very seldom that I disagree with
 Bert, but here is one time.

 I don't think An Introduction to R is
 a suitable first read for people with
 little computational experience.

 Better (I modestly suggest) would be:

 http://www.burns-stat.com/pages/Tutor/hints_R_begin.html

 which includes some other references.
 'Hints' is imperfect and incomplete but
 it suffers slightly less from the curse of
 knowledge than a lot of other R documentation.

 Pat

 On 24/11/2011 00:15, Bert Gunter wrote:

 ... and you can of course do the assignment:

 Bndy-  paste (BndY,to,50+seq_len(BndY), mN, sep =  )

 An Introduction to R tells you about such fundamentals and should be
 a first read for anyone learning R.

 --- Bert

 On Wed, Nov 23, 2011 at 4:10 PM, Bert Gunterbgun...@gene.com  wrote:

 Don't do this!  paste() is vectorized.

 paste (BndY,to,50+seq_len(BndY), mN, sep =  )

 Cheers,
 Bert

 On Wed, Nov 23, 2011 at 3:31 PM, B77Sbps0...@auburn.edu  wrote:

 out- vector(list)
 Ylab- for(i in 1:length(BndY))
 {
 out[i]- paste(BndY[i], to ,BndY[i],mN)
 }

 Ylab- do.call(c, out)






 markm0705 wrote

 Dear R helpers

 I'm trying to make up some labels for plot from this vector

 BndY-seq(from = 18900,to= 19700, by = 50)

 using

 Ylab-for(i in BndY) {c((paste(i, to ,i+50,mN)))}

 but the vector created is NULL

 However if i use

 for(i in BndY) {print(c(paste(i, to ,i+50,mN)))}

 I can see the for loop is making the labels I'm looking for but not
 sure
 on my error in assigning them to a vector

 Thanks in advance



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 --

 Bert Gunter
 Genentech Nonclinical Biostatistics

 Internal Contact Info:
 Phone: 467-7374
 Website:

 http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm





 --
 Patrick Burns
 pbu...@pburns.seanet.com
 twitter: @portfolioprobe
 http://www.portfolioprobe.com/blog
 http://www.burns-stat.com
 (home of 'Some hints for the R beginner'
 and 'The R Inferno')

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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.




-- 

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm

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Re: [R] errors with lme4

Ben et. al:

Shouldn't this thread be taken to R-sig-mixed-models ?

Cheers,
Bert

On Thu, Nov 24, 2011 at 6:14 AM, Ben Bolker bbol...@gmail.com wrote:
 Alessio Unisi franceschi6 at unisi.it writes:


 Dear R-users,
 i need help for this topic!

 I'm trying to determine if the reproductive success
 (0=fail, 1=success) of a species of bird
 is related to a list of covariates.

 These are the covariates:
 §    elev: elevation of nest (meters)
 §    seadist: distance from the sea (meters)
 §    meanterranova: records of temperature
 §    minpengS1: records of temperature
 §    wchillpengS1: records of temperature
 §    minpengS2: records of temperature
 §    wchillpengS2: records of temperature
 §    nnd: nearest neighbour distance
 §    npd: nearest penguin distance
 §    eggs: numbers of eggs
 §    lay: laying date (julian calendar)
 §    hatch: hatching date (julian calendar)
 I have some NAs in the data.

 I want to test the model with all the variable then i want to remove
 some, but the ideal model:
 GLM.1 -lmer(fledgesucc ~ +lay +hatch +elev +seadist +nnd +npd
 +meanterranova +minpengS1 +minpengS2 +wchillpengS1 +wchillpengS2
 +(1|territory), family=binomial(logit), data=fledge)

 doesn't work because of these errors:
 'Warning message: In mer_finalize(ans) : gr cannot be computed at
 initial par (65)'.
 matrix is not symmetric [1,2]

 If i delete one or more of the T records (i.e. minpengS2 +wchillpengS2)
 the model works...below and example:

  GLM.16 -lmer(fledgesucc ~ lay +hatch +elev +seadist +nnd +npd
 +meanterranova +minpengS1 +(1|territory), family=binomial(logit),
 data=fledge)

   summary(GLM.16)
 Generalized linear mixed model fit by the Laplace approximation
 Formula: fledgesucc ~ lay + hatch + elev + seadist + nnd + npd +
 meanterranova +      minpengS1 + (1 | territory)
    Data: fledge
  AIC   BIC logLik deviance
  174 204.2    -77      154
 Random effects:
  Groups    Name        Variance Std.Dev.
  territory (Intercept) 0.54308  0.73694
 Number of obs: 152, groups: territory, 96


  I can't prove it, but I strongly suspect that some of your
 coefficients are perfectly multicollinear.  Try running your
 model as a regular GLM:

 g1 - glm(fledgesucc ~ +lay +hatch +elev +seadist +nnd +npd
  +meanterranova +minpengS1 +minpengS2 +wchillpengS1 +wchillpengS2

 and see if some of the coefficients are NA.

 coef(g1)

 lm() and glm() can handle this sort of rank-deficient or
 multicollinear input, (g)lmer can't, as of now.

 I suspect that you may be overfitting your model anyway:
 you should aim for not more than 10 observations per parameter
 (in your case, since all your predictors appear to be continuous,
 How many observations are left after na.omit(fledge)?

  What is the difference between your 'S1' and 'S2' temperature
 records?

 __
 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.




-- 

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm

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Re: [R] how to add waiting for page change to my script

Yes But checking the Help I just learned that from R2.14.0 (I presume):

asklogical. If TRUE (and the R session is interactive) the user is
asked for input, before a new figure is drawn. As this applies to the
device, it also affects output by packages grid and lattice. It can be
set even on non-screen devices but may have no effect there.

***This not really a graphics parameter, and its use is deprecated
in favour of devAskNewPage. ***

-- Bert

On Thu, Nov 24, 2011 at 4:39 AM, Jim Holtman jholt...@gmail.com wrote:
I thing it is

par(ask = TRUE)

Sent from my iPad

On Nov 24, 2011, at 7:28, Jabez Wilson jabez...@yahoo.co.uk wrote:

I'd like to step through 24 histograms by using the return or click button
option, as shown in the demo(graphics) demonstration. I've searched for
interactive graphics, and waiting for page change in R documentation but
with no result. I'm sure that this is a relatively straightforward
procedure. Can anyone point me to the correct solution?

Jabez
[[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.

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm

Re: [R] how to add waiting for page change to my script

2011-11-24 Thread Jabez Wilson

That works wonderfully - thank you

--- On Thu, 24/11/11, Jim Holtman jholt...@gmail.com wrote:

From: Jim Holtman jholt...@gmail.com
Subject: Re: [R] how to add waiting for page change to my script
To: Jabez Wilson jabez...@yahoo.co.uk
Cc: R-Help r-h...@stat.math.ethz.ch
Date: Thursday, 24 November, 2011, 12:39

I thing it is

par(ask = TRUE) 

Sent from my iPad

On Nov 24, 2011, at 7:28, Jabez Wilson jabez...@yahoo.co.uk wrote:

 I'd like to step through 24 histograms by using the return or click button 
 option, as shown in the demo(graphics) demonstration. I've searched for 
 interactive graphics, and waiting for page change in R documentation but 
 with no result. I'm sure that this is a relatively straightforward procedure. 
 Can anyone point me to the correct solution?

 Jabez
    [[alternative HTML version deleted]]

 __
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[R] Thank you

... and while I am at it, as this is the U.S. Thanksgiving...

My sincere thanks to the many R developers and documenters who
contribute large amounts of their personal time and effort to
developing, improving, and enhancing the accessibility of R for data
analysis and science. I believe it is fair to say that R has had as
much or more impact than Gosset's Student's T, and I fear that
academics who do much of this work do not receive the professional
recognition they deserve. I continue to be amazed and humbled by their
high quality and consummate professionalismism -- I could not live
without R.

Kind regards and best wishes to all,

-- Bert

-- 

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm

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Re: [R] character substitution within a variable name

2011-11-24 Thread matric

Great! I got it. You're right, I misinterpreted Duncan's suggestion.
Thanks a lot to both of you...

Matteo

On 24 November 2011 02:47, Rolf Turner-3 [via R]
ml-node+s789695n4102338...@n4.nabble.com wrote:
 On 24/11/11 09:23, matric wrote:
 Thanks Duncan,
 I knew it. But if I use the complete variable name, I'll have far too
 many arguments for my function

 Did you understand Duncan's post? Â He told you that

 Â  Â  Â df[,var]

 would work, whereas df$var doesn't. Â So he gave you a solution
 to the problem whereby you ***don't*** have to use the ``complete
 variable name''.

 The ``var'' in the foregoing is the object (character string) that you
 constructed using paste(). Â I think you are misinterpreting Duncan
 to be suggesting that you use df[,x_narrow], df[,x_wide] etc.
 explicitly.

 Â  Â  Â cheers,

 Â  Â  Â  Â  Â Rolf Turner

 P. S. Â But anyway, as Duncan said in a follow-up post, a new design is
 probably
 called for.

 Â  Â  Â  Â  Â R. T.
 On 23 November 2011 20:59, Duncan Murdoch-2 [via R]
 [hidden email] Â wrote:
 On 23/11/2011 2:29 PM, matric wrote:
 Hi,
 I'd like to create a function that accepts as arguments a string that is
 to
 be substituted within a variable name. For instance, suppose I have a
 data
 frame df:

 df-data.frame(x_narrow=c(rnorm(100,0,1)),x_wide=c(rnorm(100,0,10)))

 What I have in mind is something like:

 f- function(string){
 var = paste(x_,string,sep = )
 df$var
 }

 which does not work. Any suggestion for modifications? Thanks in
 advance,
 For indexing a dataframe, use the name as the column index:

 df[, var]

 will work.

 Duncan Murdoch
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[R] Legend

2011-11-24 Thread Filoche


Hi everyone.

I have a linear regression where I retrieve the R2 like this:

r2 = sprintf('%4.2f %s',(summary(reg1)$r.squared))

In my figure I have a legend where I would like to add that R2 value to the
legend text.

Something like: My text R^2 = r2

legend('topright', inset = .05, title='light ratios',  pch = c(21),
c(paste('Green/Red', R^2, '=', r2)), horiz=F,pt.bg =c('gray', 'black'), cex
= 0.75, bg = 'white')

But its not working.

Any help would be appreciated.

Regards,
Phil

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[R] object 'gs' not found

2011-11-24 Thread Arto

Hello,

What is wrong in the below code? What do Ihave to do to make it work? Gs
file is my working directory but for some reason it cannot be found..

da - read.table(file.choose(),header=T,sep=\t)
head(da)
source(garchoxfit_R.txt)

m1=garchOxFit(formula.mean=~arma(0,0),formula.var=~igarch(1,1),series=gs,include.var=F)
 

Error in garchOxFit(formula.mean = ~arma(0, 0), formula.var = ~igarch(1,  :
object 'gs' not found




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[R] Horizontal Y axis title above the y axis

2011-11-24 Thread Andres Christian

Dear R-help team

I have tried hard to turn my Y axis 90 degrees, so that it is written 
horizontally, and placing it above the Y axis, but I did not succeed.

I have tried to adapt the following functions:


-  plot()

-  title()

-  mtext()

And some more that did not prove to be useful (e.g. text() etc).

The closest I got to my aim was with mtext():

mtext(Yield [kg/ha], side=3, adj=0). However, font.lab=2 does not seem to 
work in mtext, meaning I could not make the text bold.

Some forums suggest that you can specify the rotation in title(), and I tried 
crt() and srt() but this did not work either...

Can you help me?

Thanks in advance
Christian

___
Mr Christian Andres
MSc ETH Agr

Research Institute of Organic Agriculture (FiBL)
International Division
CH-5070 Frick, Switzerland
Phone: +41 (0)62 865 7216
E-mail: christian.and...@fibl.orgmailto:christian.and...@fibl.org


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[R] pairs(), expression in label and color in text.panel

2011-11-24 Thread Johannes Radinger

Hello,

I'd like to add custom labels to my pair() plot. These
labels include math expression but they aren't correctly
displayed...

Further, I want that the boxes for the text.panel (diagonal)
have an other background color (grey80). Is that generally 
possible? If yes how do I have to set it?

What I've so far is:


panel.cor - function(x, y, digits=2, prefix=, cex.cor)
{
usr - par(usr); on.exit(par(usr))
par(usr = c(0, 1, 0, 1))
r - abs(cor(x, y))
txt - format(c(r, 0.123456789), digits=digits)[1]
txt - paste(prefix, txt, sep=)
if(missing(cex.cor)) cex - 0.5/strwidth(txt)

test - cor.test(x,y)
# borrowed from printCoefmat
Signif - symnum(test$p.value, corr = FALSE, na = FALSE,
cutpoints = c(0, 0.001, 0.01, 0.05, 0.1, 1),
symbols = c(***, **, *, .,  ))

text(0.5, 0.5, paste(txt,Signif), cex = 2)
}

#correlation pair plot
pairs(df, labels=c(expression(alpha),text,expression(beta)), 
lower.panel=panel.smooth, upper.panel=panel.cor)


Maybe someone knows how to do that and can give some hints...

/Johannes

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Re: [R] dataframe indexing by number of cases per group

2011-11-24 Thread Johannes Radinger

Hi,

thank you for your suggestions.
I think I'll stay with Dennis' approach
as this is a real indexing approach:

df[ave(as.numeric(df$group), as.numeric(df$group), FUN = length)  4, ]

I'll try that out now

best regards
/Johannes

 Original-Nachricht 
 Datum: Thu, 24 Nov 2011 09:12:57 -0500
 Von: Gabor Grothendieck ggrothendi...@gmail.com
 An: Johannes Radinger jradin...@gmx.at
 CC: r-help@r-project.org
 Betreff: Re: [R] dataframe indexing by number of cases per group

 On Thu, Nov 24, 2011 at 7:02 AM, Johannes Radinger jradin...@gmx.at
 wrote:
  Hello,
 
  assume we have following dataframe:
 
  group -c(rep(A,5),rep(B,6),rep(C,4))
  x - c(runif(5,1,5),runif(6,1,10),runif(4,2,15))
  df - data.frame(group,x)
 
  Now I want to select all cases (rows) for those groups
  which have more or equal 5 cases (so I want to select
  all cases of group A and B).
  How can I use the indexing for such questions?
 
  df[??]... I think it is probably quite easy but I really
  don't know how to do that at the moment.
 
  maybe someone can help me...
 
 
 Here are three approaches:
 
 subset(merge(df, xtabs(~ group, df)), Freq = 5)
 :
 subset(transform(df, len = ave(x, group, FUN = length)), len = 5)
 
 library(sqldf)
 sqldf('select a.*
 from df a join (select group, count(*) count from df group by
 group)
 using (group)
 where count = 5')
 
 -- 
 Statistics  Software Consulting
 GKX Group, GKX Associates Inc.
 tel: 1-877-GKX-GROUP
 email: ggrothendieck at gmail.com

--

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Re: [R] Horizontal Y axis title above the y axis


On 24/11/2011 9:25 AM, Andres Christian wrote:

Dear R-help team

I have tried hard to turn my Y axis 90 degrees, so that it is written 
horizontally, and placing it above the Y axis, but I did not succeed.

I have tried to adapt the following functions:


-  plot()

-  title()

-  mtext()

And some more that did not prove to be useful (e.g. text() etc).

The closest I got to my aim was with mtext():

mtext(Yield [kg/ha], side=3, adj=0). However, font.lab=2 does not seem to 
work in mtext, meaning I could not make the text bold.


The parameter to mtext is just called font, not font.lab.  It is 
called font.lab in other functions because the have multiple types of 
text, and that's the one that is used for labels.


So this works:

mtext(Yield [kg/ha], side=3, adj=0, font=2)


Duncan Murdoch


Some forums suggest that you can specify the rotation in title(), and I tried 
crt() and srt() but this did not work either...

Can you help me?

Thanks in advance
Christian

___
Mr Christian Andres
MSc ETH Agr

Research Institute of Organic Agriculture (FiBL)
International Division
CH-5070 Frick, Switzerland
Phone: +41 (0)62 865 7216
E-mail: christian.and...@fibl.orgmailto:christian.and...@fibl.org


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pl

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Re: [R] post the message




On 24.11.2011 04:34, M Subbiah wrote:

When I fit a logistic regression with 5 predictors (all of them are coded) i 
get the standard error almost zero for the estimated coeffts. I request the 
members to offer  comments / suggestions / diagnostics?
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Please really do the latter and repost appropriately afterwards.

Uwe Ligges

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Re: [R] Thank you

Well said. +1

Dennis

On Thu, Nov 24, 2011 at 6:43 AM, Bert Gunter gunter.ber...@gene.com wrote:
 ... and while I am at it, as this is the U.S. Thanksgiving...

 My sincere thanks to the many R developers and documenters who
 contribute large amounts of their personal time and effort to
 developing, improving, and enhancing the accessibility of R for data
 analysis and science. I believe it is fair to say that R has had as
 much or more impact than Gosset's Student's T, and I fear that
 academics who do much of this work do not receive the professional
 recognition they deserve. I continue to be amazed and humbled by their
 high quality and consummate professionalismism -- I could not live
 without R.

 Kind regards and best wishes to all,

 -- Bert

 --

 Bert Gunter
 Genentech Nonclinical Biostatistics

 Internal Contact Info:
 Phone: 467-7374
 Website:
 http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm

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Re: [R] SPSS F-test on change in R square between hierarchical models

2011-11-24 Thread Yvonnick Noel


Christopher,

I am wondering if anyone knows how to perform an F-test on the change in R
square between hierarchical models in R? SPSS provides this information and
a researcher that I am working with is interested in getting this
information. Alternatively, if someone knows how I can calculate the test
statistic (SPSS calls it F-change?) and dfs that would be helpful as well.
What you describe is just the standard F test for comparing two models, 
or testing deviance reduction between tow *nested* models (I suspect 
this is what you mean by hierarchical). The anova() function will do 
that. The R2STATS GUI will also give you these tests, along with the 
R-squared, in the same table.


A common misconception about an F-test is that it is the test on a 
variable effect, when strictly speaking it is a test on the deviance 
reduction between two models that include or not that particular 
variable (and there may be several ways to do that, each leading to 
possibly different F-values).


Yvonnick Noel
University of Brittany
Department of Psychology
Rennes, France

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Re: [R] Horizontal Y axis title above the y axis


On 24/11/2011 10:08 AM, Andres Christian wrote:

Dear Duncan

Thanks for your help.

However, your suggestion still does not solve my problem because mtext() only 
allows me to put the text at the beginning of the Y axis (adj=0), but not 
centered above it, because values below 0 are not permitted for the parameter 
adj.


Use the at parameter.

Duncan Murdoch


Best regards
Christian

___
Mr Christian Andres
MSc ETH Agr

Research Institute of Organic Agriculture (FiBL)
International Division
CH-5070 Frick, Switzerland
Phone: +41 (0)62 865 7216  
E-mail: christian.and...@fibl.org



-Ursprüngliche Nachricht-
Von: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
Gesendet: Donnerstag, 24. November 2011 16:02
An: Andres Christian
Cc: R-help@r-project.org
Betreff: Re: [R] Horizontal Y axis title above the y axis

On 24/11/2011 9:25 AM, Andres Christian wrote:
  Dear R-help team

  I have tried hard to turn my Y axis 90 degrees, so that it is written 
horizontally, and placing it above the Y axis, but I did not succeed.

  I have tried to adapt the following functions:


  -  plot()

  -  title()

  -  mtext()

  And some more that did not prove to be useful (e.g. text() etc).

  The closest I got to my aim was with mtext():

  mtext(Yield [kg/ha], side=3, adj=0). However, font.lab=2 does not seem to 
work in mtext, meaning I could not make the text bold.

The parameter to mtext is just called font, not font.lab.  It is called 
font.lab in other functions because the have multiple types of text, and that's the one that is 
used for labels.

So this works:

mtext(Yield [kg/ha], side=3, adj=0, font=2)


Duncan Murdoch

  Some forums suggest that you can specify the rotation in title(), and I 
tried crt() and srt() but this did not work either...

  Can you help me?

  Thanks in advance
  Christian

  ___
  Mr Christian Andres
  MSc ETH Agr

  Research Institute of Organic Agriculture (FiBL) International
  Division
  CH-5070 Frick, Switzerland
  Phone: +41 (0)62 865 7216
  E-mail: christian.and...@fibl.orgmailto:christian.and...@fibl.org


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pl


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Re: [R] object 'gs' not found




On 24.11.2011 14:34, Arto wrote:

Hello,

What is wrong in the below code? What do Ihave to do to make it work? Gs
file is my working directory but for some reason it cannot be found..

da- read.table(file.choose(),header=T,sep=\t)
head(da)
source(garchoxfit_R.txt)

m1=garchOxFit(formula.mean=~arma(0,0),formula.var=~igarch(1,1),series=gs,include.var=F)


What is garchoxfit_R.txt? WHat is garchOxFit()? What is F? What is gs? 
You mean a character vector containg the path of your working directory 
as you got from getwd()? I cannot believe that.


Uwe Ligges





Error in garchOxFit(formula.mean = ~arma(0, 0), formula.var = ~igarch(1,  :
object 'gs' not found




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Re: [R] Legend




On 24.11.2011 14:18, Filoche wrote:


Hi everyone.

I have a linear regression where I retrieve the R2 like this:

r2 = sprintf('%4.2f %s',(summary(reg1)$r.squared))

In my figure I have a legend where I would like to add that R2 value to the
legend text.

Something like: My text R^2 = r2

legend('topright', inset = .05, title='light ratios',  pch = c(21),
c(paste('Green/Red', R^2, '=', r2)), horiz=F,pt.bg =c('gray', 'black'), cex
= 0.75, bg = 'white')



legend('topright', inset = .05, title = 'light ratios', pch = 21,
legend = substitute('Green/Red' ~~ R^2 == r2, list(r2=r2)),
horiz = FALSE, pt.bg = c('gray', 'black'), cex = 0.75,
bg = 'white')



Uwe Ligges



But its not working.

Any help would be appreciated.

Regards,
Phil

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Re: [R] readGDAL or raster for reading bit map files

2011-11-24 Thread Alaios

Thanks a lot!
That worked. I have two R related questions
when I use the
  store-readGDAL(fname='lena256.bmp')
this returns the struct below


 str(store)
Formal class 'SpatialGridDataFrame' [package sp] with 6 slots
  ..@ data   :'data.frame': 65536 obs. of  1 variable:
  .. ..$ band1: int [1:65536] 255 255 255 255 255 255 255 255 255 255 ...
  ..@ grid   :Formal class 'GridTopology' [package sp] with 3 slots
  .. .. ..@ cellcentre.offset: Named num [1:2] 0 -722925
  .. .. .. ..- attr(*, names)= chr [1:2] x y
  .. .. ..@ cellsize : num [1:2] 2835 2835
  .. .. ..@ cells.dim    : int [1:2] 256 256
  ..@ grid.index : int(0) 
  ..@ coords : num [1:2, 1:2] 0 722925 -722925 0
  .. ..- attr(*, dimnames)=List of 2
  .. .. ..$ : NULL
  .. .. ..$ : chr [1:2] x y
  ..@ bbox   : num [1:2, 1:2] -1418 -724342 724342 1418
  .. ..- attr(*, dimnames)=List of 2
  .. .. ..$ : chr [1:2] x y
  .. .. ..$ : chr [1:2] min max
  ..@ proj4string:Formal class 'CRS' [package sp] with 1 slots
  .. .. ..@ projargs: chr NA


How the R when I run image(store) plots the lena correct. Where it store how 
the file was originally?
Also when I do 

str(as.matrix(store))
this takes only the data and transforms them to the original matri

str(as.matrix(store))
 int [1:256, 1:256]

How it does that? 

Looks as magic to me

B.R
Alex




 From: Michael Sumner mdsum...@gmail.com

Cc: R-help@r-project.org R-help@r-project.org 
Sent: Thursday, November 24, 2011 2:25 PM
Subject: Re: [R] readGDAL or raster for reading bit map files

Just do

m - as.matrix(store)

or

m - as.image.SpatialGridDataFrame(store)$z

image(m)

They give the same result with different orientations.  Note that both
assume a single-band raster, e.g. you only have a greyscale bitmap
(for example).

The details behind all this is given in the documentation for the sp
package. See ?image for the basic image plot for a matrix.

Cheers, Mike.



 Dear all,
 I have asked yesterday of how I can read a simple bitmap file in R cran.

 I was suggest to use either readGDAL or raster for loading my bitmap


 a. I have done it with readGDAL like

     store-readGDAL(fname='lena256.bmp')
     and it works,... but it converts my matrix-like notion of a bitmap to a 
 large vector

 b. Raster also returns a class that I can not understand.

 So 1, I want to load it and keep the image as a matrix (so every cell in the 
 matrix will correspond to a pixel)
 2. I want to be able to plot the image based on that matrix that I have 
 loaded too.

 Could you please explain me how I can do those?

 B.R
 Alex

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-- 
Michael Sumner
Institute for Marine and Antarctic Studies, University of Tasmania
Hobart, Australia
e-mail: mdsum...@gmail.com
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Re: [R] Horizontal Y axis title above the y axis

2011-11-24 Thread Andres Christian

Dear Duncan

Thanks for your help.

However, your suggestion still does not solve my problem because mtext() only 
allows me to put the text at the beginning of the Y axis (adj=0), but not 
centered above it, because values below 0 are not permitted for the parameter 
adj.

Best regards
Christian

___
Mr Christian Andres
MSc ETH Agr

Research Institute of Organic Agriculture (FiBL)
International Division
CH-5070 Frick, Switzerland 
Phone: +41 (0)62 865 7216  
E-mail: christian.and...@fibl.org


-Ursprüngliche Nachricht-
Von: Duncan Murdoch [mailto:murdoch.dun...@gmail.com] 
Gesendet: Donnerstag, 24. November 2011 16:02
An: Andres Christian
Cc: R-help@r-project.org
Betreff: Re: [R] Horizontal Y axis title above the y axis

On 24/11/2011 9:25 AM, Andres Christian wrote:
 Dear R-help team

 I have tried hard to turn my Y axis 90 degrees, so that it is written 
 horizontally, and placing it above the Y axis, but I did not succeed.

 I have tried to adapt the following functions:


 -  plot()

 -  title()

 -  mtext()

 And some more that did not prove to be useful (e.g. text() etc).

 The closest I got to my aim was with mtext():

 mtext(Yield [kg/ha], side=3, adj=0). However, font.lab=2 does not seem to 
 work in mtext, meaning I could not make the text bold.

The parameter to mtext is just called font, not font.lab.  It is called 
font.lab in other functions because the have multiple types of text, and that's 
the one that is used for labels.

So this works:

mtext(Yield [kg/ha], side=3, adj=0, font=2)


Duncan Murdoch

 Some forums suggest that you can specify the rotation in title(), and I tried 
 crt() and srt() but this did not work either...

 Can you help me?

 Thanks in advance
 Christian

 ___
 Mr Christian Andres
 MSc ETH Agr

 Research Institute of Organic Agriculture (FiBL) International 
 Division
 CH-5070 Frick, Switzerland
 Phone: +41 (0)62 865 7216
 E-mail: christian.and...@fibl.orgmailto:christian.and...@fibl.org


   [[alternative HTML version deleted]]

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 http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.
pl

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Re: [R] I cannot get species scores to plot with site scores in MDS when I use a distance matrix as input. Problems with NA's?

2011-11-24 Thread B77S



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Re: [R] understanding all.equal() output: Mean relative difference

2011-11-24 Thread S Ellison

The help page says that large differences are returned as relative difference. 
A look at the code shows that all.equal.numeric, the version used for a numeric 
first argument, uses the 'target', that is, the first parametter, as the 
scaling factor. Thus

c(1,4) has a difference of 3, scaled by 1, giving 3
c(2,4) has a difference of 2, scaled by 2, giving 1

... and so on.

The other potentially useful part of the help page is the bit right at the 
beginning than says 
Don't use 'all.equal' directly in 'if'
expressions-either use 'isTRUE(all.equal())' or 'identical' if
appropriate.

which usually avoids the need to parse the result at all. 



 -Original Message-
 From: r-help-boun...@r-project.org 
 [mailto:r-help-boun...@r-project.org] On Behalf Of Liviu Andronic
 Sent: 24 November 2011 12:45
 To: r-help@r-project.org Help
 Subject: [R] understanding all.equal() output: Mean relative 
 difference
 
 Dear all
 How should one parse all.equal() output? I'm specifically 
 referring to the 'mean relative difference' messages. For example,
  all.equal(pi, 355/113)
 [1] Mean relative difference: 8.491368e-08
 
 But I'm not sure how to understand these messages. When 
 they're close to 0 (or 1xe-16), then it's intuitive. But when 
 they're big,
  all.equal(1, 4)
 [1] Mean relative difference: 3
  all.equal(2, 4)
 [1] Mean relative difference: 1
  all.equal(3, 4)
 [1] Mean relative difference: 0.333
 
 the messages start making much less sense. I tried Wikipedia 
 [1], but the description is cryptic, as is the help page. 
 Also, Fox and Weisberg (2011) don't explain this particular message.
 
 Regards
 Liviu
 
 [1] 
 http://en.wikipedia.org/wiki/Mean_difference#Relative_mean_difference
 
 
 --
 Do you know how to read?
 http://www.alienetworks.com/srtest.cfm
 http://goodies.xfce.org/projects/applications/xfce4-dict#speed-reader
 Do you know how to write?
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Re: [R] Need some vectorizing help

2011-11-24 Thread David Winsemius



On Nov 24, 2011, at 4:52 AM, Scott Tetrick wrote:

So I have a problem that I'm trying to get through, and I just can't  
seem to get it to run very fast in R.


What I'm trying to do is to find in a vector a local peak, then the  
next time that value is crossed later.  I don't care about peaks  
that may be lower than this first one - they can be ignored.  I've  
tried some sapply methods along the way, but they all are slower.   
The best solution I have is a loop, and I just know there are smart  
R folks that could help me eliminate it.


It looks as though you are reinventing hte function:

?cummax




Peak2Return - function(v) {
 Q - (1:m)[diff(v)0]; find all the peaks
 L - Q[c(TRUE,v[Q[-1]]  v[Q[-length(Q)]])]
  ;  
eliminate lower peaks
 R - sapply(L,function (x,v) { ((x+1):length(v))[v[x]  v[(x+1):m]] 
[1]; }, v)
   ;  
find the next crossing

 out - data.frame(peak=L,Return=R)
 out
}

Thanks in advance!



David Winsemius, MD
West Hartford, CT

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[R] R package for nested random-effects ANOVA models

2011-11-24 Thread syrvn

Hello,

can anyone recommend an R package which can deal with nested random-effects
ANOVA models?

Cheers

Syrvn

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Re: [R] Vegan: how to plot sites labes in diversity plot

2011-11-24 Thread David Winsemius



On Nov 24, 2011, at 8:12 AM, Alejo C.S. wrote:


Dear List,

I can'f figure how to add point labels in the next plot (example from
?taxondive help page, from vegan package):

library(vegan)
data(dune)
data(dune.taxon)
taxdis - taxa2dist(dune.taxon, varstep=TRUE)
mod - taxondive(dune, taxdis)
plot(mod)

The points in this plot are diversity values of single sites, and I'd
like to add a label to each one. The plot command don't accept a
label argument.


Right. Generally you cannot just make up argument names and expect  
plotting routines to honor them. There is no labels argument in  
`plot.default` either.


class(mod)   # to figure out what vegan thinks it object is named
[1] taxondive
 methods(plot)  # to make sure there is a specific plot method
 vegan:::plot.taxondive  # triple dots because it is hidden
function (x, ...)
{
plot(x$Species, x$Dplus, xlab = Number of Species, ylab =  
expression(Delta^+),

...)
i - order(x$Species)
abline(h = x$EDplus, ...)
lines(x$Species[i], x$EDplus - 2 * x$sd.Dplus[i], ...)
lines(x$Species[i], x$EDplus + 2 * x$sd.Dplus[i], ...)
}
environment: namespace:vegan

So from that above you see that the plotting routine is doing nothing  
special. Just plotting x,y values and a bit of annotation


So to plot labels offset a bit to the left and down you look at the  
scale of the plot dimension and take a guess at what will collide th  
least. There are also tricky routines in packages plotrix and Hmisc  
that will do the placement for you, but you clearly need to start  
learning basic R first.


 with( mod, text(Species-.3, Dplus-1, as.character(1:length(Dplus)))  )

--

David Winsemius, MD
West Hartford, CT

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Re: [R] I cannot get species scores to plot with site scores in MDS when I use a distance matrix as input. Problems with NA's?

2011-11-24 Thread B77S

Try the daisy() function from the package cluster, it seems to be able to
handle NAs and non-dummy coded character variables

metaMDS(daisy(df, metric=gower))




Edwin Lebrija Trejos wrote
 
 Hi, First I should note I am relatively new to R so I would appreciate
 answers that take this into account.
  
 I am trying to perform an MDS ordination using the function “metaMDS” of
 the “vegan” package. I want to ordinate species according to a set of
 functional traits. “Species” here refers to “sites” in traditional
 vegetation analyses while “traits” here correspond to “species” in such
 analyses.  
  
 My data looks like this:
  
  Trait1   Trait2 Trait3  Trait4  Trait5  Trait…  
 Species1 228.44   16.56   1.66   13.22 1 short 
 Species2 150.55   28.07   0.41   0.60  1 mid
 Species3 NA   25.89 NA   0.55  0 large
 Species4 147.70   17.65   0.42   1.12 NA large
 Species… 132.68  NA   1.28   2.75  0 short
 
  
 Because the traits have different variable types, different measurement
 scales, and also missing values for some species, I have calculated the
 matrix of species distances using the Gower coefficient of similarity
 available in Package “FD” (which allows missing values). 
 My problem comes when I create a bi-plot of species and traits. As I have
 used a distance matrix in function “metaMDS” there are no species scores
 available. This is given as a warning in R: 
  
  NMDSgowdis- metaMDS(SpeciesGowdis)
 plot(NMDSgowdis, type = t)
 Warning message:In ordiplot(x, choices = choices, type = type, display =
 display, :Species scores not available” 
  
 I have read from internet resources that in principle I could obtain the
 trait (species) scores to plot them in the ordination but my attempts
 have been unsuccessful. I have tried using the function “wascores” in
 package vegan and “add.spec.scores” in package BiodiversityR. For this
 purpuse I have created a new species x traits table where factor traits
 were coded into dummy variables and all integer variables (including
 binary) were coerced to numeric variables. Here are the codes used and the
 error messages I have got: 
  
 “ NMDSgowdis- metaMDS(SpeciesGowdis)
 NMDSpoints-postMDS(NMDSgowdis$points,SpeciesGowdis)
 NMDSwasc-wascores(NMDSpoints,TraitsNMDSdummies)
 Error in if (any(w  0) || sum(w) == 0) stop(weights must be non-negative
 and not all zero) : missing value where TRUE/FALSE needed” 
  
 I imagine the problem is with the NA’s in the data. 
 Alternatively, I have used the “add.spec.scores” function,
 method=”cor.scores”, found in package BiodiversityR. This seemed to work,
 as I got no error message, but the species scores were not returned. Here
 the R code and results:
 “
 A-add.spec.scores(ordi=NMDSgowdis,comm=TraitsNMDSdummies,method=cor.scores,multi=1,
 Rscale=F,scaling=1)
 plot(A)
 Warning message:In ordiplot(x, choices = choices, type = type, display =
 display, :Species scores not available“
  
 Can anyone guide me to get the trait (“species”) scores to plot together
 with my species (“site”) scores?
 Thanks in advance,
 Edwin
 
 
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Re: [R] Thank you

2011-11-24 Thread Frank Harrell

Bert you said it better than I ever could. What R creators, developers, and
documenters do for us every day by how they effect our work as statisticians
is something I would not know how to measure. THANK YOU!
Frank

Bert Gunter wrote

... and while I am at it, as this is the U.S. Thanksgiving...

My sincere thanks to the many R developers and documenters who
contribute large amounts of their personal time and effort to
developing, improving, and enhancing the accessibility of R for data
analysis and science. I believe it is fair to say that R has had as
much or more impact than Gosset's Student's T, and I fear that
academics who do much of this work do not receive the professional
recognition they deserve. I continue to be amazed and humbled by their
high quality and consummate professionalismism -- I could not live
without R.

Kind regards and best wishes to all,

-- Bert

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm

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-
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Re: [R] R package for nested random-effects ANOVA models

2011-11-24 Thread Ben Bolker

syrvn mentor_ at gmx.net writes:

 
 Hello,
 
 can anyone recommend an R package which can deal with nested random-effects
 ANOVA models?
 
 Cheers
 
 Syrvn


  lme in the nlme package; lmer in the lme4 package; and/or visit
the r-sig-mixed-models list.

  Ben Bolker

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[R] [R-pkgs] sem package (version 2.1-1)

2011-11-24 Thread John Fox

Dear R users,

Version 2.1-1 of the sem package, for structural equation modeling, is now
on CRAN. 

Unlike version 2.0-0, which was a major overhaul of the package, version
2.1-1 just sprinkles some syntactic sugar on it, introducing the
specifyEquations() and cfa() functions; specifyEquations() supports model
specification in equation (rather than path) format, and cfa() facilitates
compact specification of simple confirmatory factor analysis models. 

For example, from ?sem, the Duncan, Haller, and Portes peer-influences model
can now be specified as

model.dhp.1 - specifyEquations(covs=RGenAsp, FGenAsp)
RGenAsp = gam11*RParAsp + gam12*RIQ + gam13*RSES + gam14*FSES +
beta12*FGenAsp
FGenAsp = gam23*RSES + gam24*FSES + gam25*FIQ + gam26*FParAsp +
beta21*RGenAsp
ROccAsp = 1*RGenAsp
REdAsp = lam21(1)*RGenAsp  # to illustrate setting start values, not
necessary here
FOccAsp = 1*FGenAsp
FEdAsp = lam42(1)*FGenAsp

and the Wheaton alientation model as

model.wh - specifyEquations()
Anomia67 = 1*Alienation67
Powerless67 = lamby*Alienation67
Anomia71 = 1*Alienation71
Powerless71 = lamby*Alienation71
Education = 1*SES
SEI = lambx*SES
Alienation67 = gam1*SES
Alienation71 = gam2*SES + beta*Alienation67
V(Anomia67) = the1
V(Anomia71) = the1
V(Powerless67) = the2
V(Powerless71) = the2
V(SES) = phi
C(Anomia67, Anomia71) = the5
C(Powerless67, Powerless71) = the5

Similarly, the following are equivalent specifications of a CFA model for
the Thurstore mental-tests data:

(1) in CFA format:

mod.cfa.thur.c - cfa()
FA: Sentences, Vocabulary, Sent.Completion
FB: First.Letters, 4.Letter.Words, Suffixes
FC: Letter.Series, Pedigrees, Letter.Group

cfa.thur.c - sem(mod.cfa.thur.c, R.thur, 213)
summary(cfa.thur.c)

(2) in equation format:

mod.cfa.thur.e - specifyEquations(covs=F1, F2, F3)
Sentences = lam11*F1
Vocabulary = lam21*F1
Sent.Completion = lam31*F1
First.Letters = lam42*F2
4.Letter.Words = lam52*F2
Suffixes = lam62*F2
Letter.Series = lam73*F3
Pedigrees = lam83*F3
Letter.Group = lam93*F3
V(F1) = 1
V(F2) = 1
V(F3) = 1

cfa.thur.e - sem(mod.cfa.thur.e, R.thur, 213)
summary(cfa.thur.e)

(3) in path format:

mod.cfa.thur.p - specifyModel(covs=F1, F2, F3)
F1 - Sentences,  lam11
F1 - Vocabulary, lam21
F1 - Sent.Completion,lam31
F2 - First.Letters,  lam41
F2 - 4.Letter.Words, lam52
F2 - Suffixes,   lam62
F3 - Letter.Series,  lam73
F3 - Pedigrees,  lam83
F3 - Letter.Group,   lam93
F1 - F1,NA, 1
F2 - F2,NA, 1
F3 - F3,NA, 1


As usual, I'd be grateful for comments, suggestions, and bug reports.

Best,
 John


John Fox
Senator William McMaster
  Professor of Social Statistics
Department of Sociology
McMaster University
Hamilton, Ontario, Canada
http://socserv.mcmaster.ca/jfox

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[R] Is there way to add a new row to a data frame in a specific location

2011-11-24 Thread Sammy Zee

Is there easy way (without copying the existing rows to a temporary
location and copying back) to add a new row to a specific index location in
an existing data frame?

Example

df = data.frame( A= c('a','b','c'), B=c(1,2,3), C=(10,20,30))

newrow = c('X', 100, 200)

I want to add the newrow as the second row to the data frame df

Please suggest a solution that is efficient for a data frame that can have
millions of rows, and I want to add a new row in any given index location
of the data frame.

Thanks,
Sammy

[[alternative HTML version deleted]]

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Re: [R] Is there way to add a new row to a data frame in a specific location

2011-11-24 Thread andrija djurovic

Hi.
May be this:

df = data.frame( A=c('a','b','c'), B=c(1,2,3), C=c(10,20,30),
stringsAsFactors=FALSE)

newrow = c('X', 100, 200)

rbind(df,newrow)[c(1,4,2,3),]

Andrija


On Thu, Nov 24, 2011 at. 6:05 PM, Sammy Zee szee2...@gmail.com wrote:

 Is there easy way (without copying the existing rows to a temporary
 location and copying back) to add a new row to a specific index location in
 an existing data frame?

 Example

 df = data.frame( A= c('a','b','c'), B=c(1,2,3), C=(10,20,30))

 newrow = c('X', 100, 200)

 I want to add the newrow as the second row to the data frame df

 Please suggest a solution that is efficient for a data frame that can have
 millions of rows, and I want to add a new row in any given index location
 of the data frame.

 Thanks,
 Sammy

[[alternative HTML version deleted]]

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[[alternative HTML version deleted]]

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Re: [R] Thank you

2011-11-24 Thread christiaan pauw

And from the side of a ordinary user who opened the page that read:
Chapter 1: What is R? two years ago to all of you on this list:
Since reading that first page things have changed so that I would get
through a normal working day without the software you create and the advice
you give.

Thank you to all of you
Christiaan

On 24 November 2011 18:00, Frank Harrell f.harr...@vanderbilt.edu wrote:

 Bert you said it better than I ever could.  What R creators, developers,
 and
 documenters do for us every day by how they effect our work as
 statisticians
 is something I would not know how to measure.  THANK YOU!
 Frank

 Bert Gunter wrote
 
  ... and while I am at it, as this is the U.S. Thanksgiving...
 
  My sincere thanks to the many R developers and documenters who
  contribute large amounts of their personal time and effort to
  developing, improving, and enhancing the accessibility of R for data
  analysis and science. I believe it is fair to say that R has had as
  much or more impact than Gosset's Student's T, and I fear that
  academics who do much of this work do not receive the professional
  recognition they deserve. I continue to be amazed and humbled by their
  high quality and consummate professionalismism -- I could not live
  without R.
 
  Kind regards and best wishes to all,
 
  -- Bert
 
  --
 
  Bert Gunter
  Genentech Nonclinical Biostatistics


[[alternative HTML version deleted]]

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[R] content of global environment with dump.frames()

2011-11-24 Thread Jannis

Dear R users,


I am using dump.frames() to investigate the content of the different 
environments in cases of errors or during certain steps of a non interactive 
calculation. I am, however, wondering about how to see the content of the 
global environment at the moment that dump.fames() was invoked. Her is some 
test piece (careful about the rm(list=ls(), remove the # if you know what you 
are doing to easier see the effect):

# rm(list=ls())
a=2
test = function() {
  b=3
  dump.frames(dumpto='test', to.file = TRUE )
}
test()
# rm(list=ls())
load('test.rda')
debugger(test)

I can now investigate the value of 'b' but could not figure out a way to get 
the value of 'a'. Am I missing something or is dump.frames only intended to be 
uses with 


options(error=dump.frames) 


? Most probably some modification of save() would be more apropriate to use in 
my case but I could not (yet) figure out how to mimic the convenient behaviour 
of dump.frames() to save the whole call stack.




Thanks for any advice
Jannis


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Re: [R] content of global environment with dump.frames()

2011-11-24 Thread R. Michael Weylandt

Are perhaps you looking for options(error = recover)?

Michael

On Thu, Nov 24, 2011 at 12:52 PM, Jannis bt_jan...@yahoo.de wrote:
 Dear R users,


 I am using dump.frames() to investigate the content of the different 
 environments in cases of errors or during certain steps of a non interactive 
 calculation. I am, however, wondering about how to see the content of the 
 global environment at the moment that dump.fames() was invoked. Her is some 
 test piece (careful about the rm(list=ls(), remove the # if you know what you 
 are doing to easier see the effect):

 # rm(list=ls())
 a=2
 test = function() {
   b=3
   dump.frames(dumpto='test', to.file = TRUE )
 }
 test()
 # rm(list=ls())
 load('test.rda')
 debugger(test)

 I can now investigate the value of 'b' but could not figure out a way to get 
 the value of 'a'. Am I missing something or is dump.frames only intended to 
 be uses with


 options(error=dump.frames)


 ? Most probably some modification of save() would be more apropriate to use 
 in my case but I could not (yet) figure out how to mimic the convenient 
 behaviour of dump.frames() to save the whole call stack.




 Thanks for any advice
 Jannis


 __
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Re: [R] Is there way to add a new row to a data frame in a specific location

2011-11-24 Thread Jeff Newmiller

AFAIK all solutions to the grow object size problem in R involve creation of 
a new object to change an old one.  There is considerable sophistication 
under the hood that allows a minimum of intermediate objects to be created if 
you are careful, but actually changing the size of an object in place is not 
supported.

That doesn't mean that you have to copy... to a temporary and then copy back, 
since you can reference chunks of an existing object without actually moving 
them in memory by using indexing. But (AFAIK) you cannot escape creating at 
least one new copy of the data that becomes the object if you use rbind to 
grow your object.
---
Jeff NewmillerThe .   .  Go Live...
DCN:jdnew...@dcn.davis.ca.usBasics: ##.#.   ##.#.  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.

Sammy Zee szee2...@gmail.com wrote:

Is there easy way (without copying the existing rows to a temporary
location and copying back) to add a new row to a specific index
location in
an existing data frame?

Example

df = data.frame( A= c('a','b','c'), B=c(1,2,3), C=(10,20,30))

newrow = c('X', 100, 200)

I want to add the newrow as the second row to the data frame df

Please suggest a solution that is efficient for a data frame that can
have
millions of rows, and I want to add a new row in any given index
location
of the data frame.

Thanks,
Sammy

   [[alternative HTML version deleted]]

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Re: [R] Question on density values obtained from kde2d() from package MASS


On Thu, 24 Nov 2011, Andreas Klein wrote:


Hello,

I am a little bit confused regarding the density values obtained 
from the function kde2d() from the package MASS because the are not 
in the intervall [0,1] as I would expect them to be. Here is an


Your expectation is wrong.


example:

x - 
c(0.0036,0.0088,0.0042,0.0022,-0.0013,0.0007,0.0028,-0.0028,0.0019,0.0026,-0.0029,-0.0081,-0.0024,0.0090,0.0088,0.0038,0.0022,0.0068,0.0089,-0.0015,-0.0062,0.0066)
y - 
c(0.00614,0.00194,0.00264,0.00064,0.00344,0.00314,-0.6,-0.00066,0.00174,0.00274,-0.00076,0.00024,-0.00236,0.00234,0.00504,0.00114,0.00054,-0.00116,-0.00016,-0.00566,0.00044,0.00404)

tmp - kde2d(x=x, y=y, n=100)
range(tmp$z)
#3.621288 11989.060924

Do I have to transform them further? Or what scale are they?


They are density values, as you quote from the help page.  Try
dnorm(0, 0, 1e-6) in R.  That's a density, way above 1.

Perhaps you need to revise Probability 101.


Or did I get something wrong regarding the output because in the help file it 
reads:
zAn n[1] by n[2] matrix of the estimated density: rows

  ^

correspond to the value of x, columns to the value of y.


Regards,
Andy.



--
Brian D. Ripley,  rip...@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
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Re: [R] Is there way to add a new row to a data frame in a specific location

On Thu, 24 Nov 2011, Jeff Newmiller wrote:

AFAIK all solutions to the grow object size problem in R involve
creation of a new object to change an old one. There is
considerable sophistication under the hood that allows a minimum of
intermediate objects to be created if you are careful, but actually
changing the size of an object in place is not supported.

Just for the record, it actually is (R vectors have a LENGTH and
TRUELENGTH property at C level), but this is AFAIK only used
internally.

The better question is why you care about the order of the rows of a
data frame? A good way to think of a d.f. is like a table in a DBMS:
for efficiency the cases are unordered, but you can retrieve them in
any order you want (or no order). Indeed, for efficient operations on
millions of rows an R-DBMS interface is highly recomemded -- see the
R-data manual.

That doesn't mean that you have to copy... to a temporary and then copy back, since you
can reference chunks of an existing object without actually moving them in memory by using
indexing. But (AFAIK) you cannot escape creating at least one new copy of the data that
becomes the object if you use rbind to grow your object.
---
Jeff NewmillerThe . . Go Live...
DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. 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.

Sammy Zee szee2...@gmail.com wrote:

Is there easy way (without copying the existing rows to a temporary
location and copying back) to add a new row to a specific index
location in
an existing data frame?

Example

df = data.frame( A= c('a','b','c'), B=c(1,2,3), C=(10,20,30))

newrow = c('X', 100, 200)

I want to add the newrow as the second row to the data frame df

Please suggest a solution that is efficient for a data frame that
can have millions of rows, and I want to add a new row in any given
index location of the data frame.

Thanks,
Sammy

--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595

Re: [R] Comments disappearing from local functions (R 2.14.0)

2011-11-24 Thread Patrick Connolly

On Mon, 21-Nov-2011 at 09:46PM +1300, Rolf Turner wrote:

[]

| It *doesn't* happen to me.  Ergo it would appear to be peculiar
| to your particular set-up.
| 
| What does options()$keep.source say?  (Mine says TRUE.)
| 

Same here in both cases.


| 
| P. S.:
| 
|  sessionInfo()
| R version 2.14.0 (2011-10-31)
| Platform: i686-pc-linux-gnu (32-bit)
| 
| locale:
|  [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
|  [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
|  [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
|  [7] LC_PAPER=C LC_NAME=C
|  [9] LC_ADDRESS=C   LC_TELEPHONE=C
| [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

Both the same except the Kubuntu one is 
Platform: x86_64-unknown-linux-gnu (64-bit)


| 
| attached base packages:
| [1] stats graphics  grDevices utils datasets  methods   base
| 
| other attached packages:
| [1] misc_0.0-15

attached base packages:
[1] splines   grDevices utils stats graphics  methods   base 

other attached packages:
[1] multicore_0.1-7  gbm_1.6-3.1  survival_2.36-10 lattice_0.20-0  

loaded via a namespace (and not attached):
[1] grid_2.14.0  tools_2.14.0
 

With the one using multicore, I get a strange error that didn't occur
with R-2.13.1.  A function which runs on 7 cores produces a swag of
PDF files and then returns a list of information.  New to the 2.14.0
is an error like this:

Error in dev.off() : internal error in PDF_endpage\n

From what I can work out, that is a C message and tricky to trace.
However, if I use a postscript device instead of PDF, it works fine.
It's a simple matter to convert a postscript file to pdf, so that's
easy to deal with.  It's impossible to make a toy example of the
problem which doesn't appear when run on a single core.  Maybe if I
knew exactly where the problem arises I could make a toy example but
it's rather a lot of code I'm dealing with.  The fact that the two
problems I'm encountering did not occur with earlier versions makes me
less suspicious of my own code.


My main question is: Can I redo the updating of the packages with
checkBuilt to downgrade them back to the previous version?  Something
is not right with either of my installations and I'd like to revert.

The problem with the disappearing comments occurs when I wish to
attach to another directory.  I commonly reuse functions from previous
years and modify them for the current year.  

If my pwd is, say ~/thisYear, I'll do something like 
attach(~/lastYear/.RData)

If I then edit the function of interest, when it's saved I have the
appropriate version in ~/thisYear/.RData which I find a convenient way
to work.  If the comments aren't there, it's far less usable.  If I
can go back to R-2.13.1 I can still work that way.


TIA

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

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[R] proper work-flow with 'formula' objects and lm()

Dear all
I have a work-flow issue with lm(). When I use
 lm(y1~x1, anscombe)

Call:
lm(formula = y1 ~ x1, data = anscombe)

Coefficients:
(Intercept)   x1
 3.0001   0.5001


I get as expected the formula, y1 ~ x1, in the print()ed results or
summary(). However, if I pass through a formula object
 (form - formula(y1~x1))
y1 ~ x1
 lm(form, anscombe)

Call:
lm(formula = form, data = anscombe)

Coefficients:
(Intercept)   x1
 3.0001   0.5001


then I only get the object name in the call, 'form', instead of the
formula. When passing a 'formula' object to lm, is it possible to
retain in the resulting 'lm' object the actual formula used for the
regression: y1 ~ x1?

Regards
Liviu


-- 
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http://www.alienetworks.com/srtest.cfm
http://goodies.xfce.org/projects/applications/xfce4-dict#speed-reader
Do you know how to write?
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[R] jzoj4 43vwibnt

2011-11-24 Thread Nathaniel Saxe

5ja7o, h5ih0aufrt.
 http://yjgv6d1r.blog.com/nrd/ 
s2gqnd gkajocjaked 6fzlef, qufk5mowaax0 zcy51g1f. avgvvqnqiq79 g11hp.
  
[[alternative HTML version deleted]]

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Re: [R] proper work-flow with 'formula' objects and lm()


On 24/11/2011 2:48 PM, Liviu Andronic wrote:

Dear all
I have a work-flow issue with lm(). When I use
  lm(y1~x1, anscombe)

Call:
lm(formula = y1 ~ x1, data = anscombe)

Coefficients:
(Intercept)   x1
  3.0001   0.5001


I get as expected the formula, y1 ~ x1, in the print()ed results or
summary(). However, if I pass through a formula object
  (form- formula(y1~x1))
y1 ~ x1
  lm(form, anscombe)

Call:
lm(formula = form, data = anscombe)

Coefficients:
(Intercept)   x1
  3.0001   0.5001


then I only get the object name in the call, 'form', instead of the
formula. When passing a 'formula' object to lm, is it possible to
retain in the resulting 'lm' object the actual formula used for the
regression: y1 ~ x1?


It is retained.  terms(fit) will give it to you, if fit is an lm object.

Duncan Murdoch

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Re: [R] First read

2011-11-24 Thread Patrick Burns


Bert,

Your laziness is well founded -- it
is not on CRAN, you have to go all
the way over to another website.

And thanks for the kind words (even
though we Europeans are free to be
ingrates today).

Pat

On 24/11/2011 14:23, Bert Gunter wrote:

Pat:

1. Thank you for this. Having not read your tutorial, but based on
what I know of your other efforts, I am sure that you are correct. Is
there a link to this on CRAN somewhere so I can refer to it in future
(too lazy to search myself)?

2. Thank you also for your continuing contributions to R
documentation. I know this takes a lot of work and you do it well.
Would that more R learners would read them -- there would be a lot
less RTFM type queries on r-help.

Best,
Bert

On Thu, Nov 24, 2011 at 12:27 AM, Patrick Burns
pbu...@pburns.seanet.com  wrote:

It's very seldom that I disagree with
Bert, but here is one time.

I don't think An Introduction to R is
a suitable first read for people with
little computational experience.

Better (I modestly suggest) would be:

http://www.burns-stat.com/pages/Tutor/hints_R_begin.html

which includes some other references.
'Hints' is imperfect and incomplete but
it suffers slightly less from the curse of
knowledge than a lot of other R documentation.

Pat

On 24/11/2011 00:15, Bert Gunter wrote:


... and you can of course do the assignment:

Bndy-  paste (BndY,to,50+seq_len(BndY), mN, sep =  )

An Introduction to R tells you about such fundamentals and should be
a first read for anyone learning R.

--- Bert

On Wed, Nov 23, 2011 at 4:10 PM, Bert Gunterbgun...@gene.comwrote:


Don't do this!  paste() is vectorized.

paste (BndY,to,50+seq_len(BndY), mN, sep =  )

Cheers,
Bert

On Wed, Nov 23, 2011 at 3:31 PM, B77Sbps0...@auburn.eduwrote:


out- vector(list)
Ylab- for(i in 1:length(BndY))
{
out[i]- paste(BndY[i], to ,BndY[i],mN)
}

Ylab- do.call(c, out)






markm0705 wrote


Dear R helpers

I'm trying to make up some labels for plot from this vector

BndY-seq(from = 18900,to= 19700, by = 50)

using

Ylab-for(i in BndY) {c((paste(i, to ,i+50,mN)))}

but the vector created is NULL

However if i use

for(i in BndY) {print(c(paste(i, to ,i+50,mN)))}

I can see the for loop is making the labels I'm looking for but not
sure
on my error in assigning them to a vector

Thanks in advance




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--

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:

http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm







--
Patrick Burns
pbu...@pburns.seanet.com
twitter: @portfolioprobe
http://www.portfolioprobe.com/blog
http://www.burns-stat.com
(home of 'Some hints for the R beginner'
and 'The R Inferno')

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--
Patrick Burns
pbu...@pburns.seanet.com
twitter: @portfolioprobe
http://www.portfolioprobe.com/blog
http://www.burns-stat.com
(home of 'Some hints for the R beginner'
and 'The R Inferno')

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Re: [R] Thank you

2011-11-24 Thread Paul


On 24/11/11 14:43, Bert Gunter wrote:

... and while I am at it, as this is the U.S. Thanksgiving...

My sincere thanks to the many R developers and documenters who
contribute large amounts of their personal time and effort to
developing, improving, and enhancing the accessibility of R for data
analysis and science. I believe it is fair to say that R has had as
much or more impact than Gosset's Student's T, and I fear that
academics who do much of this work do not receive the professional
recognition they deserve. I continue to be amazed and humbled by their
high quality and consummate professionalismism -- I could not live
without R.

Kind regards and best wishes to all,

-- Bert

and even though I'm (and many others) are the 'wrong' side of the pond, 
I'd like to add my +1 to these thanks.


Thanks !

Paul.

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Re: [R] Comments disappearing from local functions (R 2.14.0)


On Fri, 25 Nov 2011, Patrick Connolly wrote:


On Mon, 21-Nov-2011 at 09:46PM +1300, Rolf Turner wrote:

[]


Please don't excise content, nor mix up topics.  I am going to reply 
here just to the subject line, and reply to your use of pdf() under 
multicore separately.




| It *doesn't* happen to me.  Ergo it would appear to be peculiar
| to your particular set-up.
|
| What does options()$keep.source say?  (Mine says TRUE.)
|

Same here in both cases.


[...]


My main question is: Can I redo the updating of the packages with
checkBuilt to downgrade them back to the previous version?  Something
is not right with either of my installations and I'd like to revert.

The problem with the disappearing comments occurs when I wish to
attach to another directory.  I commonly reuse functions from previous
years and modify them for the current year.

If my pwd is, say ~/thisYear, I'll do something like
attach(~/lastYear/.RData)

If I then edit the function of interest, when it's saved I have the
appropriate version in ~/thisYear/.RData which I find a convenient way
to work.  If the comments aren't there, it's far less usable.  If I
can go back to R-2.13.1 I can still work that way.


So you missed the NEWS item:

• The source attribute on functions created with keep.source=TRUE
  has been replaced with a srcref attribute.  The srcref
  attribute references an in-memory copy of the source file using
  the srcfilecopy class or the new srcfilealias class.

This means that if you save a function under R 2.13.1 and load/attach 
it under R 2.14.0, its kept source (with the comments) is no longer 
available.


However your original posting did not mention save/attach, nor that 
you saved under one version and attached under another.  That is hte 
only circumstance under which I can make it do what you claim.


And now you know not to do that.  Dump your functions in 2.13.1, and 
source/save in 2.14.0.



--
Brian D. Ripley,  rip...@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595__
R-help@r-project.org mailing list
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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] proper work-flow with 'formula' objects and lm()

On Thu, Nov 24, 2011 at 9:14 PM, Duncan Murdoch
murdoch.dun...@gmail.com wrote:
 It is retained.  terms(fit) will give it to you, if fit is an lm object.


Thank you. The following works nicely.
 (form - formula(y1~x1))
y1 ~ x1
 x - lm(form, anscombe)
 formula(terms(x))
y1 ~ x1


However, I was hoping that there was a way to input the 'form' object
so that summary(x) would print the underlying formula used, not the
formula object name. I was thinking of something in the style of
x - lm(deparse(form), anscombe)
summary(x)

Can this be done? Regards
Liviu

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Re: [R] pdf() under multicore (was Comments disappearing from local functions (R 2.14.0))


On Fri, 25 Nov 2011, Patrick Connolly wrote:

[... about a completely different topic]


With the one using multicore, I get a strange error that didn't occur
with R-2.13.1.  A function which runs on 7 cores produces a swag of
PDF files and then returns a list of information.  New to the 2.14.0
is an error like this:

Error in dev.off() : internal error in PDF_endpage\n


From what I can work out, that is a C message and tricky to trace.


Easy to trace; you look for it in the code! It indicates that you used 
PDF compression (new to 2.14.0) and that the page-stream file got 
corrupted.  So simply use compress=FALSE to get the previous 
behaviour.


However, mixing graphics devices with multicore is probably asking for 
trouble.  If your fork with an open graphics device you certainly are 
since the parent and child will share file handles.
But even if each child opens a separate pdf() device and closes it 
before it returns, there still are many pitfalls as the parent and 
child share a session temporary directory and all assume they have 
exclusive access to it.  My guess is that two pdf() devices in 
different processes are using the same temporary file, or the same 
FILE stream associated with a temporary file.  And only onefile=FALSE 
or compress=TRUE use such temporary files.



However, if I use a postscript device instead of PDF, it works fine.
It's a simple matter to convert a postscript file to pdf, so that's
easy to deal with.  It's impossible to make a toy example of the
problem which doesn't appear when run on a single core.  Maybe if I
knew exactly where the problem arises I could make a toy example but
it's rather a lot of code I'm dealing with.  The fact that the two
problems I'm encountering did not occur with earlier versions makes me
less suspicious of my own code.


You could at least have outlined what you are doing.

--
Brian D. Ripley,  rip...@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595

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Re: [R] proper work-flow with 'formula' objects and lm()


On Thu, 24 Nov 2011, Liviu Andronic wrote:


On Thu, Nov 24, 2011 at 9:14 PM, Duncan Murdoch
murdoch.dun...@gmail.com wrote:

It is retained.  terms(fit) will give it to you, if fit is an lm object.



Thank you. The following works nicely.

(form - formula(y1~x1))

y1 ~ x1

x - lm(form, anscombe)
formula(terms(x))

y1 ~ x1


However, I was hoping that there was a way to input the 'form' object
so that summary(x) would print the underlying formula used, not the
formula object name. I was thinking of something in the style of
x - lm(deparse(form), anscombe)
summary(x)

Can this be done? Regards


Yes.  That's a job for substitute (the second time today).


form - formula(y1~x1)
x - eval(substitute(lm(f, anscombe), list(f = form)))
summary(x)


Call:
lm(formula = y1 ~ x1, data = anscombe)
...


Liviu

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--
Brian D. Ripley,  rip...@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595__
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and provide commented, minimal, self-contained, reproducible code.

Re: [R] proper work-flow with 'formula' objects and lm()

On Thu, Nov 24, 2011 at 10:25 PM, Prof Brian Ripley
rip...@stats.ox.ac.uk wrote:
 Yes.  That's a job for substitute (the second time today).

 form - formula(y1~x1)
 x - eval(substitute(lm(f, anscombe), list(f = form)))
 summary(x)

 Call:
 lm(formula = y1 ~ x1, data = anscombe)

That's what I wanted. Thanks!

However, I do want to simplify the syntax and define a new function:
x.lm -
  function(formula, data, ...)
{
  eval(substitute(lm(f, data, ...), list(f = formula)))
}

For the simple case it works just fine
 (form - formula(y1~x1))
y1 ~ x1
 x - x.lm(form, anscombe)

But it fails when I try to input more lm() arguments:
 (x - x.lm(form, anscombe, subset=-5))
Error in eval(expr, envir, enclos) :
  ..1 used in an incorrect context, no ... to look in

Am I doing something obviously wrong? Regards
Liviu

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Re: [R] proper work-flow with 'formula' objects and lm()

2011-11-24 Thread Gabor Grothendieck

On Thu, Nov 24, 2011 at 2:48 PM, Liviu Andronic landronim...@gmail.com wrote:
 Dear all
 I have a work-flow issue with lm(). When I use
 lm(y1~x1, anscombe)

 Call:
 lm(formula = y1 ~ x1, data = anscombe)

 Coefficients:
 (Intercept)           x1
     3.0001       0.5001


 I get as expected the formula, y1 ~ x1, in the print()ed results or
 summary(). However, if I pass through a formula object
 (form - formula(y1~x1))
 y1 ~ x1
 lm(form, anscombe)

 Call:
 lm(formula = form, data = anscombe)

 Coefficients:
 (Intercept)           x1
     3.0001       0.5001


 then I only get the object name in the call, 'form', instead of the
 formula. When passing a 'formula' object to lm, is it possible to
 retain in the resulting 'lm' object the actual formula used for the
 regression: y1 ~ x1?


Try this:

 form - formula(y1~x1)
 do.call(lm, list(form, quote(anscombe)))

Call:
lm(formula = y1 ~ x1, data = anscombe)

Coefficients:
(Intercept)   x1
 3.0001   0.5001

-- 
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email: ggrothendieck at gmail.com

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Re: [R] readGDAL or raster for reading bit map files

2011-11-24 Thread Michael Sumner

It is by magic, otherwise known as R classes and methods. See

sp:::as.matrix.SpatialGridDataFrame

There's a lot of background here so I suggest you start with the
general R documentation, and the sp package documentation, including

vignette(sp)

and these

citation(sp)

Cheers, Mike.

On Fri, Nov 25, 2011 at 1:49 AM, Alaios ala...@yahoo.com wrote:
 Thanks a lot!
 That worked. I have two R related questions
 when I use the
   store-readGDAL(fname='lena256.bmp')
 this returns the struct below

 str(store)
 Formal class 'SpatialGridDataFrame' [package sp] with 6 slots
   ..@ data   :'data.frame': 65536 obs. of  1 variable:
   .. ..$ band1: int [1:65536] 255 255 255 255 255 255 255 255 255 255 ...
   ..@ grid   :Formal class 'GridTopology' [package sp] with 3 slots
   .. .. ..@ cellcentre.offset: Named num [1:2] 0 -722925
   .. .. .. ..- attr(*, names)= chr [1:2] x y
   .. .. ..@ cellsize : num [1:2] 2835 2835
   .. .. ..@ cells.dim    : int [1:2] 256 256
   ..@ grid.index : int(0)
   ..@ coords : num [1:2, 1:2] 0 722925 -722925 0
   .. ..- attr(*, dimnames)=List of 2
   .. .. ..$ : NULL
   .. .. ..$ : chr [1:2] x y
   ..@ bbox   : num [1:2, 1:2] -1418 -724342 724342 1418
   .. ..- attr(*, dimnames)=List of 2
   .. .. ..$ : chr [1:2] x y
   .. .. ..$ : chr [1:2] min max
   ..@ proj4string:Formal class 'CRS' [package sp] with 1 slots
   .. .. ..@ projargs: chr NA

 How the R when I run image(store) plots the lena correct. Where it store
 how the file was originally?
 Also when I do
 str(as.matrix(store))
 this takes only the data and transforms them to the original matri
 str(as.matrix(store))
  int [1:256, 1:256]
 How it does that?
 Looks as magic to me
 B.R
 Alex
 
 From: Michael Sumner mdsum...@gmail.com
 To: Alaios ala...@yahoo.com
 Cc: R-help@r-project.org R-help@r-project.org
 Sent: Thursday, November 24, 2011 2:25 PM
 Subject: Re: [R] readGDAL or raster for reading bit map files

 Just do

 m - as.matrix(store)

 or

 m - as.image.SpatialGridDataFrame(store)$z

 image(m)

 They give the same result with different orientations.  Note that both
 assume a single-band raster, e.g. you only have a greyscale bitmap
 (for example).

 The details behind all this is given in the documentation for the sp
 package. See ?image for the basic image plot for a matrix.

 Cheers, Mike.


 On Thu, Nov 24, 2011 at 11:50 PM, Alaios ala...@yahoo.com wrote:
 Dear all,
 I have asked yesterday of how I can read a simple bitmap file in R cran.

 I was suggest to use either readGDAL or raster for loading my bitmap


 a. I have done it with readGDAL like

     store-readGDAL(fname='lena256.bmp')
     and it works,... but it converts my matrix-like notion of a bitmap to
 a large vector

 b. Raster also returns a class that I can not understand.

 So 1, I want to load it and keep the image as a matrix (so every cell in
 the matrix will correspond to a pixel)
 2. I want to be able to plot the image based on that matrix that I have
 loaded too.

 Could you please explain me how I can do those?

 B.R
 Alex

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 PLEASE do read the posting guide
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 --
 Michael Sumner
 Institute for Marine and Antarctic Studies, University of Tasmania
 Hobart, Australia
 e-mail: mdsum...@gmail.com






-- 
Michael Sumner
Institute for Marine and Antarctic Studies, University of Tasmania
Hobart, Australia
e-mail: mdsum...@gmail.com

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R-help@r-project.org mailing list
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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] proper work-flow with 'formula' objects and lm()


You would get exactly the same problem with ...,, anway.

Here's a commonly used approach in R sources:

x.lm - function(formula, data, ...)
{
Call - match.call(expand.dots = TRUE)
Call[[1]] - as.name(lm)
Call$formula - as.formula(terms(formula))
eval(Call)
}



On Thu, 24 Nov 2011, Liviu Andronic wrote:


On Thu, Nov 24, 2011 at 10:25 PM, Prof Brian Ripley
rip...@stats.ox.ac.uk wrote:

Yes.  That's a job for substitute (the second time today).


form - formula(y1~x1)
x - eval(substitute(lm(f, anscombe), list(f = form)))
summary(x)


Call:
lm(formula = y1 ~ x1, data = anscombe)


That's what I wanted. Thanks!

However, I do want to simplify the syntax and define a new function:
x.lm -
 function(formula, data, ...)
{
 eval(substitute(lm(f, data, ...), list(f = formula)))
}

For the simple case it works just fine

(form - formula(y1~x1))

y1 ~ x1

x - x.lm(form, anscombe)


But it fails when I try to input more lm() arguments:

(x - x.lm(form, anscombe, subset=-5))

Error in eval(expr, envir, enclos) :
 ..1 used in an incorrect context, no ... to look in

Am I doing something obviously wrong? Regards
Liviu



--
Brian D. Ripley,  rip...@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] proper work-flow with 'formula' objects and lm()