date:20091006


On 06/10/2009 6:36 AM, John Maindonald wrote:

I had a large job time ago that ran fine under MacOS X.
I'd expect the same to be true under Linux.  It would run
under Windows XP only if XP had been freshly rebooted.


That sounds like you were running out of memory, or it was a bug.  Did 
you report it?


Duncan Murdoch



John Maindonald email: john.maindon...@anu.edu.au
phone : +61 2 (6125)3473fax  : +61 2(6125)5549
Centre for Mathematics  Its Applications, Room 1194,
John Dedman Mathematical Sciences Building (Building 27)
Australian National University, Canberra ACT 0200.


On 06/10/2009, at 9:00 PM, r-help-requ...@r-project.org wrote:


From: Liviu Andronic landronim...@gmail.com
Date: 6 October 2009 6:46:33 PM AEDT
To: Robert Wilkins iwriteco...@gmail.com
Cc: r-help@r-project.org
Subject: Re: [R] R on Linux, and R on Windows , any difference in  
maturity+stability?



On 10/6/09, Robert Wilkins iwriteco...@gmail.com wrote:

Will R have more glitches on one operating system as opposed to
another,


Probably not.


or is it pretty much the same?


Depending on the complexity of the code, it is pretty much the same. I
recently had a (relatively simple) group project, with the three of us
on different OSs: Win, Mac and Linux. We did not encounter one
platform specific issue.
Liviu



[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
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.

[R] Spatial Autocorrelation

2009-10-06 Thread P.Branco


Hello, 

I have a matrix with the distances among sites. And I have another matrix
with the presence and absence of  each species in each site. I would like to
test the spatial autocorrelation among sites.

I have tried to use the function gearymoran of the ade4 package, but error
messages keep popping up. Do you know any function for me to test the
spatial autocorrelation of my data?

Thanks,

Paulo Branco
-- 
View this message in context: 
http://www.nabble.com/Spatial-Autocorrelation-tp25767010p25767010.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Extracting year from a date object

2009-10-06 Thread Prof Brian Ripley


See ?weekdays, which says

Note:

 Other components such as the day of the month or the year are very
 easy to compute: just use 'as.POSIXlt' and extract the relevant
 component.

so


as.POSIXlt(MyDate)$year+1900

[1] 1994

is how you are expected to do it.

On Tue, 6 Oct 2009, joris meys wrote:


Hi all,

this one left me a bit puzzled, as I don't seem to find a function to
perform this easily. I must have overlooked the obvious, so sorry in
advance.

I have a list of dates in numerical format (i.e. 34576), defined as
the number of days that passed since january 1st 1900. So I apply the
function :


MyDate -as.Date(34576,origin=1900-01-01)
MyDate

[1] 1994-09-01

But then I want to do something like :
MyYear - a.year.function(MyDate)

MyYear should have the numerical value 1994. Alas, I don't find any
function like that. I know I can take a substring of MyDate and
convert to numeric, or even use the function seq() :


length ( seq ( as.Date(1900-01-01), MyDate, years ) ) + 1900 - 1

[1] 1994

but that seems quite a way around. Can somebody tell me where the
appropriate function is hiding?
Thank you in advance.
Joris

__
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.



--
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
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.

Re: [R] Unable to load 'doBy' package

2009-10-06 Thread joris meys

Hi Lauren,

from the error message it looks like you have a problem with the
package Hmisc. doBy is dependent on that one. Can you check whether
Hmisc is installed in your R version? For me, doBy loads without
problems.

On Tue, Oct 6, 2009 at 12:18 PM, Lauren Szathmary lszathm...@gmail.com wrote:
 Hi all,

 I am trying to load the doBy package, and I am getting the following error:

 library(doBy)
 Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) :
  there is no package called 'Hmisc'
 Error: package/namespace load failed for 'doBy'

 I tried updating R to the current version (2.9.2) and installing the most
 recent version of the doBy package (4.0.2), and the error remained the
 same.  I also tried loading the package by going to my Package Manager
 window and clicking the box to load 'doBy', but that didn't work either.  My
 other packages (e.g., lattice, chron, etc.) are loading normally with no
 problems.

 If you have any suggestions for how I can get doBy to load, please let me
 know.

 Thanks very much,
 Lauren

        [[alternative HTML version deleted]]

 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.


__
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.

Re: [R] Date-Time-Stamp input method for user-specific formats

See below.

On Mon, Oct 5, 2009 at 6:50 PM, Gabor Grothendieck
ggrothendi...@gmail.com wrote:
 Try this.  First we read a line at a time into L except for the
 header.  Then we use strapply to match on the given pattern.  It
 passes the backreferences (the portions within parentheses in the
 pattern) to the function (defined via a formula) whose implicit
 arguments are x, y and z.  That function returns two columns which are
 in the required form so that in the next statement we convert one to
 chron and the other to numeric.  See R News 4/1 for more about dates
 and times.

 library(gsubfn) # strapply
 library(chron) # as.chron
 Lines - DATETIME        FREQ
 01/09/2009      59.036
 01/09/2009 00:00:01     58.035
 01/09/2009 00:00:02     53.035
 01/09/2009 00:00:03     47.033
 01/09/2009 00:00:04     52.03
 01/09/2009 00:00:05     55.025
 L - readLines(Lines)[-1]

This line should be L - readLines(textConnection(Lines))[-1]


 pat - (../../) (..:..:..){0,1} *([0-9.]+)
 s - strapply(L, pat, ~ c(paste(x, y, 00:00:00), z), simplify = rbind)

 fmt - %m/%d/%Y %H:%M:%S
 DF - data.frame(Time = as.chron(s[,1], fmt), Freq = as.numeric(s[,2]))

 DF

 The final output looks like this:

 DF
                 Time   Freq
 1 (01/09/09 00:00:00) 59.036
 2 (01/09/09 00:00:01) 58.035
 3 (01/09/09 00:00:02) 53.035
 4 (01/09/09 00:00:03) 47.033
 5 (01/09/09 00:00:04) 52.030
 6 (01/09/09 00:00:05) 55.025

 If the times are unique you could consider making a zoo object out of
 it by replacing the DF- statement with:

 library(zoo)
 z - zoo(as.numeric(s[,2]), as.chron(s[,1], fmt))

 See the three vignettes in the zoo package.


 On Mon, Oct 5, 2009 at 5:14 PM, esp davidgary...@gmail.com wrote:

 Date-Time-Stamp input method to correctly interpret user-specific
 formats:coding is  90% there - based on exmple at
 http://tolstoy.newcastle.edu.au/R/help/05/02/12003.html
 ...anyone got the last 10% please?

 CONTEXT:

 Data is received where one of the columns is a datetimestamp.  At midnight,
 the value represented as text in this column consists of just the date part,
 e.g. 01/09/2009.  At other times, the value in the column contains both
 date and time e.g. 01/09/2009 00:00:01.  The goal is to read it into R as
 an appropriate data type, where for example date arithmetic can be
 performed.  As far as I can tell, the most appropriate such data type is
 POSIXct.  The trick then is to read in the datetimestamps in the data as
 this type.

 PROBLEM:

 POSIXct defaults to a text representation almost but not quite like my
 received data.  The main difference is that the POSIXct date part is in
 reverse order, e.g. 2009-09-01.  It is possible to define a different
 format where date and time parts look like my data but when encountering
 datetimestamps where only the the date part is present (as in the case of my
 midnight data) then this is interpreted as NA i.e. undefined.

 SOLUTION (ALMOST):

 There is a workaround (based on example at
 http://tolstoy.newcastle.edu.au/R/help/05/02/12003.html).  It is possible to
 define a class then read the data in as this class.  For such a class it is
 possible to define a class method, in terms of a function, for translating a
 text (character string) representation into a value. In that function, one
 can use a conditional expression to treat midnight datetimestamps
 differently from those at other times of day.  The example below does that.
 In order to apply this function over all of the datetimestamp values in the
 column, it is necessary to use something like R's 'sapply' function.

 SNAG:

 The function below implements this approach.  A datetimestamp with only the
 date part, including leading zeroes, is always length 10 (characters).   It
 correctly interprets the datetimestamp values, but unfortunately translates
 them into what appear to be numeric type.  I am actually uncertain precisely
 what is happening, as I am very new to R and have most certainly stretched
 myself in writing this code.  I think perhaps it returns a list and
 something associated with this aspect makes it forget the data type is
 POSIXct or at least how such a type should be displayed as text or what to
 do about it.

 PLEA:

 Please, can anyone give any help whatsoever, however tenuous?

 CODE, DATA  RESULTS:

 Function to Read required data, intended to make the datetime column of the
 data (example given further below) into POSIXct values:
 
 spot_frequency_readin - function(file,nrows=-1) {

 # create temp class
 setClass(t_class2_, representation(character))
 setAs(character, t_class2_, function(from) {sapply(from, function(x) {
  if (nchar(x)==10) {
 as.POSIXct(strptime(x,format=%d/%m/%Y))
 }
 else {
 as.POSIXct(strptime(x,format=%d/%m/%Y %H:%M:%S))
 }
 }
 )
 }
 )

 #(for format symbols, see R Reference Card)

 # read the file (TSV)
 file - read.delim(file, header=TRUE, comment.char = , nrows=nrows,
 as.is=FALSE, col.names=c(DATETIME, FREQ), colClasses=c(t_class2_,
 numeric) )

 # remove it now that

[R] Linear mixed effects model ?

2009-10-06 Thread Daniel Perkins


I am looking for some advice on an appropriate statistical analysis in R

*Experimental question* : We are interested in how communities from 
different streams may vary in their response to experimental 
temperature. Specifically we are interested to test for differences in 
the slope and intercept of the relationship between temperature and 
oxygen consumption between the different stream communities.


*Outline of experiment*

There were four streams and from each we took samples which had a 
characteristic community of organisms. These four different communities 
are labelled “S1,.. S4.


Each ‘Stream’ was incubated together in the same water bath at six 
temperatures in succession, giving covariates (~ 5,10,15,20,25,and 30°C) 
to the factor “Temp”.


However this also meant six repeated measures were made on the same 
‘Stream’ over time. As time between incubations varied ‘Time’ is given a 
categorical label a,f.


This procedure was repeated four times using different samples from the 
same streams, thus giving ‘Replicates’ labelled 1,...4. Each ‘Replicate’ 
had different temperature values but always six values in total.


The response variable measured in all 96 incubations, was the rate at 
which the communities consumed oxygen over a given time in incubation: 
‘Rate’


Some incubation’s were excluded (5 from 96)

*Models*

Ideally we would do an ANCOVA to test for differences in slope or 
intercepts for the different streams. However as there were repeated 
measures and unequal n and unbalanced design, I have used a linear mixed 
effect model (from nlme package in R) in the form:


model - lme (Rate ~ Temp* Stream, random = ~ Time|Replicate)

*Question* : Do these models appropriately account for the temporal / 
spatial pseudoreplication in the experimental design ?


Many thanks in advance

Daniel

__
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.

Re: [R] Letter-based representation of pairwise comparisons

2009-10-06 Thread goz


hello,

i try to use the multcomp letters, but i have problems with my results : 

here is my pvalue matrix (from a pairwise.t.test) : 

pair=pairwise.t.test(...)
pair$p.value

0   BBxS
B0.01727- -  
BxS 0.000130.00226   -  
S0.875550.02610   0.00027


i was thiking to have something like that : 
 0  B  S  BxS
 a  b  a  c

but function return : 

 multcompLetters(pair$p.value)
  B   BxS   S 
 a  b   a 


first question : why the 0 traitement doesn't appears in result ?
second  : why the results differs than what i expected ?

many thanks.

-- 
View this message in context: 
http://www.nabble.com/Letter-based-representation-of-pairwise-comparisons-tp21350364p25767357.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] Unable to load 'doBy' package

2009-10-06 Thread Lauren Szathmary

Hi all,

I am trying to load the doBy package, and I am getting the following error:

 library(doBy)
Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) :
  there is no package called 'Hmisc'
Error: package/namespace load failed for 'doBy'

I tried updating R to the current version (2.9.2) and installing the most
recent version of the doBy package (4.0.2), and the error remained the
same.  I also tried loading the package by going to my Package Manager
window and clicking the box to load 'doBy', but that didn't work either.  My
other packages (e.g., lattice, chron, etc.) are loading normally with no
problems.

If you have any suggestions for how I can get doBy to load, please let me
know.

Thanks very much,
Lauren

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] Viewing specific data from a dataframe

2009-10-06 Thread Krystyna Golabek


Dear R users,

Simple question. Can anyone help with the code that would allow me to view only 
the variables who's correlation output is 0.8? 

This is the code I'm using to date
cor(data, method=spearman)

Kind regards
Krys








  
_
Save time by using Hotmail to access your other email accounts.

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Spatial Autocorrelation

2009-10-06 Thread anna freni sterrantino

Hi Paulo,
you may want to take a look at

http://cran.r-project.org/web/views/Spatial.html

there, you can find all spatial packages that 
can be useful for your question.
There is also a  a mailing list R-sig-geo that where 
you can ask all those kind of question.

Hope that this helps.

Cheers

Anna



Anna Freni Sterrantino
Ph.D Student 
Department of Statistics
University of Bologna, Italy
via Belle Arti 41, 40124 BO.





Da: P.Branco pjlbra...@yahoo.com
A: r-help@r-project.org
Inviato: Martedì 6 ottobre 2009, 13:28:36
Oggetto: [R]  Spatial Autocorrelation


Hello, 

I have a matrix with the distances among sites. And I have another matrix
with the presence and absence of  each species in each site. I would like to
test the spatial autocorrelation among sites.

I have tried to use the function gearymoran of the ade4 package, but error
messages keep popping up. Do you know any function for me to test the
spatial autocorrelation of my data?

Thanks,

Paulo Branco
-- 
View this message in context: 
http://www.nabble.com/Spatial-Autocorrelation-tp25767010p25767010.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__


spazio gratuito per i tuoi file e i messaggi 

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] convert RData to txt

2009-10-06 Thread Henrique Dallazuanna

The file don't load in my computer, this give me a fatal error message.

On Tue, Oct 6, 2009 at 1:09 AM, Ilyas . mykh...@gmail.com wrote:
 thank you for your reply,,
 i tried your commands but its not working,,i have attached the RData
 file,,which i want to convert into txt..

 Ilyas
 On Mon, Oct 5, 2009 at 9:27 PM, Henrique Dallazuanna www...@gmail.com
 wrote:

 You can try something about like this:

 lapply(ls(), function(obj)cat(\n, obj, -,
 paste(deparse(get(obj)), collapse = \n), file = 'RData.txt', append
 = TRUE))
 source('RData.txt')


 On Mon, Oct 5, 2009 at 4:00 AM,  mykh...@gmail.com wrote:
  hello all,
  will you plz tell me how can i convert RData files to txt,,,
 
  __
  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.
 



 --
 Henrique Dallazuanna
 Curitiba-Paraná-Brasil
 25° 25' 40 S 49° 16' 22 O





-- 
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O

__
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.

Re: [R] 'persp' query

2009-10-06 Thread Peter Ehlers


Geoff,

One way (the only way without modifying source code?) to satisfy
your first wish is to insert a newline before your label as in

  zlab = \nMy z-text.

I don't know of an answer for your second wish other than using
the single letter Z as your label :)

 -Peter Ehlers

Geoffrey William Heard wrote:

Hi All
 
I'm creating some 3-D plots using the function 'persp', and have a query regarding the ability to make changes to the label of the z-axis.
 
There are two things I would like to do. First, the default setting places the label a little close to the axis for my liking. Is there any way of moving the label? I've tried adjustments with 'mgp' in 'par', but without success. The second is to change the direction of the label. Currently it reads top to bottom, whereas I would like it to read bottom to top, as per a y-axis on a standard plot. Is there anyway of doing so?
 
Would greatly appreciate any advice!
 
Much thanks
 
Geoff 


__
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.




__
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.

Re: [R] Viewing specific data from a dataframe

2009-10-06 Thread Paul Hiemstra

Hi,

I'm not sure I understand what you want. This would have been easier if
you had provided a reproducible example. See the following code:

bla = matrix(runif(1), 10, 10)
cor_bla = cor(bla, method = spearman)

Now what do you want to select. All the variables that have a
correlation higher than 0.8 with any of the other variables, excluding
themselves? Or a correlation higher than 0.8 in contrast to one of the
variables, e.g. the third variable?

cheers,
Paul

Krystyna Golabek wrote:

Dear R users,

Simple question. Can anyone help with the code that would allow me to view only the variables who's correlation output is 0.8?

This is the code I'm using to date

cor(data, method=spearman)

Kind regards
Krys

Save time by using Hotmail to access your other email accounts.

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone: +3130 274 3113 Mon-Tue
Phone: +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul

[R] save wmf with a batch file

2009-10-06 Thread guillaume Le Ray

Hi R users,

I'm working on a autoreporting with the batch mode of R: I would like to
save the graphs produced in wmf or emf. the problem is, it's working well
with the R gui because we print on the screen the graph devices but not with
the batch. I have used the function dev.print after encounter problem with
win.metafile.


Thanks

Guillaume

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] 'persp' query



On Oct 6, 2009, at 4:46 AM, Geoffrey William Heard wrote:


Hi All

I'm creating some 3-D plots using the function 'persp', and have a  
query regarding the ability to make changes to the label of the z- 
axis.


There are two things I would like to do. First, the default setting  
places the label a little close to the axis for my liking. Is there  
any way of moving the label? I've tried adjustments with 'mgp' in  
'par', but without success. The second is to change the direction of  
the label. Currently it reads top to bottom, whereas I would like it  
to read bottom to top, as per a y-axis on a standard plot. Is there  
anyway of doing so?


?mtext   # and use the adj argument

--
David Winsemius, MD
Heritage Laboratories
West Hartford, CT

__
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.

Re: [R] save wmf with a batch file


On 10/6/2009 9:05 AM, guillaume Le Ray wrote:

Hi R users,

I'm working on a autoreporting with the batch mode of R: I would like to
save the graphs produced in wmf or emf. the problem is, it's working well
with the R gui because we print on the screen the graph devices but not with
the batch. I have used the function dev.print after encounter problem with
win.metafile.


You should be using win.metafile.  What problems did you have?

Duncan Murdoch

__
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.

Re: [R] Viewing specific data from a dataframe

2009-10-06 Thread Paul Hiemstra


Hi Krys,

Please also cc all you responses to the list, keeping the conversation 
in the archives. The following code might be of help to you:


set.seed(1)
bla = matrix(runif(1), 10, 10)
colnames(bla) = LETTERS[1:ncol(bla)]
cor_bla = cor(bla, method = spearman)
# Assign NA to all values below 0.7 or equal to 1
cor_bla[cor_bla  0.7 | cor_bla == 1] = NA
# Are there any variables that have a correlation with another variable
# that is not NA, those are the ones you want
apply(cor_bla, 2, function(x) any(!is.na(x)))
# Show the names of the columns that fit the conditions
rownames(cor_bla)[apply(cor_bla, 2, function(x) any(!is.na(x)))]

cheers,
Paul

Paul Hiemstra wrote:

Hi,

I'm not sure I understand what you want. This would have been easier 
if you had provided a reproducible example. See the following code:


bla = matrix(runif(1), 10, 10)
cor_bla = cor(bla, method = spearman)

Now what do you want to select. All the variables that have a 
correlation higher than 0.8 with any of the other variables, excluding 
themselves? Or a correlation higher than 0.8 in contrast to one of the 
variables, e.g. the third variable?


cheers,
Paul

Krystyna Golabek wrote:

Dear R users,

Simple question. Can anyone help with the code that would allow me to 
view only the variables who's correlation output is 0.8?

This is the code I'm using to date
 

cor(data, method=spearman)



Kind regards
Krys








   
_

Save time by using Hotmail to access your other email accounts.

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide 
http://www.R-project.org/posting-guide.html

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






--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul

__
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.

Re: [R] how to fit time varying coefficient regression model?

2009-10-06 Thread Giovanni Petris


Dear rh,

You may take a look at package dlm. A vignette is included in the
documentation. 

Giovanni


 Date: Mon, 05 Oct 2009 22:30:05 -0400
 From: R_help Help rhelp...@gmail.com
 Sender: r-help-boun...@r-project.org
 Precedence: list
 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=gamma;
 DomainKey-Signature: a=rsa-sha1; c=nofws; d=gmail.com; s=gamma;
 
 Hi - I read through dse package manual a bit. I'm not quite certain
 how I can use it to estimate a time varying coefficient regression
 model? I might pick up an inappropriate package. Any suggestion would
 be greatly appreciated. Thank you.
 
 rh
 
 __
 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.
 
 


-- 

Giovanni Petris  gpet...@uark.edu
Associate Professor
Department of Mathematical Sciences
University of Arkansas - Fayetteville, AR 72701
Ph: (479) 575-6324, 575-8630 (fax)
http://definetti.uark.edu/~gpetris/

__
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.

Re: [R] Spatial Autocorrelation

2009-10-06 Thread Corey Sparks


Hi Paulo,
if your data are distance matrices, you might consider doing a Mantel test,
look at the mantel() function in package vegan.  While this is not
technically measuring spatial autocorrelation, it will test for correlation
between the attribute distances and the geographic distances.  Also, if you
can coax your data back into a point shapefile (for example), you can use
the tools in the spdep package which will measure actual spatial
autocorrelation (such as Moran's I and Geary's C). 
Best,
Corey


silcha wrote:
 
 Hi Paulo,
 you may want to take a look at
 
 http://cran.r-project.org/web/views/Spatial.html
 
 there, you can find all spatial packages that 
 can be useful for your question.
 There is also a  a mailing list R-sig-geo that where 
 you can ask all those kind of question.
 
 Hope that this helps.
 
 Cheers
 
 Anna
 
 
 
 Anna Freni Sterrantino
 Ph.D Student 
 Department of Statistics
 University of Bologna, Italy
 via Belle Arti 41, 40124 BO.
 
 
 
 
 
 Da: P.Branco pjlbra...@yahoo.com
 A: r-help@r-project.org
 Inviato: Martedì 6 ottobre 2009, 13:28:36
 Oggetto: [R]  Spatial Autocorrelation
 
 
 Hello, 
 
 I have a matrix with the distances among sites. And I have another matrix
 with the presence and absence of  each species in each site. I would like
 to
 test the spatial autocorrelation among sites.
 
 I have tried to use the function gearymoran of the ade4 package, but error
 messages keep popping up. Do you know any function for me to test the
 spatial autocorrelation of my data?
 
 Thanks,
 
 Paulo Branco
 -- 
 View this message in context:
 http://www.nabble.com/Spatial-Autocorrelation-tp25767010p25767010.html
 Sent from the R help mailing list archive at Nabble.com.
 
 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide
 http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.
 
 
 __
 
 
 spazio gratuito per i tuoi file e i messaggi 
 
   [[alternative HTML version deleted]]
 
 
 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide
 http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.
 
 

-- 
View this message in context: 
http://www.nabble.com/Spatial-Autocorrelation-tp25767010p25768890.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] save wmf with a batch file


On 10/6/2009 9:45 AM, guillaume Le Ray wrote:

I have a window with unable to create metafile  I think it is because I'm
using the function layout() in some of my graphs


I doubt if that's the cause.  More likely it's a permissions problem, or 
some other problem.  For example, this works fine:


 win.metafile(c:/temp/test.wmf)
 layout(matrix(1:4, 2,2))
 plot(1)
 plot(2)
 dev.off()
null device
  1

Duncan Murdoch

__
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.

Re: [R] else if statement error

2009/10/6 Uwe Ligges lig...@statistik.tu-dortmund.de:

 The first rule is easy: As long as you are using scalar valued (i.e. length
 1 vectors in R) cond, you should prefer
  if(cond) cons.expr  else  alt.expr
 rather than
  ifelse(cond, yes, no)
 because the latter one evaluates both yes and no while the former one
 evaluates exactly one of both expressions.

I don't think that that is true.  The false leg was not evaluated here:

 ifelse(TRUE, { cat(a); 1}, {cat(b); 2})
a[1] 1

__
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.

Re: [R] Letter-based representation of pairwise comparisons



On Oct 6, 2009, at 8:41 AM, goz wrote:



hello,

i try to use the multcomp letters, but i have problems with my  
results :


here is my pvalue matrix (from a pairwise.t.test) :

pair=pairwise.t.test(...)
pair$p.value

   0   BBxS
B0.01727- -
BxS 0.000130.00226   -
S0.875550.02610   0.00027


i was thiking to have something like that :
0  B  S  BxS
a  b  a  c

but function return :


multcompLetters(pair$p.value)

 B   BxS   S
a  b   a


first question : why the 0 traitement doesn't appears in result ?


But there is a 0 column. ???


second  : why the results differs than what i expected ?


Because your understanding of what it means to have pairwise  
comparisons differs from that of the author's.





many thanks.

--
View this message in context: 
http://www.nabble.com/Letter-based-representation-of-pairwise-comparisons-tp21350364p25767357.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


David Winsemius, MD
Heritage Laboratories
West Hartford, CT

__
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.

[R] Plot

2009-10-06 Thread Ashta

Hi All,


Days - matrix(c(Monday, Tuesday, Wed, Thu, Fri, Sat,
Sun),7,1)

Hum -matrix(c(56,57,60,75,62,67,70),

Temp-matrix(c(76,77,81,95,82,77,83),



Using the above information I want plot humidity and temperature on Y-axis
and days on X-axis

Any help is appreciated!

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] ggplot cumsum refined question (?)

2009-10-06 Thread stephen sefick

OK, so maybe last night was a little too much at one throw, so I have
reduced the data to two stations- one that has precipitation and one
that does not.  This is going to be in the context of a larger data
set.  I would like to be able to issue a ggplot command and have cum
sum just act on the facets (factors) to apply this.

library(chron)
library(ggplot2)
DF - structure(list(date_time = structure(c(14522, 14522.010417,
14522.020833, 14522.03125, 14522.041667, 14522.052083,
14522.0625, 14522.072917, 14522.08, 14522.09375,
14522.104167, 14522.114583, 14522.125, 14522.135417,
14522.145833, 14522.15625, 14522.17, 14522.177083,
14522.1875, 14522.197917, 14522.208333, 14522.21875,
14522.229167, 14522.239583, 14522.25, 14522.260417,
14522.270833, 14522.28125, 14522.291667, 14522.302083,
14522.3125, 14522.322917, 14522.33, 14522.34375,
14522.354167, 14522.364583, 14522.375, 14522.385417,
14522.395833, 14522.40625, 14522.416667, 14522.427083,
14522.4375, 14522.447917, 14522.458333, 14522.46875,
14522.479167, 14522.489583, 14522.5, 14522.510417,
14522.520833, 14522.53125, 14522.541667, 14522.552083,
14522.5625, 14522.572917, 14522.58, 14522.59375,
14522.604167, 14522.614583, 14522.625, 14522.635417,
14522.645833, 14522.65625, 14522.67, 14522.677083,
14522.6875, 14522.697917, 14522.708333, 14522.71875,
14522.729167, 14522.739583, 14522.75, 14522.760417,
14522.770833, 14522.78125, 14522.791667, 14522.802083,
14522.8125, 14522.822917, 14522.83, 14522.84375,
14522.854167, 14522.864583, 14522.875, 14522.885417,
14522.895833, 14522.90625, 14522.916667, 14522.927083,
14522.9375, 14522.947917, 14522.958333, 14522.96875,
14522.979167, 14522.989583, 14523, 14523.010417,
14523.020833, 14523.03125, 14523.041667, 14523.052083,
14523.0625, 14523.072917, 14523.08, 14523.09375,
14523.104167, 14523.114583, 14523.125, 14523.135417,
14523.145833, 14523.15625, 14523.17, 14523.177083,
14523.1875, 14523.197917, 14523.208333, 14523.21875,
14523.229167, 14523.239583, 14523.25, 14523.260417,
14523.270833, 14523.28125, 14523.291667, 14523.302083,
14523.3125, 14523.322917, 14523.33, 14523.34375,
14523.354167, 14523.364583, 14523.375, 14523.385417,
14523.395833, 14523.40625, 14522, 14522.010417, 14522.020833,
14522.03125, 14522.041667, 14522.052083, 14522.0625,
14522.072917, 14522.08, 14522.09375, 14522.104167,
14522.114583, 14522.125, 14522.135417, 14522.145833,
14522.15625, 14522.17, 14522.177083, 14522.1875,
14522.197917, 14522.208333, 14522.21875, 14522.229167,
14522.239583, 14522.25, 14522.260417, 14522.270833,
14522.28125, 14522.291667, 14522.302083, 14522.3125,
14522.322917, 14522.33, 14522.34375, 14522.354167,
14522.364583, 14522.375, 14522.385417, 14522.395833,
14522.40625, 14522.416667, 14522.427083, 14522.4375,
14522.447917, 14522.458333, 14522.46875, 14522.479167,
14522.489583, 14522.5, 14522.510417, 14522.520833,
14522.53125, 14522.541667, 14522.552083, 14522.5625,
14522.572917, 14522.58, 14522.59375, 14522.604167,
14522.614583, 14522.625, 14522.635417, 14522.645833,
14522.65625, 14522.67, 14522.677083, 14522.6875,
14522.697917, 14522.708333, 14522.71875, 14522.729167,
14522.739583, 14522.75, 14522.760417, 14522.770833,
14522.78125, 14522.791667, 14522.802083, 14522.8125,
14522.822917, 14522.83, 14522.84375, 14522.854167,
14522.864583, 14522.875, 14522.885417, 14522.895833,
14522.90625, 14522.916667, 14522.927083, 14522.9375,
14522.947917, 14522.958333, 14522.96875, 14522.979167,
14522.989583, 14523, 14523.010417, 14523.020833,
14523.03125, 14523.041667, 14523.052083, 14523.0625,
14523.072917, 14523.08, 14523.09375, 14523.104167,
14523.114583, 14523.125, 14523.135417, 14523.145833,
14523.15625, 14523.17, 14523.177083, 14523.1875,
14523.197917, 14523.208333, 14523.21875, 14523.229167,
14523.239583, 14523.25, 14523.260417, 14523.270833,
14523.28125, 14523.291667, 14523.302083, 14523.3125,
14523.322917, 14523.33, 14523.34375), format = structure(c(m/d/y,
h:m:s), .Names = c(dates, times)), origin = structure(c(1,
1, 1970), .Names = c(month, day, year)), class = c(chron,
dates, times)), gauge = c(2102908L, 2102908L, 2102908L, 2102908L,
2102908L, 2102908L, 2102908L, 2102908L, 2102908L, 2102908L, 2102908L,
2102908L, 2102908L, 2102908L, 2102908L, 2102908L, 2102908L,

[R] Fwd: Long for Loop- calling C from R - Parallel Computing

2009-10-06 Thread Antonio Paredes

-- Forwarded message --
From: Antonio Paredes antonioparede...@gmail.com
Date: Tue, Oct 6, 2009 at 9:41 AM
Subject: Re: [R] Long for Loop- calling C from R - Parallel Computing
To: Karl Ove Hufthammer k...@huftis.org

Hello again,

I'm hoping to get a response from some of the R gurus in this list. Is my
assumption that R is not designed or build to deal with high levels (a lots
of simulated data) simulation correct. For example, how to minimize system
time; do one have to call a lower level language like C or Fortran; or just,
like many of you have done,  do a lots of programing in R and eventually the
tricks will be learned.

Thanks

On Mon, Oct 5, 2009 at 8:35 AM, Antonio Paredes
antonioparede...@gmail.comwrote:

 In my case it does, because I need to preserved a high level of
 independence (lack of correlation) among the different groups of 60. Also,
 when I say final result I mean computation of standard errors and that
 source of stuff; sorry about the lack clarity in my statement.

 On Mon, Oct 5, 2009 at 9:48 AM, Karl Ove Hufthammer k...@huftis.orgwrote:

 In article 6f6f0fd60910050629p28c99209jcd7836353fd2d754
 @mail.gmail.com, antonioparede...@gmail.com says...
  I'm running the following for loop to generate random variables in
 chunks of
  60 at a time (l), here h is of order in millions (could be 5 to 6
 millions),
  note that generating all the variables at once could have an impact on
 the
  final results

 No, it will not. See this example code for an illustration:

 set.seed(1)
 rnorm(3)
 rnorm(3)
 set.seed(1)
 rnorm(6)

 So if you generate the six numbers three at a time or all at once gives
 exactly the same result.

 So my suggestion is to generate all the numbers at once. That takes next
 to no time. Or, if it takes too much memory, generate for example a
 million at once, and repeat a few times.

 --
 Karl Ove Hufthammer

 __
 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.

 --
 -Tony

-- 
-Tony

-- 
-Tony

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] else if statement error

2009-10-06 Thread Uwe Ligges




Gabor Grothendieck wrote:

2009/10/6 Uwe Ligges lig...@statistik.tu-dortmund.de:

The first rule is easy: As long as you are using scalar valued (i.e. length
1 vectors in R) cond, you should prefer
 if(cond) cons.expr  else  alt.expr
rather than
 ifelse(cond, yes, no)
because the latter one evaluates both yes and no while the former one
evaluates exactly one of both expressions.


I don't think that that is true.  The false leg was not evaluated here:


ifelse(TRUE, { cat(a); 1}, {cat(b); 2})

a[1] 1



Ah, indeed that changed at some point and I forgot that the code checks 
for the length of cond nowadays. Thanks for pointing it out.


Best wishes,
uwe

__
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.

Re: [R] Plot

2009-10-06 Thread Sarah Goslee

Did you try it? With, perhaps, plot() ? And lines() ?

You might do better with Days as a factor with the day names in order. (And
why are two full and five abbreviated?)

I don't understand why Hum and Temp are matrices rather than vectors,
and why then you didn't specify dimensions, and for that matter why you
are missing a closing paren but do have a comma in its place.

Generally this list is happy to help, but we like some evidence that the
querent has *tried* before inquiring.

Sarah

On Tue, Oct 6, 2009 at 10:05 AM, Ashta sewa...@gmail.com wrote:
 Hi All,


 Days - matrix(c(Monday, Tuesday, Wed, Thu, Fri, Sat,
 Sun),7,1)

 Hum -matrix(c(56,57,60,75,62,67,70),

 Temp-matrix(c(76,77,81,95,82,77,83),



 Using the above information I want plot humidity and temperature on Y-axis
 and days on X-axis

 Any help is appreciated!


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

__
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.

Re: [R] ggplot cumsum refined question (?)

2009-10-06 Thread ONKELINX, Thierry

Dear Stephen,

It is much easier to do you data preparation before plotting.

Cummul - ddply(subset(DF, precipitation!=NA), gauge_name,
function(x){
x$Cummul - cumsum(x$precipitation)
x
})
ggplot(Cummul, aes(x = date_time, y = Cummul)) + geom_line() +
facet_wrap(~gauge_name, scales=free_y)

HTH,

Thierry 




ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
thierry.onkel...@inbo.be
www.inbo.be

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to
say what the experiment died of.
~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of
data.
~ John Tukey

-Oorspronkelijk bericht-
Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
Namens stephen sefick
Verzonden: dinsdag 6 oktober 2009 16:07
Aan: r-help@r-project.org
Onderwerp: [R] ggplot cumsum refined question (?)

OK, so maybe last night was a little too much at one throw, so I have
reduced the data to two stations- one that has precipitation and one
that does not.  This is going to be in the context of a larger data
set.  I would like to be able to issue a ggplot command and have cum
sum just act on the facets (factors) to apply this.

library(chron)
library(ggplot2)
DF - structure(list(date_time = structure(c(14522, 14522.010417,
14522.020833, 14522.03125, 14522.041667, 14522.052083,
14522.0625, 14522.072917, 14522.08, 14522.09375,
14522.104167, 14522.114583, 14522.125, 14522.135417,
14522.145833, 14522.15625, 14522.17, 14522.177083,
14522.1875, 14522.197917, 14522.208333, 14522.21875,
14522.229167, 14522.239583, 14522.25, 14522.260417,
14522.270833, 14522.28125, 14522.291667, 14522.302083,
14522.3125, 14522.322917, 14522.33, 14522.34375,
14522.354167, 14522.364583, 14522.375, 14522.385417,
14522.395833, 14522.40625, 14522.416667, 14522.427083,
14522.4375, 14522.447917, 14522.458333, 14522.46875,
14522.479167, 14522.489583, 14522.5, 14522.510417,
14522.520833, 14522.53125, 14522.541667, 14522.552083,
14522.5625, 14522.572917, 14522.58, 14522.59375,
14522.604167, 14522.614583, 14522.625, 14522.635417,
14522.645833, 14522.65625, 14522.67, 14522.677083,
14522.6875, 14522.697917, 14522.708333, 14522.71875,
14522.729167, 14522.739583, 14522.75, 14522.760417,
14522.770833, 14522.78125, 14522.791667, 14522.802083,
14522.8125, 14522.822917, 14522.83, 14522.84375,
14522.854167, 14522.864583, 14522.875, 14522.885417,
14522.895833, 14522.90625, 14522.916667, 14522.927083,
14522.9375, 14522.947917, 14522.958333, 14522.96875,
14522.979167, 14522.989583, 14523, 14523.010417,
14523.020833, 14523.03125, 14523.041667, 14523.052083,
14523.0625, 14523.072917, 14523.08, 14523.09375,
14523.104167, 14523.114583, 14523.125, 14523.135417,
14523.145833, 14523.15625, 14523.17, 14523.177083,
14523.1875, 14523.197917, 14523.208333, 14523.21875,
14523.229167, 14523.239583, 14523.25, 14523.260417,
14523.270833, 14523.28125, 14523.291667, 14523.302083,
14523.3125, 14523.322917, 14523.33, 14523.34375,
14523.354167, 14523.364583, 14523.375, 14523.385417,
14523.395833, 14523.40625, 14522, 14522.010417,
14522.020833,
14522.03125, 14522.041667, 14522.052083, 14522.0625,
14522.072917, 14522.08, 14522.09375, 14522.104167,
14522.114583, 14522.125, 14522.135417, 14522.145833,
14522.15625, 14522.17, 14522.177083, 14522.1875,
14522.197917, 14522.208333, 14522.21875, 14522.229167,
14522.239583, 14522.25, 14522.260417, 14522.270833,
14522.28125, 14522.291667, 14522.302083, 14522.3125,
14522.322917, 14522.33, 14522.34375, 14522.354167,
14522.364583, 14522.375, 14522.385417, 14522.395833,
14522.40625, 14522.416667, 14522.427083, 14522.4375,
14522.447917, 14522.458333, 14522.46875, 14522.479167,
14522.489583, 14522.5, 14522.510417, 14522.520833,
14522.53125, 14522.541667, 14522.552083, 14522.5625,
14522.572917, 14522.58, 14522.59375, 14522.604167,
14522.614583, 14522.625, 14522.635417, 14522.645833,
14522.65625, 14522.67,

Re: [R] Viewing specific data from a dataframe

2009-10-06 Thread Peter Ehlers


If I understand correctly, you can use which( ,arr.ind=TRUE):

Assuming that you start with a data frame,

 dat - as.data.frame(matrix(runif(30), ncol=5))
 nm - names(dat)
 cormat - cor(dat)
 cormat[lower.tri(cormat, diag=TRUE)] - NA
 idx - which(cormat  0.4, arr.ind=TRUE)
 idx
 cbind(nm[idx[, row]], nm[idx[, col]])

will give you the pairs.

 -Peter Ehlers

Krystyna Golabek wrote:

Dear R users,

Simple question. Can anyone help with the code that would allow me to view only the variables who's correlation output is 0.8? 


This is the code I'm using to date

cor(data, method=spearman)


Kind regards
Krys








 		 	   		  
_

Save time by using Hotmail to access your other email accounts.

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.




__
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.

Re: [R] ggplot cumsum refined question (?)

2009-10-06 Thread hadley wickham

 It is much easier to do you data preparation before plotting.

 Cummul - ddply(subset(DF, precipitation!=NA), gauge_name,
 function(x){
        x$Cummul - cumsum(x$precipitation)
        x
 })

With a little less typing:

Cummul - ddply(subset(DF, precipitation!=NA), gauge_name, transform,
  Cummul = cumsum(precipitation))

Hadley

-- 
http://had.co.nz/

__
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.

Re: [R] R on Linux, and R on Windows , any difference in maturity+stability?

2009-10-06 Thread Jose Quesada

Robert Wilkins iwritecode2 at gmail.com writes:

 
 Will R have more glitches on one operating system as opposed to
 another, or is it pretty much the same?
 
 robert
 
 

One important difference is that, if you are unsing large datasets and need
memory, then windows is by far the worst. 
CRAN R is 32 bit and can only address 1.5 Gb of memory (or something similar; I
don't really understand why).

While there's a 64-bit version of R for windows (revolution-computing.com) I
would advise against using it, for several reasons. While revolution has
provided very nice packages to the community (e.g., foreach), the win-64 port as
of today is certainly the worst platform to do work on. Reasons:
(1) it's R 2.7.2
(2) Many important packages will never be ported
(3) Some packages (particularly those depending on Rjava) would not work 
properly
(4) There's a proprietary repository, where most packages are outrageously
outdated. 
(5) Most help you find on R-help will not apply. Instead, you have 'paid'
support. Said support is slow, and close to useless in most cases.
(6) Packages that rely on external tools (e.g., mysql) will take a lot of work
to get going. 

And of course, one have to pay for a yearly license, to have the privilege to
work under the above conditions.

If you need 64-bit right now, my advice is to switch to basically any other
platform.

Note: this may change any time, since they are working on a continuous build
that will keep the releases in sync with mainstream R.

Jose Quesada, PhD.
Max Planck Institute, Human Development, Berlin
http://www.josequesada.name/

__
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.

Re: [R] Letter-based representation of pairwise comparisons

2009-10-06 Thread hadley wickham

Please provide a reproducible example.  I've had problems with
multcompLetters in the past, because I was giving it slightly
incorrect input.

Hadley

On Tue, Oct 6, 2009 at 7:41 AM, goz garbage.collec...@hotmail.fr wrote:

 hello,

 i try to use the multcomp letters, but i have problems with my results :

 here is my pvalue matrix (from a pairwise.t.test) :

 pair=pairwise.t.test(...)
 pair$p.value

        0           B            BxS
 B    0.01727    -             -
 BxS 0.00013    0.00226   -
 S    0.87555    0.02610   0.00027


 i was thiking to have something like that :
  0  B  S  BxS
  a  b  a  c

 but function return :

 multcompLetters(pair$p.value)
  B   BxS   S
  a  b   a


 first question : why the 0 traitement doesn't appears in result ?
 second  : why the results differs than what i expected ?

 many thanks.

 --
 View this message in context: 
 http://www.nabble.com/Letter-based-representation-of-pairwise-comparisons-tp21350364p25767357.html
 Sent from the R help mailing list archive at Nabble.com.

 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.




-- 
http://had.co.nz/

__
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.

Re: [R] Plot

2009-10-06 Thread Ashta

Thanks Sara,

Yes I did try. I could not get the Days on the X-axis

blow is theerror message

plot(Temp,Days)
Error in plot.window(...) : need finite 'ylim' values
In addition: Warning messages:
1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion
2: In min(x) : no non-missing arguments to min; returning Inf
3: In max(x) : no non-missing arguments to max; returning -Inf




On Tue, Oct 6, 2009 at 10:19 AM, Sarah Goslee sarah.gos...@gmail.comwrote:

 Did you try it? With, perhaps, plot() ? And lines() ?

 You might do better with Days as a factor with the day names in order. (And
 why are two full and five abbreviated?)

 I don't understand why Hum and Temp are matrices rather than vectors,
 and why then you didn't specify dimensions, and for that matter why you
 are missing a closing paren but do have a comma in its place.

 Generally this list is happy to help, but we like some evidence that the
 querent has *tried* before inquiring.

 Sarah

 On Tue, Oct 6, 2009 at 10:05 AM, Ashta sewa...@gmail.com wrote:
  Hi All,
 
 
  Days - matrix(c(Monday, Tuesday, Wed, Thu, Fri, Sat,
  Sun),7,1)
 
  Hum -matrix(c(56,57,60,75,62,67,70),
 
  Temp-matrix(c(76,77,81,95,82,77,83),
 
 
 
  Using the above information I want plot humidity and temperature on
 Y-axis
  and days on X-axis
 
  Any help is appreciated!
 

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


[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Plot

2009-10-06 Thread joris meys

Actually, it's a bit more complex than just plot(). First you have to
make Days an ordered factor, otherwise you get indeed that error.

days - c(Mon, Tue, Wed, Thu, Fri, Sat,Sun)
Days - factor(days,levels=days,ordered=T)

Then you want to make a plot with 2 axes, you should check :
http://wiki.r-project.org/rwiki/doku.php?id=tips:graphics-base:2yaxes

and reconsider...

Kind regards

On Tue, Oct 6, 2009 at 4:19 PM, Sarah Goslee sarah.gos...@gmail.com wrote:
 Did you try it? With, perhaps, plot() ? And lines() ?

 You might do better with Days as a factor with the day names in order. (And
 why are two full and five abbreviated?)

 I don't understand why Hum and Temp are matrices rather than vectors,
 and why then you didn't specify dimensions, and for that matter why you
 are missing a closing paren but do have a comma in its place.

 Generally this list is happy to help, but we like some evidence that the
 querent has *tried* before inquiring.

 Sarah

 On Tue, Oct 6, 2009 at 10:05 AM, Ashta sewa...@gmail.com wrote:
 Hi All,


 Days - matrix(c(Monday, Tuesday, Wed, Thu, Fri, Sat,
 Sun),7,1)

 Hum -matrix(c(56,57,60,75,62,67,70),

 Temp-matrix(c(76,77,81,95,82,77,83),



 Using the above information I want plot humidity and temperature on Y-axis
 and days on X-axis

 Any help is appreciated!


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

 __
 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.


__
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.

[R] Is there a recent book on Q-Q plot and data visualization in general?

2009-10-06 Thread Peng Yu

Hi,

I want to look for some detailed explanation on the properties of Q-Q
plot and how the properties are derived.

In R, there is the following reference.
Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988) The New S
Language. Wadsworth  Brooks/Cole.

Somebody also mentioned the following book chapter to me.
Chambers et al., Graphical methods for Data Analysis, Ch.6.

But both books are old. I'm wondering if there is any more recent
(therefore, maybe better) books for Q-Q plot, and data visualization
in general.

Regards,
Peng

__
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.

Re: [R] 'persp' query

2009-10-06 Thread Peter Ehlers




David Winsemius wrote:


On Oct 6, 2009, at 4:46 AM, Geoffrey William Heard wrote:


Hi All

I'm creating some 3-D plots using the function 'persp', and have a 
query regarding the ability to make changes to the label of the z-axis.


There are two things I would like to do. First, the default setting 
places the label a little close to the axis for my liking. Is there 
any way of moving the label? I've tried adjustments with 'mgp' in 
'par', but without success. The second is to change the direction of 
the label. Currently it reads top to bottom, whereas I would like it 
to read bottom to top, as per a y-axis on a standard plot. Is there 
anyway of doing so?


?mtext   # and use the adj argument


Good idea. This works well if your z-axis is fairly vertical
on you plot.

 -Peter Ehlers

__
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.

Re: [R] Is there a recent book on Q-Q plot and data visualization in general?

2009-10-06 Thread Paul Hiemstra


Hi Peng Yu,

Chapter 13 of the following book provides a good description of the 
assumption done when using regression and other techniques. It also 
discusses the QQplot.


@BOOK{Christensen1996,
 title = {Plane Answers to Complex Questions: The Theory of Linear Models},
 publisher = {Springer, New York},
 year = {1996},
 author = {Ronald Christensen},
 edition = {Second},
 note = {496p},
}

cheers,
Paul

Peng Yu wrote:

Hi,

I want to look for some detailed explanation on the properties of Q-Q
plot and how the properties are derived.

In R, there is the following reference.
Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988) The New S
Language. Wadsworth  Brooks/Cole.

Somebody also mentioned the following book chapter to me.
Chambers et al., Graphical methods for Data Analysis, Ch.6.

But both books are old. I'm wondering if there is any more recent
(therefore, maybe better) books for Q-Q plot, and data visualization
in general.

Regards,
Peng

__
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.
  



--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul

__
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.

[R] RES: Plot

2009-10-06 Thread Rodrigo Aluizio

This may work for you.
Then you can custom your graphics with ?par.

Data-as.data.frame(matrix(c(Monday, Tuesday, Wed, Thu, Fri,
Sat,Sun,56,57,60,75,62,67,70,76,77,81,95,82,77,83),ncol=3,nrow=7,list(pa
ste('Row',1:7,sep=''),c('Days','Hum','Temp')),byrow=F))

plot(Data$Days,Data$Temp)

-Mensagem original-
De: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Em
nome de Ashta
Enviada em: terça-feira, 6 de outubro de 2009 11:36
Para: Sarah Goslee
Cc: R help
Assunto: Re: [R] Plot

Thanks Sara,

Yes I did try. I could not get the Days on the X-axis

blow is theerror message

plot(Temp,Days)
Error in plot.window(...) : need finite 'ylim' values
In addition: Warning messages:
1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion
2: In min(x) : no non-missing arguments to min; returning Inf
3: In max(x) : no non-missing arguments to max; returning -Inf




On Tue, Oct 6, 2009 at 10:19 AM, Sarah Goslee sarah.gos...@gmail.comwrote:

 Did you try it? With, perhaps, plot() ? And lines() ?

 You might do better with Days as a factor with the day names in order.
(And
 why are two full and five abbreviated?)

 I don't understand why Hum and Temp are matrices rather than vectors,
 and why then you didn't specify dimensions, and for that matter why you
 are missing a closing paren but do have a comma in its place.

 Generally this list is happy to help, but we like some evidence that the
 querent has *tried* before inquiring.

 Sarah

 On Tue, Oct 6, 2009 at 10:05 AM, Ashta sewa...@gmail.com wrote:
  Hi All,
 
 
  Days - matrix(c(Monday, Tuesday, Wed, Thu, Fri, Sat,
  Sun),7,1)
 
  Hum -matrix(c(56,57,60,75,62,67,70),
 
  Temp-matrix(c(76,77,81,95,82,77,83),
 
 
 
  Using the above information I want plot humidity and temperature on
 Y-axis
  and days on X-axis
 
  Any help is appreciated!
 

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


[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

__
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.

Re: [R] GLM quasipoisson error

2009-10-06 Thread Alain Zuur




atorso wrote:
 
 Hello,
 
 I'm having an error when trying to fit the next GLM:
 
model-glm(response ~ CLONE_M + CLONE_F + HATCHING
 +(CLONE_M*CLONE_F) + (CLONE_M*HATCHING) + (CLONE_F*HATCHING) +
 (CLONE_M*CLONE_F*HATCHING), family=quasipoisson)
 anova(model, test=Chi)
 
 
 
 
 
 I guess that those variables are factors, and that you have empty
 combinations? Make a coplot, and see whether you have data for all
 combinations of the levels of your factors. Formulated differently..does
 it make sense, or is it possible to fit the 3-way interaction for your
 data?
 
 Also..you may want to use the str command to see whether response is
 indeed coded correctly.
 
 Alain
 
Error in if (dispersion == 1) Inf else object$df.residual : 
   missing value where TRUE/FALSE needed
 
 If I fit the same model by using the Poisson distribution, it works.
 
 I have not a clue about where the problem could be. Do you have any
 idea or suggestion I could try?
 
 Thank you in advance, 
 
 Ana 
 
 __
 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.
 
 


-

Dr. Alain F. Zuur
First author of:

1. Analysing Ecological Data (2007).
Zuur, AF, Ieno, EN and Smith, GM. Springer. 680 p.

2. Mixed effects models and extensions in ecology with R. (2009).
Zuur, AF, Ieno, EN, Walker, N, Saveliev, AA, and Smith, GM. Springer.

3. A Beginner's Guide to R (2009).
Zuur, AF, Ieno, EN, Meesters, EHWG. Springer


Statistical consultancy, courses, data analysis and software
Highland Statistics Ltd.
6 Laverock road
UK - AB41 6FN Newburgh
Email: highs...@highstat.com
URL: www.highstat.com



-- 
View this message in context: 
http://www.nabble.com/GLM-quasipoisson-error-tp25754404p25770491.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Plot

2009-10-06 Thread Petr PIKAL

Hi

beside other options if you do not want to learn how to order factor 
levels

Days - c(Monday, Tuesday, Wed, Thu, Fri, Sat,Sun)
Hum -c(56,57,60,75,62,67,70)
Temp-c(76,77,81,95,82,77,83)

 limits-range(c(Hum, Temp))
 limits
[1] 56 95
 plot(1:7, Hum, ylim=limits)
 points(1:7, Temp, col=2)
 plot(1:7, Hum, ylim=limits, axes=F)
 points(1:7, Temp, col=2)
 axis(1, at=1:7, Days)
 axis(2)
 box()


this may work for you if you get rid of unnecessary matrix call.

Regards
Petr


r-help-boun...@r-project.org napsal dne 06.10.2009 16:35:44:

 Thanks Sara,
 
 Yes I did try. I could not get the Days on the X-axis
 
 blow is theerror message
 
 plot(Temp,Days)
 Error in plot.window(...) : need finite 'ylim' values
 In addition: Warning messages:
 1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion
 2: In min(x) : no non-missing arguments to min; returning Inf
 3: In max(x) : no non-missing arguments to max; returning -Inf
 
 
 
 
 On Tue, Oct 6, 2009 at 10:19 AM, Sarah Goslee 
sarah.gos...@gmail.comwrote:
 
  Did you try it? With, perhaps, plot() ? And lines() ?
 
  You might do better with Days as a factor with the day names in order. 
(And
  why are two full and five abbreviated?)
 
  I don't understand why Hum and Temp are matrices rather than vectors,
  and why then you didn't specify dimensions, and for that matter why 
you
  are missing a closing paren but do have a comma in its place.
 
  Generally this list is happy to help, but we like some evidence that 
the
  querent has *tried* before inquiring.
 
  Sarah
 
  On Tue, Oct 6, 2009 at 10:05 AM, Ashta sewa...@gmail.com wrote:
   Hi All,
  
  
   Days - matrix(c(Monday, Tuesday, Wed, Thu, Fri, Sat,
   Sun),7,1)
  
   Hum -matrix(c(56,57,60,75,62,67,70),
  
   Temp-matrix(c(76,77,81,95,82,77,83),
  
  
  
   Using the above information I want plot humidity and temperature on
  Y-axis
   and days on X-axis
  
   Any help is appreciated!
  
 
  --
  Sarah Goslee
  http://www.functionaldiversity.org
 
 
[[alternative HTML version deleted]]
 
 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide 
http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.

__
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.

Re: [R] how to fit time varying coefficient regression model?

2009-10-06 Thread Alain Zuur




R_help Help wrote:
 
 Hi - I read through dse package manual a bit. I'm not quite certain
 how I can use it to estimate a time varying coefficient regression
 model? I might pick up an inappropriate package. Any suggestion would
 be greatly appreciated. Thank you.
 
 
 Just rewrite the linear regression model into state-space equations, and
 apply Kalman filtering. See Chapter 16 or 17 in our Analysing Ecological
 Data book. There will be packages in R that can do kalman filtering and
 smoothing
 
 Alain
 
 
 
 
 
 rh
 
 __
 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.
 
 


-

Dr. Alain F. Zuur
First author of:

1. Analysing Ecological Data (2007).
Zuur, AF, Ieno, EN and Smith, GM. Springer. 680 p.

2. Mixed effects models and extensions in ecology with R. (2009).
Zuur, AF, Ieno, EN, Walker, N, Saveliev, AA, and Smith, GM. Springer.

3. A Beginner's Guide to R (2009).
Zuur, AF, Ieno, EN, Meesters, EHWG. Springer


Statistical consultancy, courses, data analysis and software
Highland Statistics Ltd.
6 Laverock road
UK - AB41 6FN Newburgh
Email: highs...@highstat.com
URL: www.highstat.com



-- 
View this message in context: 
http://www.nabble.com/how-to-fit-time-varying-coefficient-regression-model--tp25762040p25770615.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Letter-based representation of pairwise comparisons

2009-10-06 Thread goz


Ok, thanks for all your responses,

i was thinking, after reading the firsts messages that use only the $p.value
was good. By using a symetric matrix results are ok. 
It's also good with a pvalue vector (just like exemples in the help ...).

many thanks for your help




-- 
View this message in context: 
http://www.nabble.com/Letter-based-representation-of-pairwise-comparisons-tp21350364p25770624.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] ggplot cumsum refined question (?)

2009-10-06 Thread stephen sefick

The date time stamp is not the same?
data.frame(as.chron(Cumul[,date_time]), DF[,date_time])


On Tue, Oct 6, 2009 at 9:31 AM, hadley wickham h.wick...@gmail.com wrote:
 It is much easier to do you data preparation before plotting.

 Cummul - ddply(subset(DF, precipitation!=NA), gauge_name,
 function(x){
        x$Cummul - cumsum(x$precipitation)
        x
 })

 With a little less typing:

 Cummul - ddply(subset(DF, precipitation!=NA), gauge_name, transform,
  Cummul = cumsum(precipitation))

 Hadley

 --
 http://had.co.nz/

 __
 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.




-- 
Stephen Sefick

Let's not spend our time and resources thinking about things that are
so little or so large that all they really do for us is puff us up and
make us feel like gods.  We are mammals, and have not exhausted the
annoying little problems of being mammals.

-K. Mullis

__
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.

[R] RES: RES: Plot

2009-10-06 Thread Rodrigo Aluizio

Oh yeah, I forgot that, just correct this by:

Data-as.data.frame(matrix(c(Monday, Tuesday, Wed, Thu,
Fri,Sat,Sun,56,57,60,75,62,67,70,76,77,81,95,82,77,83),ncol=3,nrow=7,l
ist(paste('Row',1:7,sep=''),c('Days','Hum','Temp')),byrow=F))
Data$Hum-as.numeric(Data$Hum)
Data$Temp-as.numeric(Data$Temp)

Then you can plot it.

-Mensagem original-
De: joris meys [mailto:jorism...@gmail.com] 
Enviada em: terça-feira, 6 de outubro de 2009 12:08
Para: Rodrigo Aluizio
Assunto: Re: [R] RES: Plot

On Tue, Oct 6, 2009 at 4:56 PM, Rodrigo Aluizio r.alui...@gmail.com wrote:
 This may work for you.
 Then you can custom your graphics with ?par.

 Data-as.data.frame(matrix(c(Monday, Tuesday, Wed, Thu, Fri,

Sat,Sun,56,57,60,75,62,67,70,76,77,81,95,82,77,83),ncol=3,nrow=7,list(pa
 ste('Row',1:7,sep=''),c('Days','Hum','Temp')),byrow=F))
This won't work, as it puts also Temp en Hum as factors. A matrix can
only have 1 mode, and the matrix call you do converts everything to
factor before you put it in the dataframe.


 plot(Data$Days,Data$Temp)

 -Mensagem original-
 De: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Em
 nome de Ashta
 Enviada em: terça-feira, 6 de outubro de 2009 11:36
 Para: Sarah Goslee
 Cc: R help
 Assunto: Re: [R] Plot

 Thanks Sara,

 Yes I did try. I could not get the Days on the X-axis

 blow is theerror message

 plot(Temp,Days)
 Error in plot.window(...) : need finite 'ylim' values
 In addition: Warning messages:
 1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion
 2: In min(x) : no non-missing arguments to min; returning Inf
 3: In max(x) : no non-missing arguments to max; returning -Inf




 On Tue, Oct 6, 2009 at 10:19 AM, Sarah Goslee
sarah.gos...@gmail.comwrote:

 Did you try it? With, perhaps, plot() ? And lines() ?

 You might do better with Days as a factor with the day names in order.
 (And
 why are two full and five abbreviated?)

 I don't understand why Hum and Temp are matrices rather than vectors,
 and why then you didn't specify dimensions, and for that matter why you
 are missing a closing paren but do have a comma in its place.

 Generally this list is happy to help, but we like some evidence that the
 querent has *tried* before inquiring.

 Sarah

 On Tue, Oct 6, 2009 at 10:05 AM, Ashta sewa...@gmail.com wrote:
  Hi All,
 
 
  Days - matrix(c(Monday, Tuesday, Wed, Thu, Fri, Sat,
  Sun),7,1)
 
  Hum -matrix(c(56,57,60,75,62,67,70),
 
  Temp-matrix(c(76,77,81,95,82,77,83),
 
 
 
  Using the above information I want plot humidity and temperature on
 Y-axis
  and days on X-axis
 
  Any help is appreciated!
 

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


        [[alternative HTML version deleted]]

 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.

 __
 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.


__
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.

Re: [R] linear model with coefficient constraints

2009-10-06 Thread Dieter Menne




Rnewb wrote:
 
 I would like to perform a regression like the one below:
 
 lm(x ~ 0 + a1 + a2 + a3 + b1 + b2 + b3 + c1 + c2 + c3, data=data)
 
 However, the data has the property that a1+a2+a3 = A, b1+b2+b3 = B, and
 c1+c2+c3 = C, where A, B, 
 

Ravi Varadhan has an example how this could be done with optim

http://markmail.org/message/3dd5c4rppt2bjzwj

Dieter
-- 
View this message in context: 
http://www.nabble.com/linear-model-with-coefficient-constraints-tp25769021p25770788.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] R on Linux, and R on Windows , any difference in maturity+stability?


On 10/6/2009 10:34 AM, Jose Quesada wrote:

Robert Wilkins iwritecode2 at gmail.com writes:



Will R have more glitches on one operating system as opposed to
another, or is it pretty much the same?

robert




One important difference is that, if you are unsing large datasets and need
memory, then windows is by far the worst. 
CRAN R is 32 bit and can only address 1.5 Gb of memory (or something similar; I

don't really understand why).


By default, 32 bit Windows only gives 2 Gb for all the user processes to 
share, and saves the rest of memory for itself.  You can change this 
(see the Windows FAQ), but the most you'll ever get is 3 Gb in 32 bit 
Windows, and a bit under 4 Gb in 64 bit Windows.


Duncan Murdoch



While there's a 64-bit version of R for windows (revolution-computing.com) I
would advise against using it, for several reasons. While revolution has
provided very nice packages to the community (e.g., foreach), the win-64 port as
of today is certainly the worst platform to do work on. Reasons:
(1) it's R 2.7.2
(2) Many important packages will never be ported
(3) Some packages (particularly those depending on Rjava) would not work 
properly
(4) There's a proprietary repository, where most packages are outrageously
outdated. 
(5) Most help you find on R-help will not apply. Instead, you have 'paid'

support. Said support is slow, and close to useless in most cases.
(6) Packages that rely on external tools (e.g., mysql) will take a lot of work
to get going. 


And of course, one have to pay for a yearly license, to have the privilege to
work under the above conditions.

If you need 64-bit right now, my advice is to switch to basically any other
platform.

Note: this may change any time, since they are working on a continuous build
that will keep the releases in sync with mainstream R.

Jose Quesada, PhD.
Max Planck Institute, Human Development, Berlin
http://www.josequesada.name/

__
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.


__
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.

Re: [R] else if statement error

2009/10/6 Uwe Ligges lig...@statistik.tu-dortmund.de:


 Gabor Grothendieck wrote:

 2009/10/6 Uwe Ligges lig...@statistik.tu-dortmund.de:

 The first rule is easy: As long as you are using scalar valued (i.e.
 length
 1 vectors in R) cond, you should prefer
  if(cond) cons.expr  else  alt.expr
 rather than
  ifelse(cond, yes, no)
 because the latter one evaluates both yes and no while the former one
 evaluates exactly one of both expressions.

 I don't think that that is true.  The false leg was not evaluated here:

 ifelse(TRUE, { cat(a); 1}, {cat(b); 2})

 a[1] 1


 Ah, indeed that changed at some point and I forgot that the code checks for
 the length of cond nowadays. Thanks for pointing it out.


Modulo NAs, I think it checks whether cond is all TRUEs or all FALSEs
and in either of those cases it only evaluates one or the other.  Of
course if cond is length 1 then it necessary is all TRUE or all FALSE.
 If its a mixture of TRUE and FALSE then it evaluates both.

 ifelse(c(TRUE, TRUE), { cat(a); 1}, {cat(b); 2})
a[1] 1 1
 ifelse(c(FALSE, FALSE), { cat(a); 1}, {cat(b); 2})
b[1] 2 2
 ifelse(c(TRUE, FALSE), { cat(a); 1}, {cat(b); 2})
ab[1] 1 2

__
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.

Re: [R] Linear mixed effects model ?

2009-10-06 Thread Dieter Menne




Daniel Perkins wrote:
 
 
 Ideally we would do an ANCOVA to test for differences in slope or 
 intercepts for the different streams. However as there were repeated 
 measures and unequal n and unbalanced design, I have used a linear mixed 
 effect model (from nlme package in R) in the form:
 
 model - lme (Rate ~ Temp* Stream, random = ~ Time|Replicate)
 
 

This should rather be

model - lme (Rate ~ Temp* Stream, random = ~ 1|Time/Replicate)

Always start your model with the more parsimonious equal slopes assumption
denoted by 1|. When you place the Time variable as you did, it estimates
separate slopes for Time, which could be ill conditioned.

Dieter



-- 
View this message in context: 
http://www.nabble.com/Linear-mixed-effects-model---tp25767907p25770925.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] tkProgressBar usage

2009-10-06 Thread deepthi c

I have a frame and I want to fix the progress bar onto it.I do not want
progress bar to display as another GUI.how do i embed progress bar onto a
frame ?

-- 
Dipti

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] IRLS or other iteratively re weighted optimization algorithms with constraints in R

2009-10-06 Thread Corrado

Dear list,

is there an iterative re weighted least square based algorithm or any or other 
iteratively re weighted optimisation algorithms for non linear (and possibly 
non parametric) optimisation problems with constraints available in R?

Regards
-- 
Corrado

__
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.

[R] ggplot2: mapping categorical variable to color aesthetic with faceting

2009-10-06 Thread Bryan Hanson

Hello Again...  I¹m making a faceted plot of a response on two categorical
variables using ggplot2 and having troubles with the coloring. Here is a
sample that produces the desired plot:

compareCats - function(data, res, fac1, fac2, colors) {

require(ggplot2)
p - ggplot(data, aes(fac1, res)) + facet_grid(. ~ fac2)
jit - position_jitter(width = 0.1)
p - p + layer(geom = jitter, position = jit, color = colors)
print(p)
}

test - data.frame(res = rnorm(100), fac1 = as.factor(rep(c(A, B), 50)),
fac2 = as.factor(rep(c(lrg, lrg, sm, sm), 25)))

compareCats(data = test, res = res, fac1 = fac1, fac2 = fac2, colors =
c(red, blue))

Now, if I get away from idealized data where there are the same number of
data points per group (25 in this case), I run into problems.  So, if you
do:

rem - runif(5, 1, 100) # randomly remove a few points here and there
test - test[-rem,]
compareCats(data = test, res = res, fac1 = fac1, fac2 = fac2, colors =
c(red, blue))

R throws an error due to mismatch between the recycling of colors and the
actual number of data points:

Error in `[-.data.frame`(`*tmp*`, gp, value = list(colour = c(red,  :
  replacement element 1 has 2 rows, need 47

I'm new to ggplot2, but have been through the book and the web site enough
to know that my problem is mapping the varible to the aesthetic; I also
know I can either map or set the colors.

The question, finally:  is there an simple/elegant way to map a list of two
colors corresponding to A and B onto any random sample size of A and B with
faceting?  If not, and I must set the colors:  Do I compute the length of
all possible combos of A, B with lrg, sm, and then create one long vector of
colors for the entire plot?  I tried something like this, and was not
successful, but perhaps could be with more work.

All advice appreciated, Bryan (session info below)

*
Bryan Hanson
Professor of Chemistry  Biochemistry
DePauw University, Greencastle IN USA

 sessionInfo()
R version 2.9.2 (2009-08-24)
i386-apple-darwin8.11.1

locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] ggplot2_0.8.3  reshape_0.8.3  proto_0.3-8mvbutils_2.2.0
 [5] ChemoSpec_1.1  lattice_0.17-25mvoutlier_1.4  plyr_0.1.8
 [9] RColorBrewer_1.0-2 chemometrics_0.4   som_0.3-4
robustbase_0.4-5  
[13] rpart_3.1-45   pls_2.1-0  pcaPP_1.7  mvtnorm_0.9-7
[17] nnet_7.2-48mclust_3.2 MASS_7.2-48lars_0.9-7
[21] e1071_1.5-19   class_7.2-48  

__
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.

Re: [R] IRLS or other iteratively re weighted optimization algorithms with constraints in R



On Oct 6, 2009, at 12:14 PM, Corrado wrote:


Dear list,

is there an iterative re weighted least square based algorithm or  
any or other
iteratively re weighted optimisation algorithms for non linear (and  
possibly

non parametric) optimisation problems with constraints available in R?


Have you looked in the suggestively named Task View yet?

http://cran.r-project.org/web/views/

http://cran.r-project.org/web/views/Optimization.html

--

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

__
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.

Re: [R] Date-Time-Stamp input method for user-specific formats

2009-10-06 Thread esp



esp wrote:
 
 For the function as defined above using 'sapply'
 spot[,1]
  01/09/2009 01/09/2009 00:00:01 01/09/2009 00:00:02 01/09/2009
 00:00:03 
  1251759600  1251759601  1251759602 
 1251759603
 
 This was unexpected - it seems to have displayed the datetimestamp values
 both as per my defined character-string representation and as numeric
 values. 
 

One mystery solved (now I appreciate the existence and utility of the 'str'
and 'ls.str' functions), the apparent dual dateformat and numeric results
from my initial algorithm were in fact the associated characterstring and
numeric parts of a Named num object.

Hence for example:

 str(spot$DATETIME)
 Named num [1:4] 1.25e+09 1.25e+09 1.25e+09 1.25e+09
-   attr(*, names)= chr [1:4] 01/09/2009 01/09/2009 00:00:01 
01/09/2009
00:00:02 01/09/2009 00:00:03

 names(spot$DATETIME)
[1] 01/09/2009  01/09/2009 00:00:01 01/09/2009 00:00:02
01/09/2009 00:00:03

-- 
View this message in context: 
http://www.nabble.com/Date-Time-Stamp-input-method-for-user-specific-formats-tp25757018p25770184.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] Text editors for Sweave (rnw) files

2009-10-06 Thread Gregory Gentlemen

Hi fellow R-users,

Are there any text editors that recognize sweave (.rnw) files? I am running 
Windows Vista and in the past I used Tinn-R for R files but it (surprisingly) 
doesn't recognize rnw files and does not do any syntax highlighting for them.

Thanks in advance,
Greg



  __
Make your browsing faster, safer, and easier with the new Internet 
Explorer[[elided Yahoo spam]]
com/ca/internetexplorer/
[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Text editors for Sweave (rnw) files

2009-10-06 Thread Erik Iverson

Emacs with ESS would be one way to go.  When editing a RNW file in ESS, you can 
use a key combination to go from RNW directly to PS or PDF, which is nice. 

Erik 

 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
 On Behalf Of Gregory Gentlemen
 Sent: Tuesday, October 06, 2009 11:31 AM
 To: r-help@r-project.org
 Subject: [R] Text editors for Sweave (rnw) files

 Hi fellow R-users,

 Are there any text editors that recognize sweave (.rnw) files? I am
 running Windows Vista and in the past I used Tinn-R for R files but it
 (surprisingly) doesn't recognize rnw files and does not do any syntax
 highlighting for them.

 Thanks in advance,
 Greg

   __
 Make your browsing faster, safer, and easier with the new Internet
 Explorer[[elided Yahoo spam]]
 com/ca/internetexplorer/
   [[alternative HTML version deleted]]

 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-
 guide.html
 and provide commented, minimal, self-contained, reproducible code.

__
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.

Re: [R] Text editors for Sweave (rnw) files

vim/gvim does syntax highlighting of R, Sweave and latex.

On Tue, Oct 6, 2009 at 12:30 PM, Gregory Gentlemen
gregory_gentle...@yahoo.ca wrote:
 Hi fellow R-users,

 Are there any text editors that recognize sweave (.rnw) files? I am running 
 Windows Vista and in the past I used Tinn-R for R files but it (surprisingly) 
 doesn't recognize rnw files and does not do any syntax highlighting for them.

 Thanks in advance,
 Greg



      __
 Make your browsing faster, safer, and easier with the new Internet 
 Explorer[[elided Yahoo spam]]
 com/ca/internetexplorer/
        [[alternative HTML version deleted]]

 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.


__
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.

Re: [R] ggplot2: mapping categorical variable to color aesthetic with faceting

2009-10-06 Thread baptiste auguie

Hi,

I may be missing an important design decision, but could you not have
only a single data.frame as an argument of your function? From your
example, it seems that the colour can be mapped to the fac1 variable
of data,

compareCats - function(data) {

   require(ggplot2)
   p - ggplot(data, aes(fac1, res, color=fac1)) + facet_grid(. ~ fac2)
   jit - position_jitter(width = 0.1)
   p - p + layer(geom = jitter, position = jit) +
 scale_colour_manual(values=c(red, blue))
   print(p)
   }


test - data.frame(res = rnorm(100), fac1 = as.factor(rep(c(A, B), 50)),
   fac2 = as.factor(rep(c(lrg, lrg, sm, sm), 25)))

compareCats(data = test)

rem - runif(5, 1, 100) # randomly remove a few points here and there
last_plot() %+% test[-rem,] # replot with new dataset


HTH,

baptiste



2009/10/6 Bryan Hanson han...@depauw.edu:
 Hello Again...  I¹m making a faceted plot of a response on two categorical
 variables using ggplot2 and having troubles with the coloring. Here is a
 sample that produces the desired plot:

 compareCats - function(data, res, fac1, fac2, colors) {

    require(ggplot2)
    p - ggplot(data, aes(fac1, res)) + facet_grid(. ~ fac2)
    jit - position_jitter(width = 0.1)
    p - p + layer(geom = jitter, position = jit, color = colors)
    print(p)
    }

 test - data.frame(res = rnorm(100), fac1 = as.factor(rep(c(A, B), 50)),
    fac2 = as.factor(rep(c(lrg, lrg, sm, sm), 25)))

 compareCats(data = test, res = res, fac1 = fac1, fac2 = fac2, colors =
 c(red, blue))

 Now, if I get away from idealized data where there are the same number of
 data points per group (25 in this case), I run into problems.  So, if you
 do:

 rem - runif(5, 1, 100) # randomly remove a few points here and there
 test - test[-rem,]
 compareCats(data = test, res = res, fac1 = fac1, fac2 = fac2, colors =
 c(red, blue))

 R throws an error due to mismatch between the recycling of colors and the
 actual number of data points:

 Error in `[-.data.frame`(`*tmp*`, gp, value = list(colour = c(red,  :
  replacement element 1 has 2 rows, need 47

 I'm new to ggplot2, but have been through the book and the web site enough
 to know that my problem is mapping the varible to the aesthetic; I also
 know I can either map or set the colors.

 The question, finally:  is there an simple/elegant way to map a list of two
 colors corresponding to A and B onto any random sample size of A and B with
 faceting?  If not, and I must set the colors:  Do I compute the length of
 all possible combos of A, B with lrg, sm, and then create one long vector of
 colors for the entire plot?  I tried something like this, and was not
 successful, but perhaps could be with more work.

 All advice appreciated, Bryan (session info below)

 *
 Bryan Hanson
 Professor of Chemistry  Biochemistry
 DePauw University, Greencastle IN USA

 sessionInfo()
 R version 2.9.2 (2009-08-24)
 i386-apple-darwin8.11.1

 locale:
 en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

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

 other attached packages:
  [1] ggplot2_0.8.3      reshape_0.8.3      proto_0.3-8        mvbutils_2.2.0
  [5] ChemoSpec_1.1      lattice_0.17-25    mvoutlier_1.4      plyr_0.1.8
  [9] RColorBrewer_1.0-2 chemometrics_0.4   som_0.3-4
 robustbase_0.4-5
 [13] rpart_3.1-45       pls_2.1-0          pcaPP_1.7          mvtnorm_0.9-7
 [17] nnet_7.2-48        mclust_3.2         MASS_7.2-48        lars_0.9-7
 [21] e1071_1.5-19       class_7.2-48

 __
 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.


__
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.

[R] Way of handling empty value when reading in CSV

2009-10-06 Thread Jason Rupert

I believe I may be overlooking something simple in order address this, but I 
have searched RSeek.org and using ?, but cannot seem to find anything 
discussing this one.


I am using read.csv to read in a csv file.  Evidently in places there is 
nothing between the commas, so that when the data is read in the data.frame 
produced has values that are empty.  


Is there a way to fix this when reading the data via read.csv?  I looked at 
all the options mentioned in ?read.csv, but did not see anything to address 
this case, e.g. 


home,sqr_footage,cost
1,1500,15
2,2000,20
3,,30
4,3500,35
5,4000,45


I would like for the empty cells to have a value of NA when they are read in. 
 


Thank you for any feedback and insights.

__
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.

[R] mle from stats4

2009-10-06 Thread Stephen Collins

I am using mle as a wrapper from optim( ).  How would I extract the 
convergence code, to know that optim( ) converged properly?

Thanks,
 
 
Stephen Collins, MPP | Analyst
Global Strategy | Aon Benfield

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Date-Time-Stamp input method for user-specific formats

2009-10-06 Thread esp


Another solution, as a fix to my original algorithm, was found by a colleague
(Matthew Roberts).  While he claims not too much for its elegance, it does
seem to work.  This fix is based on the use of the 'pmax' function.  This
function is a variant of the 'max' (maximum) function to return a vector of
results corresponding to vectors of inputs.  Example: max(1:3,4:8) == 8 but
pmax(1:3,4:6) == 4 5 6.  Thanks to this, it provides appropriate results for
all rows of the data.

In the code, there are two possible datetimestamp interpretations, midnight
and non midnight, each implemented by a 'strptime' call.  When a midnight
datetimestamp is encountered, only the midnight conversion will return a
proper (non NA) value.  Thanks to the na.rm=TRUE option, the NA result is
removed so 'pmax' returns just the proper value.  For a non midnight
datetimestamp, both midnight and non midnight conversions return proper
values, but only the non midnight conversion will give a result greater than
midnight, and it is this that is returned by the 'pmax'.  

The code is as follows:

spot_frequency_readin - function(file,nrows=-1) {

# create temp class
setClass(t_class2_, representation(character))
setAs(character, t_class2_, function(from) {
as.POSIXct(pmax(strptime(from, format=%d/%m/%Y),
strptime(from, format=%d/%m/%Y %H:%M:%S),
na.rm=TRUE), tz=GMT)
}
)

#(for format symbols, see R Reference Card)

# read the file (TSV)
file - read.delim(file, header=TRUE, comment.char = , nrows=nrows,
as.is=FALSE, col.names=c(DATETIME, FREQ), colClasses=c(t_class2_,
numeric) )

# remove it now that we are done with it
removeClass(t_class2_)

return(file)
}


The result:
 spot
 DATETIME   FREQ
1 2009-09-01 00:00:00 50.036
2 2009-09-01 00:00:01 50.035
3 2009-09-01 00:00:02 50.035
4 2009-09-01 00:00:03 50.033


Confirm the nature of the result:
 str(spot)
'data.frame':   4 obs. of  2 variables:
 $ DATETIME: POSIXct, format: 2009-09-01 00:00:00 2009-09-01 00:00:01
2009-09-01 00:00:02 2009-09-01 00:00:03
 $ FREQ: num  50 50 50 50


(Note: 'str' means Compactly display the internal structure of an R
object.  I can claim from experience that his and 'ls.str' are things that
the novice R user can benefit hugely from knowing about)
-- 
View this message in context: 
http://www.nabble.com/Date-Time-Stamp-input-method-for-user-specific-formats-tp25757018p25770983.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Text editors for Sweave (rnw) files

2009-10-06 Thread Liviu Andronic

On 10/6/09, Gregory Gentlemen gregory_gentle...@yahoo.ca wrote:
  Are there any text editors that recognize sweave (.rnw) files? I am running 
 Windows Vista and in the past I used Tinn-R for R files but it (surprisingly) 
 doesn't recognize rnw files and does not do any syntax highlighting for them.

Slightly off-topic reply. You can compose Sweave documents using LyX,
in which case you would not need syntax highlighting.
Liviu

__
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.

[R] linear model with coefficient constraints

2009-10-06 Thread Rnewb


I would like to perform a regression like the one below:

lm(x ~ 0 + a1 + a2 + a3 + b1 + b2 + b3 + c1 + c2 + c3, data=data)

However, the data has the property that a1+a2+a3 = A, b1+b2+b3 = B, and
c1+c2+c3 = C, where A, B, and C are positive constants.  So there are two
extra degrees of freedom, and R handles this by producing NA for two of the
coefficients.  Instead, I would prefer to remove the degrees of freedom by
forcing constraints on the coefficients produced by the model. 
Specifically, I want

coeff(b1) + coeff(b2) + coeff(b3) = coeff(c1) + coeff(c2) + coeff(c3) = 0.

I could accomplish this by writing code to suitably shift the coefficients
after performing the basic regression above, but I'm hoping there's a better
way.  Is there?

thanks,
Rnewb
-- 
View this message in context: 
http://www.nabble.com/linear-model-with-coefficient-constraints-tp25769020p25769020.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Letter-based representation of pairwise comparisons

2009-10-06 Thread retama


Hello:

That's because the required input should be a symmetric matrix with all the
comparisons, e.g., it should have the self-comparisons diagonal. In an
hypotetical case with two treatments, the pairwise-comparison test output is
something like that:

A B 
B 0.80- 

but multcompView requires an input like that one:

 A B 
A 1 - 
B 0.80 1   

That means you should add a new row and column for your missing treatments
and, then, a diagonal of 1s meaning that each treatment compared with
itself will result in a p-value of 1 (maximal identity). Then, the new
matrix could be piped succesfully.

Regards,

Retama


goz wrote:
 
 hello,
 
 i try to use the multcomp letters, but i have problems with my results : 
 
 here is my pvalue matrix (from a pairwise.t.test) : 
 
 pair=pairwise.t.test(...)
 pair$p.value
 
 0   BBxS
 B0.01727- -  
 BxS 0.000130.00226   -  
 S0.875550.02610   0.00027
 
 
 i was thiking to have something like that : 
  0  B  S  BxS
  a  b  a  c
 
 but function return : 
 
 multcompLetters(pair$p.value)
   B   BxS   S 
  a  b   a 
 
 
 first question : why the 0 traitement doesn't appears in result ?
 second  : why the results differs than what i expected ?
 
 many thanks.
 
 

-- 
View this message in context: 
http://www.nabble.com/Letter-based-representation-of-pairwise-comparisons-tp21350364p25769894.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Way of handling empty value when reading in CSV

2009-10-06 Thread Erik Iverson

I saved your data as test.csv, and 

 read.csv(~/test.csv, header = TRUE)
  home sqr_footage   cost
111500 15
222000 20
33  NA 30
443500 35
554000 45

I am using R 2.8.1, old I know... but maybe something else is going on?  Do you 
really get a blank when you read in your sample data? 

Erik 

 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
 On Behalf Of Jason Rupert
 Sent: Tuesday, October 06, 2009 11:39 AM
 To: R-help@r-project.org
 Subject: [R] Way of handling empty value when reading in CSV
 
 I believe I may be overlooking something simple in order address this, but
 I have searched RSeek.org and using ?, but cannot seem to find anything
 discussing this one.
 
 
 I am using read.csv to read in a csv file.  Evidently in places there is
 nothing between the commas, so that when the data is read in the
 data.frame produced has values that are empty.
 
 
 Is there a way to fix this when reading the data via read.csv?  I looked
 at all the options mentioned in ?read.csv, but did not see anything to
 address this case, e.g.
 
 
 home,sqr_footage,cost
 1,1500,15
 2,2000,20
 3,,30
 4,3500,35
 5,4000,45
 
 
 I would like for the empty cells to have a value of NA when they are
 read in.
 
 
 Thank you for any feedback and insights.
 
 __
 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.

__
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.

Re: [R] Fwd: Long for Loop- calling C from R - Parallel Computing

2009-10-06 Thread jim holtman

It would help to understand the problem you are trying to solve and
the constraints that you have to live under.  I routinely process
files with millions of rows of data, do a lot of processing and create
graphics/reports from them in what I think is reasonable time (a
couple of minutes at most for the complex stuff) all within R without
having to write C/FORTRAN.  I am not sure what assumptions you are
currently operating under, but it would be good to state them so that
we know how to reply to the question that you are asking.

There are performance tips that can be provided if we knew what you
were trying to do.

On Tue, Oct 6, 2009 at 10:10 AM, Antonio Paredes
antonioparede...@gmail.com wrote:
 -- Forwarded message --
 From: Antonio Paredes antonioparede...@gmail.com
 Date: Tue, Oct 6, 2009 at 9:41 AM
 Subject: Re: [R] Long for Loop- calling C from R - Parallel Computing
 To: Karl Ove Hufthammer k...@huftis.org


 Hello again,

 I'm hoping to get a response from some of the R gurus in this list. Is my
 assumption that R is not designed or build to deal with high levels (a lots
 of simulated data) simulation correct. For example, how to minimize system
 time; do one have to call a lower level language like C or Fortran; or just,
 like many of you have done,  do a lots of programing in R and eventually the
 tricks will be learned.

 Thanks

 On Mon, Oct 5, 2009 at 8:35 AM, Antonio Paredes
 antonioparede...@gmail.comwrote:

 In my case it does, because I need to preserved a high level of
 independence (lack of correlation) among the different groups of 60. Also,
 when I say final result I mean computation of standard errors and that
 source of stuff; sorry about the lack clarity in my statement.


 On Mon, Oct 5, 2009 at 9:48 AM, Karl Ove Hufthammer k...@huftis.orgwrote:

 In article 6f6f0fd60910050629p28c99209jcd7836353fd2d754
 @mail.gmail.com, antonioparede...@gmail.com says...
  I'm running the following for loop to generate random variables in
 chunks of
  60 at a time (l), here h is of order in millions (could be 5 to 6
 millions),
  note that generating all the variables at once could have an impact on
 the
  final results

 No, it will not. See this example code for an illustration:

 set.seed(1)
 rnorm(3)
 rnorm(3)
 set.seed(1)
 rnorm(6)

 So if you generate the six numbers three at a time or all at once gives
 exactly the same result.

 So my suggestion is to generate all the numbers at once. That takes next
 to no time. Or, if it takes too much memory, generate for example a
 million at once, and repeat a few times.

 --
 Karl Ove Hufthammer

 __
 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.




 --
 -Tony




 --
 -Tony



 --
 -Tony

        [[alternative HTML version deleted]]

 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.




-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem that you are trying to solve?

__
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.

Re: [R] Text editors for Sweave (rnw) files

2009-10-06 Thread Steve Lianoglou


Hi,

On Oct 6, 2009, at 12:30 PM, Gregory Gentlemen wrote:


Hi fellow R-users,

Are there any text editors that recognize sweave (.rnw) files? I am  
running Windows Vista and in the past I used Tinn-R for R files but  
it (surprisingly) doesn't recognize rnw files and does not do any  
syntax highlighting for them.


I don't run windows, but rumor has it that the e-texteditor is  
supposed to support TextMate bundles. So, since TextMate has bundles  
to support *.R, *.Rnw, *.Rd files, I would imagine the e editor could  
work, too:


Editor:
http://www.e-texteditor.com/

Getting more bundles:
http://e-texteditor.com/wiki/index.php/Bundles#How_To_Get_More_Bundles

You'll see several R bundles here (for TextMate, which should  
theoretically work for you)

http://svn.textmate.org/trunk/Bundles/

I suspect this would be the one you want:
http://svn.textmate.org/trunk/Bundles/R.tmbundle/

Hope that helps,
-steve

--
Steve Lianoglou
Graduate Student: Computational Systems Biology
  |  Memorial Sloan-Kettering Cancer Center
  |  Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

__
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.

Re: [R] mle from stats4

2009-10-06 Thread Peter Dalgaard


Stephen Collins wrote:
I am using mle as a wrapper from optim( ).  How would I extract the 
convergence code, to know that optim( ) converged properly?


The return value from optim is contained in the details slot, so

 f...@details$convergence
[1] 0


--
   O__   Peter Dalgaard Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark  Ph:  (+45) 35327918
~~ - (p.dalga...@biostat.ku.dk)  FAX: (+45) 35327907

__
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.

Re: [R] mle from stats4

2009-10-06 Thread Ben Bolker




Stephen Collins-6 wrote:
 
 I am using mle as a wrapper from optim( ).  How would I extract the 
 convergence code, to know that optim( ) converged properly?
 
 

library(stats4)
example(mle)
slotNames(fit1)
f...@details
f...@details$convergence



-- 
View this message in context: 
http://www.nabble.com/mle-from-stats4-tp25772337p25772668.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] ggplot2: mapping categorical variable to color aesthetic with faceting

2009-10-06 Thread baptiste auguie

Further to my previous reply, it occurred to me that ggplot2 would
only ever use data and colors in your calls to compareCats(): res =
res, fac1 = fac1, fac2 = fac2 have no effect whatsoever.

If you want the user to be able to specify the variables used in the
ggplot2 call, you probably want to look at ?aes_string, as shown
below,

compareCats - function(data, fac1=fac1, fac2=fac2, res=res,
colors=c(red, blue)) {

  require(ggplot2)
  p - ggplot(data, aes_string(x=fac1, y=res, color=fac1)) +
facet_grid(paste(. ~ , fac2))
  jit - position_jitter(width = 0.1)
  p - p + layer(geom = jitter, position = jit) +
scale_colour_manual(values=colors)
  print(p)
  }

test - data.frame(res = rnorm(100), fac1 = as.factor(rep(c(A, B), 50)),
  fac2 = as.factor(rep(c(lrg, lrg, sm, sm), 25)))

compareCats(data = test)

rem - sample(10, 1:ncol(test)) # randomly remove a few points here and there
last_plot() %+% test[-rem, ] # replot with new dataset

HTH,

baptiste




2009/10/6 baptiste auguie baptiste.aug...@googlemail.com:
 Hi,

 I may be missing an important design decision, but could you not have
 only a single data.frame as an argument of your function? From your
 example, it seems that the colour can be mapped to the fac1 variable
 of data,

 compareCats - function(data) {

   require(ggplot2)
   p - ggplot(data, aes(fac1, res, color=fac1)) + facet_grid(. ~ fac2)
   jit - position_jitter(width = 0.1)
   p - p + layer(geom = jitter, position = jit) +
     scale_colour_manual(values=c(red, blue))
   print(p)
   }


 test - data.frame(res = rnorm(100), fac1 = as.factor(rep(c(A, B), 50)),
   fac2 = as.factor(rep(c(lrg, lrg, sm, sm), 25)))

 compareCats(data = test)

 rem - runif(5, 1, 100) # randomly remove a few points here and there
 last_plot() %+% test[-rem,] # replot with new dataset


 HTH,

 baptiste



 2009/10/6 Bryan Hanson han...@depauw.edu:
 Hello Again...  I¹m making a faceted plot of a response on two categorical
 variables using ggplot2 and having troubles with the coloring. Here is a
 sample that produces the desired plot:

 compareCats - function(data, res, fac1, fac2, colors) {

    require(ggplot2)
    p - ggplot(data, aes(fac1, res)) + facet_grid(. ~ fac2)
    jit - position_jitter(width = 0.1)
    p - p + layer(geom = jitter, position = jit, color = colors)
    print(p)
    }

 test - data.frame(res = rnorm(100), fac1 = as.factor(rep(c(A, B), 50)),
    fac2 = as.factor(rep(c(lrg, lrg, sm, sm), 25)))

 compareCats(data = test, res = res, fac1 = fac1, fac2 = fac2, colors =
 c(red, blue))

 Now, if I get away from idealized data where there are the same number of
 data points per group (25 in this case), I run into problems.  So, if you
 do:

 rem - runif(5, 1, 100) # randomly remove a few points here and there
 test - test[-rem,]
 compareCats(data = test, res = res, fac1 = fac1, fac2 = fac2, colors =
 c(red, blue))

 R throws an error due to mismatch between the recycling of colors and the
 actual number of data points:

 Error in `[-.data.frame`(`*tmp*`, gp, value = list(colour = c(red,  :
  replacement element 1 has 2 rows, need 47

 I'm new to ggplot2, but have been through the book and the web site enough
 to know that my problem is mapping the varible to the aesthetic; I also
 know I can either map or set the colors.

 The question, finally:  is there an simple/elegant way to map a list of two
 colors corresponding to A and B onto any random sample size of A and B with
 faceting?  If not, and I must set the colors:  Do I compute the length of
 all possible combos of A, B with lrg, sm, and then create one long vector of
 colors for the entire plot?  I tried something like this, and was not
 successful, but perhaps could be with more work.

 All advice appreciated, Bryan (session info below)

 *
 Bryan Hanson
 Professor of Chemistry  Biochemistry
 DePauw University, Greencastle IN USA

 sessionInfo()
 R version 2.9.2 (2009-08-24)
 i386-apple-darwin8.11.1

 locale:
 en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

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

 other attached packages:
  [1] ggplot2_0.8.3      reshape_0.8.3      proto_0.3-8        mvbutils_2.2.0
  [5] ChemoSpec_1.1      lattice_0.17-25    mvoutlier_1.4      plyr_0.1.8
  [9] RColorBrewer_1.0-2 chemometrics_0.4   som_0.3-4
 robustbase_0.4-5
 [13] rpart_3.1-45       pls_2.1-0          pcaPP_1.7          mvtnorm_0.9-7
 [17] nnet_7.2-48        mclust_3.2         MASS_7.2-48        lars_0.9-7
 [21] e1071_1.5-19       class_7.2-48

 __
 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.



__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the

Re: [R] Spatial Autocorrelation

2009-10-06 Thread spencerg

In addition to the taskview (below), you might consider using the sos 
package, something like the following: 



sa - ???'spatial autocorrelation' # 58 matches
sc - ???'spatial correlation' #  181 matches
s. - sa|sc # union of the to 'findFn' objects
summary(s.) # 224 links in 57 packages
installPackages(s.)  # install packages with at least 5 = 
sqrt(max(count)) matches
writeFindFn2xls(s.) # write an Excel file with 3 sheets:  PackageSum2, 
findFn, call



 This tells you that 22 help pages in spdep matched the search 
term, plus 18 pages in each of nlme, ncf, and spatstat, as well as 17 in 
ramps and 15 in geoR.  The PackageSum2 sheet also provides other 
information to help you decide which package to consider first. 



 Beyond this, you may like to uses these functions with other 
search terms;  see vignette('sos') for more information. 



 Hope this helps. 
 Spencer
Disclaimer:  I'm the lead author of sos. 



Corey Sparks wrote:

Hi Paulo,
if your data are distance matrices, you might consider doing a Mantel test,
look at the mantel() function in package vegan.  While this is not
technically measuring spatial autocorrelation, it will test for correlation
between the attribute distances and the geographic distances.  Also, if you
can coax your data back into a point shapefile (for example), you can use
the tools in the spdep package which will measure actual spatial
autocorrelation (such as Moran's I and Geary's C). 
Best,

Corey


silcha wrote:
  

Hi Paulo,
you may want to take a look at

http://cran.r-project.org/web/views/Spatial.html

there, you can find all spatial packages that 
can be useful for your question.
There is also a  a mailing list R-sig-geo that where 
you can ask all those kind of question.


Hope that this helps.

Cheers

Anna



Anna Freni Sterrantino
Ph.D Student 
Department of Statistics

University of Bologna, Italy
via Belle Arti 41, 40124 BO.





Da: P.Branco pjlbra...@yahoo.com
A: r-help@r-project.org
Inviato: Martedì 6 ottobre 2009, 13:28:36
Oggetto: [R]  Spatial Autocorrelation


Hello, 


I have a matrix with the distances among sites. And I have another matrix
with the presence and absence of  each species in each site. I would like
to
test the spatial autocorrelation among sites.

I have tried to use the function gearymoran of the ade4 package, but error
messages keep popping up. Do you know any function for me to test the
spatial autocorrelation of my data?

Thanks,

Paulo Branco
--
View this message in context:
http://www.nabble.com/Spatial-Autocorrelation-tp25767010p25767010.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__


spazio gratuito per i tuoi file e i messaggi 


[[alternative HTML version deleted]]


__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.





  



--
Spencer Graves, PE, PhD
President and Chief Operating Officer
Structure Inspection and Monitoring, Inc.
751 Emerson Ct.
San José, CA 95126
ph:  408-655-4567

__
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.

Re: [R] Way of handling empty value when reading in CSV

2009-10-06 Thread Jason Rupert

Well, I guess I posted a poor example.

This example is a little closer:
home,sqr_footage,cost,color,exterior
1,1500,15,,Siding
2,2000,20,Red,Brick
3,,30,Grey,Brick
4,3500,35,Blue,
5,4000,45,Red,Brick

This one actually shows the presence of the null fields that are loaded. 

Sorry again for the poor 1st example. 

Thank you again for your time and insight. 



--- On Tue, 10/6/09, Erik Iverson eiver...@nmdp.org wrote:

 From: Erik Iverson eiver...@nmdp.org
 Subject: RE: [R] Way of handling empty value when reading in CSV
 To: Jason Rupert jasonkrup...@yahoo.com, R-help@r-project.org 
 R-help@r-project.org
 Date: Tuesday, October 6, 2009, 11:42 AM
 I saved your data as test.csv, and 
 
  read.csv(~/test.csv, header = TRUE)
   home sqr_footage   cost
 1    1        1500 15
 2    2        2000 20
 3    3          NA
 30
 4    4        3500 35
 5    5        4000 45
 
 I am using R 2.8.1, old I know... but maybe something else
 is going on?  Do you really get a blank when you read
 in your sample data? 
 
 Erik 
 
  -Original Message-
  From: r-help-boun...@r-project.org
 [mailto:r-help-boun...@r-project.org]
  On Behalf Of Jason Rupert
  Sent: Tuesday, October 06, 2009 11:39 AM
  To: R-help@r-project.org
  Subject: [R] Way of handling empty value when reading
 in CSV
  
  I believe I may be overlooking something simple in
 order address this, but
  I have searched RSeek.org and using ?, but cannot
 seem to find anything
  discussing this one.
  
  
  I am using read.csv to read in a csv file. 
 Evidently in places there is
  nothing between the commas, so that when the data is
 read in the
  data.frame produced has values that are empty.
  
  
  Is there a way to fix this when reading the data via
 read.csv?  I looked
  at all the options mentioned in ?read.csv, but did not
 see anything to
  address this case, e.g.
  
  
  home,sqr_footage,cost
  1,1500,15
  2,2000,20
  3,,30
  4,3500,35
  5,4000,45
  
  
  I would like for the empty cells to have a value of
 NA when they are
  read in.
  
  
  Thank you for any feedback and insights.
  
  __
  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.
 




__
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.

Re: [R] R on Linux, and R on Windows , any difference in maturity+stability?

2009-10-06 Thread Kjetil Halvorsen

On Tue, Oct 6, 2009 at 11:23 AM, Duncan Murdoch murd...@stats.uwo.ca wrote:
 On 10/6/2009 10:34 AM, Jose Quesada wrote:

 Robert Wilkins iwritecode2 at gmail.com writes:


 Will R have more glitches on one operating system as opposed to
 another, or is it pretty much the same?

 robert



 One important difference is that, if you are unsing large datasets and
 need
 memory, then windows is by far the worst. CRAN R is 32 bit and can only
 address 1.5 Gb of memory (or something similar; I
 don't really understand why).

 By default, 32 bit Windows only gives 2 Gb for all the user processes to
 share, and saves the rest of memory for itself.  You can change this (see
 the Windows FAQ), but the most you'll ever get is 3 Gb in 32 bit Windows,


 _and a bit under 4 Gb in 64 bit Windows.


That sounds incredible. ¿Why so?

Kjetil

 Duncan Murdoch


 While there's a 64-bit version of R for windows (revolution-computing.com)
 I
 would advise against using it, for several reasons. While revolution has
 provided very nice packages to the community (e.g., foreach), the win-64
 port as
 of today is certainly the worst platform to do work on. Reasons:
 (1) it's R 2.7.2
 (2) Many important packages will never be ported
 (3) Some packages (particularly those depending on Rjava) would not work
 properly
 (4) There's a proprietary repository, where most packages are outrageously
 outdated. (5) Most help you find on R-help will not apply. Instead, you
 have 'paid'
 support. Said support is slow, and close to useless in most cases.
 (6) Packages that rely on external tools (e.g., mysql) will take a lot of
 work
 to get going.
 And of course, one have to pay for a yearly license, to have the privilege
 to
 work under the above conditions.

 If you need 64-bit right now, my advice is to switch to basically any
 other
 platform.

 Note: this may change any time, since they are working on a continuous
 build
 that will keep the releases in sync with mainstream R.

 Jose Quesada, PhD.
 Max Planck Institute, Human Development, Berlin
 http://www.josequesada.name/

 __
 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.

 __
 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.


__
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.

Re: [R] ggplot2: mapping categorical variable to color aesthetic with faceting

2009-10-06 Thread Bryan Hanson

Hi Baptiste:  Thanks for the suggestion.  It will work perfectly.

I would have never considered assigning a color to a variable that contained
no colors at all!  I guess this is part of the aesthetic concept, which I
haven't had time to reflect on much.  Then later, specify a manual color
scale which then maps back onto the aesthetic.  Clever.

As I stated, I'm just learning ggplot2, and I'm finding the language and
concepts a bit different (I'm not familiar with the grammar of graphics,
nor am I a computer scientist).  But, I have to say the code I am working up
replaces a much much longer code in base graphics, so I am really liking the
thought put into ggplot2 and the leanness of it - Thanks Hadley!

Thanks again, Bryan


On 10/6/09 12:36 PM, baptiste auguie baptiste.aug...@googlemail.com
wrote:

 Hi,
 
 I may be missing an important design decision, but could you not have
 only a single data.frame as an argument of your function? From your
 example, it seems that the colour can be mapped to the fac1 variable
 of data,
 
 compareCats - function(data) {
 
require(ggplot2)
p - ggplot(data, aes(fac1, res, color=fac1)) + facet_grid(. ~ fac2)
jit - position_jitter(width = 0.1)
p - p + layer(geom = jitter, position = jit) +
  scale_colour_manual(values=c(red, blue))
print(p)
}
 
 
 test - data.frame(res = rnorm(100), fac1 = as.factor(rep(c(A, B), 50)),
fac2 = as.factor(rep(c(lrg, lrg, sm, sm), 25)))
 
 compareCats(data = test)
 
 rem - runif(5, 1, 100) # randomly remove a few points here and there
 last_plot() %+% test[-rem,] # replot with new dataset
 
 
 HTH,
 
 baptiste
 
 
 
 2009/10/6 Bryan Hanson han...@depauw.edu:
 Hello Again...  I¹m making a faceted plot of a response on two categorical
 variables using ggplot2 and having troubles with the coloring. Here is a
 sample that produces the desired plot:
 
 compareCats - function(data, res, fac1, fac2, colors) {
 
    require(ggplot2)
    p - ggplot(data, aes(fac1, res)) + facet_grid(. ~ fac2)
    jit - position_jitter(width = 0.1)
    p - p + layer(geom = jitter, position = jit, color = colors)
    print(p)
    }
 
 test - data.frame(res = rnorm(100), fac1 = as.factor(rep(c(A, B), 50)),
    fac2 = as.factor(rep(c(lrg, lrg, sm, sm), 25)))
 
 compareCats(data = test, res = res, fac1 = fac1, fac2 = fac2, colors =
 c(red, blue))
 
 Now, if I get away from idealized data where there are the same number of
 data points per group (25 in this case), I run into problems.  So, if you
 do:
 
 rem - runif(5, 1, 100) # randomly remove a few points here and there
 test - test[-rem,]
 compareCats(data = test, res = res, fac1 = fac1, fac2 = fac2, colors =
 c(red, blue))
 
 R throws an error due to mismatch between the recycling of colors and the
 actual number of data points:
 
 Error in `[-.data.frame`(`*tmp*`, gp, value = list(colour = c(red,  :
  replacement element 1 has 2 rows, need 47
 
 I'm new to ggplot2, but have been through the book and the web site enough
 to know that my problem is mapping the varible to the aesthetic; I also
 know I can either map or set the colors.
 
 The question, finally:  is there an simple/elegant way to map a list of two
 colors corresponding to A and B onto any random sample size of A and B with
 faceting?  If not, and I must set the colors:  Do I compute the length of
 all possible combos of A, B with lrg, sm, and then create one long vector of
 colors for the entire plot?  I tried something like this, and was not
 successful, but perhaps could be with more work.
 
 All advice appreciated, Bryan (session info below)
 
 *
 Bryan Hanson
 Professor of Chemistry  Biochemistry
 DePauw University, Greencastle IN USA
 
 sessionInfo()
 R version 2.9.2 (2009-08-24)
 i386-apple-darwin8.11.1
 
 locale:
 en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
 
 attached base packages:
 [1] grid      datasets  tools     utils     stats     graphics  grDevices
 methods
 [9] base
 
 other attached packages:
  [1] ggplot2_0.8.3      reshape_0.8.3      proto_0.3-8        mvbutils_22.0
  [5] ChemoSpec_1.1      lattice_0.17-25    mvoutlier_1.4      plyr_0.1.8
  [9] RColorBrewer_1.0-2 chemometrics_0.4   som_0.3-4
 robustbase_0.4-5
 [13] rpart_3.1-45       pls_2.1-0          pcaPP_1.7          mvtnorm_0.9-7
 [17] nnet_7.2-48        mclust_3.2         MASS_7.2-48        lars_0.9-7
 [21] e1071_1.5-19       class_7.2-48
 
 __
 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.
 

__
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.

Re: [R] Way of handling empty value when reading in CSV

2009-10-06 Thread jim holtman

Does this do what you want:

) x - read.csv(textConnection(home,sqr_footage,cost,color,exterior
+ 1,1500,15,,Siding
+ 2,2000,20,Red,Brick
+ 3,,30,Grey,Brick
+ 4,3500,35,Blue,
+ 5,4000,45,Red,Brick), na.strings='')
 closeAllConnections()

 x
  home sqr_footage   cost color exterior
111500 15  NA   Siding
222000 20   RedBrick
33  NA 30  GreyBrick
443500 35  Blue NA
554000 45   RedBrick



On Tue, Oct 6, 2009 at 1:12 PM, Jason Rupert jasonkrup...@yahoo.com wrote:
 Well, I guess I posted a poor example.

 This example is a little closer:
 home,sqr_footage,cost,color,exterior
 1,1500,15,,Siding
 2,2000,20,Red,Brick
 3,,30,Grey,Brick
 4,3500,35,Blue,
 5,4000,45,Red,Brick

 This one actually shows the presence of the null fields that are loaded.

 Sorry again for the poor 1st example.

 Thank you again for your time and insight.



 --- On Tue, 10/6/09, Erik Iverson eiver...@nmdp.org wrote:

 From: Erik Iverson eiver...@nmdp.org
 Subject: RE: [R] Way of handling empty value when reading in CSV
 To: Jason Rupert jasonkrup...@yahoo.com, R-help@r-project.org 
 R-help@r-project.org
 Date: Tuesday, October 6, 2009, 11:42 AM
 I saved your data as test.csv, and

  read.csv(~/test.csv, header = TRUE)
   home sqr_footage   cost
 1    1        1500 15
 2    2        2000 20
 3    3          NA
 30
 4    4        3500 35
 5    5        4000 45

 I am using R 2.8.1, old I know... but maybe something else
 is going on?  Do you really get a blank when you read
 in your sample data?

 Erik

  -Original Message-
  From: r-help-boun...@r-project.org
 [mailto:r-help-boun...@r-project.org]
  On Behalf Of Jason Rupert
  Sent: Tuesday, October 06, 2009 11:39 AM
  To: R-help@r-project.org
  Subject: [R] Way of handling empty value when reading
 in CSV
 
  I believe I may be overlooking something simple in
 order address this, but
  I have searched RSeek.org and using ?, but cannot
 seem to find anything
  discussing this one.
 
 
  I am using read.csv to read in a csv file.
 Evidently in places there is
  nothing between the commas, so that when the data is
 read in the
  data.frame produced has values that are empty.
 
 
  Is there a way to fix this when reading the data via
 read.csv?  I looked
  at all the options mentioned in ?read.csv, but did not
 see anything to
  address this case, e.g.
 
 
  home,sqr_footage,cost
  1,1500,15
  2,2000,20
  3,,30
  4,3500,35
  5,4000,45
 
 
  I would like for the empty cells to have a value of
 NA when they are
  read in.
 
 
  Thank you for any feedback and insights.
 
  __
  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.





 __
 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.




-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem that you are trying to solve?

__
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.

Re: [R] R on Linux, and R on Windows , any difference in maturity+stability?


On 10/6/2009 1:17 PM, Kjetil Halvorsen wrote:

On Tue, Oct 6, 2009 at 11:23 AM, Duncan Murdoch murd...@stats.uwo.ca wrote:

On 10/6/2009 10:34 AM, Jose Quesada wrote:


Robert Wilkins iwritecode2 at gmail.com writes:



Will R have more glitches on one operating system as opposed to
another, or is it pretty much the same?

robert




One important difference is that, if you are unsing large datasets and
need
memory, then windows is by far the worst. CRAN R is 32 bit and can only
address 1.5 Gb of memory (or something similar; I
don't really understand why).


By default, 32 bit Windows only gives 2 Gb for all the user processes to
share, and saves the rest of memory for itself.  You can change this (see
the Windows FAQ), but the most you'll ever get is 3 Gb in 32 bit Windows,




_and a bit under 4 Gb in 64 bit Windows.



That sounds incredible. ¿Why so?


When running a 32 bit program, 64 bit Windows hides most of itself 
outside the address space visible to the program, so almost all of the 4 
Gb address space is available to the user.  But no more: no matter how 
much RAM you install, it's not possible to address it using a 32 bit 
address.


Duncan Murdoch



Kjetil


Duncan Murdoch



While there's a 64-bit version of R for windows (revolution-computing.com)
I
would advise against using it, for several reasons. While revolution has
provided very nice packages to the community (e.g., foreach), the win-64
port as
of today is certainly the worst platform to do work on. Reasons:
(1) it's R 2.7.2
(2) Many important packages will never be ported
(3) Some packages (particularly those depending on Rjava) would not work
properly
(4) There's a proprietary repository, where most packages are outrageously
outdated. (5) Most help you find on R-help will not apply. Instead, you
have 'paid'
support. Said support is slow, and close to useless in most cases.
(6) Packages that rely on external tools (e.g., mysql) will take a lot of
work
to get going.
And of course, one have to pay for a yearly license, to have the privilege
to
work under the above conditions.

If you need 64-bit right now, my advice is to switch to basically any
other
platform.

Note: this may change any time, since they are working on a continuous
build
that will keep the releases in sync with mainstream R.

Jose Quesada, PhD.
Max Planck Institute, Human Development, Berlin
http://www.josequesada.name/

__
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.


__
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.



__
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.

Re: [R] R on Linux, and R on Windows , any difference in maturity+stability?

2009-10-06 Thread David M Smith

On Tue, Oct 6, 2009 at 10:30 AM, Duncan Murdoch murd...@stats.uwo.ca wrote:
 When running a 32 bit program, 64 bit Windows hides most of itself outside
 the address space visible to the program, so almost all of the 4 Gb address
 space is available to the user.  But no more: no matter how much RAM you
 install, it's not possible to address it using a 32 bit address.

That's true when running a 32-bit version of R under 64-bit Windows.
But on the 64-bit version of REvolution R Enterprise for Windows, you
can create objects much larger than 4Gb, for example:

 memory.limit(2e+9)
 v-double(1e+9) # 8GB vector
 sum(v)
[1] 0

The same is true of 64-bit versions of R on other platforms, too.

# David Smith

-- 
David M Smith da...@revolution-computing.com
Director of Community, REvolution Computing www.revolution-computing.com
Tel: +1 (206) 577-4778 x3203 (San Francisco, USA)

Check out our upcoming events schedule at www.revolution-computing.com/events

__
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.

Re: [R] Robust ANOVA with variance heterogeneity

2009-10-06 Thread Kjetil Halvorsen

Hola! see below.

On Sat, Oct 3, 2009 at 2:45 PM, David Winsemius dwinsem...@comcast.net wrote:
Do you have a citation for that statement? I cannot convince myself that it
should be true.

OK. that took some time, since I have no nonparametrics book with me,
but it is a fairly
standard assumption the friedman.test shares with wilcox.test and
others. One online reference giving this is:

http://www.mathworks.com/access/helpdesk/help/toolbox/stats/index.html?/access/helpdesk/help/toolbox/stats/friedman.htmlhttp://www.google.cl/search?q=assumptions+of+friedman+testie=utf-8oe=utf-8aq=trls=com.ubuntu:en-US:unofficialclient=firefox-a

specifically:
Friedman's test makes the following assumptions about the data in X:

All data come from populations having the same continuous
distribution, apart from possibly different locations due to column
and row effects.
*

All observations are mutually independent.

This is also easy to investigate by simulation in R:

I did:
A[, 1] - rnorm(100, 0, 1)
A[, 2] - rnorm(100, 0, 5)
A[, 3] - rnorm(100, 0, 500)
friedman.test(A)

Friedman rank sum test

data: A
Friedman chi-squared = 2.96, df = 2, p-value = 0.2276

which surprised me! This test seems to be somewhat robust against
variance heterogeneity ???, but that case is not included in the
usual theory.

Kjetil

After looking at the CRAN Task View, I would suggest the OP look at
rlm(MASS) or lmrob(robustbase).

--
David

On Oct 2, 2009, at 11:05 AM, Kjetil Halvorsen wrote:

On Fri, Oct 2, 2009 at 8:45 AM, David Winsemius dwinsem...@comcast.net
wrote:

There are multiple routes to robust statistics, but the quick answer to
this question is probably friedman.test

I don't think friedman.test is robust to variance heterogeneity. It is
only robust to
non-normality.

Kjetil

I seem to remember a CRAN Task View on the area of Robust Statistics.

--
David Winsemius

On Oct 2, 2009, at 3:05 AM, Maike Luhmann wrote:

Dear list members,

I am looking for an alternative function for a two-way ANOVA in the case
of
variance heterogeneity. For one-way ANOVA, I found oneway.test(), but I
didn't find anything alike for two-way ANOVA. Does anyone have a
suggestion?

Thank you!

Maike Luhmann
Freie Universität Berlin

__
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.

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

[R] how to output profile plots for groups using lattice package

2009-10-06 Thread George Kalema

Dear R users,
I am trying to have an xyplot of a data set which has the following
variables:
case (n=10,20,30)
parameter (parm=a,b)
group (grp=g1,g2)
y (y values)
x (x=2,4,8)

My plot should be parameter by case such that I have 2 rows (each row= each
parameter) and 3 columns (each column=each case). My R-code is as follows
but I am not able to get what I want to:

tp1.sim - xyplot(y~ x | case + parm , group=group, data = data, lty = 1:4 ,
pch = 1:4)
print(tp1.sim)

How can I have two lines (for g1 and g2) in each plot (each box)?
How do I label the x-axis with only values 2, 4, 8?
How do I label each column with the corresponding case number?

My hypothetical data set is as follows:

parm x case y group
a 2 10 0.03 g1
b 2 10 0.02 g1
a 4 10 0.03 g1
b 4 10 0.02 g1
a 8 10 0.03 g1
b 8 10 0.02 g1
a 2 20 0.03 g1
b 2 20 0.02 g1
a 4 20 0.03 g1
b 4 20 0.02 g1
a 8 20 0.03 g1
b 8 20 0.02 g1
a 2 30 0.03 g1
b 2 30 0.02 g1
a 4 30 0.03 g1
b 4 30 0.02 g1
a 8 30 0.03 g1
b 8 30 0.02 g1
a 2 10 0.13 g2
b 2 10 0.12 g2
a 4 10 0.13 g2
b 4 10 0.12 g2
a 8 10 0.13 g2
b 8 10 0.12 g2
a 2 20 0.13 g2
b 2 20 0.12 g2
a 4 20 0.13 g2
b 4 20 0.12 g2
a 8 20 0.13 g2
b 8 20 0.12 g2
a 2 30 0.13 g2
b 2 30 0.12 g2
a 4 30 0.13 g2
b 4 30 0.12 g2
a 8 30 0.13 g2
b 8 30 0.12 g2

Many thanks in advance for your response.

George

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] How to extract names from a vector

2009-10-06 Thread kayj


Hi All,

I have a character vector of length=700.  The vector contains names and I
want to extract the names that contain the number 101.  The number 101 could
be anywhere within the name.

what is the best way to do this? 

-- 
View this message in context: 
http://www.nabble.com/How-to-extract-names-from-a-vector-tp25773482p25773482.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] How to extract names from a vector

2009-10-06 Thread Henrique Dallazuanna

See ?grep



On Tue, Oct 6, 2009 at 2:48 PM, kayj kjaj...@yahoo.com wrote:

 Hi All,

 I have a character vector of length=700.  The vector contains names and I
 want to extract the names that contain the number 101.  The number 101 could
 be anywhere within the name.

 what is the best way to do this?

 --
 View this message in context: 
 http://www.nabble.com/How-to-extract-names-from-a-vector-tp25773482p25773482.html
 Sent from the R help mailing list archive at Nabble.com.

 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.




-- 
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O

__
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.

Re: [R] Robust ANOVA with variance heterogeneity

On Oct 6, 2009, at 1:51 PM, Kjetil Halvorsen wrote:

On Sat, Oct 3, 2009 at 2:45 PM, David Winsemius dwinsem...@comcast.net
wrote:
Do you have a citation for that statement? I cannot convince myself
that it

should be true.

OK. that took some time, since I have no nonparametrics book with me,
but it is a fairly
standard assumption the friedman.test shares with wilcox.test and
others. One online reference giving this is:

http://www.mathworks.com/access/helpdesk/help/toolbox/stats/index.html?/access/helpdesk/help/toolbox/stats/friedman.htmlhttp://www.google.cl/search
?q=assumptions+of+friedman
+testie=utf-8oe=utf-8aq=trls=com.ubuntu:en-
US:unofficialclient=firefox-a

specifically:
Friedman's test makes the following assumptions about the data in X:
*
All data come from populations having the same continuous
distribution, apart from possibly different locations due to column
and row effects.
*
All observations are mutually independent.

This is also easy to investigate by simulation in R:

I did:

A[, 1] - rnorm(100, 0, 1)
A[, 2] - rnorm(100, 0, 5)
A[, 3] - rnorm(100, 0, 500)
friedman.test(A)

Friedman rank sum test

data: A
Friedman chi-squared = 2.96, df = 2, p-value = 0.2276

which surprised me! This test seems to be somewhat robust against
variance heterogeneity ???, but that case is not included in the
usual theory.

I do not see that your citation implied that there would be a material
impact (especially toward false positive results which I take to be
the meaning of not robust) from a violation of the equi-variance
assumption, ... only that equivariance was the basis of the
derivation of the statistical theory. The test might even be
conservative for all we know until the question has been subjected to
simulation studies. And then your simulation suggested not much of a
problem, which does not seem surprising to me given that a rank
transformation has been applied to the data. So I remain unconvinced.

--
Regards;
David.

Kjetil

After looking at the CRAN Task View, I would suggest the OP look at
rlm(MASS) or lmrob(robustbase).

--
David

On Oct 2, 2009, at 11:05 AM, Kjetil Halvorsen wrote:

On Fri, Oct 2, 2009 at 8:45 AM, David Winsemius dwinsem...@comcast.net

wrote:

There are multiple routes to robust statistics, but the quick
answer to

this question is probably friedman.test

I don't think friedman.test is robust to variance heterogeneity.
It is

only robust to
non-normality.

Kjetil

I seem to remember a CRAN Task View on the area of Robust
Statistics.

--
David Winsemius

On Oct 2, 2009, at 3:05 AM, Maike Luhmann wrote:

Dear list members,

I am looking for an alternative function for a two-way ANOVA in
the case

of
variance heterogeneity. For one-way ANOVA, I found
oneway.test(), but I

didn't find anything alike for two-way ANOVA. Does anyone have a
suggestion?

Thank you!

Maike Luhmann
Freie Universität Berlin

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

Re: [R] R on Linux, and R on Windows , any difference in maturity+stability?