Re: [R] [R-sig-Geo] envi clone in R
Dear Barry, Wednesday, February 8, 2006, 9:09:19 PM, you wrote: BR Wladimir Eremeev wrote: Hello all, Research Systems (www.rsinc.com) have developed and distributes the language IDL, and the GIS ENVI, written in IDL. BR I find it hard to believe they wrote it all in IDL! I'm guessing its BR probably scriptable in IDL, but underneath its written in something BR else... I could be wrong though! Well, not in IDL completely, I think, there is also C and Fortran code underneath. To my oppinion, R language is superior, compared to IDL, in all aspects. However, ENVI is the rather convenient and feature rich tool. By the way, even the interface to an external code is implemented in R much more conveniently, compared to IDL. It took me several hours to make IDL to call my C functions from DLL. I have read the documentation carefully 2 or 3 times... And I have done the same task in R in several minutes. --- Best regards, Wladimirmailto:[EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Plotting a count process
voodooochild at gmx.de writes: i want to plot a count process in the following way, but i don't know how i can do that. i have data for example x-(0,2,6,2,8,4,.) and dates y which is a vector of weekly dates for example (01/01/06, 08/01/06, 15/01/06, 22/01/06, ), now i want to plot the y's an the horizontal axis. On each date the count process jumps upwards 1 unit, so the vertical axis is 0, 1, 2, 3, .. the distance between the dates is shown in vector x, so for example the distance between 08/01/06 and 15/01/06 should be 2. maybe i can use some times series functions for doing this? If I understand you correctly, this means plotting equidistant point against the cumulative sum. Forgetting about the dates now, this would do it. x = floor(pmax(rnorm(30,5,2),1)) xcum = cumsum(x) plot(xcum,1:30) Dieter __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Simple optim - question
Carsten Steinhoff carsten.steinhoff at gmx.de writes:
I want to find the parameters mu and sigma that minimize the following
function.
It's important, that mu and sigma are strictly positive.
-
optimiere = function(fmean,smean,d,x,mu,sigma)
{
merk = c()
for (i in 1:length(d))
merk=c(merk,1/(d[i]^2)*(d[i]-1/(fmean*(1-plnorm(x[i],mu,sigma^2)
return(sum(merk))
}
-
Try optim or nlminb, both can be used with constraints. Or, as your example
looks like a least-square problem, reformulate optim and use nls.
Dieter
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Re: [R] logical condition in vector operation
Dear Frederico
From your example it is not clear to me what you like to obtain:
Please have a look on the slightly changed example here (I
changed two values to show a potentially undesired side effect of
your coding.
test - data.frame(rbind(c(3,3,10,21,0), c(2,3,11,12,0), c(3,4,12,23,0),
c(3,5,13,24,0)))
names(test) - c(x,y,p,d,su)
test
x y p d su
1 3 3 10 21 0
2 2 3 11 12 0
3 3 4 12 23 0
4 3 5 13 24 0
j - 3
test[test[,1] == j, 5] - test[test[,1] == j,2] + test[test[,2] == j,1]
Warning message:
longer object length
is not a multiple of shorter object length in:
test[test[, 1] == j, 2] + test[test[, 2] == j, 1]
Your code example produces now a warning for the adapted
data frame test, since one tries to add two vectors of length 2
and 3, respectively. The result is based on recycling of the
smaller vector. In your example there was no warning since the
second column had only one entry.
The result with the adapted data frame is:
test
x y p d su
1 3 3 10 21 6
2 2 3 11 12 0
3 3 4 12 23 6
4 3 5 13 24 8
Is that kind of recycling desired in your application. Otherwise
you should be careful with the coding example above.
Regards,
Christoph Buser
--
Christoph Buser [EMAIL PROTECTED]
Seminar fuer Statistik, LEO C13
ETH (Federal Inst. Technology) 8092 Zurich SWITZERLAND
phone: x-41-44-632-4673 fax: 632-1228
http://stat.ethz.ch/~buser/
--
Federico Calboli writes:
HI All,
I have a data frame such as:
test
x y p d
[1,] 1 0 10 21 0
[2,] 2 3 11 12 0
[3,] 3 4 12 23 0
[4,] 3 5 13 24 0
and I want to perfor some operations on the first two coulums,
conditional on the uneqaulity values on the 3rd and 4th columns.
For instance:
j = 3
test[test[,1] == j, 5] = test[test[,1] == j,2] + test[test[,2] == j,1]
gives me the result:
test:
x y p d
[1,] 1 0 10 21 0
[2,] 2 3 11 12 0
[3,] 3 4 12 23 6
[4,] 3 5 13 24 7
My probblem is the following: I want to perform the operation
test[test[,1] == j,2] + test[test[,2] == j,1] only if the value of
column p and column d are different at the positions where x or y = j.
In practice, I don't want to perform the first operation because
test[2,4 is 12 and test[1,3] is 12 as well.
I tried an if statement with little success:
if(test[test[,1] == j,3] != test[test[,2] == j,4]){
test[test[,1] == j, 5] = test[test[,1] == j,2] + test[test[,2] == j,1]
}
Warning message:
the condition has length 1 and only the first element will be used in:
if (test[test[, 1] == j, 3] != test[test[, 2] == j, 4]) {
Could anyone lend some advice?
Cheers,
Federico
--
Federico C. F. Calboli
Department of Epidemiology and Public Health
Imperial College, St Mary's Campus
Norfolk Place, London W2 1PG
Tel +44 (0)20 7594 1602 Fax (+44) 020 7594 3193
f.calboli [.a.t] imperial.ac.uk
f.calboli [.a.t] gmail.com
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Re: [R] writing a file using both cat() and paste()
Taka Matzmoto wrote:
Hi R users
I like to create a ASCII type file using cat() and paste()
x - round(runif(30),3)
cat(vector =( , paste(x,sep=), )\n, file = vector.dat,sep=,)
when I open vector.dat it was a long ugly file
vector =(
,0.463,0.515,0.202,0.232,0.852,0.367,0.432,0.74,0.413,0.022,0.302,0.114,0.583,0.002,0.919,0.066,0.829,0.405,0.363,0.665,0.109,0.38,0.187,0.322,0.582,0.011,0.586,0.112,0.873,0.671,
)
Also there was some problems right after opening parenthesis and before the
closing parenthesis. Two comma were there
I like to to have a nice formatted one like below. That is, 5 random values
per a line
vector =( 0.463,0.515,0.202,0.232,0.852,
0.367,0.432,0.74,0.413,0.022,
0.302,0.114,0.583,0.002,0.919,
0.066,0.829,0.405,0.363,0.665,
0.109,0.38,0.187,0.322,0.582,
0.011,0.586,0.112,0.873,0.671)
First, you might want to avoid using vector, as that is the name of an
R function. Say you have a 30 element data vector as above. If you
wanted to write a fairly general function to do this, here is a start:
vector2file-function(x,file=,values.per.line=5) {
if(nchar(file)) sink(file)
cat(deparse(substitute(x)),-c(\n)
xlen-length(x)
for(i in 1:xlen) {
cat(x[i])
if(ixlen) cat(,)
if(i%%values.per.line == 0) cat(\n)
}
cat())
if(i%%values.per.line) cat(\n)
if(nchar(file))sink()
}
Jim
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Re: [R] Plotting a count process
Thank you for your advice, but this is not the exaxt thing i'm looking for http://robotics.caltech.edu/~zoran/Research/poisson/img1.png this picture gives an example what i want to get. instead of t0, t1, t2, i want to draw my dates. In my description i forgot the the horizontal line, which indicates the time between two dates each, sorry for that. regards andreas Dieter Menne wrote: voodooochild at gmx.de writes: i want to plot a count process in the following way, but i don't know how i can do that. i have data for example x-(0,2,6,2,8,4,.) and dates y which is a vector of weekly dates for example (01/01/06, 08/01/06, 15/01/06, 22/01/06, ), now i want to plot the y's an the horizontal axis. On each date the count process jumps upwards 1 unit, so the vertical axis is 0, 1, 2, 3, .. the distance between the dates is shown in vector x, so for example the distance between 08/01/06 and 15/01/06 should be 2. maybe i can use some times series functions for doing this? If I understand you correctly, this means plotting equidistant point against the cumulative sum. Forgetting about the dates now, this would do it. x = floor(pmax(rnorm(30,5,2),1)) xcum = cumsum(x) plot(xcum,1:30) Dieter __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] echo output to screen
Hi all, I want to echo output to screen before next step, like the following when i type library(pkname), library(pkname) a few description about the package how should I do to get this? Thanks in advanced!! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] (user) ERROR: no applicable method for TukeyHSD
On Wed, 8 Feb 2006, Darren Weber wrote: Why do I see this error? Because there _is_ no applicable method. Please don't name objects after R functions, but in your case you need to do class(aov) ?TukeyHSD ?aov and see what TukeyHSD says it handles and what aov says it returns. This question has been answered at length on this list quite recently, so please also search the archives. library(stats) require(stats) [1] TRUE tHSD - TukeyHSD(aov) Error in TukeyHSD(aov) : no applicable method for TukeyHSD In case it helps: aov Call: aov(formula = roi ~ (Cue * Hemisphere) + Error(Subject/(Cue * Hemisphere)), data = roiDataframe) Grand Mean: 8.195069 Stratum 1: Subject Terms: Residuals Sum of Squares 645.7444 Deg. of Freedom 7 Residual standard error: 9.604645 Stratum 2: Subject:Cue Terms: Cue Residuals Sum of Squares 0.386987 4.015740 Deg. of Freedom1 7 Residual standard error: 0.7574148 1 out of 2 effects not estimable Estimated effects are balanced Stratum 3: Subject:Hemisphere Terms: Hemisphere Residuals Sum of Squares153.4860 827.6699 Deg. of Freedom 1 7 Residual standard error: 10.87376 1 out of 2 effects not estimable Estimated effects are balanced Stratum 4: Subject:Cue:Hemisphere Terms: Cue:Hemisphere Residuals Sum of Squares5.085930 4.279707 Deg. of Freedom 1 7 Residual standard error: 0.7819122 Estimated effects are balanced [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Brian D. Ripley, [EMAIL PROTECTED] 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] [R-sig-Geo] envi clone in R
Dear Barry, By the way... BR I settled on OpenEV - it has vector and raster support, its extensible BR in Python and uses Gtk for dialogs which you can customise. I have seen OpenEV. Unfortunately, I could not find a documentation or user guide for quick start and had not too much time to realize what is what and how to use its features with 'mouse point-and-click' :) Do you have a link to such a document? --- Best regards, Wladimirmailto:[EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] echo output to screen
Chun-Ying Lee wrote: Hi all, I want to echo output to screen before next step, like the following when i type library(pkname), library(pkname) a few description about the package how should I do to get this? ?cat Uwe Ligges Thanks in advanced!! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] echo output to screen
On Thu, 09 Feb 2006 10:02:49 +0100, Uwe Ligges wrote Chun-Ying Lee wrote: Hi all, I want to echo output to screen before next step, like the following when i type library(pkname), library(pkname) a few description about the package how should I do to get this? ?cat I know the use of cat but I mean that the description appear automatically when I type library(pkname) Uwe Ligges Thanks in advanced!! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] echo output to screen
Chun-Ying Lee wrote: On Thu, 09 Feb 2006 10:02:49 +0100, Uwe Ligges wrote Chun-Ying Lee wrote: Hi all, I want to echo output to screen before next step, like the following when i type library(pkname), library(pkname) a few description about the package how should I do to get this? ?cat I know the use of cat but I mean that the description appear automatically when I type library(pkname) See ?.onAttach (or ?.First.lib if you do not use a NAMESPACE). Uwe Ligges Uwe Ligges Thanks in advanced!! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] echo output to screen
Le 09.02.2006 10:09, Chun-Ying Lee a écrit : On Thu, 09 Feb 2006 10:02:49 +0100, Uwe Ligges wrote Chun-Ying Lee wrote: Hi all, I want to echo output to screen before next step, like the following when i type library(pkname), library(pkname) a few description about the package how should I do to get this? ?cat I know the use of cat but I mean that the description appear automatically when I type library(pkname) Hi, Your question was not too clear about that. See Writing R extensions. ?.First.lib if you don't have a NAMESPACE ?.onLoad if you do Romain -- visit the R Graph Gallery : http://addictedtor.free.fr/graphiques mixmod 1.7 is released : http://www-math.univ-fcomte.fr/mixmod/index.php +---+ | Romain FRANCOIS - http://francoisromain.free.fr | | Doctorant INRIA Futurs / EDF | +---+ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] write.table
Hello! When using the command write.table I want to convert the format: 5e-04 to .0005. How can I do it? The only option I found is to use write.matrix but then I cant add rownames. Thank you Ronen [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] write.table
See the scipen argument in ?options. write.table(data.frame(x = 0.0005)) options(scipen = 1) write.table(data.frame(x = 0.0005)) --sundar fluss wrote: Hello! When using the command write.table I want to convert the format: 5e-04 to .0005. How can I do it? The only option I found is to use write.matrix but then I cant add rownames. Thank you Ronen [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] write.table
Hello! When using the command write.table I want to convert the format: 5e-04 to .0005. How can I do it? The only option I found is to use write.matrix but then I cant add rownames. Thank you Ronen ?options, see scipen. Or, use format() to convert table before writing it. -- Brian D. Ripley, [EMAIL PROTECTED] 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] adding variable into dataframe by indice
Hi
not sure if I understand correctly but table() can be used
ttt - table(asubs112$fir)
prop - ttt/nrow(asubs112)
asubs112$prop -
prop[match(asubs112$first_drink,as.numeric(names(prop)))]
asubs112
IND_ID rs1042364 first_drink prop
2 11 (1,2) 7 0.333
5 41 (1,2) 11 0.111
6 51 (1,2) 7 0.333
7 61 (1,1) 7 0.333
8 71 (1,1) 12 0.222
10 91 (1,1) 6 0.111
11101 (1,2) 5 0.111
12111 (1,2) 13 0.111
14131 (1,2) 12 0.222
HTH
Petr
On 8 Feb 2006 at 9:40, Adrian Katschke wrote:
Date sent: Wed, 8 Feb 2006 09:40:43 -0800 (PST)
From: Adrian Katschke [EMAIL PROTECTED]
To: RHelp r-help@stat.math.ethz.ch
Subject:[R] adding variable into dataframe by indice
R-Helpers,
I am trying to insert a value into a dataframe. This value is a
proportion calculated by counting the number of those individuals
with that value and then inserting the proportion at the end of the
dataframe to only those individuals with the given value. The
problem I am running into is that the proportions are not being
attached to only those individuals with the specified value for that
proportion.
Below is an example of the code that I am using. The data is made up
for the dataframe. Should give you an idea, but the original has
'NA' in many rows. The original data is what is reported in the
output below.
#Read in Data
age.int - data.frame(IND_ID = seq(1, 140, 10), rs1042364 =
sample( c((1,1),(1,2),(2,2)),14,replace = T), first_drink =
sample(5:17,14,replace = T))
asubs112 - subset(age.int, rs1042364 != (2,2))
ages112 - sort(unique(na.omit(asubs112$first_drink)))
for ( i in ages112) {
indce - which(na.omit(asubs112$first_drink == i))
prop - length(indce)/nrow(asubs112)
asubs112[indce,4] - prop
asubs112[indce,]
}
Below is the output that I get from the script above. Notice the
proportion for the first NA but not any of the others. Not sure what
I am doing wrong, any suggestions are a big help.
TIA,
Adrian
asubs112[1:50,]
IND_ID rs1042364 first_drink age_int V5
4 10008007 (1,2) NA 16 0.003891051
6 10013012 (1,2) 13 14 0.116731518
7 10015006 (1,2) 12 17 0.105058366
8 10015007 (1,1) 12 16 0.105058366
10 10021009 (1,2) NA 15 NA
14 10039036 (1,2) NA 15 NA
15 10039037 (1,2) NA 13 NA
17 10045005 (1,2) 13 17 0.116731518
18 10045014 (1,2) 13 14 0.116731518
21 10055022 (1,2) NA 15 NA
[[alternative HTML version deleted]]
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Re: [R] logical condition in vector operation
On Thu, 2006-02-09 at 09:22 +0100, Christoph Buser wrote: Dear Frederico From your example it is not clear to me what you like to obtain: Please have a look on the slightly changed example here (I changed two values to show a potentially undesired side effect of your coding. test - data.frame(rbind(c(3,3,10,21,0), c(2,3,11,12,0), c(3,4,12,23,0), c(3,5,13,24,0))) names(test) - c(x,y,p,d,su) test x y p d su 1 3 3 10 21 0 2 2 3 11 12 0 3 3 4 12 23 0 4 3 5 13 24 0 j - 3 test[test[,1] == j, 5] - test[test[,1] == j,2] + test[test[,2] == j,1] Warning message: longer object length is not a multiple of shorter object length in: test[test[, 1] == j, 2] + test[test[, 2] == j, 1] Your code example produces now a warning for the adapted data frame test, since one tries to add two vectors of length 2 and 3, respectively. The result is based on recycling of the smaller vector. In your example there was no warning since the second column had only one entry. The result with the adapted data frame is: test x y p d su 1 3 3 10 21 6 2 2 3 11 12 0 3 3 4 12 23 6 4 3 5 13 24 8 Is that kind of recycling desired in your application. Otherwise you should be careful with the coding example above. Recycling was and is integral part of my plan. Cheers, Federico -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 7594 1602 Fax (+44) 020 7594 3193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] logical condition in vector operation
Hi
try
ifelse()
but I you probably shall put your problem clearer.
HTH
Petr
On 8 Feb 2006 at 18:12, Federico Calboli wrote:
From: Federico Calboli [EMAIL PROTECTED]
To: r-help r-help@stat.math.ethz.ch
Organization: Imperial College London
Date sent: Wed, 08 Feb 2006 18:12:37 +
Subject:[R] logical condition in vector operation
Send reply to: [EMAIL PROTECTED]
mailto:[EMAIL PROTECTED]
mailto:[EMAIL PROTECTED]
HI All,
I have a data frame such as:
test
x y p d
[1,] 1 0 10 21 0
[2,] 2 3 11 12 0
[3,] 3 4 12 23 0
[4,] 3 5 13 24 0
and I want to perfor some operations on the first two coulums,
conditional on the uneqaulity values on the 3rd and 4th columns.
For instance:
j = 3
test[test[,1] == j, 5] = test[test[,1] == j,2] + test[test[,2] == j,1]
gives me the result:
test:
x y p d
[1,] 1 0 10 21 0
[2,] 2 3 11 12 0
[3,] 3 4 12 23 6
[4,] 3 5 13 24 7
My probblem is the following: I want to perform the operation
test[test[,1] == j,2] + test[test[,2] == j,1] only if the value of
column p and column d are different at the positions where x or y = j.
In practice, I don't want to perform the first operation because
test[2,4 is 12 and test[1,3] is 12 as well.
I tried an if statement with little success:
if(test[test[,1] == j,3] != test[test[,2] == j,4]){
test[test[,1] == j, 5] = test[test[,1] == j,2] + test[test[,2] == j,1]
} Warning message: the condition has length 1 and only the first
element will be used in: if (test[test[, 1] == j, 3] != test[test[, 2]
== j, 4]) {
Could anyone lend some advice?
Cheers,
Federico
--
Federico C. F. Calboli
Department of Epidemiology and Public Health
Imperial College, St Mary's Campus
Norfolk Place, London W2 1PG
Tel +44 (0)20 7594 1602 Fax (+44) 020 7594 3193
f.calboli [.a.t] imperial.ac.uk
f.calboli [.a.t] gmail.com
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Petr Pikal
[EMAIL PROTECTED]
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Re: [R] Plotting a count process
Now my problem is solved, i thinked a while about it and rearanged my plot in the following way for everybody how is interested x-0:3 y-c(0,5,8,3) dates-c(,01.01.05,08.01.05,15.01.05) plot(x,cumsum(y),type=p,axes=FALSE,xlab=Date,ylab=Failure Number,pch=20) axis(side = 1,0:3 ,labels = dates) axis(side = 2) box() i-seq(along=x) segments(x[i],cumsum(y)[i],x[i+1],cumsum(y)[i]) segments(x[length(x)],cumsum(y)[length(y)],x[length(x)]+1,cumsum(y)[length(y)]) regards andreas [EMAIL PROTECTED] wrote: Thank you for your advice, but this is not the exaxt thing i'm looking for http://robotics.caltech.edu/~zoran/Research/poisson/img1.png this picture gives an example what i want to get. instead of t0, t1, t2, i want to draw my dates. In my description i forgot the the horizontal line, which indicates the time between two dates each, sorry for that. regards andreas Dieter Menne wrote: voodooochild at gmx.de writes: i want to plot a count process in the following way, but i don't know how i can do that. i have data for example x-(0,2,6,2,8,4,.) and dates y which is a vector of weekly dates for example (01/01/06, 08/01/06, 15/01/06, 22/01/06, ), now i want to plot the y's an the horizontal axis. On each date the count process jumps upwards 1 unit, so the vertical axis is 0, 1, 2, 3, .. the distance between the dates is shown in vector x, so for example the distance between 08/01/06 and 15/01/06 should be 2. maybe i can use some times series functions for doing this? If I understand you correctly, this means plotting equidistant point against the cumulative sum. Forgetting about the dates now, this would do it. x = floor(pmax(rnorm(30,5,2),1)) xcum = cumsum(x) plot(xcum,1:30) Dieter __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] echo output to screen
Is something like this what you want?
load_and_describe - function(pkg) {
+ eval(substitute(library(pkg)))
+ packageDescription(pkg)
+ }
load_and_describe(e1071)
Package: e1071
Version: 1.5-12
Date: 2006-01-11
Title: Misc Functions of the Department of Statistics (e1071), TU Wien
Depends: class
Imports: graphics, stats
Suggests: cluster, mlbench, nnet, randomForest, rpart, SparseM, xtable
Author: Evgenia Dimitriadou, Kurt Hornik, Friedrich Leisch, David
Meyer, and Andreas Weingessel
Maintainer: Friedrich Leisch [EMAIL PROTECTED]
Description: Functions for latent class analysis, short time Fourier
transform, fuzzy clustering, support vector machines, shortest
path computation, bagged clustering, naive Bayes classifier,
...
License: GPL version 2. See COPYRIGHT.svm.cpp for the copyright of the
svm C++ code.
SaveImage: no
LazyLoad: yes
Packaged: Wed Jan 11 17:37:06 2006; leisch
Built: R 2.2.1; i386-pc-mingw32; 2006-01-12 09:52:56; windows
Andy
From: Chun-Ying Lee
On Thu, 09 Feb 2006 10:02:49 +0100, Uwe Ligges wrote
Chun-Ying Lee wrote:
Hi all,
I want to echo output to screen before next step,
like the following when i type library(pkname),
library(pkname)
a few description about the package
how should I do to get this?
?cat
I know the use of cat
but I mean that the description appear automatically
when I type library(pkname)
Uwe Ligges
Thanks in advanced!!
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Re: [R] Using R to process spectroscopic data
In the biophysics group of Vrije Universiteit Amsterdam we are working on an R package implementing a problem solving environment for multi-way spectroscopic modeling. We do not have a public version yet, but one will be made available in the future. We plan to describe the package at useR2006. If you are interested in the sort of (parametric model-based) analysis we are doing, you can see some project documentation at http://www.nat.vu.nl/comp/proj4.html. To reply to one of your questions, for determination of the optimal number of spectrally distinct components, you could simply take the SVD of your measurements and plot the singular values. The number of values that stand out may be used as an estimate of the number of components. Feel free to contact me for more information. We look forward to providing a complete and powerful package soon! Katharine Mullen Department of Physics and Astronomy Faculty of Sciences Vrije Universiteit Amsterdam de Boelelaan 1081 1081 HV Amsterdam The Netherlands room: T.1.06 tel: +31 205987870 fax: +31 205987992 e-mail: [EMAIL PROTECTED] http://www.nat.vu.nl/~kate/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] about Cox-Box transformation
Dear R-users, I am using R version 1.8.0-1 under Suse 8.2. I need to use the boxcox command because I want to apply a Cox-Box transformation to a vector of rainfall values. Within the libraries, the MASS library is present, but I don't know whether this means that is automatically installed or not. The command doesn't work. What do I have to do in order to make it working? Is just a problem of installation or simply of recalling the right command? thank you for your help Stefano __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] about Cox-Box transformation
On Thu, 9 Feb 2006, Stefano Sofia wrote: Dear R-users, I am using R version 1.8.0-1 under Suse 8.2. That is *really* old. I need to use the boxcox command because I want to apply a Cox-Box transformation to a vector of rainfall values. Within the libraries, the MASS library is present, but I don't know whether this means that is automatically installed or not. The command doesn't work. What do I have to do in order to make it working? Is just a problem of installation or simply of recalling the right command? library(MASS), I presume. -- Brian D. Ripley, [EMAIL PROTECTED] 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] about Cox-Box transformation
Hi
1. upgrade
2. read Introduction to R shipped with the distribution
3. read documentation to MASS
4. packages not libraries
5. use library(MASS) to make functions from MASS package available
6. now you can use boxcox() but not on vectors AFAIK
probably not completely correct but this
box.cox - function(x, lambda,inv=F)
{ if (!inv)
{if(missing(lambda))
log(x)
else (x^lambda - 1)/lambda}
else (lambda*x+1)^(1/lambda)
}
you can use to perform Box-Cox transformation on vectors.
HTH
Petr
On 9 Feb 2006 at 11:51, Stefano Sofia wrote:
From: Stefano Sofia [EMAIL PROTECTED]
To: r-help@stat.math.ethz.ch
Date sent: Thu, 09 Feb 2006 11:51:02 +
Subject:[R] about Cox-Box transformation
Dear R-users,
I am using R version 1.8.0-1 under Suse 8.2.
I need to use the boxcox command because I want to apply a Cox-Box
transformation to a vector of rainfall values. Within the libraries,
the MASS library is present, but I don't know whether this means that
is automatically installed or not. The command doesn't work. What do I
have to do in order to make it working? Is just a problem of
installation or simply of recalling the right command?
thank you for your help
Stefano
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Petr Pikal
[EMAIL PROTECTED]
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Re: [R] writing a file using both cat() and paste()
With regards to the saving bit, you might want to try dput() or save()
as well.
On Thu, 2006-02-09 at 19:29 -0500, Jim Lemon wrote:
Taka Matzmoto wrote:
Hi R users
I like to create a ASCII type file using cat() and paste()
x - round(runif(30),3)
cat(vector =( , paste(x,sep=), )\n, file = vector.dat,sep=,)
when I open vector.dat it was a long ugly file
vector =(
,0.463,0.515,0.202,0.232,0.852,0.367,0.432,0.74,0.413,0.022,0.302,0.114,0.583,0.002,0.919,0.066,0.829,0.405,0.363,0.665,0.109,0.38,0.187,0.322,0.582,0.011,0.586,0.112,0.873,0.671,
)
Also there was some problems right after opening parenthesis and before the
closing parenthesis. Two comma were there
I like to to have a nice formatted one like below. That is, 5 random values
per a line
vector =( 0.463,0.515,0.202,0.232,0.852,
0.367,0.432,0.74,0.413,0.022,
0.302,0.114,0.583,0.002,0.919,
0.066,0.829,0.405,0.363,0.665,
0.109,0.38,0.187,0.322,0.582,
0.011,0.586,0.112,0.873,0.671)
First, you might want to avoid using vector, as that is the name of an
R function. Say you have a 30 element data vector as above. If you
wanted to write a fairly general function to do this, here is a start:
vector2file-function(x,file=,values.per.line=5) {
if(nchar(file)) sink(file)
cat(deparse(substitute(x)),-c(\n)
xlen-length(x)
for(i in 1:xlen) {
cat(x[i])
if(ixlen) cat(,)
if(i%%values.per.line == 0) cat(\n)
}
cat())
if(i%%values.per.line) cat(\n)
if(nchar(file))sink()
}
Jim
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[R] logLik == -Inf in gls
I am trying to fit a generalised least squares model using gls in the nlme package. The model seems to fit very well when I plot the fitted values against the original values, and the model parameters have quite narrow confidence intervals (all are significant at p5%). The problem is that the log likelihood is always given as -Inf. This doesn't seem to make sense because the model seems to fit my data so well. I have checked that the residuals are stationary using an adf test. I can't work out whether - the model really doesn't fit at all - there is something in my data that stops the implementation of logLik working correctly (the -Inf value says the calculation hasn't worked) Possible causes are: - There are lots of NAs in my data (model and response variables) - There is some autocorrelation in the data that is not accounted for by the model (most is accounted for). But, I've tried recreating the problem using a simpler data set, and have never found the same problem. The command I use to fit the model is... result2 - gls(lci4150 ~ propCapInStomachs + temperature + as.factor(monthNumber) + lagLci1 + lagcap1 + lagcap2, data = monthly, subset = subset1985, na.action = na.approx, weights = varFixed( ~ 1/numob4150) ) The output I get is... Generalized least squares fit by REML Model: lci4150 ~ propCapInStomachs + temperature + as.factor(monthNumber) + lagLci1 + lagcap1 + lagcap2 Data: monthly Subset: subset1985 AIC BIC logLik Inf Inf -Inf Variance function: Structure: fixed weights Formula: ~1/numob4150 Coefficients: Value Std.Error t-value p-value (Intercept) -0.3282412 0.5795665 -0.566356 0.5717 propCapInStomachs 0.0093283 0.0039863 2.340107 0.0202 temperature 0.4342514 0.1526104 2.845490 0.0048 as.factor(monthNumber)2 0.3990717 0.3869991 1.031195 0.3036 as.factor(monthNumber)3 1.3788334 0.3675690 3.751223 0.0002 as.factor(monthNumber)4 1.4037195 0.3857764 3.638686 0.0003 as.factor(monthNumber)5 0.9903316 0.3436177 2.882074 0.0043 as.factor(monthNumber)6 0.3453741 0.3043698 1.134719 0.2577 as.factor(monthNumber)7 0.3948442 0.3035142 1.300909 0.1946 as.factor(monthNumber)8 0.5021812 0.3532413 1.421638 0.1565 as.factor(monthNumber)9 -0.0794319 0.3598981 -0.220707 0.8255 as.factor(monthNumber)10 0.3536805 0.3790538 0.933061 0.3518 as.factor(monthNumber)11 0.7874834 0.3557116 2.213826 0.0278 as.factor(monthNumber)12 0.1854279 0.3178320 0.583415 0.5602 lagLci1 0.5488437 0.0576144 9.526151 0. lagcap1 0.0110994 0.0043669 2.541714 0.0117 lagcap2 -0.0088080 0.0041099 -2.143127 0.0332 Does anyone have any suggestions of how I can get a meaningful value for logLik? Or some other way that I can compare models. Thankyou, Lillian. -- Lillian Sandeman PhD Student School of Biological Sciences University of Aberdeen AB24 2TZ Tel.: 01224 272648 E-mail: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] about Cox-Box transformation
On Thu, 9 Feb 2006, Petr Pikal wrote:
Hi
1.upgrade
2.read Introduction to R shipped with the distribution
3.read documentation to MASS
4.packages not libraries
5.use library(MASS) to make functions from MASS package available
6.now you can use boxcox() but not on vectors AFAIK
You can by
boxcox(y ~ 1)
but car's box.cox does similar things. (I did not mention that as adding
packages to R 1.8.0 is unlikely to be easy.)
probably not completely correct but this
box.cox - function(x, lambda,inv=F)
{ if (!inv)
{if(missing(lambda))
log(x)
else (x^lambda - 1)/lambda}
else (lambda*x+1)^(1/lambda)
}
you can use to perform Box-Cox transformation on vectors.
HTH
Petr
On 9 Feb 2006 at 11:51, Stefano Sofia wrote:
From: Stefano Sofia [EMAIL PROTECTED]
To: r-help@stat.math.ethz.ch
Date sent:Thu, 09 Feb 2006 11:51:02 +
Subject: [R] about Cox-Box transformation
Dear R-users,
I am using R version 1.8.0-1 under Suse 8.2.
I need to use the boxcox command because I want to apply a Cox-Box
transformation to a vector of rainfall values. Within the libraries,
the MASS library is present, but I don't know whether this means that
is automatically installed or not. The command doesn't work. What do I
have to do in order to make it working? Is just a problem of
installation or simply of recalling the right command?
thank you for your help
Stefano
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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Re: [R] getting strata/cluster level values with survey package?
Try the examples here: ?ftable.svystat On 8/02/2006 12:23 p.m., Jeff D. Hamann wrote: First, I appoligise for the rooky question, but... I'm trying to obtain standard errors, confidence intervals, etc. from a sample design and have been trouble getting the results for anything other than the basic total or mean for the overall survey from the survey package. For example, using the following dataset, strata,cluster,vol A,1,18.58556192 A,1,12.55175443 A,1,21.65882438 A,1,17.11172946 A,1,15.41713348 A,2,13.9344623 A,2,17.13104821 A,2,14.6806479 A,2,14.68357291 A,2,18.86017714 A,2,20.67642515 A,2,15.15295351 A,2,13.82121102 A,2,12.9110477 A,2,14.83153677 A,2,21.90772687 A,3,18.69795427 A,3,18.45636428 A,3,15.77175793 A,3,15.54715217 A,3,20.31948393 A,3,19.26391445 A,3,15.54750775 A,3,19.18724018 A,4,12.89572151 A,4,12.92047701 A,4,12.64958757 A,4,19.85888418 A,4,19.64057669 A,4,19.19188964 A,4,18.81619298 A,4,21.73670878 A,5,15.99430802 A,5,18.6517 A,5,21.80441654 A,5,14.22081904 A,5,16.01576433 A,5,14.92497202 A,5,17.95123218 A,5,19.82027165 A,5,19.35698273 A,5,19.10826519 B,6,13.40892677 B,6,14.3956207 B,6,13.82113391 B,6,16.37338569 B,6,19.70159575 B,7,14.74334178 B,7,16.55125245 B,7,12.38329798 B,7,18.16472408 B,7,16.32938475 B,7,16.06465494 B,7,12.63086062 B,7,14.46114813 B,7,21.90134013 B,7,13.81025827 B,7,15.85805494 B,7,20.18195326 B,8,19.05120792 B,8,12.83856639 B,8,12.61360139 B,8,21.30434314 B,8,14.19960469 B,8,17.38397826 B,8,15.66477339 B,8,22.07182834 B,8,12.07487394 B,8,20.36357359 B,8,20.2543677 B,9,14.44499362 B,9,17.77235228 B,9,13.01620902 B,9,18.10976359 B,10,18.22350661 B,10,18.41504728 B,10,17.94735486 B,10,18.39173938 B,10,14.21729704 B,10,16.95753684 B,10,21.11643087 B,10,16.09688752 B,10,19.54707452 B,10,22.00450065 B,10,15.15308873 B,10,14.72488972 B,10,17.65280737 B,10,14.61615255 B,10,12.89525607 B,11,22.35831089 B,11,18.0853187 B,11,22.12815791 B,11,17.74562214 B,11,21.45724242 B,11,20.57933779 B,11,19.97397415 B,11,16.34967424 B,12,22.14385376 B,12,17.82816113 B,12,18.37056381 B,12,16.13152759 B,12,22.06764318 B,12,12.80924472 B,12,18.95522175 B,13,20.40554286 B,13,19.72951878 C,14,15.51581 C,14,15.4836358 C,14,13.35882363 C,14,13.16072916 C,14,21.69168971 C,14,19.09686303 C,14,14.47450457 C,14,12.04870424 C,14,13.33096141 C,14,17.38388981 C,14,16.29015289 C,14,16.32707754 C,14,16.2784054 C,15,15.0170597 C,15,14.95767365 C,15,15.20739614 C,15,22.10458509 C,15,12.3362457 C,15,19.87895753 C,15,18.8363682 C,15,16.43738666 C,15,12.84570744 C,15,15.99869357 C,15,14.42551321 C,15,13.63489872 C,15,15.67179885 C,16,14.61700901 C,16,14.64864676 C,16,14.13014582 C,16,21.7637441 C,16,20.66825543 C,16,17.05977818 C,16,17.80118916 C,16,15.16641698 where this is read into stand.data. When I use the following survey designs, srv1 - svydesign(ids=~1, strata=~strata, data=stand.data ) or, srv1 - svydesign(ids=~cluster, strata=~strata, data=stand.data ) with, print( svytotal( ~vol, srv1 ) ) I only obtain the total, print( svytotal( ~vol, srv1 ) ) total SE vol 2377 34.464 or worse, print( svytotal( ~vol + strata, srv1 ) ) total SE vol 2377.0 34.464 strataA 42.0 0.000 strataB 64.0 0.000 strataC 34.0 0.000 which reports the number of observations in each of the strata. I'm sure this is a RTFM question, but I just need a start. The size of each plot is 0.04 units (hectares) and I want to be able to quickly examine working up each sample with and without clusters (this is going to be part of a larger simulation study). I'm trying to not use SAS for this and hate to admit defeat. Thanks, Jeff. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- James Reilly Department of Statistics, University of Auckland Private Bag 92019, Auckland, New Zealand __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] logLik == -Inf in gls
Please do not repeatedly post the same thing. This is the same as https://stat.ethz.ch/pipermail/r-help/2006-February/086381.html (except you remembered to sign that one). You are fitting a weighted not a generalised least squares model: lm() will do that. On Thu, 9 Feb 2006, [EMAIL PROTECTED] wrote: I am trying to fit a generalised least squares model using gls in the nlme package. The model seems to fit very well when I plot the fitted values against the original values, and the model parameters have quite narrow confidence intervals (all are significant at p5%). The problem is that the log likelihood is always given as -Inf. This doesn't seem to make sense because the model seems to fit my data so well. I have checked that the residuals are stationary using an adf test. I can't work out whether - the model really doesn't fit at all - there is something in my data that stops the implementation of logLik working correctly (the -Inf value says the calculation hasn't worked) Possible causes are: - There are lots of NAs in my data (model and response variables) - There is some autocorrelation in the data that is not accounted for by the model (most is accounted for). But, I've tried recreating the problem using a simpler data set, and have never found the same problem. Well, how then do you expect us to be able to recreate it? As a pure guess, look at your weights. Are any numob4150 zero? The command I use to fit the model is... result2 - gls(lci4150 ~ propCapInStomachs + temperature + as.factor(monthNumber) + lagLci1 + lagcap1 + lagcap2, data = monthly, subset = subset1985, na.action = na.approx, weights = varFixed( ~ 1/numob4150) ) The output I get is... Generalized least squares fit by REML Model: lci4150 ~ propCapInStomachs + temperature + as.factor(monthNumber) + lagLci1 + lagcap1 + lagcap2 Data: monthly Subset: subset1985 AIC BIC logLik Inf Inf -Inf Variance function: Structure: fixed weights Formula: ~1/numob4150 Coefficients: Value Std.Error t-value p-value (Intercept) -0.3282412 0.5795665 -0.566356 0.5717 propCapInStomachs 0.0093283 0.0039863 2.340107 0.0202 temperature 0.4342514 0.1526104 2.845490 0.0048 as.factor(monthNumber)2 0.3990717 0.3869991 1.031195 0.3036 as.factor(monthNumber)3 1.3788334 0.3675690 3.751223 0.0002 as.factor(monthNumber)4 1.4037195 0.3857764 3.638686 0.0003 as.factor(monthNumber)5 0.9903316 0.3436177 2.882074 0.0043 as.factor(monthNumber)6 0.3453741 0.3043698 1.134719 0.2577 as.factor(monthNumber)7 0.3948442 0.3035142 1.300909 0.1946 as.factor(monthNumber)8 0.5021812 0.3532413 1.421638 0.1565 as.factor(monthNumber)9 -0.0794319 0.3598981 -0.220707 0.8255 as.factor(monthNumber)10 0.3536805 0.3790538 0.933061 0.3518 as.factor(monthNumber)11 0.7874834 0.3557116 2.213826 0.0278 as.factor(monthNumber)12 0.1854279 0.3178320 0.583415 0.5602 lagLci1 0.5488437 0.0576144 9.526151 0. lagcap1 0.0110994 0.0043669 2.541714 0.0117 lagcap2 -0.0088080 0.0041099 -2.143127 0.0332 Does anyone have any suggestions of how I can get a meaningful value for logLik? Or some other way that I can compare models. Thankyou, Lillian. -- Brian D. Ripley, [EMAIL PROTECTED] 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] lme syntax for PB examples
Paul Cossens said the following on 2006-02-09 06:21: Hi Harold, Thanks for your reply. I had already looked at all the reading material you suggested but updated to the latest Matrix as recommneded then spent all day trying to figure out what is happening. I worked through the problems and give my workings below that others may find useful. (My notation is to use lme to show lme commands and lmer to show lmer commands. I worked on two sessions in parallel. My comments are preceded by double hashes '##' and questions '##??'. I haven't included the datasets.) I have a couple of comments and outstanding issues: 1. In the Pixel data set and formulas I think the formulas are printed incorrectly in the book as some use 'I(day^2)' while others use just 'day^2'. I have used 'I(day^2)'. I'm not sure why the I() function is used. In the fm4Pixel example below the answers don't match up exactly but are close. The lme example is fm1Pixel-lme(pixel~day+I(day^2),data=Pixel,random = list(Dog=~day ,Side=~1)) fm5Pixel - update(fm1Pixel,pixel ~ day + I(day^2) + Side) which I have converted to lmer: fm4Pixel - lmer(pixel ~ day + I(day^2) +Side +(day|Dog), data = Pixel) The t-values for Side are close (sse below) but different enough to wonder if I am still doing something wrong? It's wrong. Try fm6Pixel - lmer(pixel ~ day + I(day^2) + Side + (day|Dog) + (1|Side:Dog), data = Pixel) 2. To me the specification description in the R-News article is confusing as it seems to suggest that nesting does not need to be completely specified if the groupings and nestings are clear in data set. Prof Bates article in R news vol 5/1 P 30 states It happens in this case that the grouping factors 'id' and 'sch' are not nested but if they were nested there would be no change in the model specification If the lme formula is fm1Oxide-lme(Thickness~1,Oxide) I have found the formula lmer parlance should be: 'fm1Oxide-lmer(Thickness~ (1|Lot)+(1|Lot:Wafer),data=Oxide)' not 'fm1Oxide-lmer(Thickness~ (1|Lot)+(1|Wafer),data=Oxide)' as the article reads to me. In other words you always need to explicitly specify nesting levels. 3. I still can't figue out how to replicate the lme formula fm2Oxide-update(fm1Oxide,random =~1|Lot) i.e formula(fm2Oxide) Thickness ~ 1 If I simply drop the Lot:Wafer term as in 'fm2Oxide-lmer(Thickness~ (1|Lot),data=Oxide)' I get the error 'Error in x[[3]] : object is not subsettable' what's the solution? fm3Oxide - lmer(Thickness ~ 1 + (1|Lot), data = Oxide) This seems to be a bug in `lmer', since one doesn't have to specifiy the intercept explicitly in e.g. lmer(Thickness ~ (1|Lot) + (1|Wafer), data = Oxide) HTH, Henric I'd be interested to read you article for further insights. Thanks Paul # #Oxide # PB(2000) p167-170 #NLME lme example lmedata(Oxide) lmeformula(Oxide) lmeThickness ~ 1 | Lot/Wafer lmefm1Oxide-lme(Thickness~1,Oxide) lme fm1Oxide Linear mixed-effects model fit by REML Data: Oxide Log-restricted-likelihood: -227.0110 Fixed: Thickness ~ 1 (Intercept) 2000.153 Random effects: Formula: ~1 | Lot (Intercept) StdDev:11.39768 Formula: ~1 | Wafer %in% Lot (Intercept) Residual StdDev:5.988802 3.545341 Number of Observations: 72 Number of Groups: Lot Wafer %in% Lot 8 24 lme intervals(fm1Oxide, which = var-cov) Approximate 95% confidence intervals Random Effects: Level: Lot lower est.upper sd((Intercept)) 6.38881 11.39768 20.33355 Level: Wafer lower est.upper sd((Intercept)) 4.063919 5.988802 8.825408 Within-group standard error: lower est.upper 2.902491 3.545341 4.330572 fm2Oxide-update(fm1Oxide,random =~1|Lot) lme fm2Oxide Linear mixed-effects model fit by REML Data: Oxide Log-restricted-likelihood: -245.5658 Fixed: Thickness ~ 1 (Intercept) 2000.153 Random effects: Formula: ~1 | Lot (Intercept) Residual StdDev:11.78447 6.282416 Number of Observations: 72 Number of Groups: 8 lmeintervals(fm2Oxide, which = var-cov) Approximate 95% confidence intervals Random Effects: Level: Lot lower est.upper sd((Intercept)) 6.864617 11.78447 20.23035 Within-group standard error: lower est.upper 5.283116 6.282416 7.470733 lme coef(fm1Oxide, level=1) (Intercept) 11996.689 21988.931 32001.022 41995.682 52013.616 62019.561 71991.954 81993.767 coef(fm1Oxide, level=1) (Intercept) 11996.689 21988.931 32001.022 41995.682 52013.616 62019.561 71991.954 81993.767 coef(fm1Oxide, level=2) (Intercept) 1/12003.235 1/21984.730 1/32001.146 2/11989.590
Re: [R] about Cox-Box transformation
Paulo, thank you for the straightforward hint. But then, I should use the Box-Cox transformation to a set of data, whose class at the moment is data.frame. The help says only lm and aov objects can be handled. What should I do? thank you Stefano On Thu, 2006-02-09 at 10:56 -0200, Paulo Justiniano Ribeiro Jr wrote: first load the package with: require(MASS) and then use the boxcox() function On Thu, 9 Feb 2006, Stefano Sofia wrote: Date: Thu, 09 Feb 2006 11:51:02 + From: Stefano Sofia [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch Subject: [R] about Cox-Box transformation Dear R-users, I am using R version 1.8.0-1 under Suse 8.2. I need to use the boxcox command because I want to apply a Cox-Box transformation to a vector of rainfall values. Within the libraries, the MASS library is present, but I don't know whether this means that is automatically installed or not. The command doesn't work. What do I have to do in order to make it working? Is just a problem of installation or simply of recalling the right command? thank you for your help Stefano __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Paulo Justiniano Ribeiro Jr LEG (Laboratório de Estatística e Geoinformação) Departamento de Estatística Universidade Federal do Paraná Caixa Postal 19.081 CEP 81.531-990 Curitiba, PR - Brasil Tel: (+55) 41 3361 3573 Fax: (+55) 41 3361 3141 e-mail: [EMAIL PROTECTED] http://www.est.ufpr.br/~paulojus __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] font size/disappearing labels
I am sorry if you get this email twice, but it did not show up in the digest nor on the web archive, so I am taking the chance of resending it. I am using vioplot to make nice boxplots, which I am outputting to postscript. I am using the paper=special and width and height to get the graphs to look nice. I do however have a problem with the size of the labels and titles. When I set fontsize as an option to the postscript call too high, one of the labels disappear, although there is enough space for it (imo, that is). This I have understood is an effect of the system trying to avoid overlapping numbers. Is there a way I can override this function though? Can I force it to show all of the labels, although they might be too close? Karin -- Karin Lagesen, PhD student [EMAIL PROTECTED] http://www.cmbn.no/rognes/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] bootstrapping lambda values from projections matrices
Dear all,
I'm working with a population projections matrix model from demographic
data. The dominant eigenvalue of the matrix is the growth rate of the
population (lambda). I would like to estimate confidence intervals for the
lambda values with bootstrap.
The function for calculating the eigenvalue I wrote like this:
mat.fun - function(d,i){
mat-matrix(c(0,
sum(d$klyear1[i]==1d$classyear2[i]==2)/sum(d$classyear1[i]==1),
sum(d$classyear1[i]==1d$classyear2[i]==3)/sum(d$classyear1[i]==1), 0,
sum(d$classyear1[i]==2d$classyear2[i]==2)/sum(d$classyear1[i]==2),
sum(d$classyear1[i]==2d$classyear2[i]==3)/sum(d$classyear1[i]==2),
sum(d$classyear1[i]==0d$classyear2[i]==1)/sum(d$classyear1[i]==3),
sum(d$classyear1[i]==3d$classyear2[i]==2)/sum(d$classyear1[i]==3),
sum(d$classyear1[i]==3d$classyear2[i]==2)/sum(d$classyear1[i]==3),
sum(d$classyear1[i]==3d$classyear2[i]==3)/sum(d$classyear1[i]==3)),ncol=3)
abs(eigen(mat,only.values=T)$values[1])
}
Now, in the pooled matrix from all years I would like to sample in a way
that the number of bootstrap samples taken from each year is equal to the
number of data points from each year. Therefore I'm defining strata=year.
boot1 - boot(myfile, mat.fun, 5000, strata=myfile$year); boot1
Is this the correct way to do it or did I misunderstand the
strata-argument? I checked in Davison, A.C. and Hinkley, D.V. (1997), but
I'm still not quite sure.
Thanks very much in advance for your help!
Sincerely,
Saskia Sandring
_
Saskia Sandring
Avd. för växtekologi, Evolutionsbiologiskt centrum, Uppsala universitet
Dept. of Plant Ecology, Evolutionary Biology Centre, Uppsala University
Villavägen 14 tel: 018-471 2870 (int +46 18 4712870)
SE-752 36 Uppsala fax: 018-55 34 19 (int +46 18 553419)
SWEDEN email: [EMAIL PROTECTED]
http://www.vaxtbio.uu.se/resfold/sandring.htm
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Re: [R] adding variable into dataframe by indice
Thank you for your assistance. I find that the by using the list I learn
something new everytime.
--Adrian
Hi
not sure if I understand correctly but table() can be used
ttt - table(asubs112$fir)
prop - ttt/nrow(asubs112)
asubs112$prop -
prop[match(asubs112$first_drink,as.numeric(names(prop)))]
asubs112
IND_ID rs1042364 first_drink prop
2 11 (1,2) 7 0.333
5 41 (1,2) 11 0.111
6 51 (1,2) 7 0.333
7 61 (1,1) 7 0.333
8 71 (1,1) 12 0.222
10 91 (1,1) 6 0.111
11101 (1,2) 5 0.111
12111 (1,2) 13 0.111
14131 (1,2) 12 0.222
HTH
Petr
On 8 Feb 2006 at 9:40, Adrian Katschke wrote:
Date sent: Wed, 8 Feb 2006 09:40:43 -0800 (PST)
From:Adrian Katschke [EMAIL PROTECTED]
To: RHelp r-help@stat.math.ethz.ch
Subject: [R] adding variable into dataframe by indice
R-Helpers,
I am trying to insert a value into a dataframe. This value is a
proportion calculated by counting the number of those individuals
with that value and then inserting the proportion at the end of the
dataframe to only those individuals with the given value. The
problem I am running into is that the proportions are not being
attached to only those individuals with the specified value for
that
proportion.
Below is an example of the code that I am using. The data is made
up
for the dataframe. Should give you an idea, but the original has
'NA' in many rows. The original data is what is reported in the
output below.
#Read in Data
age.int - data.frame(IND_ID = seq(1, 140, 10), rs1042364 =
sample( c((1,1),(1,2),(2,2)),14,replace = T), first_drink =
sample(5:17,14,replace = T))
asubs112 - subset(age.int, rs1042364 != (2,2))
ages112 - sort(unique(na.omit(asubs112$first_drink)))
for ( i in ages112) {
indce - which(na.omit(asubs112$first_drink == i))
prop - length(indce)/nrow(asubs112)
asubs112[indce,4] - prop
asubs112[indce,]
}
Below is the output that I get from the script above. Notice the
proportion for the first NA but not any of the others. Not sure
what
I am doing wrong, any suggestions are a big help.
TIA,
Adrian
asubs112[1:50,]
IND_ID rs1042364 first_drink age_int V5
4 10008007 (1,2) NA 16 0.003891051
6 10013012 (1,2) 13 14 0.116731518
7 10015006 (1,2) 12 17 0.105058366
8 10015007 (1,1) 12 16 0.105058366
10 10021009 (1,2) NA 15 NA
14 10039036 (1,2) NA 15 NA
15 10039037 (1,2) NA 13 NA
17 10045005 (1,2) 13 17 0.116731518
18 10045014 (1,2) 13 14 0.116731518
21 10055022 (1,2) NA 15 NA
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Petr Pikal
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[R] Tranferring R results to word prosessors
I have just started looking at R, and are getting more and more irritated at myself for not having done that before. However, one of the things I have not found in the documentation is some way of preparing output from R for convenient formatting into something like MS Word. An example: If you use summary(lm()) you get nice output. However, if you try to paste that output into the word processor, all the text elements are separated by blanks, and that is not optimal for the creation of a table (in the word processing sense). Is there an option to generate tab-separated output in R ? That would solve the problem. Tom ++ | Tom Backer Johnsen, Psychometrics Unit, Faculty of Psychology | | University of Bergen, Christies gt. 12, N-5015 Bergen, NORWAY | | Tel : +47-5558-9185Fax : +47-5558-9879 | | Email : [EMAIL PROTECTED]URL : http://www.galton.uib.no/ | ++ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Tranferring R results to word prosessors
Well, I don't know if it can be used with Word or not, but you might consider Sweave for use with LaTeX. Maybe if you use the sink() command this might work, but I haven't tried it. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Tom Backer Johnsen Sent: Thursday, February 09, 2006 9:41 AM To: r-help@stat.math.ethz.ch Subject: [R] Tranferring R results to word prosessors I have just started looking at R, and are getting more and more irritated at myself for not having done that before. However, one of the things I have not found in the documentation is some way of preparing output from R for convenient formatting into something like MS Word. An example: If you use summary(lm()) you get nice output. However, if you try to paste that output into the word processor, all the text elements are separated by blanks, and that is not optimal for the creation of a table (in the word processing sense). Is there an option to generate tab-separated output in R ? That would solve the problem. Tom ++ | Tom Backer Johnsen, Psychometrics Unit, Faculty of Psychology | | University of Bergen, Christies gt. 12, N-5015 Bergen, NORWAY | | Tel : +47-5558-9185Fax : +47-5558-9879 | | Email : [EMAIL PROTECTED]URL : http://www.galton.uib.no/ | ++ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Tranferring R results to word prosessors
In Word use a fixed font such as Courier rather than a proportional font and it will look ok. On 2/9/06, Tom Backer Johnsen [EMAIL PROTECTED] wrote: I have just started looking at R, and are getting more and more irritated at myself for not having done that before. However, one of the things I have not found in the documentation is some way of preparing output from R for convenient formatting into something like MS Word. An example: If you use summary(lm()) you get nice output. However, if you try to paste that output into the word processor, all the text elements are separated by blanks, and that is not optimal for the creation of a table (in the word processing sense). Is there an option to generate tab-separated output in R ? That would solve the problem. Tom ++ | Tom Backer Johnsen, Psychometrics Unit, Faculty of Psychology | | University of Bergen, Christies gt. 12, N-5015 Bergen, NORWAY | | Tel : +47-5558-9185Fax : +47-5558-9879 | | Email : [EMAIL PROTECTED]URL : http://www.galton.uib.no/ | ++ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Tranferring R results to word prosessors
Le 09.02.2006 15:41, Tom Backer Johnsen a écrit : I have just started looking at R, and are getting more and more irritated at myself for not having done that before. However, one of the things I have not found in the documentation is some way of preparing output from R for convenient formatting into something like MS Word. An example: If you use summary(lm()) you get nice output. However, if you try to paste that output into the word processor, all the text elements are separated by blanks, and that is not optimal for the creation of a table (in the word processing sense). Is there an option to generate tab-separated output in R ? That would solve the problem. Tom Hi , One way could be to output in html format from R (with the R2HTML package) and then read back the html from your word processor Romain -- visit the R Graph Gallery : http://addictedtor.free.fr/graphiques mixmod 1.7 is released : http://www-math.univ-fcomte.fr/mixmod/index.php +---+ | Romain FRANCOIS - http://francoisromain.free.fr | | Doctorant INRIA Futurs / EDF | +---+ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Tranferring R results to word prosessors
Tom Backer Johnsen [EMAIL PROTECTED] wrote: [...] However, one of the things I have not found in the documentation is some way of preparing output from R for convenient formatting into something like MS Word. In case you're not talking about table-like output exclusively, reading ?Devices describes all the available kinds of graphical output. Most of these can then easily be included in MS Word. Cheers, -- Sebastian P. Luque __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] lme syntax for PB examples
HaroldD == Doran, Harold [EMAIL PROTECTED] on Wed, 8 Feb 2006 08:01:03 -0500 writes: HaroldD HaroldD A few thoughts, first, use lmer in the Matrix HaroldD package and not in lme4. Well, that's potentially misleading advice: If both lme4 and Matrix are (more or less) current, it is actually better to call library(lme4) if you want to use lmer() . A more extensive advice + explanation : - lme4 is the package you should use when using lmer(). Using Matrix *instead* works as well *currently* (and yes, *currently* lmer is in the Matrix namespace). - At the moment, lme4 is an almost empty wrapper around using package Matrix, since the C code for lmer() needs to be able to call C code inside Matrix and that is not yet portably possible. For that reason, everything for lmer() is currently inside Matrix, but that should change when R will have the infrastructure for R packages to export their C API such that other R packages can reliably use that C API. HaroldD HaroldD Last, a colleague and I have a paper in press HaroldD showing how to fit models using lme which we HaroldD submitted a year or so ago. HaroldD Since lme has evolved to lmer, we created an HaroldD appendix that translates all of our lme models to HaroldD the lmer syntax so readers can see equivalences. I HaroldD am happy to send this to you (or others) upon request. That sounds quite interesting; I'll be glad to receive it as well. Martin Maechler, ETH Zurich HaroldD http://cran.r-project.org/doc/Rnews/Rnews_2005-1.pdf HaroldD Harold __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Tranferring R results to word prosessors
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Romain Francois
Sent: Thursday, February 09, 2006 3:54 PM
To: Tom Backer Johnsen
One way could be to output in html format from R (with the R2HTML
package) and then read back the html from your word processor
Romain
If you go along the HTML path, the package xtable might be also your
friend:
library(xtable)
mymat - matrix(1:9, ncol=3)
print.xtable(xtable(mymat), type=HTML)
Hope this is useful for you,
Roland
+
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Re: [R] prehistoric versions of R -- 1995!
[Martin Maechler] 2) The oldest stuff that I have is all from 1995; Mailing lists seem to go back into 1995 too. I found a few messages from around 1994 on topics to be later found within R, but I'm not sure where I got these old messages from. I did find a message really related to R-pre-alpha, which itself quotes a message written in 1994. -- François Pinard http://pinard.progiciels-bpi.ca __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Baysian model averaging method
HI, List I want to know weather any body has used BMA Package for model averaging for prediction of future values.What are the paprmeters we have to suplly to the model. Any script for the same. thanks in advance ANIL KUMAR( METEOROLOGIST) LRF SECTION NATIONAL CLIMATE CENTER ADGM(RESEARCH) INDIA METEOROLOGICAL DEPARTMENT SHIVIJI NAGAR PUNE-411005 INDIA MOBILE +919422023277 [EMAIL PROTECTED] [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] callling R from C
Can anyone please provide me with a simple example on calling R from C? Many thanks and best wishes! GT __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] (no subject)
Hi, Can you help me please. I must developp an application with the logiciel R. It 's an application for pricing. So I see it uses the langage C and I see on the net taht it 's possible in c++. Use C++ it 's better than C , we know it. However It says to use c++ with R , we must : You need to do two things: (a) Write a wrapper to export the symbols you want to call from R as extern C. (b) Include the C++ libraries in the link to make the DLL. Suppose X.cc contains your C++ code, and X_main.cc is the wrapper, as in the example in `Writing R Extensions'. Then build the DLL by (gcc) ...\bin\R CMD SHLIB X.cc X_main.cc or (VC++, which requires extension .cpp) cl /MT /c X.cpp X_main.cpp link /dll /out:X.dll /export:X_main X.obj X_main.obj or (Borland C++, which also requires extension .cpp) bcc32 -u- -WDE X.cpp X_main.cpp and call the entry point(s) in X_R, such as X_main. Construction of static variables will occur when the DLL is loaded, and destruction when the DLL is unloaded, usually when R terminates. Note that you will not see the messages from this example in the GUI console: see the next section. This example used to be in package cxx_0.0-x.tar.gz in the src/contrib/Devel section on CRAN, and could be compiled as a package in the usual way on Windows. So it doesn't run , With C it 's ok but with c++ no no. I dont understand and don' t know how write this wraper, because Compilateur Visual C++ compile C too, so I don't need wraper? Too there is a black box used in Logiciel R it is writted in R with C it 'ok but with c++ it doesn't Can you help me please. Thank you very much [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] quote problem
Hi. I'm trying to analyse information from a large database using R. I have some problems with quotes during the generation of strings. Setting: I extract data from a lot of sampling location (chemical data on water quality) and for each location I have a date of sampling and a value. I want to put everything in a list such that for each sampling point (say OS1) I have two columns (date, time). I use the function sqlQuery from the RODBC package. Here is an example that works: OxygenMeasurements$OS1 - sqlQuery(channel, SELECT saDateTime, sdValue FROM dbo_Sample WHERE (paID = 213) AND (stCode ='OS1');) To keep the code elegant and, above all, short I try to regenerate the same function call with a different query statement for each sampling point by using the paste() function. (1) sqlquery - paste(SELECT saDateTime, sdValue FROM dbo_Sample WHERE (paID = 213) AND (stCode =' , paste(stations$stCode, sep=,) , '); , sep=) This gives a vector with the sql syntax. The following line generates the whole sqlQuery-statement. (2) queries - paste(OxygenMeasurements$, paste(stations[,1]), - sqlQuery(channel, \, paste(sqlquery) , \) , sep=) This is the result for the first two elements of 'queries': OxygenMeasurements$OS1 - sqlQuery(channel, \SELECT saDateTime, sdValue FROM dbo_Sample WHERE (paID = 213) AND (stCode ='OS1'); \) OxygenMeasurements$OS2 - sqlQuery(channel, \SELECT saDateTime, sdValue FROM dbo_Sample WHERE (paID = 213) AND (stCode ='OS2'); \) If these are evaluated ( eval(queries)) it should fill the datastructure OxygenMeasurements with the desired data. The problem: The query statement containts a string and is a string in itself. In addition elements of 'queries' are strings. R doesn't seem to be able to cope with this, since it generates \ on locations where a has to be put. Is there a way to let the paste function generate a string with in it without the \ ? In a way there are 3 nested strings and R can only cope with 2 levels (by using ' and ) in my view. Does anyone know how to put IN the string instead of \? Thanks for the feedback. Tom - Win a BlackBerry device from O2 with Yahoo!. Enter now. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Tranferring R results to word prosessors
I agree that this is the best way. I often use Courier font with font size 10 that gives very good results. On Thu, 2006-02-09 at 09:47 -0500, Gabor Grothendieck wrote: In Word use a fixed font such as Courier rather than a proportional font and it will look ok. On 2/9/06, Tom Backer Johnsen [EMAIL PROTECTED] wrote: I have just started looking at R, and are getting more and more irritated at myself for not having done that before. However, one of the things I have not found in the documentation is some way of preparing output from R for convenient formatting into something like MS Word. An example: If you use summary(lm()) you get nice output. However, if you try to paste that output into the word processor, all the text elements are separated by blanks, and that is not optimal for the creation of a table (in the word processing sense). Is there an option to generate tab-separated output in R ? That would solve the problem. Tom ++ | Tom Backer Johnsen, Psychometrics Unit, Faculty of Psychology | | University of Bergen, Christies gt. 12, N-5015 Bergen, NORWAY | | Tel : +47-5558-9185Fax : +47-5558-9879 | | Email : [EMAIL PROTECTED]URL : http://www.galton.uib.no/ | ++ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Tranferring R results to word prosessors
I have added several convenient methods for sending data directly from R to Microsoft Word (report() function) in the svViews package (SciViews bundle). However, I still have to upload it to CRAN. I do it right now. It should be available in a couple of days. Best, Philippe Grosjean Romain Francois wrote: Le 09.02.2006 15:41, Tom Backer Johnsen a écrit : I have just started looking at R, and are getting more and more irritated at myself for not having done that before. However, one of the things I have not found in the documentation is some way of preparing output from R for convenient formatting into something like MS Word. An example: If you use summary(lm()) you get nice output. However, if you try to paste that output into the word processor, all the text elements are separated by blanks, and that is not optimal for the creation of a table (in the word processing sense). Is there an option to generate tab-separated output in R ? That would solve the problem. Tom Hi , One way could be to output in html format from R (with the R2HTML package) and then read back the html from your word processor Romain __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] font size/disappearing labels
Karin == Karin Lagesen [EMAIL PROTECTED] on Thu, 09 Feb 2006 14:32:53 +0100 writes: Karin I am sorry if you get this email twice, but it did not show up in the Karin digest nor on the web archive, so I am taking the chance of resending Karin it. But it's definitely there in both the digest and the web archive; here the archive entry: https://stat.ethz.ch/pipermail/r-help/2006-February/086365.html I rather think nobody felt compelled to answer you, because you didn't follow the posting guide (see link at end of *every* R-help mesage) well (look for reproducible in the guide!). Regards, Martin Maechler, ETH Zurich __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Tranferring R results to word prosessors
Tom Backer Johnsen wrote: I have just started looking at R, and are getting more and more irritated at myself for not having done that before. However, one of the things I have not found in the documentation is some way of preparing output from R for convenient formatting into something like MS Word. Well whatever you do, don't start looking at LaTeX, because that will get you even more irritated at yourself for not having done it before. LaTeX is to Word as R is to what? SPSS? I've still not seen a pretty piece of mathematics - or even text - in Word. Barry __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Point Size in plot.cox.zph
I would like control over the point size (and the type of points) when plotting a cox.zph object, but it returns the same error as when one tries to change the y-axis. I have searched the web for an answer (and the r-help list) but to no avail. What I have done is make a blank plot and use the points command as follows: plot(time, war.zph$y[,7], type=n) points(war.zph[7], ann=F, pch = .) But this causes you to lose the spline fit and seems rather cumbersome. A way to do this using the standard plot.cox.zph framework would be very helpful. Thanks Luke -- Luke Keele Assistant Professor Dept. Of Political Science Ohio State University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Color key in Heat map
Hi all, I am trying to produce a heatmap to display clustering of similar rows in the data given below. For each given row, different colors are used to represent the corresponding column value. I want to display the values of the colors in the form of a color key added to the heatmap. Is there anyway of doing this? z[1:10,1:6] [,1][,2][,3][,4][,5][,6] [1,] 403.0 409.3 611.5 569.2 536.6 580.2 [2,] 757.3 574.4 826.7 595.3 755.2 956.0 [3,] 284.4 327.3 421.6 336.6 391.3 412.6 [4,] 2314.2 1685.3 2264.7 2204.1 2233.1 2458.4 [5,] 1574.5 1273.0 1484.6 1321.2 1474.7 1774.1 [6,] 2333.7 1796.8 2464.5 2372.5 2095.9 2735.7 [7,] 13673.9 11463.9 13624.7 14513.9 12934.1 16293.1 [8,] 17778.8 15248.8 19977.2 19613.4 18609.1 18988.2 [9,] 31056.6 24869.9 30773.4 32918.6 34412.1 33954.6 [10,]36.369.892.052.057.364.9 Also, is it possible to get the order in which the rows will be clustered , starting with the first rows joined into a group and then followed by other grps added. I thought i could extract the order by using $rowInd, but looks like it's the order in which the rows are reordered in the map. Please let me know how to do this. Thanks, Vasu. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] how to clear the last error?
Hello, I would like to clear the last error that I get with geterrmessage(). Not even rm(list=ls()) clears it. Can I set it to NULL somehow? Thank you, Adrian __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] putting text in the corner
I want to write some text in a corner of my plot. Is it possible to get the xlim and ylim of an open window? Or is there anything similar like legend(x=bottomright, inset=0.01,legend=...) for text(x=1,y=2, test) Thomas __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] How to calculate the generalization error of random forests?
Hi, Perhaps this is not the proper place to ask this question but I am out of options, therefore I apologize in advance. I want to know how the (upper bound?) generalization error of the random forest is determined using the out-of-bag estimate. I read in Breiman's paper that s and p determine the generalization error: p(1-s^2)/s^2. Does s stands for the strength of the individual tree or of the entire ensemble? p stands for the correlation between the trees. If I have, let's say, built 3 trees in my forest and I know for each tree the instances that were left out during training, how do I calculate s and p, so I can calculate the error? Thanks in advance, Martin __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Tranferring R results to word prosessors
In follow up to Harold's thought of using LaTeX, I have an approach when the use of nicely formatted tables is required in a document where LaTeX is not being used for the entire document. In other words, where you need to use Word, OO.org's Writer or similar application for the majority of the document body. This involves outputting R results to LaTeX table code in a text file, processing the file with 'latex' and 'dvips' and creating an EPS file. Of course, the LaTeX text file is fully complete with preamble, etc. One can then import the EPS file to a page in the document processor file. The most recent versions of the aforementioned applications will generate a bitmapped preview of the table content to aid in placement and review. You can then print the document to a PS printer or file for subsequent use. OO.org's Writer can also use Ghostscript to print to a PDF file using a PDF Converter in the printer selection dialog. This, importantly, is different than the Export to PDF function. The latter does not properly print embedded EPS images and prints the bitmapped preview instead. The advantage of this approach is that you don't have to mess around in the word processing program doing a 'text to table' conversion and then go through the formatting of the resultant columns, borders, etc. HTH, Marc Schwartz On Thu, 2006-02-09 at 09:47 -0500, Doran, Harold wrote: Well, I don't know if it can be used with Word or not, but you might consider Sweave for use with LaTeX. Maybe if you use the sink() command this might work, but I haven't tried it. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Tom Backer Johnsen Sent: Thursday, February 09, 2006 9:41 AM To: r-help@stat.math.ethz.ch Subject: [R] Tranferring R results to word prosessors I have just started looking at R, and are getting more and more irritated at myself for not having done that before. However, one of the things I have not found in the documentation is some way of preparing output from R for convenient formatting into something like MS Word. An example: If you use summary(lm()) you get nice output. However, if you try to paste that output into the word processor, all the text elements are separated by blanks, and that is not optimal for the creation of a table (in the word processing sense). Is there an option to generate tab-separated output in R ? That would solve the problem. Tom __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] prehistoric versions of R -- 1995!
FrPi == François Pinard [EMAIL PROTECTED] on Tue, 7 Feb 2006 08:43:28 -0500 writes: FrPi [Martin Maechler] 2) The oldest stuff that I have is all from 1995; FrPi Mailing lists seem to go back into 1995 too. I found a few messages FrPi from around 1994 on topics to be later found within R, but I'm not sure FrPi where I got these old messages from. I did find a message really FrPi related to R-pre-alpha, which itself quotes a message written in 1994. Hmm, I am interested to find these. I am pretty sure the first R list was the one Ross and Robert initiated with the following e-mail (the date of which also points to that 10th anniversary date coming Sunday!): From: R Home [EMAIL PROTECTED] To: [EMAIL PROTECTED] Subject: R Code Alpha Test Date: Mon, 12 Feb 1996 16:15:53 +1300 At some point in the past you have provided comments on R which indicated that you would make a useful alpha-tester for the version we plan to release to statlib. We have put your name on a mailing list [EMAIL PROTECTED] which we will use for discussion of problems and for distributing bug-fixes and patches. We intend that that the list will only function for a short testing period. Assuming that the testing isn't too much of a disaster, we will set up a real discussion mailing list. If you don't wish to take part in the testing cycle and would like to be taken off the list please send some mail to [EMAIL PROTECTED]. If you have suggestions for other who could take part in testing let us know too. There are a number of types of input we are interested in. 1) PORTABILITY We are interested in seeing R ported to as many Unix platforms as possible. We are interested in hearing about portability and any fixes neccessary to get R running on platforms other than those we have available (SunOS, Solaris, FreeBSD, Linux, HP, SGI Irix). 2) DIFFERENCES We would like feedback on differences between R and S. We have made the decision to make R as compatible with S as possible, but have not had the chance to systematically look for differences. 3) BUGS We want to know about the bugs which are present in R. 4) EXTENSIONS What should we do next? The source code is now available by anonymous ftp from stat3.stat.auckland.ac.nz (note that this is not the usual place). Ross Ihaka + Robert Gentleman BTW, note the many (Unixy) platforms mentioned on which R was running even then. Definitely older than the above are private e-mails between Ross, Robert and various people, but these were private. An interesting one would be the first announcement of R on the S-news mailing list which I think *was* in 1994 (as you indicate above). Unfortunately the archives of S-news currently only go back to 1998. Also, further, to what I said previously on this thread, I have a nice paperback book Data Analysis - An Introduction base on R written by Alan Lee, Dept. Statistics, Auckland labeled as Course Notes of University of Auckland Papers 528.218/288 (a kind of lecture notes) which I received as gift from Ross and Robert at the Heidelberg workshop, March 25, 1995. The book has a Copyright © 1994. That seems high evidence for R to have been in use at U. of Auckland in 1994. Now if we heard even more history of R (with dates!) from Ross / Robert / Alan Lee ? Regards, Martin Maechler, ETH Zurich __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] effect sizes in lme/ multi-level models
Dear alltogether, I am searching for a way to determine effect size in multi-level models by using lme(). Coming from Psychology, for ordinary OLS there are measures (for meta-analysis, etc.) like CohensD - (mean_EG - mean_CG) / SD_pooled or (p)eta^2 - SS_effect / (SS_effect + SS_error) I do not intend to lead a discussion of the usefulness of such measures as long as the standards of psychological journals (e.g. as defined by the APA) order them. However, I wondered how to determine measures of effect size in lme. PinheiroBates (2000) do not touch that topic. I assume that as long as a grouping structure is present, the formular of CohensD (see above) has to be corrected to give respect to the grouping structure. Is there any equivalent measure like eta^2, partial-eta^2, etc.? Can anybody help me with formulas, R code or some references? Thank you very much, thanks in advance, leo gürtler -- email: [EMAIL PROTECTED] www: http://www.anicca-vijja.de/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] nice log-log plots
Dear All, I am trying to produce log-log plots in R and I was wondering if any of you have a 'template' for generating these with 'nice' labels and log-log grids? I know I can set up axes individually and use the intervals I want, however, I will be producing a large number of these plots and would not like to do this manually for each of them + I am very new to R and at the moment do not have much time that I could spend figuring this out by myself. Any help would be greatly appreciated! Thanks Tibi Alexandru Tiberiu CODILEAN PhD Candidate Departmental IT Committee PG Rep. Department of Geographical and Earth Sciences East Quadrangle, Room 309 University Avenue University of Glasgow Glasgow G12 8QQ UK Tel: +44 (0) 141 330 4872 ext. 0935 Fax: +44 (0) 141 330 4894 Email: [EMAIL PROTECTED] Home: http://web.ges.gla.ac.uk/~tcodilean/ GRASS Mirror: http://pc188.geog.gla.ac.uk/grass/ A gleekzorp without a tornpee is like a quop without a fertsneet (sort of) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Fixing AR coefficients in VAR model
I know of no existing functions in R that support fitting a multivariate autoregression while fixing some of the parameters. Of course, as Simon Blomberg famously said in April 2005, This is R. There is no if. Only how. [With library(fortunes), try 'fortune(This is R)'.] If I had to do fit a multivariate AR today with some parameters fixed, I might write a function to compute the determinant of the sample covariance matrix, and give it to optim or nlminb. I hope someone else will provide us with an easier way. hope this helps, spencer graves Daniel Medina wrote: Dear Colleague, I would like to set a few AR coefficients (not order) to zero in the multivariate AR function (mAr.est; mAr library); however, the manual for this function does not provide this information. I would appreciate any suggestions along this line. Thankfully yours, Daniel C Medina [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Tranferring R results to word prosessors
Yeah, but I don't understand LaTeX at all. Can you point me to a good beginners guide? Thanks, Roger On 2/9/06, Barry Rowlingson [EMAIL PROTECTED] wrote: Tom Backer Johnsen wrote: I have just started looking at R, and are getting more and more irritated at myself for not having done that before. However, one of the things I have not found in the documentation is some way of preparing output from R for convenient formatting into something like MS Word. Well whatever you do, don't start looking at LaTeX, because that will get you even more irritated at yourself for not having done it before. LaTeX is to Word as R is to what? SPSS? I've still not seen a pretty piece of mathematics - or even text - in Word. Barry __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Tranferring R results to word prosessors
Take a look at the facilities to write HTML output in library(R2HTML). If you write an HTML file, you can then easily copy and paste it into your Word document, or from MS Word you can use the Insert menu. i.e. library(R2HTML) x=ftable(Titanic, row.vars = 1:3) HTML(x,Titanic.html) Then from MS Word use Insert- File and select Titanic.html and see the results. I hope this helps Francisco From: Tom Backer Johnsen [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch Subject: [R] Tranferring R results to word prosessors Date: Thu, 09 Feb 2006 15:41:09 +0100 I have just started looking at R, and are getting more and more irritated at myself for not having done that before. However, one of the things I have not found in the documentation is some way of preparing output from R for convenient formatting into something like MS Word. An example: If you use summary(lm()) you get nice output. However, if you try to paste that output into the word processor, all the text elements are separated by blanks, and that is not optimal for the creation of a table (in the word processing sense). Is there an option to generate tab-separated output in R ? That would solve the problem. Tom ++ | Tom Backer Johnsen, Psychometrics Unit, Faculty of Psychology | | University of Bergen, Christies gt. 12, N-5015 Bergen, NORWAY | | Tel : +47-5558-9185Fax : +47-5558-9879 | | Email : [EMAIL PROTECTED]URL : http://www.galton.uib.no/ | ++ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] putting text in the corner
On Thu, 2006-02-09 at 17:18 +0100, Thomas Steiner wrote: I want to write some text in a corner of my plot. Is it possible to get the xlim and ylim of an open window? Or is there anything similar like legend(x=bottomright, inset=0.01,legend=...) for text(x=1,y=2, test) Thomas Try this: plot(1:10) # par(usr) defines the x/y coordinates of the plot region usr - par(usr) # Upper Left Hand Corner text(usr[1], usr[4], test, adj = c(0, 1)) # Lower Left Hand Corner text(usr[1], usr[3], test, adj = c(0, 0)) # Lower Right Hand Corner text(usr[2], usr[3], test, adj = c(1, 0)) # Upper Right Hand Corner text(usr[2], usr[4], test, adj = c(1, 1)) See ?par and ?text for more information including the 'adj' argument to text(). HTH, Marc Schwartz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] make: Target `all' not remade because of errors.
Hi: I don't know if it is a bug or what?
I followed instructions.
Jean
R version: R-2.2.1
OS: Linux RedHat 9
I followed the instructions. tar -xvf, configure, then make.
I get these error messages at the end of make and with make check.
==
==
In file included from rbitmap.c:45:
/usr/include/png.h:318:18: zlib.h: No such file or directory
In file included from /usr/include/png.h:321,
from rbitmap.c:45:
/usr/include/pngconf.h:1091: error: parse error before '*' token
/usr/include/pngconf.h:1092: error: parse error before '*' token
/usr/include/pngconf.h:1093: error: parse error before '*' token
In file included from rbitmap.c:45:
/usr/include/png.h:1034: error: parse error before z_stream
/usr/include/png.h:1262: error: parse error before '}' token
/usr/include/png.h:1821: error: parse error before png_zalloc
/usr/include/png.h:1821: error: parse error before png_ptr
/usr/include/png.h:1825: error: parse error before png_ptr
rbitmap.c: In function `my_png_error':
rbitmap.c:72: error: dereferencing pointer to incomplete type
rbitmap.c: In function `R_SaveAsPng':
rbitmap.c:121: error: dereferencing pointer to incomplete type
make[4]: *** [rbitmap.lo] Error 1
make[4]: Target `R_X11.so' not remade because of errors.
make[4]: Leaving directory `/users/cadet/R-2.2.1/src/modules/X11'
make[3]: *** [R] Error 2
make[3]: Leaving directory `/users/cadet/R-2.2.1/src/modules/X11'
make[2]: *** [R] Error 1
make[2]: Leaving directory `/users/cadet/R-2.2.1/src/modules'
make[1]: *** [R] Error 1
make[1]: Leaving directory `/users/cadet/R-2.2.1/src'
make: *** [R] Error 1
make: Target `all' not remade because of errors.
giant {122} make check
make[1]: Entering directory `/users/cadet/R-2.2.1/tests'
make[2]: Entering directory `/users/cadet/R-2.2.1/tests'
make[3]: Entering directory `/users/cadet/R-2.2.1/tests/Examples'
make[4]: Entering directory `/users/cadet/R-2.2.1/tests/Examples'
make[4]: `Makedeps' is up to date.
make[4]: Leaving directory `/users/cadet/R-2.2.1/tests/Examples'
make[4]: Entering directory `/users/cadet/R-2.2.1/tests/Examples'
make[4]: *** No rule to make target `../../src/library/base/all.R', needed
by `base-Ex.Rout'. Stop.
make[4]: Leaving directory `/users/cadet/R-2.2.1/tests/Examples'
make[3]: *** [test-Examples-Base] Error 2
make[3]: Leaving directory `/users/cadet/R-2.2.1/tests/Examples'
make[2]: *** [test-Examples] Error 2
make[2]: Leaving directory `/users/cadet/R-2.2.1/tests'
make[1]: *** [test-all-basics] Error 1
make[1]: Leaving directory `/users/cadet/R-2.2.1/tests'
make: *** [check] Error 2
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[R] glmm.admb - bug and possible solution??
Dear Dr Skaug and R users, just discovered glmm.admb in R, and it seems a very useful tool. However, I ran into a problem when I compare two models: m1-glmm.admb(survival~light*species*damage, random=~1, group=table, data=bm, family=binomial, link=logit) m1.1-glmm.admb(survival~(light+species+damage)^2, random=~1, group=table, data=bm, family=binomial, link=logit) anova(m1, m1.1) I get the following output with the warning Analysis of Variance Table Model 1: survival ~ light * species * damage Model 2: survival ~ (light + damage + species)^2 NoPar LogLik Df -2logQ P.value 1 9.000 -103.307 2 9.000 -103.781 0 -0.948 Warning message: NaNs produced in: pchisq(q, df, lower.tail, log.p) The warning is generated because the df=0. This appears to be because the number of parameters is being incorrectly calculated (they should be 9 and 8 respectively). I had a look at the function call in R, and the problem appears to be because npar is obtained from the file nbmm.par on line 140 of the function out$npar - as.numeric(scan(nbmm.par, what = , quiet = TRUE)[6]) which doesn't appear to change between calculations (the file seems to hvae been created the first time I ran glmm.admb, and not to have been modified since). Replacing this line with the following out$npar-p+m seemed to work ok. Is this a legitimate solution? I noticed that this isn't necessary for when I run the example for anova.glmm.admb (although this uses a different family). This seems to overwrite the nbmm.par file. Couldn't work out where this happens though, and take it that this occurs during the call to the ADMB program. Any thoughts? Many thanks Robert Below is the version information for R platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 2.0 year 2005 month 10 day 06 svn rev 35749 language R ADMB version Package: glmmADMB Version: 0.2 License: GPL Packaged: Thu Dec 1 07:02:40 2005; andersn Built: R 2.2.0; ; 2005-12-01 07:13:48; unix -- Robert Bagchi Animal Plant Science Alfred Denny Building University of Sheffield Western Bank Sheffield S10 2TN UK t: +44 (0)114 2220062 e: [EMAIL PROTECTED] [EMAIL PROTECTED] http://www.shef.ac.uk/aps/apsrtp/bagchi-r __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] putting text in the corner
You can get the x and y position of any place of an open graphic device with the mouse cursor, using the function locator(), and even assing this values to an object, as in: xy-locator() You will have a list with x and y positions. Then you can use: text(xy$x,xy$y,...) See ?locator. HTH, Fernando Mayer. Thomas Steiner escreveu: I want to write some text in a corner of my plot. Is it possible to get the xlim and ylim of an open window? Or is there anything similar like legend(x=bottomright, inset=0.01,legend=...) for text(x=1,y=2, test) Thomas __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Tranferring R results to word prosessors
Marc Schwartz (via MN) wrote: In follow up to Harold's thought of using LaTeX, I have an approach when the use of nicely formatted tables is required in a document where LaTeX is not being used for the entire document. In other words, where you need to use Word, OO.org's Writer or similar application for the majority of the document body. This involves outputting R results to LaTeX table code in a text file, processing the file with 'latex' and 'dvips' and creating an EPS file. Of course, the LaTeX text file is fully complete with preamble, etc. One can then import the EPS file to a page in the document processor file. The most recent versions of the aforementioned applications will generate a bitmapped preview of the table content to aid in placement and review. You can then print the document to a PS printer or file for subsequent use. OO.org's Writer can also use Ghostscript to print to a PDF file using a PDF Converter in the printer selection dialog. This, importantly, is different than the Export to PDF function. The latter does not properly print embedded EPS images and prints the bitmapped preview instead. The advantage of this approach is that you don't have to mess around in the word processing program doing a 'text to table' conversion and then go through the formatting of the resultant columns, borders, etc. HTH, Marc Schwartz In addition to Marc's nice idea, I have had luck with Linux programs latex2rtf (.tex to .rtf) and hevea (.tex to .html). Most often I use hevea and let Word users quickly convert from .html to .doc. Of course doing everything in LaTeX is far better, using either Sweave or http://biostat.mc.vanderbilt.edu/StatReport . Personal productivity with LaTeX is amazingly greater than with Word. Frank On Thu, 2006-02-09 at 09:47 -0500, Doran, Harold wrote: Well, I don't know if it can be used with Word or not, but you might consider Sweave for use with LaTeX. Maybe if you use the sink() command this might work, but I haven't tried it. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Tom Backer Johnsen Sent: Thursday, February 09, 2006 9:41 AM To: r-help@stat.math.ethz.ch Subject: [R] Tranferring R results to word prosessors I have just started looking at R, and are getting more and more irritated at myself for not having done that before. However, one of the things I have not found in the documentation is some way of preparing output from R for convenient formatting into something like MS Word. An example: If you use summary(lm()) you get nice output. However, if you try to paste that output into the word processor, all the text elements are separated by blanks, and that is not optimal for the creation of a table (in the word processing sense). Is there an option to generate tab-separated output in R ? That would solve the problem. Tom __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] main parameter in plot.default vs plot.formula
Folks: R 2.2.0 on Windows. I find the following somewhat puzzling: a-1; x-0:1; y-x ## following works fine: plot(x,y ,main= bquote(n[1] == .(a) )) ## following produces an error: plot(y~x ,main= bquote(n[1] == .(a) )) Error in paste(n[1] == 1, and , n[2] == 2) : object n not found *** Note 1: I assume that this is due to the following documented behavior of plot.formula(): Both the terms in the formula and the ... arguments are evaluated in data enclosed in parent.frame() if data is a list or a data frame. Nevertheless, the behavior seems inconsistent to me. Am I missing something (including the I assume ... comment)? Note 2: If one uses substitute() instead, it works fine: plot(y~x ,main= substitute(bquote(n[1] == a),list(a=a))) Any illumination, public or private, would be appreciated. Cheers, Bert -- Bert Gunter Genentech Non-Clinical Statistics South San Francisco, CA The business of the statistician is to catalyze the scientific learning process. - George E. P. Box __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] minimum adequate model using contrasts
I am trying to model a set of data that I am working on using contrasts. Since the data set is too large, I am interested in scripting the entire process to arrive at the minimum adequate model. Has anyone in the group done this before? If you I would appreciate their comments. Cheers ../Murli __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] how to clear the last error?
On 2/9/2006 11:11 AM, Adrian Dragulescu wrote: Hello, I would like to clear the last error that I get with geterrmessage(). Not even rm(list=ls()) clears it. Can I set it to NULL somehow? Not from R, but there is a C-level way to do it in src/main/errors.c. It's marked as temporary, but it's been there since R 1.3.x. The declaration is void R_SetErrmessage(char *s); Alternatively, you could just cover up the last error with a new one by calling stop, e.g. try(stop(),TRUE) geterrmessage() [1] Error in try(stop(\\), TRUE) : \n Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] putting text in the corner
On 2/9/2006 11:18 AM, Thomas Steiner wrote: I want to write some text in a corner of my plot. Is it possible to get the xlim and ylim of an open window? Or is there anything similar like legend(x=bottomright, inset=0.01,legend=...) for text(x=1,y=2, test) par(usr) gives you the limits. Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] putting text in the corner
?par, look at usr (which is how legend does it) On Thu, 9 Feb 2006, Thomas Steiner wrote: I want to write some text in a corner of my plot. Is it possible to get the xlim and ylim of an open window? Or is there anything similar like legend(x=bottomright, inset=0.01,legend=...) for text(x=1,y=2, test) -- Brian D. Ripley, [EMAIL PROTECTED] 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] minimal adequate model
I am trying to model a set of data that I am working on using contrasts. Since the data set is too large, I am interested in scripting the entire process to arrive at the minimum adequate model. Has anyone in the group done this before? If you I would appreciate their comments. Cheers ../Murli [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Tranferring R results to word prosessors
There is some documentation online at: http://www.latex-project.org/guides/ which would be a good starting place. If you prefer a good book, The LaTeX Companion (aka TLC) is the place to begin: http://www.amazon.com/gp/product/0201362996 There is also a boxed set (expensive) of several books (including TLC) available: http://www.amazon.com/gp/product/0321269446 Finally, for dealing with EPS (or PDF) graphics (ie. R plots), the online document Using Imported Graphics in LaTeX and pdfLaTeX is excellent: http://www.ctan.org/tex-archive/info/epslatex.pdf HTH, Marc Schwartz On Thu, 2006-02-09 at 12:33 -0500, roger bos wrote: Yeah, but I don't understand LaTeX at all. Can you point me to a good beginners guide? Thanks, Roger On 2/9/06, Barry Rowlingson [EMAIL PROTECTED] wrote: Tom Backer Johnsen wrote: I have just started looking at R, and are getting more and more irritated at myself for not having done that before. However, one of the things I have not found in the documentation is some way of preparing output from R for convenient formatting into something like MS Word. Well whatever you do, don't start looking at LaTeX, because that will get you even more irritated at yourself for not having done it before. LaTeX is to Word as R is to what? SPSS? I've still not seen a pretty piece of mathematics - or even text - in Word. Barry __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Shapefiles
Dear List, I have examined the sp, maptools, and shapefiles packages (Windows) but cannot seem to figure out a solution for writing shapefiles for 'curvy shapes'. The scenario is that I generate a series of polygons, circles, and ellipses on a plot and would like to convert them to shapefiles. Since the circles and ellipses are do not return a coordinate list during the plotting sequence (e.g., all I need supply are the lengths of axes and rotation angle), is there an easy way by which the plot window can be converted to a shapefile? Thank you, Tarmo __ Tarmo Remmel Ph.D. GUESS Lab, Department of Geography University of Toronto at Mississauga Mississauga, Ontario, L5L 1C6 Tel: 905-569-4382 Lab: 905-828-3868 Fax: 905-828-5273 Skype: tarmoremmel http://eratos.erin.utoronto.ca/remmelt __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] New user: Custom probability distribution
Hello, Given a probability function: p(x) = 12 / (25(x+1)) , x=0, 1, 2, 3 we generate the following values: C1 C2 0 0.48 1 0.24 2 0.16 3 0.12 Now, I'm supposed to create 50 random values using this table. In MiniTab, I simply selected Calc - Random Data - Discrete, and selected the columns, and it created 50 random values in a new column.[1] How do I do the same thing in R? [1] You may be wondering why I'm telling you this. Well, it's because if I were in your shoes, I'd think Oh, someone wants me to solve his homework.. I have already solved it using MiniTab, but I want to be able to use R instead (since I prefer NetBSD). -- Kind Regards, Jan Danielsson Te audire non possum. Musa sapientum fixa est in aure. signature.asc Description: OpenPGP digital signature __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] New psi with rlm
Hi, How can I define a new psi function in the rlm comand? In particular I would like to implement the case for \rho(u)=0.5*(u^2) and \psi(u)=u in order to assume normally distributed errors. Any help? Thanks -- Angelo Secchi PGP Key ID:EA280337 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Tranferring R results to word prosessors
One approach is to use LyX (http://www.lyx.org/). This is a lot like using Word or other word processors but it creates LaTeX. You probably won't need to know anything about TeX for a long time unless you are doing really weird things. Patrick Burns [EMAIL PROTECTED] +44 (0)20 8525 0696 http://www.burns-stat.com (home of S Poetry and A Guide for the Unwilling S User) roger bos wrote: Yeah, but I don't understand LaTeX at all. Can you point me to a good beginners guide? Thanks, Roger On 2/9/06, Barry Rowlingson [EMAIL PROTECTED] wrote: Tom Backer Johnsen wrote: I have just started looking at R, and are getting more and more irritated at myself for not having done that before. However, one of the things I have not found in the documentation is some way of preparing output from R for convenient formatting into something like MS Word. Well whatever you do, don't start looking at LaTeX, because that will get you even more irritated at yourself for not having done it before. LaTeX is to Word as R is to what? SPSS? I've still not seen a pretty piece of mathematics - or even text - in Word. Barry __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Tranferring R results to word prosessors
roger bos [EMAIL PROTECTED] 2/9/2006 12:33 pm wrote Yeah, but I don't understand LaTeX at all. Can you point me to a good beginners guide? I like Math into LaTeX, by Gratzer. For a real beginners guide, there's one called first steps in LaTeX. You might also want to look at issues of the PracTEX journal, many of which are for beginners (It's an online journal) Peter Peter L. Flom, PhD Assistant Director, Statistics and Data Analysis Core Center for Drug Use and HIV Research National Development and Research Institutes 71 W. 23rd St http://cduhr.ndri.org www.peterflom.com New York, NY 10010 (212) 845-4485 (voice) (917) 438-0894 (fax) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] iteration history
Hi Bob ! It possible See the first element of controle argument set it to a positive integer ! --- Robert Mcfadden [EMAIL PROTECTED] a écrit : Dear R Users I would like to use optim function to optimize a function. I read help but I couldn't find what I need: is it possible to get information after each iteration, for example as there is in MATLAB: Gradient's Iteration Func-count f(x)Step-size infinity-norm 0 24 388.976 14 1 72 385.67 0.0292637 16.8 2 96 383.54 1 4.15 3 120 383.412 1 0.108 4 144 383.412 1 0.002 5 168 383.412 1 0.00149 6 192 383.412 1 6.23e-005 7 216 383.412 1 1.01e-005 It is useful when iteration takes long time - I know what's happen I would appreciate any suggestion Robert __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] R2WinBUGS - formating data for winbugs
I am currently running analyses in winbugs with two different formats of data: matrix and list. The data in the list have different dimensions than the matrix. Do I need to create a single format for entry into R which R passes to WinBUGS? Thanks, Chris Christopher Behr Principal Analyst eDesign Dynamics www.edesigndynamics.com 4024 Calvert St. NW Washington DC 20007 (202) 298-6437 (t/f) (551) 998-4823 (c) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] problem with simple if() statement
Hi Norman ! I observe that R syntax is very close to C/C++ or Java --- Philippe Grosjean [EMAIL PROTECTED] a écrit : Norman Goodacre wrote: the following code apprantely, for some grand old reason, induces a syntax error: if (seq[i] = A) m - trans[1,] where seq is a vector and trans is a matrix. I cannot for the life of me see why this is wrong. Syntax error is: Error: syntax error in if (seq[i] = Sincerely, Norman Goodacre Please, read An Introduction to R provided with any version of R. The correct syntax for an equality condition is ==, not =, so: if (seq[i] == A) Best, Philippe Grosjean __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Fixing AR coefficients in VAR model
You can do this with dse. See
require(dse1)
?fixConstants
Paul Gilbert
Spencer Graves wrote:
I know of no existing functions in R that support fitting a
multivariate autoregression while fixing some of the parameters.
Of course, as Simon Blomberg famously said in April 2005, This is R.
There is no if. Only how. [With library(fortunes), try 'fortune(This
is R)'.] If I had to do fit a multivariate AR today with some
parameters fixed, I might write a function to compute the determinant of
the sample covariance matrix, and give it to optim or nlminb.
I hope someone else will provide us with an easier way.
hope this helps,
spencer graves
Daniel Medina wrote:
Dear Colleague,
I would like to set a few AR coefficients (not order) to zero in the
multivariate AR function (mAr.est; mAr library); however, the manual for
this function does not provide this information. I would appreciate any
suggestions along this line.
Thankfully yours,
Daniel C Medina
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La version française suit le texte anglais.
This email message from the Bank of Canada is given in good faith, and shall
not be
binding or construed as constituting any obligation on the part of the Bank.
This email may contain privileged and/or confidential inform...{{dropped}}
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[R] Plotting 27 line plots in one page
Dear group,
I am a novice programmer in R. I have a list that
has a length of 27 elements. Each element is derived
from table function.
lls - table(drres)
legnth(lls)
27
I want to plot all these elements in 9x3 plot (9 rows
and 3 columns)
par(9,3)
mypltfunc - function(mydata){
+ for (i in 1:27){
+ plot(unlist(mydata[i]))
+ }
+ }
mypltfunc(lls)
In the graphics window, all 27 figures are drawn in
fraction of sec, one by one and I get to see the last
graph. It is not drawing into this 9X3 grid.
Could any one help me please.
Thanks
sri
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[R] converting lat-long coordinates to Albers Conical Equal Area coordinates
We have used maptools to construct state, county, township, census-tract, and zipcode level R maps with an Albers Conical Equal Area projection. We would like to be able to plot the location of weather stations or other point locations on the maps. The data the point locations are in latitude-longitude units and we must convert the coordinates to the Albers Conical Equal Area coordinates. However, as of yet, we have not been able to obtain satisfactory results using mapproj. Given the specs below can someone please tell us how to use mapproj (or some other R library) to convert lat-long coordinates into the appropriate Albers Conical Equal Area coordinates? Thanks in advance Joe Atwood Montana State University [EMAIL PROTECTED] The material at the bottom of this message is the metadata from the shapefile we are using (as created in Arc-GIS). --- Horizontal coordinate system Projected coordinate system name: NAD_1927_Albers Geographic coordinate system name: GCS_North_American_1927 Details Map Projection Name: Albers Conical Equal Area Standard Parallel: 29.50 Standard Parallel: 45.50 Longitude of Central Meridian: -96.00 Latitude of Projection Origin: 23.00 False Easting: 0.00 False Northing: 0.00 Planar Coordinate Information Planar Distance Units: meters Coordinate Encoding Method: coordinate pair Coordinate Representation Abscissa Resolution: 0.008192 Ordinate Resolution: 0.008192 Geodetic Model Horizontal Datum Name: North American Datum of 1927 Ellipsoid Name: Clarke 1866 Semi-major Axis: 6378206.40 Denominator of Flattening Ratio: 294.978698 _ Bounding coordinates Horizontal In decimal degrees West: -127.889829 East: -65.349890 North: 51.606167 South: 22.862978 In projected or local coordinates Left: -2356341.706499 Right: 2257925.009693 Top: 3172647.320063 Bottom: 268329.067476 ### __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] main parameter in plot.default vs plot.formula
I cannot explain it but I must have come across it since I noticed in various places in some of my code I have used, in terms of your example, the following: plot(y ~ x, main = as.expression(bquote(m[1] == .(a plot(y ~ x, main = list(bquote(m[1] == .(a both of which work as expected. On 2/9/06, Berton Gunter [EMAIL PROTECTED] wrote: Folks: R 2.2.0 on Windows. I find the following somewhat puzzling: a-1; x-0:1; y-x ## following works fine: plot(x,y ,main= bquote(n[1] == .(a) )) ## following produces an error: plot(y~x ,main= bquote(n[1] == .(a) )) Error in paste(n[1] == 1, and , n[2] == 2) : object n not found *** Note 1: I assume that this is due to the following documented behavior of plot.formula(): Both the terms in the formula and the ... arguments are evaluated in data enclosed in parent.frame() if data is a list or a data frame. Nevertheless, the behavior seems inconsistent to me. Am I missing something (including the I assume ... comment)? Note 2: If one uses substitute() instead, it works fine: plot(y~x ,main= substitute(bquote(n[1] == a),list(a=a))) Any illumination, public or private, would be appreciated. Cheers, Bert -- Bert Gunter Genentech Non-Clinical Statistics South San Francisco, CA The business of the statistician is to catalyze the scientific learning process. - George E. P. Box __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Fixing AR coefficients in VAR model
Hi, Paul: Thanks very much. I'd forgotten that. Moreover, you provide very nice vignettes. Daniel C Medina: If you are not familiar with vignettes, you may wish to review http://finzi.psych.upenn.edu/R/Rhelp02a/archive/67006.html; in addition to the vignette help page. Best Wishes, spencer graves Paul Gilbert wrote: You can do this with dse. See require(dse1) ?fixConstants Paul Gilbert Spencer Graves wrote: I know of no existing functions in R that support fitting a multivariate autoregression while fixing some of the parameters. Of course, as Simon Blomberg famously said in April 2005, This is R. There is no if. Only how. [With library(fortunes), try 'fortune(This is R)'.] If I had to do fit a multivariate AR today with some parameters fixed, I might write a function to compute the determinant of the sample covariance matrix, and give it to optim or nlminb. I hope someone else will provide us with an easier way. hope this helps, spencer graves Daniel Medina wrote: Dear Colleague, I would like to set a few AR coefficients (not order) to zero in the multivariate AR function (mAr.est; mAr library); however, the manual for this function does not provide this information. I would appreciate any suggestions along this line. Thankfully yours, Daniel C Medina [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html La version française suit le texte anglais. This email message from the Bank of Canada is given in good faith, and shall not be binding or construed as constituting any obligation on the part of the Bank. This email may contain privileged and/or confidential information, and the Bank of Canada does not waive any related rights. Any distribution, use, or copying of this email or the information it contains by other than the intended recipient is unauthorized. If you received this email in error please delete it immediately from your system and notify the sender promptly by email that you have done so. Recipients are advised to apply their own virus checks to this message upon receipt. L'information communiquée dans les courriels en provenance de la Banque du Canada est soumise de bonne foi, mais elle ne saurait lier la Banque et ne doit aucunement être interprétée comme constituant une obligation de sa part. Le présent courriel peut contenir de l'information privilégiée ou confidentielle. La Banque du Canada ne renonce pas aux droits qui s'y rapportent. Toute diffusion, utilisation ou copie de ce courriel ou des renseignements qu'il contient par une personne autre que le ou les destinataires désignés est interdite. Si vous recevez ce courriel par erreur, veuillez le supprimer immédiatement et envoyer sans délai à l'expéditeur un message électronique pour l'aviser que vous avez éliminé de votre ordinateur toute copie du courriel reçu. Dès la réception du présent message, le ou les destinataires doivent activer leur programme de détection de virus pour éviter toute contamination possible. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] New user: Custom probability distribution
On 2/9/2006 2:02 PM, Jan Danielsson wrote: Hello, Given a probability function: p(x) = 12 / (25(x+1)) , x=0, 1, 2, 3 we generate the following values: C1 C2 0 0.48 1 0.24 2 0.16 3 0.12 Now, I'm supposed to create 50 random values using this table. In MiniTab, I simply selected Calc - Random Data - Discrete, and selected the columns, and it created 50 random values in a new column.[1] How do I do the same thing in R? [1] You may be wondering why I'm telling you this. Well, it's because if I were in your shoes, I'd think Oh, someone wants me to solve his homework.. I have already solved it using MiniTab, but I want to be able to use R instead (since I prefer NetBSD). You want to use the sample() function. See ?sample. Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] New user: Custom probability distribution
rbinom(50,5,c(0.48,0.24,0.16,0.12)) On Thu, 2006-09-02 at 20:02 +0100, Jan Danielsson wrote: Hello, Given a probability function: p(x) = 12 / (25(x+1)) , x=0, 1, 2, 3 we generate the following values: C1 C2 0 0.48 1 0.24 2 0.16 3 0.12 Now, I'm supposed to create 50 random values using this table. In MiniTab, I simply selected Calc - Random Data - Discrete, and selected the columns, and it created 50 random values in a new column.[1] How do I do the same thing in R? [1] You may be wondering why I'm telling you this. Well, it's because if I were in your shoes, I'd think Oh, someone wants me to solve his homework.. I have already solved it using MiniTab, but I want to be able to use R instead (since I prefer NetBSD). __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] putting text in the corner
par('usr') will give you the coordinates of the corners of the current plot.
If you want to go a little beyond this (more like your legend example) by
specifying that you want your text to be some distance from the bottom and left
of the plot and have the distance not affected by the scale of the data then
you might want to look at the cnvrt.coords function in the TeachingDemos
package.
-Original Message-
From: [EMAIL PROTECTED] on behalf of Thomas Steiner
Sent: Thu 2/9/2006 9:18 AM
To: r-help@stat.math.ethz.ch
Subject: [R] putting text in the corner
I want to write some text in a corner of my plot.
Is it possible to get the xlim and ylim of an open window?
Or is there anything similar like
legend(x=bottomright, inset=0.01,legend=...)
for
text(x=1,y=2, test)
Thomas
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Re: [R] Shapefiles
On Thu, 9 Feb 2006, Tarmo Remmel wrote: Dear List, I have examined the sp, maptools, and shapefiles packages (Windows) but cannot seem to figure out a solution for writing shapefiles for 'curvy shapes'. The scenario is that I generate a series of polygons, circles, and ellipses on a plot and would like to convert them to shapefiles. Since the circles and ellipses are do not return a coordinate list during the plotting sequence (e.g., all I need supply are the lengths of axes and rotation angle), is there an easy way by which the plot window can be converted to a shapefile? No, the plot window is committed to the device, and (re)-capturing the objects there as polygon objects will be messy. You'll need to generate an object that can be drawn as a sequence of straight line segments, and create a polygon object from that, from the x,y coordinates of the centre and the radius, or major/minor axes lengths and orientations. There is some code on: http://finzi.psych.upenn.edu/R/Rhelp02a/archive/56190.html (see RSiteSearch(circle)) but I don't know if it will suit your purposes. Once constructed, the polygons can be built into an object for exporting. Thank you, Tarmo __ Tarmo Remmel Ph.D. GUESS Lab, Department of Geography University of Toronto at Mississauga Mississauga, Ontario, L5L 1C6 Tel: 905-569-4382 Lab: 905-828-3868 Fax: 905-828-5273 Skype: tarmoremmel http://eratos.erin.utoronto.ca/remmelt __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 e-mail: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] putting text in the corner
Fernando Mayer wrote: You can get the x and y position of any place of an open graphic device with the mouse cursor, using the function locator(), and even assing this values to an object, as in: xy-locator() You will have a list with x and y positions. Then you can use: text(xy$x,xy$y,...) or even text(locator(), test, ...) Kjetil See ?locator. HTH, Fernando Mayer. Thomas Steiner escreveu: I want to write some text in a corner of my plot. Is it possible to get the xlim and ylim of an open window? Or is there anything similar like legend(x=bottomright, inset=0.01,legend=...) for text(x=1,y=2, test) Thomas __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] New user: Custom probability distribution
Jan Danielsson wrote: Hello, Given a probability function: p(x) = 12 / (25(x+1)) , x=0, 1, 2, 3 we generate the following values: C1 C2 0 0.48 1 0.24 2 0.16 3 0.12 Now, I'm supposed to create 50 random values using this table. In MiniTab, I simply selected Calc - Random Data - Discrete, and selected the columns, and it created 50 random values in a new column.[1] How do I do the same thing in R? sample( 0:3, 50, prob=c(0.48, 0.24, 0.26, 0.12)) Kjetil [1] You may be wondering why I'm telling you this. Well, it's because if I were in your shoes, I'd think Oh, someone wants me to solve his homework.. I have already solved it using MiniTab, but I want to be able to use R instead (since I prefer NetBSD). __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] problem to install R on linux
For the rpm install you may also need to install a package called info-x.x.x.x-x.rpm. For the compilation you'll need to be certain that you've installed readline-x.x.x.x.x.rpm and and perhaps readline-devel-x.x.x.x.rpm Those should be in your mandriva distn André Beló wrote: Dear members, this can sound trivial for some people but I don't have experience on compilation. I'm trying to install R-2.2.1 on a laptop running Mandriva 2006. I already installed many of the recommended packages/libraries but it seems that something is still missing. The problem is that I cannot identify... Could somebody give me some advise? I put the output of the command ./configure bellow. When I tryed to install the R-2.0.0-1mdk.i586.rpm I got: [EMAIL PROTECTED] Download]# rpm -i R-2.0.0-1mdk.i586.rpm warning: R-2.0.0-1mdk.i586.rpm: Header V3 DSA signature: NOKEY, key ID 6c60ceea error: Failed dependencies: info is needed by R-2.0.0-1mdk.i586 [EMAIL PROTECTED] Download]# Thanks in advance, AB [EMAIL PROTECTED] R-2.2.1]# ./configure checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu loading site script './config.site' loading build specific script './config.site' checking for pwd... /bin/pwd checking whether builddir is srcdir... yes checking for working aclocal... found checking for working autoconf... found checking for working automake... found checking for working autoheader... found checking for working makeinfo... found checking for gawk... gawk checking for egrep... grep -E checking whether ln -s works... yes checking for ranlib... ranlib checking for bison... no checking for byacc... no checking for ar... ar checking for a BSD-compatible install... /usr/bin/install -c checking for sed... /bin/sed checking for less... /usr/bin/less checking for perl... /usr/bin/perl checking whether perl version is at least 5.004... yes checking for dvips... /usr/bin/dvips checking for tex... /usr/bin/tex checking for latex... /usr/bin/latex checking for makeindex... /usr/bin/makeindex checking for pdftex... /usr/bin/pdftex checking for pdflatex... /usr/bin/pdflatex checking for makeinfo... /usr/bin/makeinfo checking for unzip... /usr/bin/unzip checking for zip... /usr/bin/zip checking for gzip... /bin/gzip checking for firefox... no checking for mozilla... no checking for netscape... no checking for galeon... no checking for kfmclient... no checking for opera... no checking for gnome-moz-remote... /usr/bin/gnome-moz-remote using default browser ... /usr/bin/gnome-moz-remote checking for acroread... /usr/bin/acroread checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -E checking whether gcc needs -traditional... no checking how to run the C preprocessor... gcc -E checking for gfortran... gfortran checking whether we are using the GNU Fortran 77 compiler... no checking whether gfortran accepts -g... no checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C++ preprocessor... g++ -E checking for a sed that does not truncate output... /bin/sed checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from gcc object... ok checking for objdir... .libs checking for ranlib... (cached) ranlib checking for strip... strip checking if gcc static flag works... yes checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC checking if gcc PIC flag -fPIC works... yes checking if gcc supports -c -o file.o... yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode
Re: [R] New user: Custom probability distribution
Hi, you can use our package distr respectively distrEx. require(distrEx) D1 - DiscreteDistribution(supp=0:3, prob = 12/(25*(1:4))) plot(D1) r(D1)(50) hth Matthias Hello, Given a probability function: p(x) = 12 / (25(x+1)) , x=0, 1, 2, 3 we generate the following values: C1 C2 0 0.48 1 0.24 2 0.16 3 0.12 Now, I'm supposed to create 50 random values using this table. In MiniTab, I simply selected Calc - Random Data - Discrete, and selected the columns, and it created 50 random values in a new column.[1] How do I do the same thing in R? [1] You may be wondering why I'm telling you this. Well, it's because if I were in your shoes, I'd think Oh, someone wants me to solve his homework.. I have already solved it using MiniTab, but I want to be able to use R instead (since I prefer NetBSD). __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- StaMatS - Statistik + Mathematik Service Dr. rer. nat. Matthias Kohl Gottlieb-Keim-Straße 60 95448 Bayreuth Phone: +49 921 50736457 E-Mail: [EMAIL PROTECTED] Home: www.stamats.de __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] latent class modle for rater agreement
Hello there, I would like to test the agreement amongst 6 raters for nominal data on a scale from 1-4, and conduct a latent class analysis in R. How should the data be formatted and what code should I use? Thank you very much Lisa Wang Princess Margaret Hospital Biostatistics tel:416 946 4501 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Transferring R results to word prosessors
There has been an incredible number of responses in a short time, with a number of different suggestions. With hindsight, I must admit I have not been quite clear, so additional (somewhat lengthy) explanation is needed. I want to use R in an introductory course on multiple regression (among other things) starting in two weeks time for students of psychology at my University. These students are very much used to MS Word, it is in principle possible to get them to adopt OpenOffice (which I would like to), but I regard Latex to be out of the question. One of the things they are drilled on is that they have to produce term papers etc. based on a template in APA (American Psychological Association) format. Among other things, this means that the document must be all text apart from the graphics. Therefore any kind of solution involving pictures of tables rather than the tables / results as text is out. Same holds for all kinds of mixed output, so combinations of text with PDF elements. Besides, the tables in R are not that nice in respect to the formatting. Since the content is the main thing anyhow, that does not matter. In most cases, the tables have to be tweaked as least to some extent. Given my inexperience, it seems that the R2HTML path is so far the most promising (but for me untried so far) One of the nice things about SPSS and Statistica is that it is VERY easy to copy and paste output from the program right into the paper / paper. A commmon trick when using SPSS is to first paste the output into a spreadsheet (e.g. Excel), and from there into the document. In any case, the outcome is that the output is a table (not a table in the R sense) in the document, which may be edited, tweaked, adding borders etc.. So, what I am looking for is a process starting with output from R (like what is obtained from the summary(lm (...)) command, the output of a correlation matrix, or ...) that could end up as a table in MS Word (and probably in OpenOffice as well) in the smallest number of steps. For instance, if there was an option in R which had the effect that the spaces separating things (e.g. the columns in the output of a correlation matrix or the elements in an ANOVA table) were replaced by tabs, everything would be very simple. Then, you could (a) paste the output into the document, and (b) do a simple text-to-table conversion in Word after the paste. A simple affair with a few simple steps. Ideally, what I want for me and my students is this or a similar solution to this problem. That might be a good selling argument for R as well. Tom __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Plotting 27 line plots in one page
I want to plot all these elements in 9x3 plot (9 rows and 3 columns) par(9,3) You need to specify what par you want - see ?par for details. In this case, either par(mfrow=c(9,3)) or par(mfcol=c(9, 3)) will do what you want. Sarah -- Sarah Goslee http://www.stringpage.com [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Tranferring R results to word prosessors
Marc Schwartz (via MN) [EMAIL PROTECTED] 2/9/2006 If you prefer a good book, The LaTeX Companion (aka TLC) is the place to begin: http://www.amazon.com/gp/product/0201362996 Peter L. Flom, PhD Assistant Director, Statistics and Data Analysis Core Center for Drug Use and HIV Research National Development and Research Institutes 71 W. 23rd St http://cduhr.ndri.org www.peterflom.com New York, NY 10010 (212) 845-4485 (voice) (917) 438-0894 (fax) I respectfully disagree. TLC is a great book. Absolutely. But I think it is overwhelming for a beginner. Peter __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
