Re: [R] Identify and plotting symbols.

[Prof Brian Ripley]

On Thu, 20 Sep 2007, Rolf Turner wrote:

> I have been trying, unsuccessfully, to use identify() to (simply) return 
> a list of the indices of points clicked on and overplot (with say a 
> solid dot) each clicked-on point so that I can see where I've been. 
> I.e. I don't want to see the indices printed on the screen; I just want 
> the points I've already selected to be highlighted.
>
> I tried
>
>   ind <- identify(x,y,labels=rep("\021",length(x)),offset=0)
>
> Two problems:
>
>   (1) Instead of getting a solid dot --- which I thought I should 
> get from "\021", I got a small rectangle outlined in dotted lines. 
> (Which I would've thought I'd get from "\177".)

Why did you think so?

What glyphs (if any) you get from non-ASCII characters depends on the OS, 
locale, graphics device and font, none of which we know.
(It can be even more specific than that: it may depend on what font 
variants you have installed, as on both X11 and Windows there can be 
multiple fonts of the same name with different encodings.)

In particular in a UTF-8 locale (and you seem latterly to be using MacOS X 
which has UTF-8 locales), you probably need to select characters by 
Unicode points, e.g. \u2022 or \u22c5.

>   I seem to get the dotted rectangle no matter what 3 digit string I
> use in "\xxx".

I am surprised: does "\088" not give "H" ?

>   (2) Despite setting offset=0 the superimposed symbol is not 
> actually superimposed, but is jittered off the location of the existing 
> point by a small amount.

Ah, what do you mean by 'superimposed'?  What you should find is the 
appropriate edge of the bounding box of the character is on the point 
identified.  See the 'value' section of the help page for what is meant by 
'appropriate edge'.

> Another minor annoyance is having to use rep("\021",length(x)) rather 
> than simply "\021".  I.e. the vector supplied for labels does not get 
> ``recycled'' the way col and pch etc. are recycled.

Which is as documented, and contrasts with e.g. text() which says its 
'labels' argument is recycled.

> Is there any way of resolving these difficulties?

Yes, use identify(plot=FALSE) in a loop and manage the plotting yourself.
Something like

myidentify <- function(x, y, pch=19, n, ...)
{
 res <- integer(0)
 for(i in seq_len(n)) {
 ans <- identify(x, y, plot=FALSE, n=1, ...)
if(length(ans) == 0) break
 points(x[ans], y[ans], pch=pch)
res <- c(res, ans)
 }
 res
}

and you can refine this by using xy.coords and not allowing repeats.

-- 
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] SHLIB problem under Vista

[Prof Brian Ripley]

This is a known problem with your compiler installation, discussed in the 
R-admin manual.  From the version in R-patched:

   There are known problems with one of the compilers sets in this toolset
   on Windows Vista: see the workaround below. (With that workaround it has
   been used on both 32- and 64-bit versions of Vista.)

   ...

   On Vista systems you will need to add

   c:\Rtools\MinGW\libexec\gcc\mingw\3.4.5

   to the path.

This is not relevant to the recommended compiler set for R 2.6.0.


On Wed, 19 Sep 2007, Anand Patil wrote:

> Hi all,
>
>
> I'd like to distribute an R package that compiles some (small) C functions
> every time it's sourced. The relevant code in the top level R script is as
> follows:
>
> system("R CMD SHLIB Selma_extensions.c")
> if (.Platform$OS.type=="windows") {
>slash = '\\'
>dyn.load("Selma_extensions.dll")
> }
> if (.Platform$OS.type=="unix") {
>slash = '/'
>dyn.load("Selma_extensions.so")
> }

Hmm, all the information you need is already in .Platform, $file.sep and 
$dynlib.ext: the latter varies by OS.type.

> This works fine on a Mac, but I tried it under Windows Vista, after
> installing RTools and telling it to put itself on the system path, and got
> the following:
>
> making Selma_extensions.d from Selma_extensions.c
> gcc.exe: installation problem, cannot exec `cc1': No such file or directory
> make: *** [Selma_extensions.d] Error 1
> Error in dyn.load(x, as.logical(local), as.logical(now)) :
>unable to load shared library
> 'C:/Users/anand/Desktop/Selma/Selma_extensions.dll':
>  LoadLibrary failure:  The specified module could not be found.
>
> Can this be fixed without requiring the user to do anything?

The fix requires 'the user' to read the documentation.

-- 
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] SEM - standardized path coefficients? - significant style

[Steve Powell]

Dear John
Being an R user is like having Christmas every day and having a direct line
to Santa for present suggestions. 
How about if path.diagram.sem had the ability to print non-significant paths
in, for example dotted style? I had a go myself but couldn't see how to get
(summary(model)$coeff)$"Pr(>|z|)" into the loop.
Very best wishes
Steve Powell

 
proMENTE social research 
research | evaluation | training & consulting 
Kranjčevićeva 35, 71000 Sarajevo 
mobile: +387 61 215 997 | office: +387 33 556 865 | fax: +387 33 556 866
skype: stevepowell99 
www.promente.org  |  www.mojakarijera.com  |  www.psih.org  

-Original Message-
From: John Fox [mailto:[EMAIL PROTECTED] 
Sent: 19 September 2007 13:55
To: 'Steve Powell'
Cc: [EMAIL PROTECTED]
Subject: RE: [R] SEM - standardized path coefficients?

Dear Steve,

My intention was to provide this flexibility via the parameters argument to
path.diagram.sem(), but it isn't implemented. Here's a version that should
do what you want:

- snip 

path.diagram.sem <- function (model, out.file, min.rank = NULL, max.rank =
NULL, 
same.rank = NULL, variables = model$var.names, parameters, 
ignore.double = TRUE, edge.labels = c("names", "values"), 
size = c(8, 8), node.font = c("Helvetica", 14), edge.font =
c("Helvetica", 
10), rank.direction = c("LR", "TB"), digits = 2, ...) {
if (!missing(out.file)) {
handle <- file(out.file, "w")
on.exit(close(handle))
}
else handle <- stdout()
edge.labels <- match.arg(edge.labels)
rank.direction <- match.arg(rank.direction)
cat(file = handle, paste("digraph \"", deparse(substitute(model)), 
"\" {\n", sep = ""))
cat(file = handle, paste("  rankdir=", rank.direction, ";\n", 
sep = ""))
cat(file = handle, paste("  size=\"", size[1], ",", size[2], 
"\";\n", sep = ""))
cat(file = handle, paste("  node [fontname=\"", node.font[1], 
"\" fontsize=", node.font[2], " shape=box];\n", sep = ""))
cat(file = handle, paste("  edge [fontname=\"", edge.font[1], 
"\" fontsize=", edge.font[2], "];\n", sep = ""))
cat(file = handle, "  center=1;\n")
if (!is.null(min.rank)) {
min.rank <- paste("\"", min.rank, "\"", sep = "")
min.rank <- gsub(",", "\" \"", gsub(" ", "", min.rank))
cat(file = handle, paste("  {rank=min ", min.rank, "}\n", 
sep = ""))
}
if (!is.null(max.rank)) {
max.rank <- paste("\"", max.rank, "\"", sep = "")
max.rank <- gsub(",", "\" \"", gsub(" ", "", max.rank))
cat(file = handle, paste("  {rank=max ", max.rank, "}\n", 
sep = ""))
}
if (!is.null(same.rank)) {
for (s in 1:length(same.rank)) {
same <- paste("\"", same.rank[s], "\"", sep = "")
same <- gsub(",", "\" \"", gsub(" ", "", same))
cat(file = handle, paste("  {rank=same ", same, "}\n", 
sep = ""))
}
}
latent <- variables[-(1:model$n)]
for (lat in latent) {
cat(file = handle, paste("  \"", lat, "\" [shape=ellipse]\n", 
sep = ""))
}
ram <- model$ram
ram[names(model$coeff), 5] <- model$coeff
rownames(ram)[model$fixed] <- ram[model$fixed, 5]
names <- rownames(ram)
values <- round(ram[, 5], digits)
heads <- ram[, 1]
to <- ram[, 2]
from <- ram[, 3]
labels <- if (!missing(parameters)){ 
if (is.numeric(parameters)) round(parameters, digits) 
else parameters
}
else if (edge.labels == "names") names
else values
direction <- ifelse((heads == 2), " dir=both", "")
for (par in 1:nrow(ram)) {
if ((!ignore.double) || (heads[par] == 1)) 
cat(file = handle, paste("  \"", variables[from[par]], 
"\" -> \"", variables[to[par]], "\" [label=\"", 
labels[par], "\"", direction[par], "];\n", sep = ""))
}
cat(file = handle, "}\n")
}

- snip 

E.g., continuing the example in ?path.diagram,

path.diagram(sem.dhp, min.rank='RIQ, RSES, RParAsp, FParAsp, FSES, FIQ', 
max.rank='ROccAsp, REdAsp, FEdAsp, FOccAsp', 
parameters=standardized.coefficients(sem.dhp)$"Std. Estimate")

I'll put the updated path.diagram.sem() in the sem package when I have a
chance.

I hope this helps,
 John


John Fox, Professor
Department of Sociology
McMaster University
Hamilton, Ontario
Canada L8S 4M4
905-525-9140x23604
http://socserv.mcmaster.ca/jfox
 

> -Original Message-
> From: Steve Powell [mailto:[EMAIL PROTECTED]
> Sent: Wednesday, September 19, 2007 3:33 AM
> To: [EMAIL PROTECTED]
> Cc: [EMAIL PROTECTED]
> Subject: Re: [R] SEM - standardized path coefficients?
> 
> Dear list members,
> In sem, std.coef() will give me standardized coefficients from a sem 
> model.
> But is there a trick so that path.diagram can use 

[R] Ambiguities in vector

[Birgit Lemcke]

Hello all you helpful people out there!

I am stil R Beginner using R 2.5.1 on a Apple Power Book G4 with Mac
OS X 10.4.10 .

Perhaps you haven´t understood my question in the mail yesterday. So  
I will try to describe my problem in a different way

You see the tables. I would like to test the variables between the  
tables. But for some variables in some species , I have more than 1  
possibility.
Example: if the variable is leaf form coded by numbers. The species  
Anth-crin could have the form round or elliptic coded with 1 and 2.  
So there is written 12. But the two numbers should be treated  
separately. Is there a possibility in R to have a classe with  
ambiguities? Or do I have to recode my variables in a different way  
to handle this?

I really hope you understand now what I mean. If not please ask me.

I would be very pleased, if somebody could help me.

Here are the two tables:

MalTabChi
X1 X4 X6 X8  X10  X14  X21  X24   X29  X38  X43 X50
X67  X76  X78 X80 X82 X84
Anth_cap   1  1  1  1651   45124   12   6
5652   4   1   1
Anth_crin 12  1  1  2   7651   45   2562   25  56
56  3452  23   1   2
Anth_eck  12  1 12  175   12514   452  56
452  34   1  12
Anth_gram  2  1  1  1651   2525   23   25  45
5   452  23   1  12
Anth_insi  2  1  1  2   63514 222  45
45   45   12   3   1  23
Anth_laxi 12  1  1 127   4515   245   235  46
56  3452  23   1  12
Anth_sing  1  1  2  17 234514   129 2345   12  46
45   23   2   1   1
Aski_albo_ari  3  1  1  2652   46 2   34   15  34
553   4   1   1
Aski_alt  13  1  1  26524 23   15  46
552  34   3   1
Aski_and   1  1  2  26525   1  36
453   3   3   1
Aski_capi  3  1  1  2   63525 235  45
453   3   1   1.

FemTabChi
  X1 X4   X6 X8  X10  X14 X21 X24   X29  X38  X43 X50
X67 X76  X78 X80 X82 X84
Anth_cap 1  11  244   1   5 6   142   6
56   52  23   1   1
Anth_crin1  11  2   475   1  45 612
455  342   3   1  23
Anth_eck 1  11  245   1  45 612  56
46 3452   3   1  12
Anth_gram1  11  2 5   2   5  4   56
56   52   3   1   1
Anth_insi1  11  235   1   426   252
45   52   3   1 234
Anth_laxi1  11  2   475   1  56 6   242
45 345   21  23   1   1
Anth_sing1  11  2   47   24   1   22422
44   52  12   1   1
Aski_albo_ari2  11  245   2   4 2   34   15
45   53   4   1   1
Aski_alt12  11  245   2   4895   15
465   52   3   3   1
Aski_and 1  11  245   2   5   25951  46
25   52  23   1   1
Aski_capi   23  11  2  2345   2   5  2459  2355
465  343   3   1   1
Aski_chart  12  11  245   2   4292   15   4
25   52  34   3   1
Aski_deli2  11  245  12   4 625
465   33   4   1   1..

Greetings

Birgit




Birgit Lemcke
Institut für Systematische Botanik
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
[EMAIL PROTECTED]






[[alternative HTML version deleted]]

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Re: [R] RE : Must be easy, but haven't found the function (numerical integration)

[Ptit_Bleu]

Hello Ravi,

I was also trying to write down such a calculation but I did not manage (I
didn't use diff(x)).
Thank you for the solution.
Ptit Bleu.



Ravi Varadhan wrote:
> 
> Here is a simple trapezoidal rule integrator:
> 
> x <- time
> y <- value
> 
> area <- sum(diff(x)*(y[-1]+y[-length(y)]))/2
> 
> Ravi.
> 
> 
> 
> ---
> 
> Ravi Varadhan, Ph.D.
> 
> Assistant Professor, The Center on Aging and Health
> 
> Division of Geriatric Medicine and Gerontology 
> 
> Johns Hopkins University
> 
> Ph: (410) 502-2619
> 
> Fax: (410) 614-9625
> 
> Email: [EMAIL PROTECTED]
> 
> Webpage:  http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
> 
> 
> 
> 
> 
> 
> -Original Message-
> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
> On
> Behalf Of Ptit_Bleu
> Sent: Tuesday, September 18, 2007 11:24 AM
> To: r-help@r-project.org
> Subject: Re: [R] RE : Must be easy, but haven't found the function
> (numerical integration)
> 
> 
> Thanks to all.
> 
> cumsum can be helpful but the solution given by David seems to match my
> request.
> I will test it as soon as possible (before the end of the week, I hope).
> 
> Have a nice end of day,
> Ptit Bleu.
> 
> 
> 
> GOUACHE David wrote:
>> 
>> try :
>> 
>> library(Bolsatd)
>> ?sintegral
>> 
>> or:
>> 
>> library(caTools)
>> ?trapz
>> 
>> David Gouache
>> Arvalis - Institut du Végétal
>> Station de La Minière
>> 78280 Guyancourt
>> Tel: 01.30.12.96.22 / Port: 06.86.08.94.32
>> 
>> 
>> -Message d'origine-
>> De : Ptit_Bleu [mailto:[EMAIL PROTECTED] 
>> Envoyé : lundi 17 septembre 2007 12:09
>> À : [EMAIL PROTECTED]
>> Objet : [R] Must be easy,but haven't found the function (numerical
>> integration)
>> 
>> 
>> Hi,
>> 
>> I have a data frame of 2 columns with the following types :
>> data$day char
>> data$value num
>> 
>> And I plot my data with :
>> plot(strptime(donnees$day,format="%Y-%m-%d %H:%M:%S"),donnees$value,
>> type="l")
>> 
>> And I'd just like to get the numerical value of the integration of this
>> graph.
>> I looked at ?integrate but, as far as I understood (that is, not very
>> much,
>> due to my poor english), it seems that it doesn't work with values in
>> data
>> frame.
>> 
>> Could you please help me to do this ?
>> 
>> Thanks in advance,
>> Have a nice week,
>> Ptit Bleu.
>> -- 
>> View this message in context:
>>
> http://www.nabble.com/Must-be-easy%2C-but-haven%27t-found-the-function-%28nu
> merical-integration%29-tf4465684.html#a12732936
>> Sent from the R help mailing list archive at Nabble.com.
>> 
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>> 
>> 
> 
> -- 
> View this message in context:
> http://www.nabble.com/Must-be-easy%2C-but-haven%27t-found-the-function-%28nu
> merical-integration%29-tf4465684.html#a12759423
> Sent from the R help mailing list archive at Nabble.com.
> 
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
> 
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
> 
> 

-- 
View this message in context: 
http://www.nabble.com/Must-be-easy%2C-but-haven%27t-found-the-function-%28numerical-integration%29-tf4465684.html#a12792420
Sent from the R help mailing list archive at Nabble.com.

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[R] problem with generalized singular value decomposition using LAPACK

[Altuna Akalin]

Hi All,
I'm trying to run  generalized singular value decomposition (GSVD)   function
from LAPACK library. Basically my problem is that I can not run it for large
matrices, I get a memory error.
I'm using R 2.5.1.  I tried this on  intel centos5 machines with 2 GB memory 
and 8 GB memory. I have unlimited max memory,cpu time and virtual memory.

LAPACK is already compiled for R (libRlapack.so ) and using dyn.load and
.Fortran functions it's possible to call LAPACK functions(I don't if it's the
best way to do it)
. I pasted the function below.
As I said,  it's not possible to run GSVD on large matrices. Here is couple of
examples:

>  res=GSVD( matrix(1:35000,5000,6), matrix(1:35000,5000,6)  ) #runs without
problems
>  res=GSVD( matrix(1:36000,6000,6), matrix(1:36000,6000,6)  )
Error: cannot allocate vector of size 274.7 Mb

when tried with 8gig machine:
res=GSVD(matrix(1:36000,6000,6), matrix(1:36000,6000,6)  ) #runs without 
problems
>  res=GSVD(matrix(1:42000,7000,6), matrix(1:36000,6000,6)  )
Error: cannot allocate vector of size 373.8 Mb

when I tried this with equivalent built-in matlab GSVD function, I get a similar
memory error as well. matlab also uses LAPACK for this.

Is there a workaround for this problem without increasing the memory? Does using
.Fortran makes it worse (memory wise)?
I need to work with matrices 4 times larger than the ones I tried.

I would be grateful if anyone can help on these issues
Best,
Altuna

# function
GSVD<-function(A,B)
{   
# A=U*E1*Q'
# B=V*E2*Q'
dyn.load("/usr/local/lib/R/lib/libRlapack.so")
#is.loaded("dggsvd") # returns TRUE
 
z <- .Fortran("dggsvd",
as.character('N'),
as.character('N'),
as.character('Q'),
as.integer(nrow(A)),
as.integer(ncol(A)),
as.integer(nrow(B)),
integer(1),
integer(1),
as.double(A),
as.integer(nrow(A)),
as.double(B),
as.integer(nrow(B)),
 double(ncol(A)),
double(ncol(A)),
double(nrow(A)*nrow(A)),
as.integer(nrow(A)),
double(nrow(B)*nrow(B)),
as.integer(nrow(B)),
double(ncol(A)*ncol(A)),
as.integer(ncol(A)),
double(max(c(3*ncol(A),nrow(A),nrow(B)))+ncol(A)),
integer(ncol(A)),
integer(1),dup=FALSE)
K=z[7][[1]]
L=z[8][[1]]
U=z[15][[1]]
V=z[17][[1]]
Q=z[19][[1]]
ALPHA=z[13][[1]]
BETA=z[14][[1]]
R=matrix(z[9][[1]],ncol(A),nrow=nrow(A),byrow=FALSE)
U=matrix(U,ncol=nrow(A),nrow=nrow(A),byrow=FALSE)
V=matrix(V,ncol=nrow(B),nrow=nrow(B),byrow=FALSE)
  Q=matrix(Q,ncol=ncol(A),nrow=ncol(A),byrow=FALSE)
D1=mat.or.vec(nrow(A),K+L)
D2=mat.or.vec(nrow(B),K+L)

oR=mat.or.vec((K+L),ncol(A))
if(K > 0)
{
if(K==1)
{ D1[1:K,1:K] =rep(1,K)
}
else
{
  diag(D1[1:K,1:K])=rep(1,K)
}
 diag(D1[(K+1):(K+L),(K+1):(K+L)])=ALPHA[(K+1):(K+L)]
diag(D2[1:L,(K+1):(K+L)])=BETA[(K+1):(K+L)]
   
}

if(K ==0)
{
diag(D1[(K+1):(K+L),(K+1):(K+L)])=ALPHA[(K+1):(K+L)]
diag(D2[1:L,(K+1):(K+L)])=BETA[(K+1):(K+L)]

}
   
Ci=ALPHA[(K+1):(K+L)]
S=BETA[(K+1):(K+L)]

oR[(1):(K+L),(ncol(A)-K-L+1):(ncol(A))]=R[(1):(K+L),(ncol(A)-K-L+1):(ncol(A))]
   
return(list(U=U,V=V,Q=Q,D1=D1,D2=D2,oR=oR,C=Ci,S=S,K=K,L=L))
   
}

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Re: [R] Smooth line in graph

[Nestor Fernandez]

Both worked, thanks!

N. Fernandez

> Katharine Mullen:
>
> require(splines)
> x<-1:5
> y <- c(0.31, 0.45, 0.84, 0.43, 0.25)
> yy <-predict(interpSpline(x, y))
> plot(x, y)
> lines(yy)
>   

> Greg Snow:
> lines(spline(x,y, method='n', n=250))

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[R] R

[mohammad sahebhonar]

I am going to fit my model with R-2.5.1.tar
my model is y=fixed effect+b(x) and I have three column in my
data file (y a x) and about 20 observation(y) 
but I had some problems. I was wondering If you could help me
the error massage is:
> res <- read.table("pro.sdf")
> fm <- glm(y=A+x,data=res)
Error: NA/NaN/Inf in foreign function call (arg 4)
In addition: Warning messages:
1: - not meaningful for factors in: Ops.factor(y, mu)
2: - not meaningful for factors in: Ops.factor(eta, offset)
3: - not meaningful for factors in: Ops.factor(y, mu)
thank you
sincerely
M.Sahebhonar

 Send instant messages to your online friends http://uk.messenger.yahoo.com 
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Re: [R] R

[Ted Harding]

On 20-Sep-07 08:45:43, mohammad sahebhonar wrote:
> I am going to fit my model with R-2.5.1.tar
> my model is y=fixed effect+b(x) and I have three column in my
> data file (y a x) and about 20 observation(y) 
> but I had some problems. I was wondering If you could help me
> the error massage is:
>> res <- read.table("pro.sdf")
>> fm <- glm(y=A+x,data=res)
> Error: NA/NaN/Inf in foreign function call (arg 4)
> In addition: Warning messages:
> 1: - not meaningful for factors in: Ops.factor(y, mu)
> 2: - not meaningful for factors in: Ops.factor(eta, offset)
> 3: - not meaningful for factors in: Ops.factor(y, mu)
> thank you
> sincerely
> M.Sahebhonar
> 
>  Send instant messages to your online friends
> http://uk.messenger.yahoo.com 
>   [[alternative HTML version deleted]]

There are two points to investigate in your description above.

1. You describe your datafile as having three columns "y", "a", "x",
   but in your formular you wrote "A+x". If the column-name is "a"
   then "A+x" will not work since "a" and "A" are different names.
   Either the column name in the datafile really is "A", and
   there is no problem (you simply typed it wrong above),
   or it is really "a" and you should use "y ~ a+x" (see below).

2. The way to specify a model formula to glm (also lm, etc.)
   is to write the formula as

  y ~ A+x  (or y ~ a+x, depending on which one is correct)

   Do not use "y = a+x"!

Best woishes,
Ted.


E-Mail: (Ted Harding) <[EMAIL PROTECTED]>
Fax-to-email: +44 (0)870 094 0861
Date: 20-Sep-07   Time: 10:50:24
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[R] combine mathematical expressions with plain text

[squall44]

Hello,

I would like to create a mtext. The argument 'text' should combine the
mathematical expressions 'bar' with the plain text ' = 3.07'. Is that
possible?

mtext(text=expression(bar(x)) ...)
' = 3.07'

Thanks for any ideas
Tobias
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View this message in context: 
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Re: [R] Smooth line in graph

[Nestor Fernandez]

Sorry, I answered too quickly.
It worked with the "simplified" example I provided but not with 
non-regular intervals in x:

x<-c(-45,67,131,259,347)
y <- c(0.31, 0.45, 0.84, 0.43, 0.25)

plot(x,y)
lines(spline(x,y, method='n', n=250))
#or:
lines(predict(interpSpline(x, y)))

Produce the same decrease between first two points and the shape is 
quite different to that produced by sigmaplot -I need comparable 
figures. Changing "method" and "n" arguments did not help.

Sorry for bothering. Any other suggestion?




Greg Snow escribió:
> Try:
>
>   
>> lines(spline(x,y, method='n', n=250))
>> 
>
>

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Re: [R] problem with generalized singular value decomposition using LAPACK

[elw]

> I'm trying to run generalized singular value decomposition (GSVD) 
> function from LAPACK library. Basically my problem is that I can not run 
> it for large matrices, I get a memory error. I'm using R 2.5.1.  I tried 
> this on intel centos5 machines with 2 GB memory and 8 GB memory. I have 
> unlimited max memory,cpu time and virtual memory.
>
>>  res=GSVD( matrix(1:35000,5000,6), matrix(1:35000,5000,6)  ) #runs 
>> without
> problems
>>  res=GSVD( matrix(1:36000,6000,6), matrix(1:36000,6000,6)  )
> Error: cannot allocate vector of size 274.7 Mb


Did you examine R's internal memory limits, e.g. ?memory for help...

that should help.  [You should, most likely, be able to allocate a ~274MB 
vector on a 2GB machine... but you might have to coerce R into taking that 
much memory from the system, rather than trying to be conservative.]

--elijah

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Re: [R] combine mathematical expressions with plain text

[Scionforbai]

plot(0,0,"n")
mtext( expression( bar(x) == 3.07) )

but you can also simply 'paste' things:

text(0,0,labels=expression(paste(bar(omega), " = 1")),srt=90)

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Re: [R] Need help on "date"

[Arun Kumar Saha]

This mail is continuation of my previous one. i have some raw data from
Excel which was carried to R:

data = read.delim(file="clipboard", header=T)
> data
   Date Price
1  09/01/05   365
2  09/02/05   360
3  09/03/05   360
4  09/05/05   370
5  09/06/05   370
6  09/08/05   365
7  09/09/05   365
8  09/10/05   365
9  09/12/05   365
10 09/13/05   360
11 09/14/05   360
12 09/15/05   360

and, using the input from R-help I exctracted day, month, and year, from
"Date"

year = as.numeric(format(as.Date(data[,1],"%m/%d/%y"),"%Y"))
month = as.numeric(format(as.Date(data[,1],"%m/%d/%y"),"%m"))
day = as.numeric(format(as.Date(data[,1],"%m/%d/%y"),"%d"))

Now I want to create a date-variable and put it in actual data:

library(date)
data1 = cbind(mdy.date(month, day, year), data[,-1])
> data1
   [,1] [,2]
 [1,] 16680  365
 [2,] 16681  360
 [3,] 16682  360
 [4,] 16684  370
 [5,] 16685  370
 [6,] 16687  365
 [7,] 16688  365
 [8,] 16689  365
 [9,] 16691  365
[10,] 16692  360
[11,] 16693  360
[12,] 16694  360

However this is not that thing what I wanted, first column has been jumbled,
it is not in actual date format.

Can anyone tell me what should i do here?

Regards,






On 9/18/07, Arun Kumar Saha <[EMAIL PROTECTED]> wrote:
>
> Dear all,
>
> I have a variable 'x' like that:
>
> > x
> [1] "2005-09-01"
>
> Here, 2005 represents year, 09 month and 01 day.
>
> Now I want to create three variables naming: y, m, and d such that:
>
> y = 2005
> m = 09
> d = 01
>
> can anyone tell me how to do that?
>
> Regards,
>
>

[[alternative HTML version deleted]]

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Re: [R] combine mathematical expressions with plain text

[Fernando Mayer]

Hi,

have you tried:

mtext(expression(bar(x) == 3.07), ...)

or

mtext(bquote(bar(x) == 3.07), ...)

?

Fernando Mayer.

squall44 escreveu:
> Hello,
> 
> I would like to create a mtext. The argument 'text' should combine the
> mathematical expressions 'bar' with the plain text ' = 3.07'. Is that
> possible?
> 
> mtext(text=expression(bar(x)) ...)
> ' = 3.07'
> 
> Thanks for any ideas
> Tobias

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Re: [R] Need help on "date"

[Gabor Grothendieck]

Since this is a time series you might want to look at the zoo package:

Lines <- "Date Price
09/01/05   365
09/02/05   360
09/03/05   360
09/05/05   370
09/06/05   370
09/08/05   365
09/09/05   365
09/10/05   365
09/12/05   365
09/13/05   360
09/14/05   360
09/15/05   360
"

library(zoo)
# replace with
#z <- read.zoo("myfile.dat", header = TRUE,format = "%m/%d/%Y")
z <- read.zoo(textConnection(Lines), header = TRUE, format = "%m/%d/%Y")
plot(z)

vignette("zoo") # info on zoo
vignette("zoo-quickref") # more info on zoo



On 9/20/07, Arun Kumar Saha <[EMAIL PROTECTED]> wrote:
> This mail is continuation of my previous one. i have some raw data from
> Excel which was carried to R:
>
> data = read.delim(file="clipboard", header=T)
> > data
>   Date Price
> 1  09/01/05   365
> 2  09/02/05   360
> 3  09/03/05   360
> 4  09/05/05   370
> 5  09/06/05   370
> 6  09/08/05   365
> 7  09/09/05   365
> 8  09/10/05   365
> 9  09/12/05   365
> 10 09/13/05   360
> 11 09/14/05   360
> 12 09/15/05   360
>
> and, using the input from R-help I exctracted day, month, and year, from
> "Date"
>
> year = as.numeric(format(as.Date(data[,1],"%m/%d/%y"),"%Y"))
> month = as.numeric(format(as.Date(data[,1],"%m/%d/%y"),"%m"))
> day = as.numeric(format(as.Date(data[,1],"%m/%d/%y"),"%d"))
>
> Now I want to create a date-variable and put it in actual data:
>
> library(date)
> data1 = cbind(mdy.date(month, day, year), data[,-1])
> > data1
>   [,1] [,2]
>  [1,] 16680  365
>  [2,] 16681  360
>  [3,] 16682  360
>  [4,] 16684  370
>  [5,] 16685  370
>  [6,] 16687  365
>  [7,] 16688  365
>  [8,] 16689  365
>  [9,] 16691  365
> [10,] 16692  360
> [11,] 16693  360
> [12,] 16694  360
>
> However this is not that thing what I wanted, first column has been jumbled,
> it is not in actual date format.
>
> Can anyone tell me what should i do here?
>
> Regards,
>
>
>
>
>
>
> On 9/18/07, Arun Kumar Saha <[EMAIL PROTECTED]> wrote:
> >
> > Dear all,
> >
> > I have a variable 'x' like that:
> >
> > > x
> > [1] "2005-09-01"
> >
> > Here, 2005 represents year, 09 month and 01 day.
> >
> > Now I want to create three variables naming: y, m, and d such that:
> >
> > y = 2005
> > m = 09
> > d = 01
> >
> > can anyone tell me how to do that?
> >
> > Regards,
> >
> >
>
>[[alternative HTML version deleted]]
>
> __
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

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[R] referencing packages?

[Rainer M. Krug]

Hi

I know how to referenc R in a scientific paper - but is there a 
standardised way to reference packages?

Thanks

Rainer

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Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)

Plant Conservation Unit
Department of Botany
University of Cape Town
Rondebosch 7701
South Africa

Tel:+27 - (0)21 650 5776 (w)
Fax:+27 - (0)86 516 2782
Fax:+27 - (0)21 650 2440 (w)
Cell:   +27 - (0)83 9479 042

Skype:  RMkrug

email:  [EMAIL PROTECTED]
[EMAIL PROTECTED]

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Re: [R] referencing packages?

[Katharine Mullen]

use citation("pkg-name")

On Thu, 20 Sep 2007, Rainer M. Krug wrote:

> Hi
>
> I know how to referenc R in a scientific paper - but is there a
> standardised way to reference packages?
>
> Thanks
>
> Rainer
>
> --
> NEW EMAIL ADDRESS AND ADDRESS:
>
> [EMAIL PROTECTED]
>
> [EMAIL PROTECTED] WILL BE DISCONTINUED END OF MARCH
>
> Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
> Biology (UCT)
>
> Plant Conservation Unit
> Department of Botany
> University of Cape Town
> Rondebosch 7701
> South Africa
>
> Tel:  +27 - (0)21 650 5776 (w)
> Fax:  +27 - (0)86 516 2782
> Fax:  +27 - (0)21 650 2440 (w)
> Cell: +27 - (0)83 9479 042
>
> Skype:RMkrug
>
> email:[EMAIL PROTECTED]
>   [EMAIL PROTECTED]
>
> __
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> and provide commented, minimal, self-contained, reproducible code.
>

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Re: [R] referencing packages?

[Rainer M. Krug]

Thanks a million

Rainer

Katharine Mullen wrote:
> use citation("pkg-name")
> 
> On Thu, 20 Sep 2007, Rainer M. Krug wrote:
> 
>> Hi
>>
>> I know how to referenc R in a scientific paper - but is there a
>> standardised way to reference packages?
>>
>> Thanks
>>
>> Rainer
>>
>> --
>> NEW EMAIL ADDRESS AND ADDRESS:
>>
>> [EMAIL PROTECTED]
>>
>> [EMAIL PROTECTED] WILL BE DISCONTINUED END OF MARCH
>>
>> Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
>> Biology (UCT)
>>
>> Plant Conservation Unit
>> Department of Botany
>> University of Cape Town
>> Rondebosch 7701
>> South Africa
>>
>> Tel: +27 - (0)21 650 5776 (w)
>> Fax: +27 - (0)86 516 2782
>> Fax: +27 - (0)21 650 2440 (w)
>> Cell:+27 - (0)83 9479 042
>>
>> Skype:   RMkrug
>>
>> email:   [EMAIL PROTECTED]
>>  [EMAIL PROTECTED]
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
> 
> __
> R-help@r-project.org mailing list
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.


-- 
NEW EMAIL ADDRESS AND ADDRESS:

[EMAIL PROTECTED]

[EMAIL PROTECTED] WILL BE DISCONTINUED END OF MARCH

Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)

Plant Conservation Unit
Department of Botany
University of Cape Town
Rondebosch 7701
South Africa

Tel:+27 - (0)21 650 5776 (w)
Fax:+27 - (0)86 516 2782
Fax:+27 - (0)21 650 2440 (w)
Cell:   +27 - (0)83 9479 042

Skype:  RMkrug

email:  [EMAIL PROTECTED]
[EMAIL PROTECTED]

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[R] Cutting & pasting help examples into script window

[Muenchen, Robert A (Bob)]

Hi All,

When I cut & paste help file examples into a script window, about half
the time it pastes as a single long line. 

The steps I follow are:

1. Open a help file e.g. ?data.frame.
2. Select the examples at the bottom.
3. Choose File: Copy.
4. Return to the console.
5. Choose File: New script.
6. Choose File: Paste or do CTRL-V. The examples frequently paste as a
single long line. 

I came across this in 2.6.0 beta on Windows XP & thought it was related
to the cut/paste changes in that version. I went back to 2.5.1 and at
first it worked fine, verifying my suspicion that it was a 2.6.0
problem. I double-checked my steps before posting, and to my surprise
found that in both versions this problem is intermittent.

I thought it might be a menu vs. keyboard CTRL-V difference, but found
it happens with both, and in both versions. I have also fiddled with
sizing or moving the Help window but that doesn't seem to be related. I
did discover that may be a problem on the paste side of things, as so
far it *always* pastes into Notepad correctly.

Any ideas?

Thanks,
Bob

P.S. What would really be slick would be to select the example in Help,
right-click and choose Run Line or Selection. Perhaps in version 2.7.
;-) .

=
Bob Muenchen (pronounced Min'-chen), 
Manager, Statistical Consulting Center 
U of TN Office of Information Technology
Stokely Management Center, Suite 200
916 Volunteer Blvd., Knoxville, TN 37996-0520
Voice: (865) 974-5230
FAX: (865) 974-4810
Email: [EMAIL PROTECTED]
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[R] SEM - singularity error

[nicolette . cagle]

Good morning,

I am trying to develop a structural equation model of snake abundance using
habitat variables. In attempting to estimate the model using the "sem" package
in R version 2.4.0, I receive the following error message:

"Error in solve.default(C) : system is computationally singular: reciprocal
condition number = 1.75349e-16"

MAIN PROBLEM: I am hoping to discover why I am receiving the aforementioned
error message and how to successfully estimate the model.

OTHER INFORMATION:
1. I believe the model is over-identified rather than under-identified (based on
my understanding of the t-rule). I have observed data for 10 variables (9
exogenous, 1 endogenous).

2. I am not certain that I have used the proper tool to estimate the covariance
matrix. In this case, I used the "VAR" function.

3. I am most concerned that I have improperly coded the RAM file. For example,
in a case where I have three exogenous indicators of one exogenous latent
variable, I specify a start value of 1 for one of the exogenous indicators. I
am not sure if this is proper or necessary.

4. I am new to SEM; this is the first model I have ever tried to estimate.

R CODE: Below is the r-code I have used to estimate the structural equation
model --

# LOADING R PACKAGES
library(sem)

# READING IN THE CSV FILES
thsi.2006<-read.csv("thsi_ab_env_space_sem.csv")
thsi<-thsi.2006

# MAKING "RAM" FILE 2
model2.nlc <-specify.model()
Moist->slope, NA, 1
Moist->sand, lamda21, NA
Moist->clay, lamda31, NA
Hab->isol, NA, 1
Hab->edgedist_a, lamda52, NA
Hab->ag10, lamda62, NA
Hab->urb10, lamda72, NA
Hab->rd10, lamda82, NA
Hab->y, lamda92, NA
Moist->this, gamma11, NA
Hab->this, gamma12, NA
slope<->slope, theta11, NA
sand<->sand, theta22, NA
clay<->clay, theta33, NA
isol<->isol, theta44, NA
edgedist_a<->edgedist_a, theta55, NA
ag10<->ag10, theta66, NA
urb10<->urb10, theta77, NA
rd10<->rd10, theta88, NA
y<->y, the99, NA
Moist<->Moist, phi11, NA
Hab<->Hab, phi22, NA
this<->this, theps11, NA

model2.nlc
end

# MAKING S (COVARIANCE MATRIX)
thsi.var <- var(thsi)

# MAKING UNSCALED SEM MODEL
sem2<-sem(ram=model2.nlc, S=thsi.var, N=22)

I am also attaching a jpeg diagram of the model I am trying to estimate. Please
let me know if there is any additional information that I should add to this
posting.

Thank you so much for your time.
Nicolette Cagle
-- 
Ecology Ph.D. Candidate
Duke University
Durham, NC 27708
www.duke.edu/~nlc4__
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[R] How to find "p"(proportion) in binomial(n, p)?

[fang liu]

Hi,

I got a problem. I am trying to find "p" in binomial.
X~bin(n, p)
I want to find value "p", so that Pr(X <= k) <= alpha.
Here, n, k are known.

Thank you for helping me with this!

Catherine

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[R] The Survey package again

[eugen pircalabelu]

Good afternoon! 
   
  1 I have a bit of a problem with the Survey package, but one that is
 more theoretical than practical. If for example on wishes to use some
 additional information  which comprises of 4 variables with 7, 5,5 and 5
 categories (resulting in 875 post-strata if the whole crossing were to
 be constructed) and if only the marginal distribution of each variable
 is known, would it be better to rake or to calibrate? 
   
  2 Is calibrating affected by the cells with 0 frequency, as raking
 is?  
   
  3 when a sample is already stratified and one wishes to post stratify
 by other variables, do the new weights take account of the fact that
 the sample is stratified and that sampling weights could be determined;
 and what is the algorithm for determining these new weights; are the new 
weights determined for each strata taking account of the sampling weights for 
each strata ?
   
  Thank you and have a good day!

   
-

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Re: [R] Identify and plotting symbols.

[D L McArthur]

Rolf Turner  auckland.ac.nz> writes:
...
> I tried
> 
>   ind <- identify(x,y,labels=rep("\021",length(x)),offset=0)

Have you tried "\225" or "\244" or "\370" (which can be previewed by 
typing > "\225" etc), and clicking just above the plotted datapoints?

D L McArthur, UCLA Sch of Medicine   dmca  ucla.edu

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[R] ggplot and xlim/ylim

[jiho]

Hello everyone,

I am (happily) using ggplot2 for all my plotting now and I wondered  
is there is an easy way to specify xlim and ylim somewhere when using  
the ggplot syntax, as opposed to the qplot syntax. Eg.

  qplot(data=mtcars,y=wt, x=qsec,xlim=c(0,30))

<->

ggplot(mtcars, aes(y=wt, x=qsec)) + geom_point() + ???

Indeed the ggplot syntax is in general more flexible and powerful and  
I usually rely on it in scripts. It would be nice to know how to use  
xlim/ylim with this syntax.

Thank you in advance.

JiHO
---
http://jo.irisson.free.fr/

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Re: [R] Cutting & pasting help examples into script window

[Stefan Grosse]

On Thursday 20 September 2007 15:08:45 Muenchen, Robert A (Bob) wrote:
MR > Hi All,
MR >
MR > When I cut & paste help file examples into a script window, about half
MR > the time it pastes as a single long line.
MR >
MR > Any ideas?
MR >
MR > Thanks,
MR > Bob
MR >
MR > P.S. What would really be slick would be to select the example in Help,
MR > right-click and choose Run Line or Selection. Perhaps in version 2.7.
MR > ;-) .

What I do not understand is why you not just type example(yourcommand)?

Stefan

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[R] Comprehensive New Learning Resource for R

[Rob Kabacoff]

Hi Folks,

I have created a website with over 70 R tutorials on a wide range of subjects. 
The site is aimed at data analysts who have an idea about what they would like 
to do, but don't know how to do it in R. The site should be particularly useful 
for users of statistical packages like SAS, SPSS, Stata, and Systat who would 
like to get up and running in R quickly. However, I think that it will also be 
useful for even veteran R users.

The URL is http://www.statmethods.net

Topics are organized around these headings:
* The R Interface
* Data Input
* Data Management
* Basic Statistics
* Advanced Statistics
* Basic Graphs
* Advanced Graphs

Topic range from GUIs to creating publication quality output, from database 
access to date values, from t-tests to generalized linear models, from 
barcharts to interactive multivariate graphics.

I hope that you find this useful. Please feel free to link to the site.

Feedback is always welcome.

Sincerely,

Rob Kabacoff, Ph.D.
[EMAIL PROTECTED]
www.statmethods.net

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[R] Package Survey

[Rita Sousa]

Hello,

 

How I use the function as.svrepdesign without memory.size problems?

 

desenho_npc_JK <- as.svrepdesign(desenho_npc,type="JKn")

Error: cannot allocate vector of size 161.3 Mb

In addition: Warning messages:

1: Reached total allocation of 1022Mb: see help(memory.size) 

2: Reached total allocation of 1022Mb: see help(memory.size) 

3: Reached total allocation of 1022Mb: see help(memory.size) 

4: Reached total allocation of 1022Mb: see help(memory.size)

 

Many thanks,

---
Rita Sousa
Departamento de Metodologia e Sistemas de Informação

INE - DP: Instituto Nacional de Estatística - Delegação do Porto 

Tel.: 22 6072016 (Extensão: 4116)
--- 




[[alternative HTML version deleted]]

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Re: [R] Must be easy, but haven't found the function (numerical integration)

[John Wilkinson_dsl]

Ptit Bleu.

try the  'adapt' function for multi-dimensional numerical integration.

library(adapt)
Adaptive Numerical Integration in 2–20 Dimensions

John



Checked by AVG Free Edition.

11:53

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Re: [R] Cutting & pasting help examples into script window

[Muenchen, Robert A (Bob)]

Stephan Grosse replied:

> 
> What I do not understand is why you not just type
example(yourcommand)?
> 
> Stefan

That's a good question. I want to play around with variations of the
examples rather than run them exactly as they are.

Thanks,
Bob

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[R] comparing survival curves(weighted log rank test)

[raymond chiruka]

hie
   
  I know I can use the log rank test for comparing survival curves but my 
problem is that the G(rho) by fleming & harrington(1982) which is the one in R 
seems to be inadequate are they any other test ie fleming & harrington (1991) 
as there are some some differences on the survival curves I need to compare.
  if some one can suggest a weighted log rank in  R i will be very greatful

   
-

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Re: [R] ggplot and xlim/ylim

[hadley wickham]

Hi Jiho,

To figure this out, you need to think about exactly what you are doing
when you change the limits - what part of the plot are you changing?
You are changing the scales, and if you have a look at
http://had.co.nz/ggplot2/scale_continuous.html, you'll see you need
something like:

+ scale_y_continuous(limits=c(0,10)

Remember, you can also modify qplot in the same way as ggplot:

qplot(...) + geom_point() + ...

Regards,

Hadley

On 9/20/07, jiho <[EMAIL PROTECTED]> wrote:
> Hello everyone,
>
> I am (happily) using ggplot2 for all my plotting now and I wondered
> is there is an easy way to specify xlim and ylim somewhere when using
> the ggplot syntax, as opposed to the qplot syntax. Eg.
>
>   qplot(data=mtcars,y=wt, x=qsec,xlim=c(0,30))
>
> <->
>
> ggplot(mtcars, aes(y=wt, x=qsec)) + geom_point() + ???
>
> Indeed the ggplot syntax is in general more flexible and powerful and
> I usually rely on it in scripts. It would be nice to know how to use
> xlim/ylim with this syntax.
>
> Thank you in advance.
>
> JiHO
> ---
> http://jo.irisson.free.fr/
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


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

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Re: [R] Package Survey

[Thomas Lumley]

On Thu, 20 Sep 2007, Rita Sousa wrote:


How I use the function as.svrepdesign without memory.size problems?

desenho_npc_JK <- as.svrepdesign(desenho_npc,type="JKn")

Error: cannot allocate vector of size 161.3 Mb


There is currently no easy way to affect the amount of memory that this 
uses, unless you can divide the data into pieces -- for example, use only 
some variables, or create separate design objects for strata.


The surveyNG package, which can handle very large designs, does not yet do 
replicate-weight analyses.



One question is how big the design actually is.
161.3Mb looks like a vector of length 21 million

If this is the number of observations in the study then you need a 
larger computer.  If it is the total number of replicate weights then you 
may just be able to increase the memory limit for R  on your computer 
using the memory.size() function, as the warning method suggests.


-thomas


In addition: Warning messages:

1: Reached total allocation of 1022Mb: see help(memory.size)

2: Reached total allocation of 1022Mb: see help(memory.size)

3: Reached total allocation of 1022Mb: see help(memory.size)

4: Reached total allocation of 1022Mb: see help(memory.size)



Many thanks,

---
Rita Sousa
Departamento de Metodologia e Sistemas de Informa??o

INE - DP: Instituto Nacional de Estat?stica - Delega??o do Porto

Tel.: 22 6072016 (Extens?o: 4116)
---




[[alternative HTML version deleted]]




Thomas Lumley   Assoc. Professor, Biostatistics
[EMAIL PROTECTED]   University of Washington, Seattle__
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Re: [R] Comprehensive New Learning Resource for R

[Wiebke Timm]

On 20.09.2007, at 09:24, Rob Kabacoff wrote:

> I hope that you find this useful. Please feel free to link to the  
> site.

Very nicely done from what I saw by browsing the site a little. Good  
colors, good content, easy to navigate. Thanks!

You might want to add self-organizing maps as a cross-over of  
clustering and visualization. Maybe statistical learning methods as  
well.

Regards,
Wiebke

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Re: [R] Comprehensive New Learning Resource for R

[Gabor Grothendieck]

Also use of T and F is bad form since its possible to
define variables T and F.  Use TRUE and FALSE.

On 9/20/07, Ted Harding <[EMAIL PROTECTED]> wrote:
> Excellent! Thanks. Just what I need for referring
> friends to.
>
> However, your very first feedback:
>
> Under http://www.statmethods.net/input/datatypes.html
> you have:
>
> ##Vectors
>
> a <- c(1,2,5.3,6,-2,4) # numberic vector
> b <- c("one","two","three") # character vector
> c <- c(T,T,T,F,T,F) #logical vector
>
> ##Refer to elements of a vector using subscripts.
>
> a[2,4] # 2nd and 4th elements of vector
>
> ## Err, no! a[c(2,4)] of course!
>
> More {when|if} I spot them!
> Best wishes,
> Ted.
>
> On 20-Sep-07 13:24:22, Rob Kabacoff wrote:
> > Hi Folks,
> >
> > I have created a website with over 70 R tutorials on a wide range of
> > subjects. The site is aimed at data analysts who have an idea about
> > what they would like to do, but don't know how to do it in R. The site
> > should be particularly useful for users of statistical packages like
> > SAS, SPSS, Stata, and Systat who would like to get up and running in R
> > quickly. However, I think that it will also be useful for even veteran
> > R users.
> >
> > The URL is http://www.statmethods.net
> >
> > Topics are organized around these headings:
> > * The R Interface
> > * Data Input
> > * Data Management
> > * Basic Statistics
> > * Advanced Statistics
> > * Basic Graphs
> > * Advanced Graphs
> >
> > Topic range from GUIs to creating publication quality output, from
> > database access to date values, from t-tests to generalized linear
> > models, from barcharts to interactive multivariate graphics.
> >
> > I hope that you find this useful. Please feel free to link to the site.
> >
> > Feedback is always welcome.
> >
> > Sincerely,
> >
> > Rob Kabacoff, Ph.D.
> > [EMAIL PROTECTED]
> > www.statmethods.net
> >
> > __
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
> 
> E-Mail: (Ted Harding) <[EMAIL PROTECTED]>
> Fax-to-email: +44 (0)870 094 0861
> Date: 20-Sep-07   Time: 15:17:14
> -- XFMail --
>
> __
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> and provide commented, minimal, self-contained, reproducible code.
>

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Re: [R] warnings although R CMD check runs without any problem

[Uwe Ligges]

Can you give examples?

Uwe


Christian Kohler wrote:
> Dear list members,
> 
> as I am new to R, I would kindly like to ask for your help.
> 
> I checked a package with the 'R CMD check' command and all worked out
> well, (only 'OK' status). Loading its vignette afterwards with
> 'source("package.Rcheck/inst/doc/vignette.R")' yields a message saying
> that several (well, in my case more than 50) warnings still exist and
> can be viewed via the 'warnings()' command.
> 
> My question now is: why are there still warnings even though the check
> has been passed without any problems? Generally speaking, would it be
> possible to submit this package e.g. to the Bioconductor project, even
> if these warnings still exist?
> 
> 
> Thanks in advance,
> Christian
> 
> 
>

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Re: [R] Comprehensive New Learning Resource for R

[Ted Harding]

Excellent! Thanks. Just what I need for referring
friends to.

However, your very first feedback:

Under http://www.statmethods.net/input/datatypes.html
you have:

##Vectors

a <- c(1,2,5.3,6,-2,4) # numberic vector
b <- c("one","two","three") # character vector
c <- c(T,T,T,F,T,F) #logical vector

##Refer to elements of a vector using subscripts.

a[2,4] # 2nd and 4th elements of vector

## Err, no! a[c(2,4)] of course!

More {when|if} I spot them!
Best wishes,
Ted.

On 20-Sep-07 13:24:22, Rob Kabacoff wrote:
> Hi Folks,
> 
> I have created a website with over 70 R tutorials on a wide range of
> subjects. The site is aimed at data analysts who have an idea about
> what they would like to do, but don't know how to do it in R. The site
> should be particularly useful for users of statistical packages like
> SAS, SPSS, Stata, and Systat who would like to get up and running in R
> quickly. However, I think that it will also be useful for even veteran
> R users.
> 
> The URL is http://www.statmethods.net
> 
> Topics are organized around these headings:
> * The R Interface
> * Data Input
> * Data Management
> * Basic Statistics
> * Advanced Statistics
> * Basic Graphs
> * Advanced Graphs
> 
> Topic range from GUIs to creating publication quality output, from
> database access to date values, from t-tests to generalized linear
> models, from barcharts to interactive multivariate graphics.
> 
> I hope that you find this useful. Please feel free to link to the site.
> 
> Feedback is always welcome.
> 
> Sincerely,
> 
> Rob Kabacoff, Ph.D.
> [EMAIL PROTECTED]
> www.statmethods.net
> 
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.


E-Mail: (Ted Harding) <[EMAIL PROTECTED]>
Fax-to-email: +44 (0)870 094 0861
Date: 20-Sep-07   Time: 15:17:14
-- XFMail --

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[R] warnings although R CMD check runs without any problem

[Christian Kohler]

Dear list members,

as I am new to R, I would kindly like to ask for your help.

I checked a package with the 'R CMD check' command and all worked out
well, (only 'OK' status). Loading its vignette afterwards with
'source("package.Rcheck/inst/doc/vignette.R")' yields a message saying
that several (well, in my case more than 50) warnings still exist and
can be viewed via the 'warnings()' command.

My question now is: why are there still warnings even though the check
has been passed without any problems? Generally speaking, would it be
possible to submit this package e.g. to the Bioconductor project, even
if these warnings still exist?


Thanks in advance,
Christian



-- 

Christian Kohler
Institute of Functional Genomics
Computational Diagnostics
University of Regensburg
D-93147 Regensburg (Germany)

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Re: [R] SEM - standardized path coefficients? - significant style

[John Fox]

Dear Steve,

I'll file this suggestion for when I next revise the sem package. I'm
unlikely to get to it soon since I rarely use the graph-drawing program dot
and would have to figure out how to do what you want. As well, I think that
I'd more likely allow the user to specify the line type for each edge in the
graph rather than hard-coding this to significance/non-significance.

Regards,
 John


John Fox, Professor
Department of Sociology
McMaster University
Hamilton, Ontario
Canada L8S 4M4
905-525-9140x23604
http://socserv.mcmaster.ca/jfox 
 

> -Original Message-
> From: Steve Powell [mailto:[EMAIL PROTECTED] 
> Sent: Thursday, September 20, 2007 3:40 AM
> To: 'John Fox'
> Cc: [EMAIL PROTECTED]; [EMAIL PROTECTED]
> Subject: RE: [R] SEM - standardized path coefficients? - 
> significant style
> 
> Dear John
> Being an R user is like having Christmas every day and having 
> a direct line to Santa for present suggestions. 
> How about if path.diagram.sem had the ability to print 
> non-significant paths in, for example dotted style? I had a 
> go myself but couldn't see how to get 
> (summary(model)$coeff)$"Pr(>|z|)" into the loop.
> Very best wishes
> Steve Powell
> 
>  
> proMENTE social research
> research | evaluation | training & consulting Kranjčevićeva 
> 35, 71000 Sarajevo
> mobile: +387 61 215 997 | office: +387 33 556 865 | fax: +387 
> 33 556 866
> skype: stevepowell99
> www.promente.org  |  www.mojakarijera.com  |  www.psih.org  
> 

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[R] Problem with lars

[Wiebke Timm]

Hi!

Ok, probably my last mail was too long. Questions are:

* Did someone try lars on data with much more components than data  
points? Did you observe bad overfitting, too? Any other observations?

* Why might the lars (least angle regression from lars package)  
method produce beta values that shoot up into the sky (until they  
overflow), and why might the Cp values start at a _negative_ value in  
step 1, growing linearly? That's not normal behaviour. What might be  
wrong there?

For details see my last mail. :)

Regards,
Wiebke

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[R] It works but I don't know how (nice scientific notation with Lattice)

[Ptit_Bleu]

Hi,

I had problems to display my results in a nice way (according to me).
Thanks to posts of people of this forum, I solved my problems (ticks with a
scientific notation and how to write nicely "V/m2" in the label of the
x-axis) but ... I don't understand the script.

Can somebody explain me how the short script below writes the scientific
notation ?
I guess it is the result of 

ans$bottom$labels$labels <- parse(text = ans$bottom$labels$labels)

but it is really not clear to me.

Thanks in advance for your explainations
Ptit Bleu.




library(lattice)

x<-c(10,100,1000,1,10,20,200,2000,2,20)
y<-c(1,2,3,4,5,2,4,6,8,10)
z<-c(1,1,1,1,1,2,2,2,2,2)

xyplot(y ~ x | z,
  scales = list(x = list(log = T)),
  xscale.components = function(...) {
  ans <- xscale.components.default(...)
  ans$bottom$labels$labels <- parse(text
= ans$bottom$labels$labels)
  ans
}
  , xlab=(expression(paste("X (V/",m^2,")"))) , ylab="Y (arb. unit)")

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[R] SUPER PARAMAGNETIC CLUSTERING

[Silvia Figini]

Dear all,
we would like to know if there exist some routines (software) to build
models based on the super paramagnetic clustering.

Best regards,
Silvia Figini


-- 
Silvia Figini
Department of Statistics "L. Lenti"
University of Pavia
Via Strada Nuova, 65 - 27100 - Pavia, Italy
tel.+39- 0382-984660
http://musing.unipv.it/datamining

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Re: [R] warnings although R CMD check runs without any problem

[Christian Kohler]

Uwe Ligges wrote:
> Can you give examples?
>
> Uwe
>
>
> Christian Kohler wrote:
>   
>> Dear list members,
>>
>> as I am new to R, I would kindly like to ask for your help.
>>
>> I checked a package with the 'R CMD check' command and all worked out
>> well, (only 'OK' status). Loading its vignette afterwards with
>> 'source("package.Rcheck/inst/doc/vignette.R")' yields a message saying
>> that several (well, in my case more than 50) warnings still exist and
>> can be viewed via the 'warnings()' command.
>>
>> My question now is: why are there still warnings even though the check
>> has been passed without any problems? Generally speaking, would it be
>> possible to submit this package e.g. to the Bioconductor project, even
>> if these warnings still exist?
>>
>>
>> Thanks in advance,
>> Christian
>>
>>
>>
>> 
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>   
Hello Uwe,

as the package is to submit to Bioconductor, I should have posted to the
BioC-Help instead but initially it was rather a 'R'-specific question to me.
My apology for that.

Examples for warning messages are

>warnings()
>1:The exprSet class is deprecated, use ExpressionSet instead
...
>6: The phenoData class is deprecated, use AnnotatedDataFrame (with
ExpressionSet) instead
>13: In s[v == x[1]] <- r : Number of elements to be replaced is not a
multiple of the substitution length.


In my opinion, these messages solely indicate some 'hints' which do not
interfere with any functionality within the package. Right?
As there is no reference to a file, which triggers these messages, I
have currently no idea where to take a closer look at.

Regards,
Christian

-- 

Christian Kohler
Institute of Functional Genomics
Computational Diagnostics
University of Regensburg
D-93147 Regensburg (Germany)

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Re: [R] warnings although R CMD check runs without any problem

[Robert Gentleman]

Hi,

Christian Kohler wrote:
> Uwe Ligges wrote:
>> Can you give examples?
>>
>> Uwe
>>
>>
>> Christian Kohler wrote:
>>   
>>> Dear list members,
>>>
>>> as I am new to R, I would kindly like to ask for your help.
>>>
>>> I checked a package with the 'R CMD check' command and all worked out
>>> well, (only 'OK' status). Loading its vignette afterwards with
>>> 'source("package.Rcheck/inst/doc/vignette.R")' yields a message saying
>>> that several (well, in my case more than 50) warnings still exist and
>>> can be viewed via the 'warnings()' command.
>>>
>>> My question now is: why are there still warnings even though the check
>>> has been passed without any problems? Generally speaking, would it be
>>> possible to submit this package e.g. to the Bioconductor project, even
>>> if these warnings still exist?
>>>
>>>
>>> Thanks in advance,
>>> Christian
>>>
>>>
>>>
>>> 
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>   
> Hello Uwe,
> 
> as the package is to submit to Bioconductor, I should have posted to the
> BioC-Help instead but initially it was rather a 'R'-specific question to me.
> My apology for that.
> 
> Examples for warning messages are
> 
>> warnings()
>> 1:The exprSet class is deprecated, use ExpressionSet instead
> ...
>> 6: The phenoData class is deprecated, use AnnotatedDataFrame (with
> ExpressionSet) instead

  These tell you that you are using data structures that are no longer 
supported and should not be used. You need to fix them - the appropriate 
replacements are also indicated in the help message.

>> 13: In s[v == x[1]] <- r : Number of elements to be replaced is not a
> multiple of the substitution length.

   This is also serious. It suggests that you have an error in your 
code. Typically if one replaces the elements in one vector
s[v == x[1]], with those in another vector, namely r, the two sets 
should be the same length. In most (but not all) cases where this 
happens there is a bug.

> 
> 
> In my opinion, these messages solely indicate some 'hints' which do not
> interfere with any functionality within the package. Right?

   No, wrong - the first two tell you that you are badly (at least one 
year) out of date in your use of data structures and the last one tells 
you that you probably have a serious problem with your code.


> As there is no reference to a file, which triggers these messages, I
> have currently no idea where to take a closer look at.

   Well, you did not give the whole output, and in it there really are 
names of files and locations.  You can also use an editor to search for
  1) any instance of the work exprSet or phenoData and replace those 
parts of the code with the new classes

  2) search for s[v == x[1]], and then use some of R's debugging methods 
to determine whether there is a bug or not.

  best wishes
Robert

> 
> Regards,
> Christian
> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
[EMAIL PROTECTED]

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Re: [R] warnings although R CMD check runs without any problem

[Prof Brian Ripley]

On Thu, 20 Sep 2007, Christian Kohler wrote:

> Dear list members,
>
> as I am new to R, I would kindly like to ask for your help.
>
> I checked a package with the 'R CMD check' command and all worked out
> well, (only 'OK' status). Loading its vignette afterwards with
> 'source("package.Rcheck/inst/doc/vignette.R")' yields a message saying
> that several (well, in my case more than 50) warnings still exist and
> can be viewed via the 'warnings()' command.
>
> My question now is: why are there still warnings even though the check
> has been passed without any problems? Generally speaking, would it be

Because the check process does not consider R-level warnings in examples 
or vignettes, only errors.  Only someone who understands the code will 
know if the warnings are pedagogical, innocuous or serious.  No one says 
that examples should not give warnings, and it may be helpful to 
illustrate when they might occur.

> possible to submit this package e.g. to the Bioconductor project, even
> if these warnings still exist?

It is possible to submit it, and very likely that it would be acceptable. 
Distributing a package with warnings you do not understand is not a good 
idea, though.

-- 
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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[R] Plotmath issue superscript "-"

[Gavin Simpson]

Dear List,

I'm trying to typeset some chemical ions in axis labels. These have both
super and subscript components, and for some, I need a superscript "-".
In LaTeX I might use $NO_3^-$ to do the typesetting, but I'm having a
problem getting the correct invocation for expression:

> expression(NO^{-}[3])
Error: syntax error, unexpected '}' in "expression(NO^{-}"
> expression(NO^-[3])
Error: syntax error, unexpected '[' in "expression(NO^-["
> expression(NO^-)
Error: syntax error, unexpected ')' in "expression(NO^-)"
> expression(NO^{-})
Error: syntax error, unexpected '}' in "expression(NO^{-}"

This is with R 2.5.1 (exact version info below).

I suspect this is something to do with my use of the "-", which has some
special meaning.

Is there a way to achieve a superscript "-" (or similar looking
character) using the plotmath routines in R?

Thanks in advance,

G

> version
   _  
platform   i686-pc-linux-gnu  
arch   i686   
os linux-gnu  
system i686, linux-gnu
status Patched
major  2  
minor  5.1
year   2007   
month  07 
day05 
svn rev42131  
language   R  
version.string R version 2.5.1 Patched (2007-07-05 r42131)

-- 
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
 Gavin Simpson [t] +44 (0)20 7679 0522
 ECRC, UCL Geography,  [f] +44 (0)20 7679 0565
 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
 Gower Street, London  [w] http://www.ucl.ac.uk/~ucfagls/
 UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%

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

Re: [R] warnings although R CMD check runs without any problem

[Christian Kohler]

Prof Brian Ripley wrote:
> On Thu, 20 Sep 2007, Christian Kohler wrote:
>
>   
>> Dear list members,
>>
>> as I am new to R, I would kindly like to ask for your help.
>>
>> I checked a package with the 'R CMD check' command and all worked out
>> well, (only 'OK' status). Loading its vignette afterwards with
>> 'source("package.Rcheck/inst/doc/vignette.R")' yields a message saying
>> that several (well, in my case more than 50) warnings still exist and
>> can be viewed via the 'warnings()' command.
>>
>> My question now is: why are there still warnings even though the check
>> has been passed without any problems? Generally speaking, would it be
>> 
>
> Because the check process does not consider R-level warnings in examples 
> or vignettes, only errors.  Only someone who understands the code will 
> know if the warnings are pedagogical, innocuous or serious.  No one says 
> that examples should not give warnings, and it may be helpful to 
> illustrate when they might occur.
>
>   
>> possible to submit this package e.g. to the Bioconductor project, even
>> if these warnings still exist?
>> 
>
> It is possible to submit it, and very likely that it would be acceptable. 
> Distributing a package with warnings you do not understand is not a good 
> idea, though.
>
>   
Dear Prof Ripley & Mr Ligges,

thanks for your help and the quick responses.

Regards,
Christian


-- 

Christian Kohler
Institute of Functional Genomics
Computational Diagnostics
University of Regensburg
D-93147 Regensburg (Germany)

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Re: [R] Plotmath issue superscript "-"

[Scionforbai]

Try:

  plot(0,0,"n")
  text(0,0,expression( {NO[3]}^'-'))

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Re: [R] Plotmath issue superscript "-"

[Peter Dalgaard]

Gavin Simpson wrote:
> Dear List,
>
> I'm trying to typeset some chemical ions in axis labels. These have both
> super and subscript components, and for some, I need a superscript "-".
> In LaTeX I might use $NO_3^-$ to do the typesetting, but I'm having a
> problem getting the correct invocation for expression:
>
>   
>> expression(NO^{-}[3])
>> 
> Error: syntax error, unexpected '}' in "expression(NO^{-}"
>   
>> expression(NO^-[3])
>> 
> Error: syntax error, unexpected '[' in "expression(NO^-["
>   
>> expression(NO^-)
>> 
> Error: syntax error, unexpected ')' in "expression(NO^-)"
>   
>> expression(NO^{-})
>> 
> Error: syntax error, unexpected '}' in "expression(NO^{-}"
>
> This is with R 2.5.1 (exact version info below).
>
> I suspect this is something to do with my use of the "-", which has some
> special meaning.
>
> Is there a way to achieve a superscript "-" (or similar looking
> character) using the plotmath routines in R?
>
>   
It's an operator, it needs something to operate on.

Try

 plot(0,main=quote(NO^-{}))



> Thanks in advance,
>
> G
>
>   
>> version
>> 
>_  
> platform   i686-pc-linux-gnu  
> arch   i686   
> os linux-gnu  
> system i686, linux-gnu
> status Patched
> major  2  
> minor  5.1
> year   2007   
> month  07 
> day05 
> svn rev42131  
> language   R  
> version.string R version 2.5.1 Patched (2007-07-05 r42131)
>
>   


-- 
   O__   Peter Dalgaard Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark  Ph:  (+45) 35327918
~~ - ([EMAIL PROTECTED])  FAX: (+45) 35327907

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Re: [R] Smooth line in graph

[Greg Snow]

I don't know what SigmaPlot and Excel are doing for you, but I would guess that 
they are not doing cubic splines (as a general rule, when R and Excel differ, 
it is safest to assume that R is not the one doing something wrong)

Often differences between packages are due to differences in assumptions or 
model specifications.  I don't know SigmaPlot to be able to say what it is 
doing and a quick search of the excel help for 'spline' was not enlightening.

Perhaps what you are looking for is not a cubic spline.  Another option is an 
xspline.  These are implemented in the grid package.  Try:

library(grid)
library(lattice)

x<-c(-45,67,131,259,347)
y <- c(0.31, 0.45, 0.84, 0.43, 0.25)

s <- seq(-1,1, .25)

tmp.df <- data.frame(x=rep(x,9), y=rep(y,9), s=rep(s, each=5))

xyplot(y~x|factor(s), data=tmp.df, tmp.s=tmp.df$s, 
panel=function(x,y,subscripts,tmp.s,...){
 grid.points(x,y)
 tmp2.s <- tmp.s[subscripts]
print(tmp2.s)
 grid.xspline(x,y, default.units='native', shape=tmp2.s)
 })

Hope this helps,

-- 
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
(801) 408-8111
 
 

> -Original Message-
> From: Nestor Fernandez [mailto:[EMAIL PROTECTED] 
> Sent: Thursday, September 20, 2007 4:02 AM
> To: [EMAIL PROTECTED]
> Cc: Greg Snow
> Subject: Re: [R] Smooth line in graph
> 
> Sorry, I answered too quickly.
> It worked with the "simplified" example I provided but not 
> with non-regular intervals in x:
> 
> x<-c(-45,67,131,259,347)
> y <- c(0.31, 0.45, 0.84, 0.43, 0.25)
> 
> plot(x,y)
> lines(spline(x,y, method='n', n=250))
> #or:
> lines(predict(interpSpline(x, y)))
> 
> Produce the same decrease between first two points and the 
> shape is quite different to that produced by sigmaplot -I 
> need comparable figures. Changing "method" and "n" arguments 
> did not help.
> 
> Sorry for bothering. Any other suggestion?
> 
> 
> 
> 
> 
> 
> Greg Snow escribió:
> > Try:
> >
> >   
> >> lines(spline(x,y, method='n', n=250))
> >> 
> >
> >   
> 
> 

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[R] Portfolio Optimization

[livia]

Hello,

I would like to solve a portfolio optimization problem in R. As far as I
searched, I found the example of "solve.QP" &"portfolio.optim". In my
understanding, both of them are based on given expected return, finding the
minimum variance. Is there a way of doing this in an opposite way?i.e
maximize the expected return subject to fixed variance? Or even better, like
combining these two together?

I would be grateful if anyone give me some advice or share the codes?
-- 
View this message in context: 
http://www.nabble.com/Portfolio-Optimization-tf4488519.html#a12800372
Sent from the R help mailing list archive at Nabble.com.

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Re: [R] SEM - singularity error

[Chuck Cleland]

[EMAIL PROTECTED] wrote:
> Good morning,
> 
> I am trying to develop a structural equation model of snake abundance using
> habitat variables. In attempting to estimate the model using the "sem" package
> in R version 2.4.0, I receive the following error message:
> 
> "Error in solve.default(C) : system is computationally singular: reciprocal
> condition number = 1.75349e-16"
> 
> MAIN PROBLEM: I am hoping to discover why I am receiving the aforementioned
> error message and how to successfully estimate the model.
> 
> OTHER INFORMATION:
> 1. I believe the model is over-identified rather than under-identified (based 
> on
> my understanding of the t-rule). I have observed data for 10 variables (9
> exogenous, 1 endogenous).
> 
> 2. I am not certain that I have used the proper tool to estimate the 
> covariance
> matrix. In this case, I used the "VAR" function.
> 
> 3. I am most concerned that I have improperly coded the RAM file. For example,
> in a case where I have three exogenous indicators of one exogenous latent
> variable, I specify a start value of 1 for one of the exogenous indicators. I
> am not sure if this is proper or necessary.
> 
> 4. I am new to SEM; this is the first model I have ever tried to estimate.
> 
> R CODE: Below is the r-code I have used to estimate the structural equation
> model --
> 
> # LOADING R PACKAGES
> library(sem)
> 
> # READING IN THE CSV FILES
> thsi.2006<-read.csv("thsi_ab_env_space_sem.csv")
> thsi<-thsi.2006
> 
> # MAKING "RAM" FILE 2
> model2.nlc <-specify.model()
> Moist->slope, NA, 1
> Moist->sand, lamda21, NA
> Moist->clay, lamda31, NA
> Hab->isol, NA, 1
> Hab->edgedist_a, lamda52, NA
> Hab->ag10, lamda62, NA
> Hab->urb10, lamda72, NA
> Hab->rd10, lamda82, NA
> Hab->y, lamda92, NA
> Moist->this, gamma11, NA
> Hab->this, gamma12, NA
> slope<->slope, theta11, NA
> sand<->sand, theta22, NA
> clay<->clay, theta33, NA
> isol<->isol, theta44, NA
> edgedist_a<->edgedist_a, theta55, NA
> ag10<->ag10, theta66, NA
> urb10<->urb10, theta77, NA
> rd10<->rd10, theta88, NA
> y<->y, the99, NA
> Moist<->Moist, phi11, NA
> Hab<->Hab, phi22, NA
> this<->this, theps11, NA
> 
> model2.nlc
> end
> 
> # MAKING S (COVARIANCE MATRIX)
> thsi.var <- var(thsi)
> 
> # MAKING UNSCALED SEM MODEL
> sem2<-sem(ram=model2.nlc, S=thsi.var, N=22)
> 
> I am also attaching a jpeg diagram of the model I am trying to estimate. 
> Please
> let me know if there is any additional information that I should add to this
> posting.
> 
> Thank you so much for your time.
> Nicolette Cagle

  Your specification of the model seems OK and it is over-identified (21
free parameters and 34 df).  I suspect the problem is that one or more
of your 10 variables is a linear function of the remaining variables.
If that is the case, then the following should give the same singularity
error:

factanal(thsi, factors=1)

  You may be able to drop one or more of the 10 variables from
consideration and successfully estimate a conceptually similar model.

hope this helps,

Chuck Cleland

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

-- 
Chuck Cleland, Ph.D.
NDRI, Inc.
71 West 23rd Street, 8th floor
New York, NY 10010
tel: (212) 845-4495 (Tu, Th)
tel: (732) 512-0171 (M, W, F)
fax: (917) 438-0894

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[R] help with making a function of scatter plot with multiple variables

[Tom Cohen]

Dear list,
   
  I have done a scatter plot of  multiple variables in the same graph, with 
different col and pch. I managed to do it with the following code but not know 
how to make a function of these so that next time if I want to do similar graph 
but with new variables, I dont have to copy the code and then change the old 
variables with the new ones but just call a function with the new variables. I 
dont have any experience in making a function and would be very grateful if you 
can help me. A function will shorten my prog dramatically, since I repeat tthis 
type of graph alots in my analysis.
   
  Thanks in advance,
  Tom
   
  op <- par(bg = "grey97")
par(mfrow=c(1,2))
plot(d1,v1, pch="v", col="orange",cex=0.6, lwd=2,
xlab="day", ylab="resp",cex.main =1,font.main= 1,main=" Surv 
data",ylim=y,xlim=x,
col.main="navyblue",col.lab="navyblue",cex.lab=0.7)

points(s1,t1, pch="A", col="green4", cex=1)
points(s2,t2, pch="B",col="navyblue", cex=1)
points(s3,t3, pch="C",col="red", cex=1)
points(s4,t4, pch="D",col="darkviolet", cex=1)
points(s5,t5, pch="E",col="blue", cex=1)
  
legend("topright",lbels,col=c("orange","green4","navyblue","red","darkviolet","blue"),
 text.col=c("orange","green4","navyblue","red","darkviolet","steelblue"),
 pch=c("v","A","B","C","D","E"),bg='gray100',cex=0.7,box.lty=1,box.lwd=1)
abline(h = -1:9, v = 0:8, col = "lightgray", lty=3) 
par(op)
  
  

   
-

Jämför pris på flygbiljetter och hotellrum: 
http://shopping.yahoo.se/c-169901-resor-biljetter.html
[[alternative HTML version deleted]]

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Re: [R] Plotmath issue superscript "-"

[P Ehlers]

If you need a subscript as well, I like

  plot(0, main=quote({NO^'\x96'}[3]))

Peter Ehlers

Peter Dalgaard wrote:
> Gavin Simpson wrote:
>> Dear List,
>>
>> I'm trying to typeset some chemical ions in axis labels. These have both
>> super and subscript components, and for some, I need a superscript "-".
>> In LaTeX I might use $NO_3^-$ to do the typesetting, but I'm having a
>> problem getting the correct invocation for expression:
>>
>>   
>>> expression(NO^{-}[3])
>>> 
>> Error: syntax error, unexpected '}' in "expression(NO^{-}"
>>   
>>> expression(NO^-[3])
>>> 
>> Error: syntax error, unexpected '[' in "expression(NO^-["
>>   
>>> expression(NO^-)
>>> 
>> Error: syntax error, unexpected ')' in "expression(NO^-)"
>>   
>>> expression(NO^{-})
>>> 
>> Error: syntax error, unexpected '}' in "expression(NO^{-}"
>>
>> This is with R 2.5.1 (exact version info below).
>>
>> I suspect this is something to do with my use of the "-", which has some
>> special meaning.
>>
>> Is there a way to achieve a superscript "-" (or similar looking
>> character) using the plotmath routines in R?
>>
>>   
> It's an operator, it needs something to operate on.
> 
> Try
> 
>  plot(0,main=quote(NO^-{}))
> 
> 
> 
>> Thanks in advance,
>>
>> G
>>
>>   
>>> version
>>> 
>>_  
>> platform   i686-pc-linux-gnu  
>> arch   i686   
>> os linux-gnu  
>> system i686, linux-gnu
>> status Patched
>> major  2  
>> minor  5.1
>> year   2007   
>> month  07 
>> day05 
>> svn rev42131  
>> language   R  
>> version.string R version 2.5.1 Patched (2007-07-05 r42131)
>>
>>   
> 
>

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Re: [R] SEM - singularity error

[nicolette . cagle]

Good afternoon Chuck,

I really appreciate your help. I just ran the factor analysis and did not
receive the singularity error (please see results below).

Do you happen to have any additional ideas or suggestions?

Thank you so much.
Nicki

FACTANAL RESULTS:
Call: factanal(x = thsi, factors = 1)

Uniquenesses:
  this edgedist_a   isol   ag10  urb10   rd10  slope
 0.705  0.914  0.232  0.124  0.136  0.017  0.952
  clay   sand  y
 0.534  0.485  0.144

Loadings:
   Factor1
this0.543
edgedist_a  0.293
isol0.876
ag10   -0.936
urb10   0.930
rd100.992
slope  -0.220
clay   -0.682
sand0.718
y  -0.925

   Factor1
SS loadings  5.757
Proportion Var   0.576

Test of the hypothesis that 1 factor is sufficient.
The chi square statistic is 120.94 on 35 degrees of freedom.
The p-value is 2.17e-11

Quoting Chuck Cleland <[EMAIL PROTECTED]>:

> [EMAIL PROTECTED] wrote:
>> Good morning,
>>
>> I am trying to develop a structural equation model of snake abundance using
>> habitat variables. In attempting to estimate the model using the 
>> "sem" package
>> in R version 2.4.0, I receive the following error message:
>>
>> "Error in solve.default(C) : system is computationally singular: reciprocal
>> condition number = 1.75349e-16"
>>
>> MAIN PROBLEM: I am hoping to discover why I am receiving the aforementioned
>> error message and how to successfully estimate the model.
>>
>> OTHER INFORMATION:
>> 1. I believe the model is over-identified rather than 
>> under-identified (based on
>> my understanding of the t-rule). I have observed data for 10 variables (9
>> exogenous, 1 endogenous).
>>
>> 2. I am not certain that I have used the proper tool to estimate the 
>> covariance
>> matrix. In this case, I used the "VAR" function.
>>
>> 3. I am most concerned that I have improperly coded the RAM file. 
>> For example,
>> in a case where I have three exogenous indicators of one exogenous latent
>> variable, I specify a start value of 1 for one of the exogenous 
>> indicators. I
>> am not sure if this is proper or necessary.
>>
>> 4. I am new to SEM; this is the first model I have ever tried to estimate.
>>
>> R CODE: Below is the r-code I have used to estimate the structural equation
>> model --
>>
>> # LOADING R PACKAGES
>> library(sem)
>>
>> # READING IN THE CSV FILES
>> thsi.2006<-read.csv("thsi_ab_env_space_sem.csv")
>> thsi<-thsi.2006
>>
>> # MAKING "RAM" FILE 2
>> model2.nlc <-specify.model()
>> Moist->slope, NA, 1
>> Moist->sand, lamda21, NA
>> Moist->clay, lamda31, NA
>> Hab->isol, NA, 1
>> Hab->edgedist_a, lamda52, NA
>> Hab->ag10, lamda62, NA
>> Hab->urb10, lamda72, NA
>> Hab->rd10, lamda82, NA
>> Hab->y, lamda92, NA
>> Moist->this, gamma11, NA
>> Hab->this, gamma12, NA
>> slope<->slope, theta11, NA
>> sand<->sand, theta22, NA
>> clay<->clay, theta33, NA
>> isol<->isol, theta44, NA
>> edgedist_a<->edgedist_a, theta55, NA
>> ag10<->ag10, theta66, NA
>> urb10<->urb10, theta77, NA
>> rd10<->rd10, theta88, NA
>> y<->y, the99, NA
>> Moist<->Moist, phi11, NA
>> Hab<->Hab, phi22, NA
>> this<->this, theps11, NA
>>
>> model2.nlc
>> end
>>
>> # MAKING S (COVARIANCE MATRIX)
>> thsi.var <- var(thsi)
>>
>> # MAKING UNSCALED SEM MODEL
>> sem2<-sem(ram=model2.nlc, S=thsi.var, N=22)
>>
>> I am also attaching a jpeg diagram of the model I am trying to 
>> estimate. Please
>> let me know if there is any additional information that I should add to this
>> posting.
>>
>> Thank you so much for your time.
>> Nicolette Cagle
>
>  Your specification of the model seems OK and it is over-identified (21
> free parameters and 34 df).  I suspect the problem is that one or more
> of your 10 variables is a linear function of the remaining variables.
> If that is the case, then the following should give the same singularity
> error:
>
> factanal(thsi, factors=1)
>
>  You may be able to drop one or more of the 10 variables from
> consideration and successfully estimate a conceptually similar model.
>
> hope this helps,
>
> Chuck Cleland
>
>> 
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> --
> Chuck Cleland, Ph.D.
> NDRI, Inc.
> 71 West 23rd Street, 8th floor
> New York, NY 10010
> tel: (212) 845-4495 (Tu, Th)
> tel: (732) 512-0171 (M, W, F)
> fax: (917) 438-0894
>
>



-- 
Ecology Ph.D. Candidate
Duke University
Durham, NC 27708
www.duke.edu/~nlc4

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[R] how can I attach a variable stored in

[Peter Waltman]

Hi -

Any help would be greatly appreciated.

I'm loading a list variable that's stored in an .RData file and would 
like attach it.

I've used attach(  ), but that only lets me see the variable 
that's stored in the file. 

As the variable name is of the form "comp.x.x", I've tried using attach( 
ls( pat="comp" ) ), but get an error as ls() just gives back a string.

I've also played around with eval(), but don't really quite get what 
that function does since it seems to get into the R internals which I 
don't entirely understand and I haven't found any great unified 
documentation on R's handling environment and scoping.

Thanks,

Peter Waltman

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[R] Superimposing vector polygons over raster grid in a plot

[Rick Reeves]

Hello:

I would like to superimpose vector polygons (state outlines) from a 
Shape file on top of a satellite image,
imported into a SpatialGridDataFrame from GEOTIFF via gdal_translate and 
readGDAL.


When I plot polygon and point shape files in R, into 
SpatialPointDataFrame and SpatialPolygonDataFrame,
the two feature sets line up geographically, so it seems logical that a 
SpatialGridDataFrame should behave

in the same way.

From my initial research, the spplot function is the correct function 
for plotting grids/images with axes and

annotation.

The big question is, how do I incorporate a Spatial(Points or 
Polygons)DataFrame into the spplot display list?


It seems as though many scientists would like to create such plots 
without resorting to GRASS or

another GIS.

Thanks for any advice,
Rick Reeves

Rick Reeves 
Scientific Programmer / Analyst 
National Center for Ecological Analysis and Synthesis
UC Santa Barbara
[EMAIL PROTECTED]
www.nceas.ucsb.edu
805 892 2533

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Re: [R] Plotmath issue superscript "-"

[Scionforbai]

Hallo,

> If you need a subscript as well, I like
>
>   plot(0, main=quote({NO^'\x96'}[3]))


I tried this but I get:

>  plot(0, main=quote({NO^'\x96'}[3]))
Errore in title(...) : stringa multibyte non valida ('invalid multibyte string')

My R version is:
platform   i686-redhat-linux-gnu
version.string R version 2.4.1 (2006-12-18)

locale is: LANG=it_IT.UTF-8

What is this multibyte string? Does it depend on LOCALE settings?
Where can I find further docs on this way to pass character
descriptors?
Thanks,
ScionForbai

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Re: [R] Cutting & pasting help examples into script window

[Muenchen, Robert A (Bob)]

Does this look like a bug? If so, is there a different way to report it?
Thanks, Bob

> -Original Message-
> From: Dirk Eddelbuettel [mailto:[EMAIL PROTECTED]
> Sent: Thursday, September 20, 2007 10:17 AM
> To: Muenchen, Robert A (Bob)
> Subject: Re: [R] Cutting & pasting help examples into script window
> 
> On Thu, Sep 20, 2007 at 10:01:03AM -0400, Muenchen, Robert A (Bob)
> wrote:
> > Stephan Grosse replied:
> >
> > >
> > > What I do not understand is why you not just type
> > example(yourcommand)?
> > >
> > > Stefan
> >
> > That's a good question. I want to play around with variations of the
> > examples rather than run them exactly as they are.
> 
> In Emacs' wonderful ESS mode, you just press 'l' and the line of
> example code you're on gets sent to R.  You can then 'pick it up' in
> the R buffer and play with it.  I do that all the time ...
> 
> Dirk
> 
> --
> Three out of two people have difficulties with fractions.

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[R] Time series graphs

[Bill Pepe]

I'm fairly new to S-Plus and I need to get this done quickly. Suppose I have 
the following fake data below:
   
  There are two companies, call them Bob and Tom. Each have two variables, call 
them A and B, that have observations.
   
 Bob Tom

A BAB
  Jan  84 9 8
  Feb 7 5 4 7
  Mar 6 8 4 4
  Apr 3 7  6 2
  May5 1 8 5
  Jun 6 4  71
  July 2 8 3 4
  Aug 12  4 8
  Sep4  3  19
   
  Here is what I want to do: I want to make two different graphs, one for Bob 
and one for Tom. For each graph, plot both variables A and B. Connect the A 
values with a line, and connect the B values with a different type of line. So 
there should be two lines for each graph. For the A line, at each time point, 
the letter A should be on the line. And the same goes for the B line. Either R 
or S-Plus since they are essentially the same.
   
  I'm sure this is easy, but any help would be greatly appreciated.
   
  Thanks,
   
  Bill

   
-
Pinpoint customers who are looking for what you sell. 
[[alternative HTML version deleted]]

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Re: [R] SEM - singularity error

[John Fox]

Dear Nicolette and Chuck,

I apologize for not seeing Nicolette's original posting.

The model does appear to be correctly specified (though I didn't see
the path diagram) and over-identified. I assume that all of the
variables with lower-case names are observed variables and that "Moist"
and "Hab" are latent variables. (Simply comparing the number of free
parameters to the number of unique covariances among observed variables
provides a necessary but not sufficient condition for identification.
This model is identified because there more than two unique indicators
for each latent variable and because the structural submodel relating
"this" to "Moist" and "Hab" is identified.)

I suspect that the problem here is the restriction that "Moist" and
"Hab" are uncorrelated, which follows from the lack of a double-headed
arrow connecting these variables. You might try adding Moist <-> Hab to
the model.

I hope this helps,
 John


On Thu, 20 Sep 2007 12:40:06 -0400
 Chuck Cleland <[EMAIL PROTECTED]> wrote:
> [EMAIL PROTECTED] wrote:
> > Good morning,
> > 
> > I am trying to develop a structural equation model of snake
> abundance using
> > habitat variables. In attempting to estimate the model using the
> "sem" package
> > in R version 2.4.0, I receive the following error message:
> > 
> > "Error in solve.default(C) : system is computationally singular:
> reciprocal
> > condition number = 1.75349e-16"
> > 
> > MAIN PROBLEM: I am hoping to discover why I am receiving the
> aforementioned
> > error message and how to successfully estimate the model.
> > 
> > OTHER INFORMATION:
> > 1. I believe the model is over-identified rather than
> under-identified (based on
> > my understanding of the t-rule). I have observed data for 10
> variables (9
> > exogenous, 1 endogenous).
> > 
> > 2. I am not certain that I have used the proper tool to estimate
> the covariance
> > matrix. In this case, I used the "VAR" function.
> > 
> > 3. I am most concerned that I have improperly coded the RAM file.
> For example,
> > in a case where I have three exogenous indicators of one exogenous
> latent
> > variable, I specify a start value of 1 for one of the exogenous
> indicators. I
> > am not sure if this is proper or necessary.
> > 
> > 4. I am new to SEM; this is the first model I have ever tried to
> estimate.
> > 
> > R CODE: Below is the r-code I have used to estimate the structural
> equation
> > model --
> > 
> > # LOADING R PACKAGES
> > library(sem)
> > 
> > # READING IN THE CSV FILES
> > thsi.2006<-read.csv("thsi_ab_env_space_sem.csv")
> > thsi<-thsi.2006
> > 
> > # MAKING "RAM" FILE 2
> > model2.nlc <-specify.model()
> > Moist->slope, NA, 1
> > Moist->sand, lamda21, NA
> > Moist->clay, lamda31, NA
> > Hab->isol, NA, 1
> > Hab->edgedist_a, lamda52, NA
> > Hab->ag10, lamda62, NA
> > Hab->urb10, lamda72, NA
> > Hab->rd10, lamda82, NA
> > Hab->y, lamda92, NA
> > Moist->this, gamma11, NA
> > Hab->this, gamma12, NA
> > slope<->slope, theta11, NA
> > sand<->sand, theta22, NA
> > clay<->clay, theta33, NA
> > isol<->isol, theta44, NA
> > edgedist_a<->edgedist_a, theta55, NA
> > ag10<->ag10, theta66, NA
> > urb10<->urb10, theta77, NA
> > rd10<->rd10, theta88, NA
> > y<->y, the99, NA
> > Moist<->Moist, phi11, NA
> > Hab<->Hab, phi22, NA
> > this<->this, theps11, NA
> > 
> > model2.nlc
> > end
> > 
> > # MAKING S (COVARIANCE MATRIX)
> > thsi.var <- var(thsi)
> > 
> > # MAKING UNSCALED SEM MODEL
> > sem2<-sem(ram=model2.nlc, S=thsi.var, N=22)
> > 
> > I am also attaching a jpeg diagram of the model I am trying to
> estimate. Please
> > let me know if there is any additional information that I should
> add to this
> > posting.
> > 
> > Thank you so much for your time.
> > Nicolette Cagle
> 
>   Your specification of the model seems OK and it is over-identified
> (21
> free parameters and 34 df).  I suspect the problem is that one or
> more
> of your 10 variables is a linear function of the remaining variables.
> If that is the case, then the following should give the same
> singularity
> error:
> 
> factanal(thsi, factors=1)
> 
>   You may be able to drop one or more of the 10 variables from
> consideration and successfully estimate a conceptually similar model.
> 
> hope this helps,
> 
> Chuck Cleland
> 
> >
>

> > 
> > __
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> 
> -- 
> Chuck Cleland, Ph.D.
> NDRI, Inc.
> 71 West 23rd Street, 8th floor
> New York, NY 10010
> tel: (212) 845-4495 (Tu, Th)
> tel: (732) 512-0171 (M, W, F)
> fax: (917) 438-0894
> 
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-proje

[R] Non-metric multidimensional scaling

[Friedman, Steven]

Hello everyone,

 

I'm working with R 2.4.1 on a PC running with XP.

 

Trying to run isoMDS as follows:

 

Gquad.mat <- Gquads[4:10]   # extracts only the metric data variables

Gquad.dist <- dist(Gquad.mat) 

Gquad.mds <- isoMDS(Gquad.dist)

plot(Gquad.mds$points, type = "n")

text(Gquad.mds$points, labels = as.character(Gquads$Quadname), cex = .5)

 

 

The data.frame includes 711 records, and the first 3 columns contain
categorical variables which I exclude from the analysis.

 

When I invoke the script above an error message is returned.

 

Error in isoMDS(Gquad.dist) : zero or negative distance between objects
179 and 180.

 

How can I handle this, is it valid to add 0.5 to every element in the
distance matrix or is someother  alternative more appropriate?

 

Thanks in advance

Steve

 

 

Steve Friedman, PhD

Everglades Division

Senior Environmental Scientist, Landscape Ecology

South Florida Water Management District

3301 Gun Club Road

West Palm Beach, Florida 33406

email:  [EMAIL PROTECTED]

Office:  561 - 682 - 6312

Fax:  561 - 682 - 5980

 

If you are not doing what you truly enjoy its your obligation to
yourself to change.

 


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Re: [R] Strange behaviour of lars method

[Wiebke Timm]

Thanks for your answer!

On 20.09.2007, at 12:48, Tim Hesterberg wrote:

> Might you be having numerical problems?

That might very well be what's happening. Did hope that it only  
happens late in the procedure so I can ignore it, but those Cp values  
indicate I maybe can't.

> If you're using the "lars"
> library, it uses cross-product matrices, which are notoriously
> numerically unstable in regression calculations when there is
> high multiple correlation among the x's.

...as is the case in my data. Good to know...

> We have a prototype package that offers more stable calculations,
> using QR decompositions.
> See http://www.insightful.com/Hesterberg/glars
> Let me know if you'd like to try this.

Yes, please!

Just also had a peak at the ProcASA paper that's linked there... I  
did not know about elastic net before, maybe I will try that too for  
comparison... In fact (like always) I don't really know what method  
would be best.

Did you try lars or glars on some more noisy/bad/difficult data sets?  
How good is its stability/generalization capability on these?
You write the original LARS method is for linear regression. But it  
includes the lasso solutions. Lasso can have nonlinear solutions  
because of the penalty used. Or did I misunderstand something?

Regards,
Wiebke

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Re: [R] Time series graphs

[Gabor Grothendieck]

Using plot.zoo in the zoo package try this:

Lines <- "Bob.A Bob.BTom.ATom.B
 Jan  84 9 8
 Feb 7 5 4 7
 Mar 6 8 4 4
 Apr 3 7  6 2
 May5 1 8 5
 Jun 6 4  71
 July 2 8 3 4
 Aug 12  4 8
 Sep4  3  19
"
DF <- read.table(textConnection(Lines))

library(zoo)
z <- zooreg(as.matrix(DF), start = as.yearmon(as.Date("2007-01-01")), freq = 12)
z <- aggregate(z, as.Date, tail, 1)
plot(z, plot.type = "single",  type = "o",
pch = c("A", "A", "B", "B"), lty = 1:2)
legend("bottomleft", c("Bob", "Tom"), lty = 1:2)



On 9/20/07, Bill Pepe <[EMAIL PROTECTED]> wrote:
> I'm fairly new to S-Plus and I need to get this done quickly. Suppose I have 
> the following fake data below:
>
>  There are two companies, call them Bob and Tom. Each have two variables, 
> call them A and B, that have observations.
>
> Bob Tom
>
>A BAB
>  Jan  84 9 8
>  Feb 7 5 4 7
>  Mar 6 8 4 4
>  Apr 3 7  6 2
>  May5 1 8 5
>  Jun 6 4  71
>  July 2 8 3 4
>  Aug 12  4 8
>  Sep4  3  19
>
>  Here is what I want to do: I want to make two different graphs, one for Bob 
> and one for Tom. For each graph, plot both variables A and B. Connect the A 
> values with a line, and connect the B values with a different type of line. 
> So there should be two lines for each graph. For the A line, at each time 
> point, the letter A should be on the line. And the same goes for the B line. 
> Either R or S-Plus since they are essentially the same.
>
>  I'm sure this is easy, but any help would be greatly appreciated.
>
>  Thanks,
>
>  Bill
>
>
> -
> Pinpoint customers who are looking for what you sell.
>[[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

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[R] Conditional Logit and Mixed Logit

[David U.]

Hello,

Could anybody provide me with codes (procedure) how to obtain Conditional
Logit (McFadden) and Mixed Logit (say, assuming normal distribution)
estimates in R?

Thanks,
David U.
-- 
View this message in context: 
http://www.nabble.com/Conditional-Logit-and-Mixed-Logit-tf4489238.html#a12802959
Sent from the R help mailing list archive at Nabble.com.

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Re: [R] Ambiguities in vector

[bbolker]

Birgit Lemcke wrote:
> 
> 
> Perhaps you haven´t understood my question in the mail yesterday. So  
> I will try to describe my problem in a different way
> 
> You see the tables. I would like to test the variables between the  
> tables. 
> 

I'm afraid that even before we start to deal with the ambiguities
your question is not clear.   What do you want to know, and before
you sat down at the computer what statistical test did you intend
to use?  (For better or worse, most of the documentation of R
_assumes_ you know what you want to test and how you want to
do it.)   I'm supposing you want to do some kind of comparison
across communities (tables 1 and 2), but I don't know what kind.
Comparing a single cell of the table to another just asks if
the leaf form is the same in the two communities.  Do you just
want to ask if leaf forms of a given species are significantly different
in different communities?  I'm not sure what the null hypothesis
would be here.  What are the rows and columns?  Can we use
them to develop a hypothesis?

If you can say precisely what your question is and how you would
test it in the _absence_ of ambiguity (i.e., specify a statistical test --
you don't need to know how to run it in R, that's what the list is
actually for), then we can help you decide how to handle the
multiple coding problem.

  good luck
Ben Bolker
-- 
View this message in context: 
http://www.nabble.com/Ambiguities-in-vector-tf4485921.html#a12802997
Sent from the R help mailing list archive at Nabble.com.

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[R] convert data from

[Pan Zheng]

Hi,

I am trying to convert a data frame from:

X1X2
A12
B34
C56

to:
A01 1
A02 2
B013
B024
C015
C026.

How can I do it in R?

I appreciate your help.

Zheng

   
-

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Re: [R] how can I attach a variable stored in

[Leeds, Mark (IED)]

I don't think I understand your question but John Fox has written a very
nice documentat about scoping and environments on his website.
It's probably easy to find the site by googling "John Fox" but, if you
can't find it, let me know.
 
As I said, I don't think that I understand your question but, if you
loaded a list variable using load("whatever.Rdata"), the variable will 
just be suitting in  your workspace. You don't need to attach anything
because load just loads the data right into the workspace.
So typing the variable name should show the data.




-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Peter Waltman
Sent: Thursday, September 20, 2007 1:32 PM
To: r-help@r-project.org
Subject: [R] how can I attach a variable stored in

Hi -

Any help would be greatly appreciated.

I'm loading a list variable that's stored in an .RData file and would
like attach it.

I've used attach(  ), but that only lets me see the variable
that's stored in the file. 

As the variable name is of the form "comp.x.x", I've tried using attach(
ls( pat="comp" ) ), but get an error as ls() just gives back a string.

I've also played around with eval(), but don't really quite get what
that function does since it seems to get into the R internals which I
don't entirely understand and I haven't found any great unified
documentation on R's handling environment and scoping.

Thanks,

Peter Waltman

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


This is not an offer (or solicitation of an offer) to buy/se...{{dropped}}

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

Re: [R] Non-metric multidimensional scaling

[Silvia Lomascolo]

>Error in isoMDS(Gquad.dist) : zero or negative distance between objects
>179 and 180.
>How can I handle this, is it valid to add 0.5 to every element in the
>distance matrix or is someother  alternative more appropriate?

This means that your objects 179 and 180 are identical so just remove one of
the two.  They both have the same distance to all other objects so your
results shouldn't change.  Whatever conclusion you draw from the location of
one on your plot, you can say the same for the other. 

Silvia.





 

Thanks in advance

Steve

 

 

Steve Friedman, PhD

Everglades Division

Senior Environmental Scientist, Landscape Ecology

South Florida Water Management District

3301 Gun Club Road

West Palm Beach, Florida 33406

email:  [EMAIL PROTECTED]

Office:  561 - 682 - 6312

Fax:  561 - 682 - 5980

 

If you are not doing what you truly enjoy its your obligation to
yourself to change.

 


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Re: [R] random Forests

[Liaw, Andy]

1) See the help pages for save() and load().  We do this all the time. 

2) Prediction (or what you call scoring) given the matrix structure is
quite simple.  Take a look at the underlying C source code.  You can
write that in any language you want without much problem.

Andy

From: David Montgomery
> 
> Hi,
>  
> I am new to R and have a specific question about the 
> randomForest package and the saving of trees and scoring.
>  
> 1) I am looking to save the trees and score at a later time.  
> Is there a way to load the saved trees and use the predict 
> function?  Can objects be saved and loaded i.e. the 
> randomForest function call?  I dont want to have to rerun 
> trees.  Hopefully this applies to any stat type procedure 
> that requires scoring.
>  
> 2) Has anybody written any code in any other language that 
> optimizes scoring using the format that the trees are saved 
> in?  Ideally I would like to do real time scoring outside of 
> R and hoping that someone has code in python or c++developed 
> around the matrix format of the tree structure.
>  
> Thanks,
>  
> David
>  
>  
>  
>  
>   [[alternative HTML version deleted]]
> 
> __
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> 
> 
> 


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Re: [R] SEM - singularity error

[nicolette . cagle]

Dear John,

Thank you so much for your assistance, it is greatly appreciated. You are
correct in your interpretation of the variables (Moist and Hab are latent, the
other, lower case variables are observed). I've attempted to run the model
again adding Moist <-> Hab (please see code below) and still receive the same
error message:

"Error in solve.default(C) : system is computationally singular: reciprocal
condition number = 6.59035e-17."

Is it possible that something is wrong with the variance-covariance matrix
(please see pasted below r code)? Are extremely small values (e.g., 4e-4)
problematic? Do you have any additional suggestions as to how I might go about
trouble shooting this problem?

I am also attaching the jpeg model diagram, in case it could be of use to you.

Thank you so much for your time.
Best wishes,
Nicki

R CODE USED:
# 20 Sep 2007 SEM of Thamnophis abundance

# LOADING R PACKAGES
library(sem)

# READING IN THE CSV FILES
thsi.2006<-read.csv("thsi_ab_env_space_sem.csv")
thsi<-thsi.2006

# MAKING "RAM" FILE 3
model3.nlc <-specify.model()
Moist->slope, NA, 1
Moist->sand, lamda21, NA
Moist->clay, lamda31, NA
Hab->isol, NA, 1
Hab->edgedist_a, lamda52, NA
Hab->ag10, lamda62, NA
Hab->urb10, lamda72, NA
Hab->rd10, lamda82, NA
Hab->y, lamda92, NA
Moist->this, gamma11, NA
Hab->this, gamma12, NA
slope<->slope, theta11, NA
sand<->sand, theta22, NA
clay<->clay, theta33, NA
isol<->isol, theta44, NA
edgedist_a<->edgedist_a, theta55, NA
ag10<->ag10, theta66, NA
urb10<->urb10, theta77, NA
rd10<->rd10, theta88, NA
y<->y, the99, NA
Moist<->Moist, phi11, NA
Hab<->Hab, phi22, NA
Moist<->Hab, phi21, NA
this<->this, theps11, NA

model3.nlc
end

# MAKING S (COVARIANCE MATRIX)
thsi.var <- var(thsi)

# MAKING UNSCALED SEM MODEL
sem3<-sem(ram=model3.nlc, S=thsi.var, N=22)

VARIANCE-COVARIANCE MATRIX (AKA: thsi.var):
  this
this  8.88528139
edgedist_a   44.91469329
isol   2678.38321991
ag10 -0.38967619
urb10 0.11704827
rd10  0.02132100
slope-2.25074394
clay-36.19339827
sand 19.66753247
y-0.95970602
 edgedist_a
this  44.9146933
edgedist_a 17491.7873712
isol   96122.5594957
ag10  -9.1045614
urb10  1.9439758
rd10   0.5333281
slope 24.4351358
clay   -1360.1102116
sand 619.1507519
y-15.4852253
   isol
this  2678.38322
edgedist_a   96122.55950
isol   4167108.48214
ag10  -347.26757
urb10   91.79339
rd1025.71996
slope -392.44092
clay-42236.76039
sand 19461.19308
y -868.20597
   ag10
this -0.38967619
edgedist_a   -9.10456137
isol   -347.26756672
ag10  0.05167298
urb10-0.01314388
rd10 -0.00297957
slope 0.06923224
clay  3.17604271
sand -1.61043719
y 0.11896881
 urb10
this0.117048268
edgedist_a  1.943975810
isol   91.793388529
ag10   -0.013143880
urb10   0.003733677
rd100.000784747
slope  -0.039094302
clay   -0.907067141
sand0.491619654
y  -0.034343332
   rd10
this0.0213209957
edgedist_a  0.5333280831
isol   25.7199633947
ag10   -0.0029795700
urb10   0.0007847471
rd100.0001987203
slope  -0.0041496227
clay   -0.2726142316
sand0.1286087229
y  -0.0078502982
  slope
this   -2.250744e+00
edgedist_a  2.443514e+01
isol   -3.924409e+02
ag106.923224e-02
urb10  -3.909430e-02
rd10   -4.149623e-03
slope   2.520968e+00
clay3.343637e+00
sand   -2.202094e+00
y   3.306712e-01
   clay
this   -3.619340e+01
edgedist_a -1.360110e+03
isol   -4.223676e+04
ag103.176043e+00
urb10  -9.070671e-01
rd10   -2.726142e-01
slope   3.343637e+00
clay7.962072e+02
sand   -3.410372e+02
y   1.096320e+01
   sand
this  19.6675325
edgedist_a   619.1507519
isol   19461.1930766
ag10  -1.6104372
urb10  0.4916197
rd10   0.1286087
slope -2.2020936
clay-341.0372225
sand 165.1578113
y -5.4148540
  y
this   -9.597060e-01
edgedist_a -1.548523e+01
isol   -8.682060e+02
ag101.189688e-01
urb10  -3.434333e-02
rd10   -7.850298e-03
slope   3.306712e-01
clay1.096320e+01
sand   -5.414854e+00
y   3.694397e-01


Quoting John Fox <[EMAIL PROTECTED]>:


Dear Nicolette and Chuck,

I apologize for not seeing Nicolette's original posting.

The model does appear to be correctly specified (though I didn't see
the path diagram) and over-identified. I assume that all of the
variables with lower-case names are observed variables and that "Moist"
and "Hab" are latent variables. (Simply comparing the number of free
parameters to the number of unique covarianc

Re: [R] Ambiguities in vector

[Birgit Lemcke]

First thanks for your answer.
Now I try to explain better:

I have species in the rows and morphological attributes in the  
columns coded by numbers (qualitative variables; nominal and ordinal).
In one table for the male plants of every species and in the other  
table for the female plants of every species. The variables contain  
every possible occurrence in this species and this gender.
I would like to compare every variable between male and female plants  
for example using a ChiSquare Test.
The Null-hypothesis could be: Variable male is equal to variable Female.

The question behind all is, if male and female plants in this species  
are significantly different and which attributes are responsible for  
this difference.

I really hope that this is better understandable. If not please ask.

Thanks a million in advance.


Greetings

Birgit






Am 20.09.2007 um 20:24 schrieb bbolker:

>
>
>
> Birgit Lemcke wrote:
>>
>>
>> Perhaps you haven´t understood my question in the mail yesterday. So
>> I will try to describe my problem in a different way
>>
>> You see the tables. I would like to test the variables between the
>> tables.
>>
>
> I'm afraid that even before we start to deal with the ambiguities
> your question is not clear.   What do you want to know, and before
> you sat down at the computer what statistical test did you intend
> to use?  (For better or worse, most of the documentation of R
> _assumes_ you know what you want to test and how you want to
> do it.)   I'm supposing you want to do some kind of comparison
> across communities (tables 1 and 2), but I don't know what kind.
> Comparing a single cell of the table to another just asks if
> the leaf form is the same in the two communities.  Do you just
> want to ask if leaf forms of a given species are significantly  
> different
> in different communities?  I'm not sure what the null hypothesis
> would be here.  What are the rows and columns?  Can we use
> them to develop a hypothesis?
>
> If you can say precisely what your question is and how you would
> test it in the _absence_ of ambiguity (i.e., specify a statistical  
> test --
> you don't need to know how to run it in R, that's what the list is
> actually for), then we can help you decide how to handle the
> multiple coding problem.
>
>   good luck
> Ben Bolker
> -- 
> View this message in context: http://www.nabble.com/Ambiguities-in- 
> vector-tf4485921.html#a12802997
> Sent from the R help mailing list archive at Nabble.com.
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting- 
> guide.html
> and provide commented, minimal, self-contained, reproducible code.

Birgit Lemcke
Institut für Systematische Botanik
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
[EMAIL PROTECTED]






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Re: [R] Time series graphs

[Scionforbai]

In pure R (without other packages) is IMHO simpler to understand (at
least if data are so simple: months 1 till 9 with no missing
values...). All you need is:

dummybob <- ' month A B
 Jan   8 4
 Feb   7 5
 Mar   6 8
 Apr   3 7
 May   5 1
 Jun   6 4
 Jul   2 8
 Aug   1 2
 Sep   4 3
'

bob <- read.table(textConnection(dummybob), head=TRUE,
stringsAsFactors = FALSE)

plot(0,0,"n",xlim=c(1,9),ylim=c(0,9),xlab="Month",ylab="Value",axes=FALSE)
title(main="Bob")
lines(1:9,bob$A,lty="solid",col="black")
lines(1:9,bob$B,lty="dotted",col="green")
axis(1,1:9,bob$month)
axis(2)

text(1:9,bob$A,"A",pos=3)
text(1:9,bob$B,"B",pos=3)
box()

And then repeat with the other dataset.

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Re: [R] Superimposing vector polygons over raster grid in a plot

[Dylan Beaudette]

On Thursday 20 September 2007, Rick Reeves wrote:
> Hello:
>
> I would like to superimpose vector polygons (state outlines) from a
> Shape file on top of a satellite image,
> imported into a SpatialGridDataFrame from GEOTIFF via gdal_translate and
> readGDAL.
>
> When I plot polygon and point shape files in R, into
> SpatialPointDataFrame and SpatialPolygonDataFrame,
> the two feature sets line up geographically, so it seems logical that a
> SpatialGridDataFrame should behave
> in the same way.
>
>  From my initial research, the spplot function is the correct function
> for plotting grids/images with axes and
> annotation.
>
> The big question is, how do I incorporate a Spatial(Points or
> Polygons)DataFrame into the spplot display list?
>
> It seems as though many scientists would like to create such plots
> without resorting to GRASS or
> another GIS.

While GRASS and GMT are excellent tools, here are some ideas on how to make 
composite maps in R:

http://casoilresource.lawr.ucdavis.edu/drupal/node/442

cheers,

Dylan



> Thanks for any advice,
> Rick Reeves
>
> Rick Reeves
> Scientific Programmer / Analyst
> National Center for Ecological Analysis and Synthesis
> UC Santa Barbara
> [EMAIL PROTECTED]
> www.nceas.ucsb.edu
> 805 892 2533



-- 
Dylan Beaudette
Soils and Biogeochemistry Graduate Group
University of California at Davis
530.754.7341

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Re: [R] Plotmath issue superscript "-"

[P Ehlers]

Yes, sorry, I should have said that I was on Windows.
In a UTF-8 locale, you could try \u2013 in place of \x96.
The character is an endash.

Peter Ehlers

Scionforbai wrote:
> Hallo,
> 
>> If you need a subscript as well, I like
>>
>>   plot(0, main=quote({NO^'\x96'}[3]))
> 
> 
> I tried this but I get:
> 
>>  plot(0, main=quote({NO^'\x96'}[3]))
> Errore in title(...) : stringa multibyte non valida ('invalid multibyte 
> string')
> 
> My R version is:
> platform   i686-redhat-linux-gnu
> version.string R version 2.4.1 (2006-12-18)
> 
> locale is: LANG=it_IT.UTF-8
> 
> What is this multibyte string? Does it depend on LOCALE settings?
> Where can I find further docs on this way to pass character
> descriptors?
> Thanks,
> ScionForbai
> 
>

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Re: [R] how can I attach a variable stored in

[Peter Waltman]

Hi Mark -

Thanks for the reply.  Sorry I didn't really clarify too well what I'm 
trying to do.  The issue is not that I can't see the variable that gets 
loaded. 

The issue is that the variable is a list variable, and I'd like to write 
a function that will take the .RData filename and attach the variable it 
contains so that I can more easily access its contents, i.e.

foo.bar <- list( "a"= "a", "b"=1 )
save( file="foo.bar.RData", foo.bar )
rm( foo.bar )

my.fn <- function( fname ) {
   load( fname )
   attach( ls( pat="foo" ) ) #  I want to attach( foo.bar ), but
this doesn't work
}

ls()  # prints out "foo.bar"

attach( ls( ) )   # still doesn't work
attach( foo.bar )  # works

So, basically, the question is how can I attach the variable that's 
stored in a file if I don't already know it's name?

Thanks again!

Peter

Leeds, Mark (IED) wrote:
> I don't think I understand your question but John Fox has written a very
> nice documentat about scoping and environments on his website.
> It's probably easy to find the site by googling "John Fox" but, if you
> can't find it, let me know.
>  
> As I said, I don't think that I understand your question but, if you
> loaded a list variable using load("whatever.Rdata"), the variable will 
> just be suitting in  your workspace. You don't need to attach anything
> because load just loads the data right into the workspace.
> So typing the variable name should show the data.
>
>
>
>
> -Original Message-
> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
> On Behalf Of Peter Waltman
> Sent: Thursday, September 20, 2007 1:32 PM
> To: r-help@r-project.org
> Subject: [R] how can I attach a variable stored in
>
> Hi -
>
> Any help would be greatly appreciated.
>
> I'm loading a list variable that's stored in an .RData file and would
> like attach it.
>
> I've used attach(  ), but that only lets me see the variable
> that's stored in the file. 
>
> As the variable name is of the form "comp.x.x", I've tried using attach(
> ls( pat="comp" ) ), but get an error as ls() just gives back a string.
>
> I've also played around with eval(), but don't really quite get what
> that function does since it seems to get into the R internals which I
> don't entirely understand and I haven't found any great unified
> documentation on R's handling environment and scoping.
>
> Thanks,
>
> Peter Waltman
>
> __
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Re: [R] Conditional Logit and Mixed Logit

[Charles C. Berry]

On Thu, 20 Sep 2007, David U. wrote:

>
> Hello,
>
> Could anybody provide me with codes (procedure) how to obtain Conditional
> Logit (McFadden) and Mixed Logit (say, assuming normal distribution)
> estimates in R?


RSiteSearch("conditional logit")

as the posting guide tells you!

>
> Thanks,
> David U.
> -- 
> View this message in context: 
> http://www.nabble.com/Conditional-Logit-and-Mixed-Logit-tf4489238.html#a12802959
> Sent from the R help mailing list archive at Nabble.com.
>
> __
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

Charles C. Berry(858) 534-2098
 Dept of Family/Preventive Medicine
E mailto:[EMAIL PROTECTED]  UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901

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[R] error in manova

[Silvia Lomascolo]

I work with Windows, R 2.4.1.  I'm a beginner with R!

After doing a Discriminant Function Analysis, I am trying to run manova to
get a measure of significance of my lda results. I want to predict groups 1
through 4 using 78 variables (bad group/var ratio, I know, but I'm just
exploring the possibilities right now).  I've tried with a test matrix and I
get my results fine, so I think it might have something to do with the
matrix I'm using (hence, the sample of my matrix I show below). My matrix,
called disperser.mx in my code, looks like:

disperser   P5.38   P6.45   P6.55   P6.63   P7.12   P7.42   P8.10   P8.30   
P8.88   P9.09   P9.30
3   0.001.340.000.000.000.000.000.000.00
0.000.00
2   0.000.00131.56  0.000.000.000.000.000.00
0.000.00
2   0.005.050.000.000.000.000.000.000.00
0.000.00
3   0.0072.65   103.26  1.090.000.000.000.000.00
0.000.00
2   0.000.000.000.000.000.000.000.000.00
0.000.00
2   0.880.480.890.000.000.160.000.000.00
0.000.00
2   0.000.000.000.000.000.750.000.000.00
0.000.00
4   0.000.000.000.000.000.000.000.000.00
0.000.00
2   0.000.000.000.000.005.4120.62   0.008.13
8.878.27
4   0.000.000.000.000.000.000.000.000.00
0.000.00
2   0.000.000.000.000.000.000.000.000.00
0.000.00
2   0.000.000.000.000.000.000.000.000.00
0.000.00
2   0.00133.24  0.000.730.000.001.342.130.00
0.000.00
1   0.0011.08   3.160.760.000.000.000.000.00
0.000.00
4   0.000.000.000.000.000.000.000.000.00
0.000.00
4   0.820.000.000.004.790.000.0033.69   0.00
0.0011.44
2   0.000.000.000.000.000.000.000.000.00
0.000.00
4   0.000.000.000.000.000.000.000.000.00
0.000.00
2   0.001.810.000.000.000.000.000.000.00
0.000.00
1   0.000.000.000.000.006.890.000.000.00
0.000.00
2   7.268.161.500.001.971.280.004.080.00
0.001.16
4   0.000.000.000.000.003.130.000.000.00
0.000.00
4   0.000.000.000.000.000.830.000.000.00
0.000.00
1   0.000.000.000.000.000.000.000.000.00
0.000.00
2   0.001.480.220.000.000.001.800.000.66
0.470.47
1   0.000.000.000.000.000.000.000.000.00
0.000.00
1   0.000.000.000.004.780.000.000.000.00
0.000.00

...with a lot more variables.  The code I am writing to get a manova is:

##first, the code for the discriminant function, just in case it has
something to do with the error I get later##
disperser.mx$disperser<- as.factor (disperser.mx$disperser)
disperser.df <- lda(disperser~., data=disperser.mx)
predict(disperser.df)
attach(disperser.mx)
table(disperser, predict(disperser.df)$class)  ## so far so good.  I get my
discriminant analysis fine
volatileVar <- disperser.mx[c(2:79)] ## these are all the variables that I
want to use
summary (manova(as.matrix(volatileVar)~disperser.mx$disperser),
test='Wilks')  ## here is where I get an error that says "Error in
summary.manova(manova(as.matrix(volatileVar) ~ disperser.mx$disperser),  : 
residuals have rank 23 < 78"


I would appreciate any help you can offer! Silvia.


-- 
View this message in context: 
http://www.nabble.com/error-in-manova-tf4489610.html#a12804209
Sent from the R help mailing list archive at Nabble.com.

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Re: [R] how can I attach a variable stored in

[jim holtman]

try:

attach(get(ls(pat="^foo")))

On 9/20/07, Peter Waltman <[EMAIL PROTECTED]> wrote:
> Hi Mark -
>
> Thanks for the reply.  Sorry I didn't really clarify too well what I'm
> trying to do.  The issue is not that I can't see the variable that gets
> loaded.
>
> The issue is that the variable is a list variable, and I'd like to write
> a function that will take the .RData filename and attach the variable it
> contains so that I can more easily access its contents, i.e.
>
>foo.bar <- list( "a"= "a", "b"=1 )
>save( file="foo.bar.RData", foo.bar )
>rm( foo.bar )
>
>my.fn <- function( fname ) {
>   load( fname )
>   attach( ls( pat="foo" ) ) #  I want to attach( foo.bar ), but
>this doesn't work
>}
>
>ls()  # prints out "foo.bar"
>
>attach( ls( ) )   # still doesn't work
>attach( foo.bar )  # works
>
> So, basically, the question is how can I attach the variable that's
> stored in a file if I don't already know it's name?
>
> Thanks again!
>
> Peter
>
> Leeds, Mark (IED) wrote:
> > I don't think I understand your question but John Fox has written a very
> > nice documentat about scoping and environments on his website.
> > It's probably easy to find the site by googling "John Fox" but, if you
> > can't find it, let me know.
> >
> > As I said, I don't think that I understand your question but, if you
> > loaded a list variable using load("whatever.Rdata"), the variable will
> > just be suitting in  your workspace. You don't need to attach anything
> > because load just loads the data right into the workspace.
> > So typing the variable name should show the data.
> >
> >
> >
> >
> > -Original Message-
> > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
> > On Behalf Of Peter Waltman
> > Sent: Thursday, September 20, 2007 1:32 PM
> > To: r-help@r-project.org
> > Subject: [R] how can I attach a variable stored in
> >
> > Hi -
> >
> > Any help would be greatly appreciated.
> >
> > I'm loading a list variable that's stored in an .RData file and would
> > like attach it.
> >
> > I've used attach(  ), but that only lets me see the variable
> > that's stored in the file.
> >
> > As the variable name is of the form "comp.x.x", I've tried using attach(
> > ls( pat="comp" ) ), but get an error as ls() just gives back a string.
> >
> > I've also played around with eval(), but don't really quite get what
> > that function does since it seems to get into the R internals which I
> > don't entirely understand and I haven't found any great unified
> > documentation on R's handling environment and scoping.
> >
> > Thanks,
> >
> > Peter Waltman
> >
> > __
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> > 
> >
> > This is not an offer (or solicitation of an offer) to buy/sell the 
> > securities/instruments mentioned or an official confirmation.  Morgan 
> > Stanley may deal as principal in or own or act as market maker for 
> > securities/instruments mentioned or may advise the issuers.  This is not 
> > research and is not from MS Research but it may refer to a research 
> > analyst/research report.  Unless indicated, these views are the author's 
> > and may differ from those of Morgan Stanley research or others in the Firm. 
> >  We do not represent this is accurate or complete and we may not update 
> > this.  Past performance is not indicative of future returns.  For 
> > additional information, research reports and important disclosures, contact 
> > me or see https://secure.ms.com/servlet/cls.  You should not use e-mail to 
> > request, authorize or effect the purchase or sale of any security or 
> > instrument, to send transfer instructions, or to effect any other 
> > transactions.  We cannot guarantee that any such requests received !
 vi!
>  a e-mail will be processed in a timely manner.  This communication is solely 
> for the addressee(s) and may contain confidential information.  We do not 
> waive confidentiality by mistransmission.  Contact me if you do not wish to 
> receive these communications.  In the UK, this communication is directed in 
> the UK to those persons who are market counterparties or intermediate 
> customers (as defined in the UK Financial Services Authority's rules).
> >
> >
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


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

What is the problem you are trying to solve?

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Re: [R] convert data from

[jim holtman]

This should get you close to what you want:

> x <- read.table(textConnection("   X1X2
+ A12
+ B34
+ C56"), header=TRUE)
> # add rownames to the dataframe
> x$name <- row.names(x)
> require(reshape)  # use reshape package
[1] TRUE
> melt(x, id='name')
  name variable value
1A   X1 1
2B   X1 3
3C   X1 5
4A   X2 2
5B   X2 4
6C   X2 6


On 9/20/07, Pan Zheng <[EMAIL PROTECTED]> wrote:
> Hi,
>
> I am trying to convert a data frame from:
>
>X1X2
> A12
> B34
> C56
>
> to:
> A01 1
> A02 2
> B013
> B024
> C015
> C026.
>
> How can I do it in R?
>
> I appreciate your help.
>
> Zheng
>
>
> -
>
>[[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


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

What is the problem you are trying to solve?

__
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Re: [R] Identify and plotting symbols. [SEC=UNCLASSIFIED]

[Rolf Turner]

On 20/09/2007, at 4:35 PM, Crombie, Joe wrote:

> Or maybe:
>
>> while(length(ind <- identify(x,y,n = 1, plot = F)))
>>   points(x[ind], y[ind], pch = 19)
>
> (highlights each point as you select it, until you click _stop_)

Bewdy!!!  That's eggs-actly what I was looking for.  Thanks very much.

cheers,

Rolf

##
Attention:\ This e-mail message is privileged and confidenti...{{dropped}}

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Re: [R] help with making a function of scatter plot with multiple variables

[jim holtman]

The simple way is to enclose it in a 'function' and pass parameters.
Assuming that you have the same number of parameters, then the
following will do:

my.func <- function(x,y,d1,v1,s1,t1,s2,t2,s3,t3,s4,t4,s5,t5)
{
op <- par(bg = "grey97")
par(mfrow=c(1,2))
plot(d1,v1, pch="v", col="orange",cex=0.6, lwd=2,
   xlab="day", ylab="resp",cex.main =1,font.main= 1,main=" Surv
data",ylim=y,xlim=x,
   col.main="navyblue",col.lab="navyblue",cex.lab=0.7)

   points(s1,t1, pch="A", col="green4", cex=1)
   points(s2,t2, pch="B",col="navyblue", cex=1)
   points(s3,t3, pch="C",col="red", cex=1)
   points(s4,t4, pch="D",col="darkviolet", cex=1)
   points(s5,t5, pch="E",col="blue", cex=1)
 
legend("topright",lbels,col=c("orange","green4","navyblue","red","darkviolet","blue"),
text.col=c("orange","green4","navyblue","red","darkviolet","steelblue"),
pch=c("v","A","B","C","D","E"),bg='gray100',cex=0.7,box.lty=1,box.lwd=1)
   abline(h = -1:9, v = 0:8, col = "lightgray", lty=3)
par(op)
}

# call it with

my.func(x,y,d1,v1,s1,t1,s2,t2,s3,t3,s4,t4,s5,t5)

You might also include the data in a list to make it easier



On 9/20/07, Tom Cohen <[EMAIL PROTECTED]> wrote:
> Dear list,
>
>  I have done a scatter plot of  multiple variables in the same graph, with 
> different col and pch. I managed to do it with the following code but not 
> know how to make a function of these so that next time if I want to do 
> similar graph but with new variables, I dont have to copy the code and then 
> change the old variables with the new ones but just call a function with the 
> new variables. I dont have any experience in making a function and would be 
> very grateful if you can help me. A function will shorten my prog 
> dramatically, since I repeat tthis type of graph alots in my analysis.
>
>  Thanks in advance,
>  Tom
>
>  op <- par(bg = "grey97")
> par(mfrow=c(1,2))
> plot(d1,v1, pch="v", col="orange",cex=0.6, lwd=2,
>xlab="day", ylab="resp",cex.main =1,font.main= 1,main=" Surv 
> data",ylim=y,xlim=x,
>col.main="navyblue",col.lab="navyblue",cex.lab=0.7)
>
>points(s1,t1, pch="A", col="green4", cex=1)
>points(s2,t2, pch="B",col="navyblue", cex=1)
>points(s3,t3, pch="C",col="red", cex=1)
>points(s4,t4, pch="D",col="darkviolet", cex=1)
>points(s5,t5, pch="E",col="blue", cex=1)
>  
> legend("topright",lbels,col=c("orange","green4","navyblue","red","darkviolet","blue"),
> text.col=c("orange","green4","navyblue","red","darkviolet","steelblue"),
> pch=c("v","A","B","C","D","E"),bg='gray100',cex=0.7,box.lty=1,box.lwd=1)
>abline(h = -1:9, v = 0:8, col = "lightgray", lty=3)
> par(op)
>
>
>
>
> -
>
> Jämför pris på flygbiljetter och hotellrum: 
> http://shopping.yahoo.se/c-169901-resor-biljetter.html
>[[alternative HTML version deleted]]
>
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>


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

What is the problem you are trying to solve?

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

Re: [R] how can I attach a variable stored in

[Tony Plate]

Here's a function that does what I think you want to do:

 > attach.firstvar <- function(file) {
+ tmpenv <- new.env()
+ vars <- load(file, envir=tmpenv)
+ x <- get(vars[1], envir=tmpenv, inherits=FALSE)
+ if (is.list(x))
+ attach(x, name=vars[1])
+ return(vars)
+ }
 > x <- list(xa=1, xb=2, xc=3)
 > save(list="x", file="tmp1.rda")
 > remove(list="x")
 > attach.firstvar("tmp1.rda")
[1] "x"
 > ls(pos=2)
[1] "xa" "xb" "xc"
 > find("xa")
[1] "x"
 > search()
  [1] ".GlobalEnv""x" "package:stats"
  [4] "package:graphics"  "package:grDevices" "package:utils"
  [7] "package:datasets"  "package:methods"   "Autoloads"
[10] "package:base"
 > xa
[1] 1
 > xb
[1] 2
 >

Peter Waltman wrote:
> Hi Mark -
> 
> Thanks for the reply.  Sorry I didn't really clarify too well what I'm 
> trying to do.  The issue is not that I can't see the variable that gets 
> loaded. 
> 
> The issue is that the variable is a list variable, and I'd like to write 
> a function that will take the .RData filename and attach the variable it 
> contains so that I can more easily access its contents, i.e.
> 
> foo.bar <- list( "a"= "a", "b"=1 )
> save( file="foo.bar.RData", foo.bar )
> rm( foo.bar )
> 
> my.fn <- function( fname ) {
>load( fname )
>attach( ls( pat="foo" ) ) #  I want to attach( foo.bar ), but
> this doesn't work
> }
> 
> ls()  # prints out "foo.bar"
> 
> attach( ls( ) )   # still doesn't work
> attach( foo.bar )  # works
> 
> So, basically, the question is how can I attach the variable that's 
> stored in a file if I don't already know it's name?
> 
> Thanks again!
> 
> Peter
> 
> Leeds, Mark (IED) wrote:
>> I don't think I understand your question but John Fox has written a very
>> nice documentat about scoping and environments on his website.
>> It's probably easy to find the site by googling "John Fox" but, if you
>> can't find it, let me know.
>>  
>> As I said, I don't think that I understand your question but, if you
>> loaded a list variable using load("whatever.Rdata"), the variable will 
>> just be suitting in  your workspace. You don't need to attach anything
>> because load just loads the data right into the workspace.
>> So typing the variable name should show the data.
>>
>>
>>
>>
>> -Original Message-
>> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
>> On Behalf Of Peter Waltman
>> Sent: Thursday, September 20, 2007 1:32 PM
>> To: r-help@r-project.org
>> Subject: [R] how can I attach a variable stored in
>>
>> Hi -
>>
>> Any help would be greatly appreciated.
>>
>> I'm loading a list variable that's stored in an .RData file and would
>> like attach it.
>>
>> I've used attach(  ), but that only lets me see the variable
>> that's stored in the file. 
>>
>> As the variable name is of the form "comp.x.x", I've tried using attach(
>> ls( pat="comp" ) ), but get an error as ls() just gives back a string.
>>
>> I've also played around with eval(), but don't really quite get what
>> that function does since it seems to get into the R internals which I
>> don't entirely understand and I haven't found any great unified
>> documentation on R's handling environment and scoping.
>>
>> Thanks,
>>
>> Peter Waltman
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>> 
>>
>> This is not an offer (or solicitation of an offer) to buy/sell the 
>> securities/instruments mentioned or an official confirmation.  Morgan 
>> Stanley may deal as principal in or own or act as market maker for 
>> securities/instruments mentioned or may advise the issuers.  This is not 
>> research and is not from MS Research but it may refer to a research 
>> analyst/research report.  Unless indicated, these views are the author's and 
>> may differ from those of Morgan Stanley research or others in the Firm.  We 
>> do not represent this is accurate or complete and we may not update this.  
>> Past performance is not indicative of future returns.  For additional 
>> information, research reports and important disclosures, contact me or see 
>> https://secure.ms.com/servlet/cls.  You should not use e-mail to request, 
>> authorize or effect the purchase or sale of any security or instrument, to 
>> send transfer instructions, or to effect any other transactions.  We cannot 
>> guarantee that any such requests received v
i!
>  a e-mail will be processed in a timely manner.  This communication is solely 
> for the addressee(s) and may contain confidential information.  We do not 
> waive confidentiality by mistransmission.  Contact me if you do not wish to 
> receive these communications.  In the UK, this communication is directed in 
> the UK to those persons

Re: [R] Robust or Sandwich estimates in lmer2

[David Duffy]

Abdus Sattar <[EMAIL PROTECTED]> asked:

>
> I am trying to find the robust (or sandwich) estimates of the standard
> error of fixed effects parameter estimates using the package "lmer2".
>
Others have already pointed out that this is not implemented in lmer2.

You could try a delete-n jackknife, which you would have to implement
yourself. An ordinary delete-1 jackknife does not work for
clustered/correlated data.  This would also give you bias-corrected
point estimates.  I should add that, in the limited simulations I have
done (for Gaussian mixed model analysis of pedigree data), the jackknife
standard errors seemed a bit conservative (too big).

David Duffy.
-- 
| David Duffy (MBBS PhD) ,-_|\
| email: [EMAIL PROTECTED]  ph: INT+61+7+3362-0217 fax: -0101  / *
| Epidemiology Unit, Queensland Institute of Medical Research   \_,-._/
| 300 Herston Rd, Brisbane, Queensland 4029, Australia  GPG 4D0B994A v

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Re: [R] Superimposing vector polygons over raster grid in a plot

[Dylan Beaudette]

On Thursday 20 September 2007, Rick Reeves wrote:
> Thanks for this, Dylan. Great example. One question: 'elev.pred' and
> 'elev.var' are columns in the result 'p' from predict?
> thanks, RR

Hi,

elev.pred and elev.var are the 'zcol' attribute, or rather the value at each 
cell within the spatial dataframe object 'p' in that example. here is the 
construct for spplot() ... note that i left off the 'zcol=' bit on the first 
call to spplot... i will fix that.

spplot(p, zcol='elev.var', ...


cheers,

Dylan

> Dylan Beaudette wrote:
> > On Thursday 20 September 2007, Rick Reeves wrote:
> >> Hello:
> >>
> >> I would like to superimpose vector polygons (state outlines) from a
> >> Shape file on top of a satellite image,
> >> imported into a SpatialGridDataFrame from GEOTIFF via gdal_translate and
> >> readGDAL.
> >>
> >> When I plot polygon and point shape files in R, into
> >> SpatialPointDataFrame and SpatialPolygonDataFrame,
> >> the two feature sets line up geographically, so it seems logical that a
> >> SpatialGridDataFrame should behave
> >> in the same way.
> >>
> >>  From my initial research, the spplot function is the correct function
> >> for plotting grids/images with axes and
> >> annotation.
> >>
> >> The big question is, how do I incorporate a Spatial(Points or
> >> Polygons)DataFrame into the spplot display list?
> >>
> >> It seems as though many scientists would like to create such plots
> >> without resorting to GRASS or
> >> another GIS.
> >
> > While GRASS and GMT are excellent tools, here are some ideas on how to
> > make composite maps in R:
> >
> > http://casoilresource.lawr.ucdavis.edu/drupal/node/442
> >
> > cheers,
> >
> > Dylan
> >
> >> Thanks for any advice,
> >> Rick Reeves
> >>
> >> Rick Reeves
> >> Scientific Programmer / Analyst
> >> National Center for Ecological Analysis and Synthesis
> >> UC Santa Barbara
> >> [EMAIL PROTECTED]
> >> www.nceas.ucsb.edu
> >> 805 892 2533



-- 
Dylan Beaudette
Soils and Biogeochemistry Graduate Group
University of California at Davis
530.754.7341

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Re: [R] Time series graphs, question about using zoo

[fang liu]

Hi,
Can you tell me what is the meaning for "tail, 1"  in "aggregate"?
I also want to get some similar graph, but the data is not time series data.
Suppose here is my data one, I want a graph with x-axis is just the 
index(1:9).
The graph plot all the variable A, B,C,D. So there should be 4 lines for 
each graph. For the A line, at each time point, the letter A should be on 
the line. And the same goes for the B line.
A   BCD
>  8   4 9 8
>  7   5 4 7
>  6   8 4 4
>  3   7  6 2
>  5   1 8 5
>  6   4  71
>  2   8 3 4
>  1   2  4 8
>  4   3  19

So I add a name for each row
rownames(one) <- c(1:9)
z <- zooreg(as.matrix(one), start = 1, freq = 1)
z <- aggregate(z, as.Date, tail, 1)
plot(z, plot.type = "single",  type = "o",
pch = c("A", "B", "C", "D"), lty = 1:2)

I get the plot, which I think it should be right. but the problem is that 
the x-axis still have month (Jan, ) on it and I didnot get "A,B,C,D" on my 
graph, is there any thing wrong?



>From: "Gabor Grothendieck" <[EMAIL PROTECTED]>
>To: "Bill Pepe" <[EMAIL PROTECTED]>
>CC: r-help@r-project.org
>Subject: Re: [R] Time series graphs
>Date: Thu, 20 Sep 2007 14:15:54 -0400
>
>Using plot.zoo in the zoo package try this:
>
>Lines <- "Bob.A Bob.BTom.ATom.B
>  Jan  84 9 8
>  Feb 7 5 4 7
>  Mar 6 8 4 4
>  Apr 3 7  6 2
>  May5 1 8 5
>  Jun 6 4  71
>  July 2 8 3 4
>  Aug 12  4 8
>  Sep4  3  19
>"
>DF <- read.table(textConnection(Lines))
>
>library(zoo)
>z <- zooreg(as.matrix(DF), start = as.yearmon(as.Date("2007-01-01")), freq 
>= 12)
>z <- aggregate(z, as.Date, tail, 1)
>plot(z, plot.type = "single",  type = "o",
>   pch = c("A", "A", "B", "B"), lty = 1:2)
>legend("bottomleft", c("Bob", "Tom"), lty = 1:2)
>
>
>
>On 9/20/07, Bill Pepe <[EMAIL PROTECTED]> wrote:
> > I'm fairly new to S-Plus and I need to get this done quickly. Suppose I 
>have the following fake data below:
> >
> >  There are two companies, call them Bob and Tom. Each have two 
>variables, call them A and B, that have observations.
> >
> > Bob Tom
> >
> >A BAB
> >  Jan  84 9 8
> >  Feb 7 5 4 7
> >  Mar 6 8 4 4
> >  Apr 3 7  6 2
> >  May5 1 8 5
> >  Jun 6 4  71
> >  July 2 8 3 4
> >  Aug 12  4 8
> >  Sep4  3  19
> >
> >  Here is what I want to do: I want to make two different graphs, one for 
>Bob and one for Tom. For each graph, plot both variables A and B. Connect 
>the A values with a line, and connect the B values with a different type of 
>line. So there should be two lines for each graph. For the A line, at each 
>time point, the letter A should be on the line. And the same goes for the B 
>line. Either R or S-Plus since they are essentially the same.
> >
> >  I'm sure this is easy, but any help would be greatly appreciated.
> >
> >  Thanks,
> >
> >  Bill
> >
> >
> > -
> > Pinpoint customers who are looking for what you sell.
> >[[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide 
>http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
>__
>R-help@r-project.org mailing list
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide 
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.

_
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Re: [R] SEM - singularity error

[John Fox]

Dear Nicki,

> -Original Message-
> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] 
> Sent: Thursday, September 20, 2007 3:06 PM
> To: John Fox
> Cc: Chuck Cleland; [EMAIL PROTECTED]
> Subject: Re: [R] SEM - singularity error
> 
> Dear John,
> 
> Thank you so much for your assistance, it is greatly 
> appreciated. You are correct in your interpretation of the 
> variables (Moist and Hab are latent, the other, lower case 
> variables are observed). I've attempted to run the model 
> again adding Moist <-> Hab (please see code below) and still 
> receive the same error message:
> 
> "Error in solve.default(C) : system is computationally 
> singular: reciprocal condition number = 6.59035e-17."
> 
> Is it possible that something is wrong with the 
> variance-covariance matrix (please see pasted below r code)? 
> Are extremely small values (e.g., 4e-4) problematic? Do you 
> have any additional suggestions as to how I might go about 
> trouble shooting this problem?

You could set the argument debug=TRUE in the call to sem(), which will give
you more detail about what's going on. But I suspect that the problem is the
very large differences in size among the variances of your observed
variances, differences of many orders of magnitude. You could try the
following: (1) set the argument par.size="start.values"; and, if that
doesn't work, (2) alternatively see what happens when you try to estimate
the model from a correlation rather than a covariance matrix.

> 
> I am also attaching the jpeg model diagram, in case it could 
> be of use to you.

The diagram is identical to the one that I inferred from your model
specification. I still think that you probably want to allow the two latent
exogenous variables to be correlated.

If neither of these approaches works, then please send me (privately) the
input covariance matrix and model specification as files so that I can take
a closer look.

Regards,
 John

> 
> Thank you so much for your time.
> Best wishes,
> Nicki
> 
> R CODE USED:
> # 20 Sep 2007 SEM of Thamnophis abundance
> 
> # LOADING R PACKAGES
> library(sem)
> 
> # READING IN THE CSV FILES
> thsi.2006<-read.csv("thsi_ab_env_space_sem.csv")
> thsi<-thsi.2006
> 
> # MAKING "RAM" FILE 3
> model3.nlc <-specify.model()
> Moist->slope, NA, 1
> Moist->sand, lamda21, NA
> Moist->clay, lamda31, NA
> Hab->isol, NA, 1
> Hab->edgedist_a, lamda52, NA
> Hab->ag10, lamda62, NA
> Hab->urb10, lamda72, NA
> Hab->rd10, lamda82, NA
> Hab->y, lamda92, NA
> Moist->this, gamma11, NA
> Hab->this, gamma12, NA
> slope<->slope, theta11, NA
> sand<->sand, theta22, NA
> clay<->clay, theta33, NA
> isol<->isol, theta44, NA
> edgedist_a<->edgedist_a, theta55, NA
> ag10<->ag10, theta66, NA
> urb10<->urb10, theta77, NA
> rd10<->rd10, theta88, NA
> y<->y, the99, NA
> Moist<->Moist, phi11, NA
> Hab<->Hab, phi22, NA
> Moist<->Hab, phi21, NA
> this<->this, theps11, NA
> 
> model3.nlc
> end
> 
> # MAKING S (COVARIANCE MATRIX)
> thsi.var <- var(thsi)
> 
> # MAKING UNSCALED SEM MODEL
> sem3<-sem(ram=model3.nlc, S=thsi.var, N=22)
> 
> VARIANCE-COVARIANCE MATRIX (AKA: thsi.var):
>this
> this  8.88528139
> edgedist_a   44.91469329
> isol   2678.38321991
> ag10 -0.38967619
> urb10 0.11704827
> rd10  0.02132100
> slope-2.25074394
> clay-36.19339827
> sand 19.66753247
> y-0.95970602
>   edgedist_a
> this  44.9146933
> edgedist_a 17491.7873712
> isol   96122.5594957
> ag10  -9.1045614
> urb10  1.9439758
> rd10   0.5333281
> slope 24.4351358
> clay   -1360.1102116
> sand 619.1507519
> y-15.4852253
> isol
> this  2678.38322
> edgedist_a   96122.55950
> isol   4167108.48214
> ag10  -347.26757
> urb10   91.79339
> rd1025.71996
> slope -392.44092
> clay-42236.76039
> sand 19461.19308
> y -868.20597
> ag10
> this -0.38967619
> edgedist_a   -9.10456137
> isol   -347.26756672
> ag10  0.05167298
> urb10-0.01314388
> rd10 -0.00297957
> slope 0.06923224
> clay  3.17604271
> sand -1.61043719
> y 0.11896881
>   urb10
> this0.117048268
> edgedist_a  1.943975810
> isol   91.793388529
> ag10   -0.013143880
> urb10   0.003733677
> rd100.000784747
> slope  -0.039094302
> clay   -0.907067141
> sand0.491619654
> y  -0.034343332
> rd10
> this0.0213209957
> edgedist_a  0.5333280831
> isol   25.7199633947
> ag10   -0.0029795700
> urb10   0.0007847471
> rd100.0001987203
> slope  -0.0041496227
> clay   -0.2726142316
> sand0.1286087229
> y  -0.0078502982
>slope
> this   -2.250744e+00
> edgedist_a  2.443514e+01
> isol   -3.924409e+02
> ag106.923224e-02
> urb10  

Re: [R] Cutting & pasting help examples into script window

[Duncan Murdoch]

On 20/09/2007 1:49 PM, Muenchen, Robert A (Bob) wrote:
> Does this look like a bug? If so, is there a different way to report it?

It sounds like a bug, but I can't reproduce it.  You said it is 
intermittent on your system.  Can you try to work out the conditions 
that reliably trigger it?

It might be something specific to your system; does anyone else see this?

Duncan Murdoch

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Re: [R] Time series graphs, question about using zoo

[Gabor Grothendieck]

Try this:

Lines <- "A   BCD
   8   4 9 8
   7   5 4 7
   6   8 4 4
   3   7  6 2
   5   1 8 5
   6   4  71
   2   8 3 4
   1   2  4 8
   4   3  19
"
one <- read.table(textConnection(Lines), header = TRUE)
library(zoo)
z <- zoo(as.matrix(one))
plot(z, plot.type = "single", pch = colnames(z), type = "o", col =
1:4, lty = 1:4)
legend("bottomleft", colnames(z), col = 1:4, lty = 1:4)

# or use matplot
matplot(as.matrix(one), pch = colnames(z), type = "o")
legend("bottomleft", colnames(z), col = 1:4, lty = 1:4)


On 9/20/07, fang liu <[EMAIL PROTECTED]> wrote:
> Hi,
> Can you tell me what is the meaning for "tail, 1"  in "aggregate"?
> I also want to get some similar graph, but the data is not time series data.
> Suppose here is my data one, I want a graph with x-axis is just the
> index(1:9).
> The graph plot all the variable A, B,C,D. So there should be 4 lines for
> each graph. For the A line, at each time point, the letter A should be on
> the line. And the same goes for the B line.
>A   BCD
> >  8   4 9 8
> >  7   5 4 7
> >  6   8 4 4
> >  3   7  6 2
> >  5   1 8 5
> >  6   4  71
> >  2   8 3 4
> >  1   2  4 8
> >  4   3  19
>
> So I add a name for each row
> rownames(one) <- c(1:9)
> z <- zooreg(as.matrix(one), start = 1, freq = 1)
> z <- aggregate(z, as.Date, tail, 1)
> plot(z, plot.type = "single",  type = "o",
>pch = c("A", "B", "C", "D"), lty = 1:2)
>
> I get the plot, which I think it should be right. but the problem is that
> the x-axis still have month (Jan, ) on it and I didnot get "A,B,C,D" on my
> graph, is there any thing wrong?
>
>
>
> >From: "Gabor Grothendieck" <[EMAIL PROTECTED]>
> >To: "Bill Pepe" <[EMAIL PROTECTED]>
> >CC: r-help@r-project.org
> >Subject: Re: [R] Time series graphs
> >Date: Thu, 20 Sep 2007 14:15:54 -0400
> >
> >Using plot.zoo in the zoo package try this:
> >
> >Lines <- "Bob.A Bob.BTom.ATom.B
> >  Jan  84 9 8
> >  Feb 7 5 4 7
> >  Mar 6 8 4 4
> >  Apr 3 7  6 2
> >  May5 1 8 5
> >  Jun 6 4  71
> >  July 2 8 3 4
> >  Aug 12  4 8
> >  Sep4  3  19
> >"
> >DF <- read.table(textConnection(Lines))
> >
> >library(zoo)
> >z <- zooreg(as.matrix(DF), start = as.yearmon(as.Date("2007-01-01")), freq
> >= 12)
> >z <- aggregate(z, as.Date, tail, 1)
> >plot(z, plot.type = "single",  type = "o",
> >   pch = c("A", "A", "B", "B"), lty = 1:2)
> >legend("bottomleft", c("Bob", "Tom"), lty = 1:2)
> >
> >
> >
> >On 9/20/07, Bill Pepe <[EMAIL PROTECTED]> wrote:
> > > I'm fairly new to S-Plus and I need to get this done quickly. Suppose I
> >have the following fake data below:
> > >
> > >  There are two companies, call them Bob and Tom. Each have two
> >variables, call them A and B, that have observations.
> > >
> > > Bob Tom
> > >
> > >A BAB
> > >  Jan  84 9 8
> > >  Feb 7 5 4 7
> > >  Mar 6 8 4 4
> > >  Apr 3 7  6 2
> > >  May5 1 8 5
> > >  Jun 6 4  71
> > >  July 2 8 3 4
> > >  Aug 12  4 8
> > >  Sep4  3  19
> > >
> > >  Here is what I want to do: I want to make two different graphs, one for
> >Bob and one for Tom. For each graph, plot both variables A and B. Connect
> >the A values with a line, and connect the B values with a different type of
> >line. So there should be two lines for each graph. For the A line, at each
> >time point, the letter A should be on the line. And the same goes for the B
> >line. Either R or S-Plus since they are essentially the same.
> > >
> > >  I'm sure this is easy, but any help would be greatly appreciated.
> > >
> > >

Re: [R] Time series graphs, question about using zoo [SEC=UNCLASSIFIED]

[Crombie, Joe]

Hi Fang,

An easy way of doing this is by:

> matplot(one, pch = LETTERS[1:4], type = 'b')

Cheers  Joe

 
Joe Crombie
 
Information and Risk Sciences
Bureau of Rural Science
Canberra  Australia
 
p: +61 2 6272 5906
e: [EMAIL PROTECTED]


-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of fang liu
Sent: Friday, 21 September 2007 8:35 AM
To: r-help@r-project.org
Subject: Re: [R] Time series graphs, question about using zoo

Hi,
Can you tell me what is the meaning for "tail, 1"  in "aggregate"?
I also want to get some similar graph, but the data is not time series
data.
Suppose here is my data one, I want a graph with x-axis is just the
index(1:9).
The graph plot all the variable A, B,C,D. So there should be 4 lines for
each graph. For the A line, at each time point, the letter A should be
on the line. And the same goes for the B line.
A   BCD
>  8   4 9 8
>  7   5 4 7
>  6   8 4 4
>  3   7  6 2
>  5   1 8 5
>  6   4  71
>  2   8 3 4
>  1   2  4 8
>  4   3  19

So I add a name for each row
rownames(one) <- c(1:9)
z <- zooreg(as.matrix(one), start = 1, freq = 1) z <- aggregate(z,
as.Date, tail, 1) plot(z, plot.type = "single",  type = "o",
pch = c("A", "B", "C", "D"), lty = 1:2)

I get the plot, which I think it should be right. but the problem is
that the x-axis still have month (Jan, ) on it and I didnot get
"A,B,C,D" on my graph, is there any thing wrong?



>From: "Gabor Grothendieck" <[EMAIL PROTECTED]>
>To: "Bill Pepe" <[EMAIL PROTECTED]>
>CC: r-help@r-project.org
>Subject: Re: [R] Time series graphs
>Date: Thu, 20 Sep 2007 14:15:54 -0400
>
>Using plot.zoo in the zoo package try this:
>
>Lines <- "Bob.A Bob.BTom.ATom.B
>  Jan  84 9 8
>  Feb 7 5 4 7
>  Mar 6 8 4 4
>  Apr 3 7  6 2
>  May5 1 8 5
>  Jun 6 4  71
>  July 2 8 3 4
>  Aug 12  4 8
>  Sep4  3  19
>"
>DF <- read.table(textConnection(Lines))
>
>library(zoo)
>z <- zooreg(as.matrix(DF), start = as.yearmon(as.Date("2007-01-01")),
>freq = 12) z <- aggregate(z, as.Date, tail, 1) plot(z, plot.type = 
>"single",  type = "o",
>   pch = c("A", "A", "B", "B"), lty = 1:2) legend("bottomleft",
c("Bob", 
>"Tom"), lty = 1:2)
>
>
>
>On 9/20/07, Bill Pepe <[EMAIL PROTECTED]> wrote:
> > I'm fairly new to S-Plus and I need to get this done quickly. 
> > Suppose I
>have the following fake data below:
> >
> >  There are two companies, call them Bob and Tom. Each have two
>variables, call them A and B, that have observations.
> >
> > Bob Tom
> >
> >A BAB
> >  Jan  84 9 8
> >  Feb 7 5 4 7
> >  Mar 6 8 4 4
> >  Apr 3 7  6 2
> >  May5 1 8 5
> >  Jun 6 4  71
> >  July 2 8 3 4
> >  Aug 12  4 8
> >  Sep4  3  19
> >
> >  Here is what I want to do: I want to make two different graphs, one

> > for
>Bob and one for Tom. For each graph, plot both variables A and B. 
>Connect the A values with a line, and connect the B values with a 
>different type of line. So there should be two lines for each graph.
>For the A line, at each time point, the letter A should be on the line.

>And the same goes for the B line. Either R or S-Plus since they are
essentially the same.
> >
> >  I'm sure this is easy, but any help would be greatly appreciated.
> >
> >  Thanks,
> >
> >  Bill
> >
> >
> > -
> > Pinpoint customers who are looking for what you sell.
> >[[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
>__
>R-help@r-projec

[R] Help create a loopto conduct multiple pairwise operations

[Luke Neraas]

#Hello,


#I have three data frames, X,Y and Z with two columns each and different
numbers of rows.

# creation of data frame X

X.alleles  <- c(1,5,6,7,8)
X.Freq<- c(0.35, 0.15, 0.05 , 0.10, 0.35)
Loc1  <- cbind( X.alleles,X.Freq)
X   <- data.frame(Loc1)

#creation of data frame Y

Y.alleles  <- c(1,4,6,8)
Y.Freq <- c(0.35, 0.35, 0.10, 0.20 )
Loc2<- cbind(Y.alleles, Y.Freq)
Y <- data.frame (Loc2)

# creation of data frame Z

Z.alleles  <- c(1,4,5,6,8)
Z.Freq <- c(0.35, 0.35, 0.05, 0.05, 0.20)
Loc3   <- cbind(Z.alleles, Z.Freq)
Z<- data.frame (Loc3)

X
Y
Z

#  I want to create a pair wise multiplication for all of the second columns
of my dataframe X,Y and Z

# Here is a way to get two of the data frames to create a pairwise
multiplication.

X.Freq_times_Y.Freq<- matrix(Y[,2] %o% X[,2], ncol=1)
X.Freq_times_Y.Freq

# I would like to create a loop to calculate all possible pairwise
multiplications for the
# second columns of my X,Y, and Z data frames.
# I will be conducting pair wise comparisons for up to 50 different data
frames so I need the code to be
# as flexible as possible

Any help would be greatly appreciated.

Thanks in advance


Luke Neraas
[EMAIL PROTECTED]

University of Alaska Fairbanks
School of Fisheries and Ocean Sciences
11120 Glacier Highway
UAF Fisheries Division
Juneau, AK 99801

[[alternative HTML version deleted]]

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

Re: [R] Help create a loopto conduct multiple pairwise operations

[jim holtman]

You can put the dataframes in a list and then use 'combn' to determine
the possible pairwise combinations and then use this in an lapply to
compute the products which is also in a list:

>
> X.alleles  <- c(1,5,6,7,8)
> X.Freq<- c(0.35, 0.15, 0.05 , 0.10, 0.35)
> Loc1  <- cbind( X.alleles,X.Freq)
> X   <- data.frame(Loc1)
>
> #creation of data frame Y
>
> Y.alleles  <- c(1,4,6,8)
> Y.Freq <- c(0.35, 0.35, 0.10, 0.20 )
> Loc2<- cbind(Y.alleles, Y.Freq)
> Y <- data.frame (Loc2)
>
> # creation of data frame Z
>
> Z.alleles  <- c(1,4,5,6,8)
> Z.Freq <- c(0.35, 0.35, 0.05, 0.05, 0.20)
> Loc3   <- cbind(Z.alleles, Z.Freq)
> Z<- data.frame (Loc3)
>
> X
  X.alleles X.Freq
1 1   0.35
2 5   0.15
3 6   0.05
4 7   0.10
5 8   0.35
> Y
  Y.alleles Y.Freq
1 1   0.35
2 4   0.35
3 6   0.10
4 8   0.20
> Z
  Z.alleles Z.Freq
1 1   0.35
2 4   0.35
3 5   0.05
4 6   0.05
5 8   0.20
> # create a list of the dataframes you want to multiply
> dfList <- list(X, Y, Z)
> # get possible pairwise matches
> combo <- combn(length(dfList), 2)
> result <- lapply(seq(ncol(combo)), function(.col){
+ dfList[[combo[1, .col]]][, 2] %o% dfList[[combo[2, .col]]][, 2]
+ })
>
> result
[[1]]
   [,1]   [,2]  [,3] [,4]
[1,] 0.1225 0.1225 0.035 0.07
[2,] 0.0525 0.0525 0.015 0.03
[3,] 0.0175 0.0175 0.005 0.01
[4,] 0.0350 0.0350 0.010 0.02
[5,] 0.1225 0.1225 0.035 0.07

[[2]]
   [,1]   [,2]   [,3]   [,4] [,5]
[1,] 0.1225 0.1225 0.0175 0.0175 0.07
[2,] 0.0525 0.0525 0.0075 0.0075 0.03
[3,] 0.0175 0.0175 0.0025 0.0025 0.01
[4,] 0.0350 0.0350 0.0050 0.0050 0.02
[5,] 0.1225 0.1225 0.0175 0.0175 0.07

[[3]]
   [,1]   [,2]   [,3]   [,4] [,5]
[1,] 0.1225 0.1225 0.0175 0.0175 0.07
[2,] 0.1225 0.1225 0.0175 0.0175 0.07
[3,] 0.0350 0.0350 0.0050 0.0050 0.02
[4,] 0.0700 0.0700 0.0100 0.0100 0.04

> dfList
[[1]]
  X.alleles X.Freq
1 1   0.35
2 5   0.15
3 6   0.05
4 7   0.10
5 8   0.35

[[2]]
  Y.alleles Y.Freq
1 1   0.35
2 4   0.35
3 6   0.10
4 8   0.20

[[3]]
  Z.alleles Z.Freq
1 1   0.35
2 4   0.35
3 5   0.05
4 6   0.05


On 9/20/07, Luke Neraas <[EMAIL PROTECTED]> wrote:
> #Hello,
>
>
> #I have three data frames, X,Y and Z with two columns each and different
> numbers of rows.
>
> # creation of data frame X
>
> X.alleles  <- c(1,5,6,7,8)
> X.Freq<- c(0.35, 0.15, 0.05 , 0.10, 0.35)
> Loc1  <- cbind( X.alleles,X.Freq)
> X   <- data.frame(Loc1)
>
> #creation of data frame Y
>
> Y.alleles  <- c(1,4,6,8)
> Y.Freq <- c(0.35, 0.35, 0.10, 0.20 )
> Loc2<- cbind(Y.alleles, Y.Freq)
> Y <- data.frame (Loc2)
>
> # creation of data frame Z
>
> Z.alleles  <- c(1,4,5,6,8)
> Z.Freq <- c(0.35, 0.35, 0.05, 0.05, 0.20)
> Loc3   <- cbind(Z.alleles, Z.Freq)
> Z<- data.frame (Loc3)
>
> X
> Y
> Z
>
> #  I want to create a pair wise multiplication for all of the second columns
> of my dataframe X,Y and Z
>
> # Here is a way to get two of the data frames to create a pairwise
> multiplication.
>
> X.Freq_times_Y.Freq<- matrix(Y[,2] %o% X[,2], ncol=1)
> X.Freq_times_Y.Freq
>
> # I would like to create a loop to calculate all possible pairwise
> multiplications for the
> # second columns of my X,Y, and Z data frames.
> # I will be conducting pair wise comparisons for up to 50 different data
> frames so I need the code to be
> # as flexible as possible
>
> Any help would be greatly appreciated.
>
> Thanks in advance
>
>
> Luke Neraas
> [EMAIL PROTECTED]
>
> University of Alaska Fairbanks
> School of Fisheries and Ocean Sciences
> 11120 Glacier Highway
> UAF Fisheries Division
> Juneau, AK 99801
>
>[[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


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

What is the problem you are trying to solve?

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Re: [R] Cutting & pasting help examples into script window

[Muenchen, Robert A (Bob)]

Now I'm working in 2.5.1 on a home machine also running XP. It has the
same problem, and I think I finally figured it out. 

I've noticed that if the cursor is directly over the text, it becomes an
I-beam. When hovering over the blank space around the text, the cursor
becomes an arrow. Selections via the arrow almost always paste properly
into a script window. Copies made while selecting with the I-beam cursor
almost always fail.

Regardless of how the selection is done, a paste into Notepad never
fails. Copying from Notepad to a script window never fails, regardless
of how the paste into Notepad was selected.

Very strange!

Bob

P.S. almost the testing has been with the ?data.frame and ?summary
examples.

> -Original Message-
> From: Duncan Murdoch [mailto:[EMAIL PROTECTED]
> Sent: Thursday, September 20, 2007 7:59 PM
> To: Muenchen, Robert A (Bob)
> Cc: [EMAIL PROTECTED]
> Subject: Re: [R] Cutting & pasting help examples into script window
> 
> On 20/09/2007 1:49 PM, Muenchen, Robert A (Bob) wrote:
> > Does this look like a bug? If so, is there a different way to report
> it?
> 
> It sounds like a bug, but I can't reproduce it.  You said it is
> intermittent on your system.  Can you try to work out the conditions
> that reliably trigger it?
> 
> It might be something specific to your system; does anyone else see
> this?
> 
> Duncan Murdoch

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[R] BRugs package question

[sk]

Hi there,
  I installed the latest OpenBUGS version (3.0.3) in program files folder but 
it seems that bugs use its own version of OpenBUGS. 
  here is part of the message bugs returns
  . 
  Welcome to BRugs running on OpenBUGS version 2.2.0 beta 
   
  how can i configure BRugs  to use the mine version of OpenBUGS?
  Cheers, SK
   

   
-

[[alternative HTML version deleted]]

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[R] Line Graph - Greater than 2 variables on plot

[Wayne Aldo Gavioli]

Hello all,

I was wondering if anyone knew how to construct a multiple line graph on R,
where there are 2 (or more) sets of data points plotted against some x axis of
data, and you can draw a line on the graph connecting each set of data points.

For example:

A   B  C  D
0.65662.11851.23205
0.647 2.08651.232510
0.65322.10601.228715
0.64872.12901.231320
0.65942.12851.234125
0.65772.10701.234330
0.65792.13451.234035
0.67342.17051.236240
0.675 2.18451.237245
0.65922.15501.234050
0.66472.17101.230555



Would there be a way:
a) To graph all the points of data in sets A, B and C as Y coordinates on one
graph, using the points in set D as the X-axis/coordinates for all 3 sets (A, B
and C)?
b) To be able to draw 3 lines on the graph that connect each set of data (1 line
connects all the A points, one line connects all the B points, one line connects
all the C points)


I couldn't find anything in the examples or the help section about multiple
lines on the same graph, only one line.


Thanks,



Wayne

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Re: [R] Line Graph - Greater than 2 variables on plot

[Rolf Turner]

On 21/09/2007, at 1:57 PM, Wayne Aldo Gavioli wrote:

>
>
> Hello all,
>
> I was wondering if anyone knew how to construct a multiple line  
> graph on R,
> where there are 2 (or more) sets of data points plotted against  
> some x axis of
> data, and you can draw a line on the graph connecting each set of  
> data points.
>
> For example:
>
> A   B  C  D
> 0.65662.11851.23205
> 0.647 2.08651.232510
> 0.65322.10601.228715
> 0.64872.12901.231320
> 0.65942.12851.234125
> 0.65772.10701.234330
> 0.65792.13451.234035
> 0.67342.17051.236240
> 0.675 2.18451.237245
> 0.65922.15501.234050
> 0.66472.17101.230555
>
>
>
> Would there be a way:
> a) To graph all the points of data in sets A, B and C as Y  
> coordinates on one
> graph, using the points in set D as the X-axis/coordinates for all  
> 3 sets (A, B
> and C)?
> b) To be able to draw 3 lines on the graph that connect each set of  
> data (1 line
> connects all the A points, one line connects all the B points, one  
> line connects
> all the C points)
>
>
> I couldn't find anything in the examples or the help section about  
> multiple
> lines on the same graph, only one line.

?points
?lines
?matplot

##
Attention:\ This e-mail message is privileged and confidenti...{{dropped}}

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[R] RJDBC connection help needed

[Jim Porzak]

Hi everyone,

I'm obviously missing something simple here...

Trying to connect to an external db with RJDBC. (I can connect OK with
ROLAP and with other java apps, eg dbVisualizer)

JDBC call seems to work ok:

> driverClass <- "net.sourceforge.jtds.jdbc.Driver"
> classPath <- "C:\\Dwns\\jtds\\jtds-1.2.jar"
> identifier.quote <- '"'
> drv <- JDBC(driverClass, classPath, identifier.quote)
> summary(drv)
JDBCDriver
name = JDBC
driver.version = 0.1-1
DBI.version = 0.1-1
client.version = NA
max.connections = NA
>

but attempting to connect gives:
> dbURL <- "jdbc:jtds:sqlserver://..com;DatabaseName=sunms"
> con <- dbConnect(drv, dbURL, uid = "jporzak", pwd = "")
Error in .local(drv, ...) : Unable to connect JDBC to
jdbc:jtds:sqlserver://..com;DatabaseName=sunms
>

where "", "", "" are changed to protect the innocent.

note that the dbURL string is exactly what I use in dbVisualizer with success

(using WinXP SP2, R 2.5.1,  RJDBC 0.1-3)

-- 
TIA,
Jim Porzak
http://www.linkedin.com/in/jimporzak

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Re: [R] Line Graph - Greater than 2 variables on plot

[jim holtman]

This should do it for you:

> x <- read.table(textConnection("A   B  C  D
+ 0.65662.11851.23205
+ 0.647 2.08651.232510
+ 0.65322.10601.228715
+ 0.64872.12901.231320
+ 0.65942.12851.234125
+ 0.65772.10701.234330
+ 0.65792.13451.234035
+ 0.67342.17051.236240
+ 0.675 2.18451.237245
+ 0.65922.15501.234050
+ 0.66472.17101.230555"), header=TRUE)
>
> matplot(x[, 4], x[, -4], type='o')
>


On 9/20/07, Wayne Aldo Gavioli <[EMAIL PROTECTED]> wrote:
>
>
> Hello all,
>
> I was wondering if anyone knew how to construct a multiple line graph on R,
> where there are 2 (or more) sets of data points plotted against some x axis of
> data, and you can draw a line on the graph connecting each set of data points.
>
> For example:
>
> A   B  C  D
> 0.65662.11851.23205
> 0.647 2.08651.232510
> 0.65322.10601.228715
> 0.64872.12901.231320
> 0.65942.12851.234125
> 0.65772.10701.234330
> 0.65792.13451.234035
> 0.67342.17051.236240
> 0.675 2.18451.237245
> 0.65922.15501.234050
> 0.66472.17101.230555
>
>
>
> Would there be a way:
> a) To graph all the points of data in sets A, B and C as Y coordinates on one
> graph, using the points in set D as the X-axis/coordinates for all 3 sets (A, 
> B
> and C)?
> b) To be able to draw 3 lines on the graph that connect each set of data (1 
> line
> connects all the A points, one line connects all the B points, one line 
> connects
> all the C points)
>
>
> I couldn't find anything in the examples or the help section about multiple
> lines on the same graph, only one line.
>
>
> Thanks,
>
>
>
> Wayne
>
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


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

What is the problem you are trying to solve?

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[R] Estimate correlation with bootstrap

[Andreas Klein]

Hello.

I would like to estimate the correlation coefficient
from two samples with Bootstrapping using the
R-function sample().

The problem is, that I have to sample pairwise. For
example if I have got two time series and I draw from
the first series the value from 1912 I need the value
from 1912 from the second sample, too.

Example:

Imagine that a and b are two time series with returns
for example: 

a <- c(1,2,3,4,5,6,7,8,9,10)
b <- c(1,1,56,3,6,6,6,7,2,10)

a.sample <- numeric(10)
b.sample <- numeric(10)
boot.cor.a.b <- numeric(1000)

for (i in 1:1000)

{

 for (j in 1:10)

 {

  a.sample[j] <- sample(a,1,replace=TRUE)
  b.sample[j] <- sample(b,1,replace=TRUE)

 }

 boot.cor.a.b[i] <- cor(a,b)

}

The problem here is, that the sampling is independent
from each other.

So how do I have to change the R-code to get the
pairwise sampling mentioned above?

I hope you can help me.

Sincerely
Klein.


  

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