[R] Quadratic Optimization

2006-11-27 Thread amit soni
Hi,

I need to solve an optimization problem in R having linear objective function 
and quadratic constraints(number of variables is around 80).  What are the 
possible choices to do this in R.
optim() function only allows box constrained problems. Is it possible in nlm()? 
Or please tell me if there is any other routine.

Thanks

Amit




 

Cheap talk?


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Re: [R] Questions about generating samples in R

2006-11-27 Thread Peter Dalgaard
Christian Schulz [EMAIL PROTECTED] writes:

 split - sample(2,nrow(dataframe),replace=T,prob=c(0.04,0.96))
 
 dataframe[split==1,]  # 200
 dataframe[split==2,] # 4800
 
 regards, christian
 
  ?sample should tell you what you need to know.

It does, but the above is not how. To get exactly 200 samples, use

sel - sample(200, nrow(dataframe))
dataframe[sel,]

  On 26/11/06, Alexander Geisler [EMAIL PROTECTED] wrote:

  Hello!
 
  I have a data set with 8 columns and in about 5000 rows. What I want to
  do is to generate samples of this data set.
 
  Samples of a special size, as example 200.
 
  What is the easiest way to do this? No special things are needed, only
  the random selection of 200 rows of the data set.
 
  Thanks
  Alex
 
  --
  Alexander Geisler * Kaltenbach 151 * A-6272 Kaltenbach
  email: [EMAIL PROTECTED] | [EMAIL PROTECTED]
  phone: +43 650 / 811 61 90 | skpye: al1405ex
 
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[R] Package Installation Error: Ruuid, RBGL,-- RGui2.4.0

2006-11-27 Thread j.joshua thomas
Dear All,


I added packages using :Install Packages from Local Zip files.
I have downloaded Ruuid,RGraphviz,graph from BioConductor:
I try installed the packages then i tried the following line of code:

library(RBGL)

the popup message from RGUI 2.4.0 :

RGUI:Rgui.exe- Entry point not Found

followed by:

Loading required package: graph
Loading required package: Ruuid
Error in dyn.load(x, as.logical(local), as.logical(now)) :
unable to load shared library
'C:/PROGRA~1/R/R-24~1.0/library/Ruuid/libs/Ruuid.dll':
  LoadLibrary failure:  The specified procedure could not be found.

Error: package 'Ruuid' could not be loaded

*Then i tried to install Ruuid etc: again the same ERROR:*

Error in dyn.load(x, as.logical(local), as.logical(now)) :
unable to load shared library
'C:/PROGRA~1/R/R-24~1.0/library/Ruuid/libs/Ruuid.dll':
  LoadLibrary failure:  The specified procedure could not be found.

Error: package/namespace load failed for 'Ruuid'



Need Help!
JJ


-- 
Lecturer J. Joshua Thomas
KDU College Penang Campus
Research Student,
University Sains Malaysia

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Re: [R] Splitting criterion in tree and rpart

2006-11-27 Thread Jens Röder
Datum: Fri, 24 Nov 2006 17:54:38 +0100
Von: Paolo Radaelli [EMAIL PROTECTED]
An: r-help@stat.math.ethz.ch
Betreff: [R] Splitting criterion in tree and rpart

 Dear all,
 I'm interested in fitting a classification tree by using a
 user-specified splitting criterion. If I am right,  Tree package allows to 
 use only
 deviance or gini while rpart package offers  anova, poisson, class
 or exp. and tries to make an intelligent guess if method is missing. 

anova, ... are not splitting criteria, but the kind of tree you want to 
construct, which depends on the dependent variable of your data.

 I also found that, in rpart, method can be a list of functions named init,
 split and eval but I really don't know how can I do it.  Does someone can
 suggest me some documentation I can have a look do define my splitting
 criterion and pass it to rpart ?

Here you can find an Technical Report that might help you:
http://www.mayo.edu/hsr/techrpt/61.pdf

Henri 

 Thanks
 Paolo
 
 Paolo Radaelli
 Dipartimento di Metodi Quantitativi per le Scienze Economiche ed Aziendali
 Facoltà di Economia
 Università degli Studi di Milano-Bicocca
 e-mail [EMAIL PROTECTED]
 
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Re: [R] random effect question and glm

2006-11-27 Thread Michael Dewey
At 06:28 26/11/2006, you wrote:
Below is the output for p5.random.p,p5.random.p1 and m0
My question is
in p5.random.p, variance for P is 5e-10.
But in p5.random.p1,variance for P is 0.039293.
Why they are so different?

Please do as the posting guide asks and reply to the list, not just 
the individual.
a - I might not know the answer
b - the discussion might help others

You give very brief details of the underlying problem so it is hard 
to know what information will help you most.

Remember, if a computer estimates a non-negative quantity as very 
small perhaps it is really zero.

I think you might benefit from reading Pinheiro and Bates, again see 
the posting list.

Is that wrong to write Y~P+(1|P) if I consider P as random effect?

I suppose terminology differs but I would have said the model with 
Y~1+(1|P) was a random intercept model

Also in p5.random.p and m0, it seems that there are little 
difference in estimate for P. Why?

thanks,

Aimin Yan

  p5.random.p - 
 lmer(Y~P+(1|P),data=p5,family=binomial,control=list(usePQL=FALSE,msV=1))
  summary(p5.random.p)
Generalized linear mixed model fit using Laplace
Formula: Y ~ P + (1 | P)
Data: p5
  Family: binomial(logit link)
   AIC  BIC logLik deviance
  1423 1452 -705.4 1411
Random effects:
  Groups NameVariance Std.Dev.
  P  (Intercept) 5e-102.2361e-05
number of obs: 1030, groups: P, 5

Estimated scale (compare to  1 )  0.938

Fixed effects:
  Estimate Std. Error z value Pr(|z|)
(Intercept)  0.153404   0.160599  0.9552   0.3395
P8ABP   -0.422636   0.202181 -2.0904   0.0366 *
P8adh0.009634   0.194826  0.0495   0.9606
P9pap0.108536   0.218875  0.4959   0.6200
P9RNT0.376122   0.271957  1.3830   0.1667
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Correlation of Fixed Effects:
   (Intr) P8ABP  P8adh  P9pap
P8ABP -0.794
P8adh -0.824  0.655
P9pap -0.734  0.583  0.605
P9RNT -0.591  0.469  0.487  0.433
  p5.random.p1 - 
 lmer(Y~1+(1|P),data=p5,family=binomial,control=list(usePQL=FALSE,msV=1))
  summary(p5.random.p1)
Generalized linear mixed model fit using Laplace
Formula: Y ~ 1 + (1 | P)
Data: p5
  Family: binomial(logit link)
   AIC  BIC logLik deviance
  1425 1435 -710.6 1421
Random effects:
  Groups NameVariance Std.Dev.
  P  (Intercept) 0.039293 0.19823
number of obs: 1030, groups: P, 5

Estimated scale (compare to  1 )  0.9984311

Fixed effects:
 Estimate Std. Error z value Pr(|z|)
(Intercept)   0.1362 0.1109   1.2280.219

  m0-glm(Y~P,data=p5,family=binomial(logit))
  summary(m0)

Call:
glm(formula = Y ~ P, family = binomial(logit), data = p5)

Deviance Residuals:
 Min   1Q   Median   3Q  Max
-1.4086  -1.2476   0.9626   1.1088   1.2933

Coefficients:
  Estimate Std. Error z value Pr(|z|)
(Intercept)  0.154151   0.160604   0.960   0.3371
P8ABP   -0.422415   0.202180  -2.089   0.0367 *
P8adh0.009355   0.194831   0.048   0.9617
P9pap0.108214   0.218881   0.494   0.6210
P9RNT0.374693   0.271945   1.378   0.1683
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

(Dispersion parameter for binomial family taken to be 1)

 Null deviance: 1425.5  on 1029  degrees of freedom
Residual deviance: 1410.8  on 1025  degrees of freedom
AIC: 1420.8

Number of Fisher Scoring iterations: 4


At 06:13 AM 11/24/2006, you wrote:
At 21:52 23/11/2006, Aimin Yan wrote:
consider p as random effect with 5 levels, what is difference between these
two models?

   p5.random.p - lmer(Y
~p+(1|p),data=p5,family=binomial,control=list(usePQL=FALSE,msV=1))
   p5.random.p1 - lmer(Y
~1+(1|p),data=p5,family=binomial,control=list(usePQL=FALSE,msV=1))

Well, try them and see. Then if you cannot understand the output tell us
a) what you found
b) how it differed from what you expected

in addtion, I try these two models, it seems they are same.
what is the difference between these two model. Is this a cell means model?
m00 - glm(sc ~aa-1,data = p5)
m000 - glm(sc ~1+aa-1,data = p5)

See above


thanks,

Aimin Yan

Michael Dewey
http://www.aghmed.fsnet.co.uk





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Re: [R] GLM and LM singularities

2006-11-27 Thread Michael Dewey
At 23:12 26/11/2006, Tim Sippel wrote:
Hi-

I'm wrestling with some of my data apparently not being called into a GLM or
an LM.  I'm looking at factors affecting fish annual catch rates (ie. CPUE)
over 30 years.  Two of the factors I'm using are sea surface temperature and
sea surface temperature anomaly.  A small sample of my data is below:



I could not make much sense of the dataset and your output is 
incomplete (what happened to Year?) but usually the message you 
received means that one of your predictors is a linear combination of 
some of the others.



CPUE

Year

Vessel_ID

Base_Port

Boat_Lgth

Planing

SST

Anomaly


0.127

1976

2

BOI

40

Planing

19.4

-0.308


0.059

1976

30

BOI

40

Displacement

19.4

-0.308


0.03

1977

46

BOI

45

Displacement

18.5

-1.008


0.169231

1977

2

BOI

40

Planing

18.5

-1.008


0.044118

1977

19

BOI

34

Planing

18.5

-1.008


0.114286

1977

29

WHANGAROA

42

Displacement

18.5

-1.008



Have defined Year, Vessel_ID, Base_Port, Boat_Lgth, Planing as factors, and
CPUE, SST, Anomaly are continuous variables.



The formula I'm calling is: glm(formula = log(CPUE) ~ Year + Vessel_ID +
SST, data = marlin).  A summary of the glm includes the following output:



Coefficients: (1 not defined because of singularities)

 Estimate Std. Error t value Pr(|t|)

Vessel_ID80 -0.540930.23380  -2.314 0.021373 *

Vessel_ID83 -0.364990.20844  -1.751 0.080977 .

Vessel_ID84 -0.233860.19098  -1.225 0.221718

SST   NA NA  NA   NA



Can someone explain the output Coefficients: (1 not defined because of
singularities)? What does this mean?  I'm guessing that something to do
with my SST data is causing a singularity but I don't know where to go
from there?  Have inspected various R discussions on this, but I haven't
found the information I need.



Many thanks,



Tim Sippel (MSc)

School of Biological Sciences

Auckland University

Private Bag 92019

Auckland 1020

New Zealand

+64-9-373-7599 ext. 84589 (work)

+64-9-373-7668 (Fax)

+64-21-593-001 (mobile)




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Re: [R] Erosion, mathematical morphology

2006-11-27 Thread Oleg Sklyar
Hi. My bioconductor.org package, EBImage, should do that -- it allows you to
specify the structuring element, which can be a circle of any given radius
if you want. The package includes erosion, dilation, opening and closing. It
is also a general package for image analysis and processing built around
ImageMagick library with many functions added. The only minus, still no
Windows support -- Linux, Unix or Mac.

Best, Oleg Sklyar

On 20/11/06, Milton Cezar Ribeiro [EMAIL PROTECTED] wrote:

 Hi there,

   Try this
  require(adehabitat)
  ?morphology

   You can also try this for binary image
  require(rimage)
  ?maxImg

   HTP

   Miltinho
   Brazil


 [EMAIL PROTECTED] escreveu:
   Hello!
 I need a function to compute the erosion of a binary image by a
 structuring element. I need the structuring element to be a ball of a
 given radius.
 As far as I know the libraries adehabitat and spatstat include
 functions of mathematical morphology but I couldn't find a function
 which computes the erosion by a ball. Any idea?

 Thanks!

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[R] quantile regression - estimation of CAViaR

2006-11-27 Thread jacinthe
How is it possible to estimate the conditional autoregressive Value-at-Risk 
model

qantile_t(tau)=a0+a1*qantile_(t-1)(tau)+a2*abs(r_(t-1))

see http://www.faculty.ucr.edu/~taelee/paper/BLSpaper1.pdf (page 10)) of Engle 
 Manganelli in R?  The qantile_(t-1)(tau)-term causes headache.


Kind regards,

Jaci
-- 
Ein Herz für Kinder - Ihre Spende hilft! Aktion: www.deutschlandsegelt.de
Unser Dankeschön: Ihr Name auf dem Segel der 1. deutschen America's Cup-Yacht!

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Re: [R] odfTable: how to escape

2006-11-27 Thread Kuhn, Max
Francesco,

odfTable writes out a table in xml format directly into an xml file. The
issues is that the characters  and  (among others) have to be
converted to gt; and lt;.

I will build a new version where this happens automatically. In the
meantime, you should be able to use the colnames argument of odfTable
and odfTranslate to convert the column headings:

   odfTranslate(these need to be fixed:  and , toR = FALSE)
  [1] these need to be fixed: lt; and gt;

Max


-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Francesco Cernuto
Sent: Friday, November 24, 2006 10:06 AM
To: r-help@stat.math.ethz.ch
Subject: [R] odfTable: how to escape 

Dear All,

I'm appreciating odfWeave as a nice reporting tool, but I had some pain 
in producing tables with odfTable command
where the first column began with  or  such as in age class heading, 
for example:
35
35-39
40-49
50-50
 60
In this case, to avoid a content.xml error, I had to change 35 in less 
than 35 and  60 in over 60.

Anyone knows how to escape those characters while producing a table in R

or in a document chunk?


Thanks in advance,

Francesco Cernuto

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[R] NaN with ccf() for vector with all same element

2006-11-27 Thread colliera
hello,

i have been using ccf() to look at the correlation between lightning and 
electrogamnetic data. for the most part it has worked exactly as expected. 
however, i have come across something that puzzles me a bit:

 x - c(1, 0, 1, 0, 1, 0)
 y - c(0, 0, 0, 0, 0, 0)
 ccf(x, x, plot = FALSE)

Autocorrelations of series 'X', by lag

-4 -3 -2 -1  0  1  2  3  4 
 0.333 -0.500  0.667 -0.833  1.000 -0.833  0.667 -0.500  0.333 
 ccf(x, y, plot = FALSE)

Autocorrelations of series 'X', by lag

 -4  -3  -2  -1   0   1   2   3   4 
NaN NaN NaN NaN NaN NaN NaN NaN NaN 
 y - c(1, 1, 1, 1, 1, 1)
 ccf(x, y, plot = FALSE)

Autocorrelations of series 'X', by lag

 -4  -3  -2  -1   0   1   2   3   4 
NaN NaN NaN NaN NaN NaN NaN NaN NaN

i don't see why the result from ccf() would be NaN if the elements of y are all 
the same... perhaps i am just being silly or missing something. but if i work 
this out by hand, then i get a proper result. so, why not with ccf()?

thanks for the help!

best regards,
andrew.

-- 
Andrew B. Collier

Space Physics Group
Hermanus Magnetic Observatory

Antarctic Research Fellow   tel: +27 31 2601157
Space Physics Research Institutefax: +27 31 2616550
University of KwaZulu-Natal, Durban, 4041, South Africa gsm: +27 83 3813655

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Re: [R] question about capscale (vegan)

2006-11-27 Thread Alicia Amadoz
Hi Gavin,

I have been analyzing real data (sorry but I am not allowed to post
these data here) and what I got was this,

mydistmat_f.cap - capscale(distmat_f ~ F + L + F:L, mfactors_frame)

Warning messages:
1: some of the first 30 eigenvalues are  0 in: cmdscale(X, k = k, eig =
TRUE, add = add)
2: Se han producido NaNs in: sqrt(ev)

 mydistmat_f.cap

Call:
capscale(formula = distmat_f ~ F + L + F:L, data = mfactors_frame)

  Inertia Rank
Total  0.3758
Constrained0.21104
Unconstrained  0.16484
Inertia is squared  distance
Some constraints were aliased because they were collinear (redundant)

Eigenvalues for constrained axes:
 CAP1  CAP2  CAP3  CAP4
1.679e-01 2.954e-02 1.349e-02 1.233e-05

Eigenvalues for unconstrained axes:
 MDS1  MDS2  MDS3  MDS4
1.388e-01 2.601e-02 4.076e-05 2.064e-07

So, by these results I can tell that there are 4 axes that explain
0.1648 of the total variance and another 4 axes that explain 0.2110 of
the total variance. But I don't understand the difference between
constrained and unconstrained.

 anova(mydistmat_f.cap)

Permutation test for capscale under direct model

Model: capscale(formula = distmat_f ~ F + L + F:L, data = mfactors_frame)
 DfVar  F N.Perm Pr(F)
Model 4   0.21 1.2798 400.00 0.0875 .
Residual  4   0.16
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

 summary(anova(mydistmat_f.cap))
   Df Var   F N.PermPr(F)
 Min.   :4   Min.   :0.1648   Min.   :1.280   Min.   :200   Min.   :0.12
 1st Qu.:4   1st Qu.:0.1764   1st Qu.:1.280   1st Qu.:200   1st Qu.:0.12
 Median :4   Median :0.1879   Median :1.280   Median :200   Median :0.12
 Mean   :4   Mean   :0.1879   Mean   :1.280   Mean   :200   Mean   :0.12
 3rd Qu.:4   3rd Qu.:0.1994   3rd Qu.:1.280   3rd Qu.:200   3rd Qu.:0.12
 Max.   :4   Max.   :0.2110   Max.   :1.280   Max.   :200   Max.   :0.12
  NA's   :1.000   NA's   :  1   NA's   :1.00

Then, I want to know the sum of squares of anova to check with other
analysis that we performed but I can't see them by the output of anova.
Besides, I am wondering if there is any manner to identify the main
effects, factor effects and interaction in this anova analysis. I would
be very grateful if you could help me to understand these results.

Thank you very much,
Alicia

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Re: [R] NaN with ccf() for vector with all same element

2006-11-27 Thread Gabor Grothendieck
The denominator holds the variance and since the variance is zero you
get that.  Calculate the covariance instead of the correlation:

ccf(x, y, plot = FALSE, type = cov)




On 11/27/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote:
 hello,

 i have been using ccf() to look at the correlation between lightning and 
 electrogamnetic data. for the most part it has worked exactly as expected. 
 however, i have come across something that puzzles me a bit:

  x - c(1, 0, 1, 0, 1, 0)
  y - c(0, 0, 0, 0, 0, 0)
  ccf(x, x, plot = FALSE)

 Autocorrelations of series 'X', by lag

-4 -3 -2 -1  0  1  2  3  4
  0.333 -0.500  0.667 -0.833  1.000 -0.833  0.667 -0.500  0.333
  ccf(x, y, plot = FALSE)

 Autocorrelations of series 'X', by lag

  -4  -3  -2  -1   0   1   2   3   4
 NaN NaN NaN NaN NaN NaN NaN NaN NaN
  y - c(1, 1, 1, 1, 1, 1)
  ccf(x, y, plot = FALSE)

 Autocorrelations of series 'X', by lag

  -4  -3  -2  -1   0   1   2   3   4
 NaN NaN NaN NaN NaN NaN NaN NaN NaN

 i don't see why the result from ccf() would be NaN if the elements of y are 
 all the same... perhaps i am just being silly or missing something. but if i 
 work this out by hand, then i get a proper result. so, why not with ccf()?

 thanks for the help!

 best regards,
 andrew.

 --
 Andrew B. Collier

 Space Physics Group
 Hermanus Magnetic Observatory

 Antarctic Research Fellow   tel: +27 31 
 2601157
 Space Physics Research Institutefax: +27 31 
 2616550
 University of KwaZulu-Natal, Durban, 4041, South Africa gsm: +27 83 
 3813655

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Re: [R] question about capscale (vegan)

2006-11-27 Thread Gavin Simpson
On Mon, 2006-11-27 at 15:37 +0100, Alicia Amadoz wrote:
 Hi Gavin,
 
 I have been analyzing real data (sorry but I am not allowed to post
 these data here) and what I got was this,
 
 mydistmat_f.cap - capscale(distmat_f ~ F + L + F:L, mfactors_frame)

I believe you can write that formula as: distmat_f ~ F * L

 
 Warning messages:
 1: some of the first 30 eigenvalues are  0 in: cmdscale(X, k = k, eig =
 TRUE, add = add)
 2: Se han producido NaNs in: sqrt(ev)

Sorry, I don't know enough about this method to know whether this a
problem you should worry about or not. You should read up on the method
some more to decide if the first warning is something you should be
worried about. IIRC, negative eigenvalues are to be expected with this
method as they are handled explicitly by capscale, and as this is a
warning coming from cmdscale(), I suspect it is a helpful feature of
that function, which you don't need to worry about when used in
capscale().

 
  mydistmat_f.cap
 
 Call:
 capscale(formula = distmat_f ~ F + L + F:L, data = mfactors_frame)
 
   Inertia Rank
 Total  0.3758
 Constrained0.21104
 Unconstrained  0.16484
 Inertia is squared  distance
 Some constraints were aliased because they were collinear (redundant)
 
 Eigenvalues for constrained axes:
  CAP1  CAP2  CAP3  CAP4
 1.679e-01 2.954e-02 1.349e-02 1.233e-05
 
 Eigenvalues for unconstrained axes:
  MDS1  MDS2  MDS3  MDS4
 1.388e-01 2.601e-02 4.076e-05 2.064e-07
 
 So, by these results I can tell that there are 4 axes that explain
 0.1648 of the total variance and another 4 axes that explain 0.2110 of
 the total variance. But I don't understand the difference between
 constrained and unconstrained.

The constrained axes are axes that are linear combinations of your
explanatory variables (F, L and F:L), so this is the bit of your genomic
data that is explained by those explanatory factors. The unconstrained
bit is the remaining variance not explained, and are MDS (PCoord) axes.

So you can explain c. 56% of the variance in your genomic data with F,
L, and F:L.

Note the warning about aliased constraints - this means that at least
the variance of one variable in the model (inc interactions) is
completely correlated with another variable (or combination of
variables?) and is redundant.

Type alias(mydistmat_f.cap) to see which coefficients are aliased
and ?alias to see what this means.

 
  anova(mydistmat_f.cap)
 
 Permutation test for capscale under direct model
 
 Model: capscale(formula = distmat_f ~ F + L + F:L, data = mfactors_frame)
  DfVar  F N.Perm Pr(F)
 Model 4   0.21 1.2798 400.00 0.0875 .
 Residual  4   0.16
 ---
 Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
 
  summary(anova(mydistmat_f.cap))
Df Var   F N.PermPr(F)
  Min.   :4   Min.   :0.1648   Min.   :1.280   Min.   :200   Min.   :0.12
  1st Qu.:4   1st Qu.:0.1764   1st Qu.:1.280   1st Qu.:200   1st Qu.:0.12
  Median :4   Median :0.1879   Median :1.280   Median :200   Median :0.12
  Mean   :4   Mean   :0.1879   Mean   :1.280   Mean   :200   Mean   :0.12
  3rd Qu.:4   3rd Qu.:0.1994   3rd Qu.:1.280   3rd Qu.:200   3rd Qu.:0.12
  Max.   :4   Max.   :0.2110   Max.   :1.280   Max.   :200   Max.   :0.12
   NA's   :1.000   NA's   :  1   NA's   :1.00
 
 Then, I want to know the sum of squares of anova to check with other
 analysis that we performed but I can't see them by the output of anova.
 Besides, I am wondering if there is any manner to identify the main
 effects, factor effects and interaction in this anova analysis. I would
 be very grateful if you could help me to understand these results.

There isn't a summary method for anova.cca, and anyway, this anova isn't
working on sums of squares, but on other measures of variance. It is a
permutation test, and simply works out with brute force how likely you
are to have a model explaining 56% of the total variance given your
sample size and model complexity, under a null/random model.

It sounds like you haven't grasped fully the fundamentals of the methods
you are employing, and I would strongly advise you to do some more
reading up on these methods. I can, at best, only guide you as I am not
that familiar with the technique myself.

A good start would be the refs in ?capscale and then search for papers
that cite Anderson  Willis and that use the methodology.

 
 Thank you very much,
 Alicia

HTH

G

-- 
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
 Gavin Simpson [t] +44 (0)20 7679 0522
 ECRC  ENSIS, 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
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%


[R] [R-pkgs] kernlab 0.9-0 on CRAN

2006-11-27 Thread Alexandros Karatzoglou

A new version of kernlab has just been released.
kernlab is a kernel-based Machine Learning package for R.

kernlab includes the following functions:

 o ksvm() : Support Vector Machines for classification, regression,
novelty detection, native multi-class classification, support
for class-probability output and confidence intervals in
regression.

 o gausspr() : Gaussian Processes for classification and regression

 o lssvm() : Least Squares Support Vector Machines for classification

 o rvm() : Relevance Vector Machines for regression

 o specc() : Spectral Clustering

 o kkmeans() : Kernel k-means clustering

 o ranking() : Kernel-based ranking method

 o onlearn() : Kernel-based Online Learning algorithms for classification,
   novelty detection and regression

 o kpca() : Kernel Pricipal Components Analysis

 o kcca() : Kernel Canonical Correlation Analysis

 o kfa() : Kernel Feature Analysis

 o sigest() : Hyperparameter estimation for the Gaussian and the Laplacian 
kernels

 o inchol() : Incomplete Cholesky decomposition method

 o csi() : Cholesky decomposition with side information

 o ipop() : Interior point-based Quadratic Optimizer

Kernlab also includes a range of functions enabling the easy implementation of
new kernel methods including functions for computing commonly used kernel
expressions (e.g. kernel matrix, kernel expansion, etc.) and
implementations of nine kernels (e.g. Linear, Gaussian, Polynomial,
Sigmoid, Laplace, String kernels, etc.) which can be used with any of the
functions included in the package.
Ready computed kernel matrices and user defined kernel functions can also
be used.

kernlab is based on the S4 object model.
A vignette describing a large portion of the functions and features is
included.

cheers
Alexandros

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Re: [R] NaN with ccf() for vector with all same element

2006-11-27 Thread Prof Brian Ripley
On Mon, 27 Nov 2006, [EMAIL PROTECTED] wrote:

 hello,

 i have been using ccf() to look at the correlation between lightning and 
 electrogamnetic data. for the most part it has worked exactly as 
 expected. however, i have come across something that puzzles me a bit:

 x - c(1, 0, 1, 0, 1, 0)
 y - c(0, 0, 0, 0, 0, 0)
 ccf(x, x, plot = FALSE)

 Autocorrelations of series 'X', by lag

-4 -3 -2 -1  0  1  2  3  4
 0.333 -0.500  0.667 -0.833  1.000 -0.833  0.667 -0.500  0.333
 ccf(x, y, plot = FALSE)

 Autocorrelations of series 'X', by lag

 -4  -3  -2  -1   0   1   2   3   4
 NaN NaN NaN NaN NaN NaN NaN NaN NaN
 y - c(1, 1, 1, 1, 1, 1)
 ccf(x, y, plot = FALSE)

 Autocorrelations of series 'X', by lag

 -4  -3  -2  -1   0   1   2   3   4
 NaN NaN NaN NaN NaN NaN NaN NaN NaN

 i don't see why the result from ccf() would be NaN if the elements of y 
 are all the same... perhaps i am just being silly or missing something. 
 but if i work this out by hand, then i get a proper result. so, why not 
 with ccf()?

How do you get a non-zero value for the variance of y?  Dividing zero by 
zero is NaN, and that is what is happening here.

-- 
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] Using a specified splitting criterion in tree and rpart

2006-11-27 Thread Paolo Radaelli
Dear all
I'm interested in fitting a classification tree by using a user-specified 
splitting criterion. If I am right,  Tree package allows to use only 
deviance or gini while the rpart package offers the possibility to 
specify, in the parms optional parameters for the splitting function, the 
component split (index) that can be chosen between gini and information.
Does someone can suggest me some documentation I can have a look do define 
my splitting criterion and pass it to rpart ?
Thanks
Paolo

Paolo Radaelli
Dipartimento di Metodi Quantitativi per le Scienze Economiche ed Aziendali
Facoltà di Economia
Università degli Studi di Milano-Bicocca
P.zza dell'Ateneo Nuovo, 1
20126 Milano
Italy
e-mail [EMAIL PROTECTED]
Tel +39 02 6448 3163
Fax +39 02 6448 3105

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[R] EM algorithm for truncated multivariate mixture of normals

2006-11-27 Thread Jeff D. Hamann
I couldn't find a direct answer in CRAN to this question, so I'm asking
with some trepidation. I have a multivariate dataset (data.frame) with
columns that can be expressed as a set of mixed normals (at least I think)
and need to impute values that have constraints (truncated mixture of
normals where the values cannot be below zero). If there isn't a package
that can do this, is there a package similar to em.norm() that can be used
for truncated data?

I'm not sure if this is a pie in the sky question or not.

Thanks,
Jeff.

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[R] ANN: BioC Advanced Course, Jan 10-12 in Seattle

2006-11-27 Thread Seth Falcon
Hello all,

We will be holding an advanced BioC course January 10th-12th in
Seattle.  

Lectures will be based on content from _Bioinformatics and
Computational Biology Solutions Using R and Bioconductor_. During the
hands-on labs, attendees will learn how to use R and Bioconductor to:

  * perform quality assessment on microarray experiments

  * use Hypergeometric and GSEA tools for carrying out downstream
analyses

  * integrate related, but different microarray experiments

For more information and details on registering for this course,
please visit:

https://secure.bioconductor.org/biocadv/



+ seth

--
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org

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Re: [R] Questions about generating samples in R

2006-11-27 Thread Mark Na
Further to Alexander's question ... could anyone provide assistance
with random stratified sampling? Let's say we have Alex's dataframe
and we want to stratify the random selection by group membership
(which is contained in one of the eight columns).

We might want to randomly select:

1) a constant number (e.g., 5) of rows from each group, or
2) a percentage (e.g. 10%) of rows from each group resulting in groups
being represented proportionally in the sample (with respect to the
population).

I am aware of stratsrs but this function does not seem to allow the
second of the above two options.

Any ideas how to achieve this in R?

Thanks, Mark



On 11/26/06, Alexander Geisler [EMAIL PROTECTED] wrote:
 Hello!

 I have a data set with 8 columns and in about 5000 rows. What I want to
 do is to generate samples of this data set.

 Samples of a special size, as example 200.

 What is the easiest way to do this? No special things are needed, only
 the random selection of 200 rows of the data set.

 Thanks
 Alex

 --
 Alexander Geisler * Kaltenbach 151 * A-6272 Kaltenbach
 email: [EMAIL PROTECTED] | [EMAIL PROTECTED]
 phone: +43 650 / 811 61 90 | skpye: al1405ex

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[R] calling R from cmd line, loading in data sets on the call

2006-11-27 Thread Matt Anthony
Hi -

 

I have read the archives on R cmd and passing parameters, and I guess I
am not totally clear if that solved this problem ...

 

I would like to call an R script from the command line, and in the
process pass in data sets and parameters ... right now, I manually
specify the files to be read in as the data sets for the script, and
then it processes, but I need to be able to automate this action from
the cmd line. 

 

Rcmd myprogram.R  is clearly documented as unable to take parameters
passed to it ...

 

 

I am on Windows, R 2.3.1 

 

 

 

Thanks

 

Matt

 

 

 

 


[[alternative HTML version deleted]]

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[R] RSQLite basic

2006-11-27 Thread Alexander Nervedi
Hi.

I am still trying to figure out how connection and RSQLIte function. When i 
run the following commands

library(RSQLite)
m - dbDriver(SQLite, max.con = 25)
con - dbConnect(m, dbname=sqlite.db)

on my windows laptop everthing works fine. For example:

m - dbDriver(SQLite, max.con = 25)
con - dbConnect(m, dbname=sqlite.db)
version
   _
platform   i386-pc-mingw32
arch   i386
os mingw32
system i386, mingw32
status
major  2
minor  4.0
year   2006
month  10
day03
svn rev39566
language   R
version.string R version 2.4.0 (2006-10-03)


However, this gives all kinds of errors when I run it on a linux box and I 
am not sure what the error message is telling me. I thought I'd crave your 
indulgence and ask for advice.


m - dbDriver(SQLite, max.con = 25)
con - dbConnect(m, dbname=sqlite.db)
Error in sqliteNewConnection(drv, ...) : RS-DBI driver: (could not connect 
to dbname sqlite.db
)


version
   _
platform   i686-pc-linux-gnu
arch   i686
os linux-gnu
system i686, linux-gnu
status
major  2
minor  4.0
year   2006
month  10
day03
svn rev39566
language   R
version.string R version 2.4.0 (2006-10-03)

thanks

- the nerdy.

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[R] automatic cleaning of workspace

2006-11-27 Thread Leeds, Mark \(IED\)
I'm having that problem where I am sometimes using an object that's from
a previous workspace when I don't want to be doing that. I was thinking
of putting rm(objects=ls()) in my first.R function But, the problem with
doing this, is that it doesn't prompt you with are you sure and there
could be very rare cases where I don't want to delete the workspace ? Is
there a way to
make the cleaning of the workspace automatic but still prompt you ? I
guess I can always just try to remember to manually 
do rm(objects=ls())when I start up in whatever workspace I am in but I
don't think I can trust my memory. Thanks.


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

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Re: [R] [R-sig-Geo] plot() and Jpeg() increase font size and resolution

2006-11-27 Thread Alexander.Herr
Hi Edzer,

png also does not increase the file size. 

Following the commands. The data are located at
ftp://ftp.csiro.au/Herry, file qldproperty.Rdata.


trellis.par.get(fontsize)-fontsize
 fontsize$default-16
 fontsize$points-16
 fontsize$text-18
  trellis.par.set(fontsize,fontsize)
trellis.par.get(fontsize)
 
 
 
plot(v1,plot.number=F, model=m2, ylim=c(4,9))

plt1-plot(v1,plot.number=F, model=m1, ylim=c(4,9), col=black,
pch=+, scales=list(cex=1.5,)) 

jpeg(file=LOTPLAN_variogram_mod.png, bg=white, res=300,
pointsize=16, width=800, height=800)
 plt1
dev.off()
XXX


SessionInfo:
R version 2.4.0 (2006-10-03)
i686-pc-linux-gnu

locale:
LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=e
n_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHON
E=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C

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

other attached packages:
geoRgstat MCMCpack MASS coda
lattice
1.6-11 0.9-34  0.7-4 7.2-29 0.10-7
0.14-13
mcmc RColorBrewer maps maptools   sp
foreign
 0.5-1  0.2-3 2.0-32  0.6-3  0.9-4
0.8-17
 spatial
7.2-29


Thanks
Herry


Dr Alexander Herr
Spatial and statistical analyst
CSIRO, Sustainable Ecosystems
Davies Laboratory,
University Drive, Douglas, QLD 4814 
Private Mail Bag, Aitkenvale, QLD 4814
 
Phone/www 
(07) 4753 8510; 4753 8650(fax)
Home: http://herry.ausbats.org.au
Webadmin ABS: http://ausbats.org.au
Sustainable Ecosystems: http://www.cse.csiro.au/



-Original Message-
From: Edzer J. Pebesma [mailto:[EMAIL PROTECTED] 
Sent: Monday, November 27, 2006 5:34 PM
To: Herr, Alexander Herr - Herry (CSE, Townsville)
Cc: r-help@stat.math.ethz.ch; r-sig-geo@stat.math.ethz.ch
Subject: Re: [R-sig-Geo] plot() and Jpeg() increase font size and
resolution

[EMAIL PROTECTED] wrote:
 Thanks to Edzer and Roger,
 I can now plot with increased font sizes. However, jpeg still does not

 reproduce these, nor does it show up in high quality. What I would 
 like to do is produce some highresolution jpegs.
   
Please specify the commands that you used, preferrably such that we can
reproduce them, and specify which worked and which didn't the way you
expected. Also please give the output of sessionInfo(), and tell us the
platform you work on. Have you tried producing png, did that work?
--
Edzer
 Any help would be appreciated

 Thanx
 Herry


 R2.4 on Mandriva 10.2 linux.

 Dr Alexander Herr
 Spatial and statistical analyst
 CSIRO, Sustainable Ecosystems
 Davies Laboratory,
 University Drive, Douglas, QLD 4814
 Private Mail Bag, Aitkenvale, QLD 4814
  
 Phone/www
 (07) 4753 8510; 4753 8650(fax)
 Home: http://herry.ausbats.org.au
 Webadmin ABS: http://ausbats.org.au
 Sustainable Ecosystems: http://www.cse.csiro.au/
 


 -Original Message-
 From: Edzer J. Pebesma [mailto:[EMAIL PROTECTED]
 Sent: Friday, November 24, 2006 5:37 PM
 To: Herr, Alexander Herr - Herry (CSE, Townsville)
 Cc: r-help@stat.math.ethz.ch; r-sig-geo@stat.math.ethz.ch
 Subject: Re: [R-sig-Geo] plot() and Jpeg() increase font size and 
 resolution

 plotting variograms in gstat is done through xyplot in lattice; you'll

 find where it gets it's defaults by

 library(lattice)
 trellis.par.get()
 ?trellis.par.set
 --
 Edzer

 [EMAIL PROTECTED] wrote:
   
  
 Dear list,

 I am having troubles increasing the fontize when plotting a 
 variogram{gstat} and its model (vgm) with plot and using jpeg(). Also

 the resolution in the jpeg call does not work. I am using R2.4 on 
 Mandriva 10.2 linux.

 I can change fontsize with cex.axis in a normal plot, so I presume it

 has to do with plotting the variogram model. Any help on how to 
 increase the font size and resolution would be appreciated?

 R-calls:
 v1-variogram(log(z)~x+y, loc=coordinates(shp1),data=shp1) 
 m1-vgm(0.0175, Gau, 20,0.052)

 jpeg(file=LOTPLAN_variogram_mod.jpg, bg=white, res=300, 
 pointsize=16, width=1200, height=1200, quality=100)

  plot(v1,plot.number=F, model=m1, ylim=c(0.04,0.08), col=black,
 cex.axis=1.5)

 dev.off()

 Thanks Herry

 Dr Alexander Herr
 Spatial and statistical analyst
 CSIRO, Sustainable Ecosystems
 Davies Laboratory,
 University Drive, Douglas, QLD 4814
 Private Mail Bag, Aitkenvale, QLD 4814
  
 Phone/www
 (07) 4753 8510; 4753 8650(fax)
 Home: http://herry.ausbats.org.au
 Webadmin ABS: http://ausbats.org.au
 Sustainable Ecosystems: http://www.cse.csiro.au/

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[R] comments in scan

2006-11-27 Thread Jarrett Byrnes
I had a question about scan in R.  For better code readability, I  
would like to have lines in the block of data to be scanned that are  
commented - not just lines that have a comment at the end.  For example

#age, weight, height
33,128,65
34,56,155

instead of having to do something like

33,128,65 #age, weight, height
34,56,155


Is this at all possible?

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Re: [R] automatic cleaning of workspace

2006-11-27 Thread Gavin Simpson
On Mon, 2006-11-27 at 18:29 -0500, Leeds, Mark (IED) wrote:
 I'm having that problem where I am sometimes using an object that's from
 a previous workspace when I don't want to be doing that. I was thinking
 of putting rm(objects=ls()) in my first.R function But, the problem with
 doing this, is that it doesn't prompt you with are you sure and there
 could be very rare cases where I don't want to delete the workspace ? Is
 there a way to
 make the cleaning of the workspace automatic but still prompt you ? I
 guess I can always just try to remember to manually 
 do rm(objects=ls())when I start up in whatever workspace I am in but I
 don't think I can trust my memory. Thanks.

I assume you are saving your workspace when exiting R, and then when
restarting R in same directory it is auto loading the saved workspace?

If so, try not saving the workspace at the end of the session when
quitting, but explicitly save the objects you wish to save using save()
and load() it when restarting.

You might need to locate and delete the file .Rdata in the working
directory first, before you start R for example, to stop it being loaded
when you start R again. Alternatively, give it a new name with a .Rdata
extension, so you can load the workspace again if needed.

You might also want save.image if you are interested in saving
workspaces rather than individual objects.

This way you are in control of what is and is not saved/reloaded and you
won't have to rely on your memory.

HTH

G

-- 
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
 Gavin Simpson [t] +44 (0)20 7679 0522
 ECRC  ENSIS, 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/cv/
 London, UK. WC1E 6BT. [w] http://www.ucl.ac.uk/~ucfagls/
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Re: [R] comments in scan

2006-11-27 Thread Duncan Murdoch
On 11/27/2006 7:25 PM, Jarrett Byrnes wrote:
 I had a question about scan in R.  For better code readability, I  
 would like to have lines in the block of data to be scanned that are  
 commented - not just lines that have a comment at the end.  For example
 
 #age, weight, height
 33,128,65
 34,56,155
 
 instead of having to do something like
 
 33,128,65 #age, weight, height
 34,56,155
 
 
 Is this at all possible?

If it's on the first line, it's easy:  just use skip=1 to skip the first 
line.

The general case

#age, weight, height
33,128,65
# and now for something completely different
34,56,155

probably needs something like this:

  scan(foo, what=list(0,0,0), comment.char=#, sep=,, multi.line=T)

i.e. you need to tell it how many objects are in a record, and allow 
records to span multiple lines.  Watch out for typos in the file that 
put different numbers of entries on each line, because scan() won't 
complain about it.

Duncan Murdoch

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Re: [R] automatic cleaning of workspace

2006-11-27 Thread Bert Gunter
I believe the usal advice here is to store data and associated functions
together in separate .Rdata datasets (workspaces) via ?save. You can ?load
them as needed. 

Bert Gunter
Genentech Nonclinical Statistics
South San Francisco, CA 94404


-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Leeds, Mark (IED)
Sent: Monday, November 27, 2006 3:30 PM
To: r-help@stat.math.ethz.ch
Subject: [R] automatic cleaning of workspace

I'm having that problem where I am sometimes using an object that's from
a previous workspace when I don't want to be doing that. I was thinking
of putting rm(objects=ls()) in my first.R function But, the problem with
doing this, is that it doesn't prompt you with are you sure and there
could be very rare cases where I don't want to delete the workspace ? Is
there a way to
make the cleaning of the workspace automatic but still prompt you ? I
guess I can always just try to remember to manually 
do rm(objects=ls())when I start up in whatever workspace I am in but I
don't think I can trust my memory. Thanks.


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

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[R] RSQLite +textConnection()

2006-11-27 Thread Alexander Nervedi
Hi !

I am trying to read in 1000 really small text files.  When on adams, R bails 
out after reading 125 files with the error message

Error in textConnection(readLines(f, n = 2)) :
all connections are in use

I have traced this to a call to the scan() function which is at that point 
trying to read tge 126th data file.  I have tried specifically closing each 
connection i open after loading a file to avoid this. But that fails and I 
get the same error message. I googled and hit on a conversation between 
Professor Ripley and Dirk Eddelbuettel  
https://stat.ethz.ch/pipermail/r-sig-db/2006-July/000208.html that talks 
about a similar problem  - there the suggestion made which apparently worked 
was to fix a function called mysqlImportFile(). But i dont see this function 
being even in memory now.

Peculiarly, I am able to read upto 200 files when i am in windows.

I am hoping someone with more expereince with linux and/or RSQLite will have 
some suggestions. thanks!

Alex

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Re: [R] RSQLite basic

2006-11-27 Thread Alexander Nervedi
Hi Seth,

I didn't realize that this conversation went off the list with Bentilon. It 
turns out the source of the problem was that I was trying to write into a 
linux sub-directory to which I didn't have write permissions. I am able to 
read and write now using dbWriteTale()

thanks for suggesting using sessionInfo() - i didn't know of the command.

Al




From: Seth Falcon [EMAIL PROTECTED]
To: Alexander Nervedi [EMAIL PROTECTED]
CC: r-help@stat.math.ethz.ch
Subject: Re: [R] RSQLite basic
Date: Mon, 27 Nov 2006 16:47:40 -0800

Hi Alexander,

Alexander Nervedi [EMAIL PROTECTED] writes:
  However, this gives all kinds of errors when I run it on a linux box and 
I
  am not sure what the error message is telling me. I thought I'd crave 
your
  indulgence and ask for advice.
 
 
 m - dbDriver(SQLite, max.con = 25)
 con - dbConnect(m, dbname=sqlite.db)
  Error in sqliteNewConnection(drv, ...) : RS-DBI driver: (could not 
connect
  to dbname sqlite.db
  )

What is your working directory when you run this command?  getwd()
will tell you.  You should verify that you have write access there.

Does sqlite.db already exist?  If so, was it created with a different
version of sqlite than you are running?

Which brings me to:

it would be helpful to see the output of sessionInfo() so we know what
versions of DBI and RSQLite you are running.

+ seth

_
Share your latest news with your friends with the Windows Live Spaces 
friends module.

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Re: [R] RSQLite basic

2006-11-27 Thread Seth Falcon
Hi Alexander,

Alexander Nervedi [EMAIL PROTECTED] writes:
 However, this gives all kinds of errors when I run it on a linux box and I 
 am not sure what the error message is telling me. I thought I'd crave your 
 indulgence and ask for advice.


m - dbDriver(SQLite, max.con = 25)
con - dbConnect(m, dbname=sqlite.db)
 Error in sqliteNewConnection(drv, ...) : RS-DBI driver: (could not connect 
 to dbname sqlite.db
 )

What is your working directory when you run this command?  getwd()
will tell you.  You should verify that you have write access there.

Does sqlite.db already exist?  If so, was it created with a different
version of sqlite than you are running?

Which brings me to:

it would be helpful to see the output of sessionInfo() so we know what
versions of DBI and RSQLite you are running.

+ seth

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Re: [R] comments in scan

2006-11-27 Thread Simon Blomberg
 From ?scan :

If |comment.char| occurs (except inside a quoted character field), it 
signals that the rest of the line should be regarded as a comment and be 
discarded. Lines beginning with a comment character (possibly after 
white space with the default separator) are treated as blank lines.

So, set comment.char=#

and you should be fine.

Cheers,

Simon.

Jarrett Byrnes wrote:
 I had a question about scan in R.  For better code readability, I  
 would like to have lines in the block of data to be scanned that are  
 commented - not just lines that have a comment at the end.  For example

 #age, weight, height
 33,128,65
 34,56,155

 instead of having to do something like

 33,128,65 #age, weight, height
 34,56,155


 Is this at all possible?

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

   


-- 
Simon Blomberg, B.Sc.(Hons.), Ph.D, M.App.Stat. 
Centre for Resource and Environmental Studies
The Australian National University  
Canberra ACT 0200   
Australia   
T: +61 2 6125 7800 email: Simon.Blomberg_at_anu.edu.au
F: +61 2 6125 0757
CRICOS Provider # 00120C

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

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[R] pivot algorithm

2006-11-27 Thread sethlatimer

I am trying to simulate a self avoiding random walk in 2d of length 100. So I
am using two vectors of length 100 to encode the x and y coordinates.  At
each step I want apply a orthogonal transformation at a random point and
then check to see if the walk intersects with itself. This amounts to simply
checking to see if any of the ordered pairs of (x,y) coordinates in 1:j are
repeated in j+1:100. This seems like it should be really easy. But I cannot
find a simple method.

I have been calling the pivoted portion of the walk (xn[],yn[])



for(i in  1:j) for(m in {j+1}:100) if(xn[m]==x[i])  if(yn[m]==y[i])
dont_transform=1 else dont_transform=0
if(dont_transform==0) for(g in j:100) {x[g]=xn[g] ; y[g]=yn[g]}
z=c(x,y)
dim(z)=c(100,2)
z
 
maybe the right solution would be to use intersection() but I couldnt figure
out how to make it work.
Any advice would be appreciated.

Thanks 
Seth Latimer
-- 
View this message in context: 
http://www.nabble.com/pivot-algorithm-tf2715472.html#a7571334
Sent from the R help mailing list archive at Nabble.com.

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Re: [R] comments in scan

2006-11-27 Thread Simon Blomberg
You may want to set blank.lines.skip=TRUE too.

Simon.

 From ?scan :
 
 If |comment.char| occurs (except inside a quoted character field), it 
 signals that the rest of the line should be regarded as a comment and be 
 discarded. Lines beginning with a comment character (possibly after 
 white space with the default separator) are treated as blank lines.
 
 So, set comment.char=#
 
 and you should be fine.
 
 Cheers,
 
 Simon.
 
 Jarrett Byrnes wrote:


 I had a question about scan in R.  For better code readability, I  
 would like to have lines in the block of data to be scanned that are  
 commented - not just lines that have a comment at the end.  For example

 #age, weight, height
 33,128,65
 34,56,155

 instead of having to do something like

 33,128,65 #age, weight, height
 34,56,155


 Is this at all possible?

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

   


-- 
Simon Blomberg, B.Sc.(Hons.), Ph.D, M.App.Stat.
Centre for Resource and Environmental Studies
The Australian National University
Canberra ACT 0200
Australia
T: +61 2 6125 7800 email: Simon.Blomberg_at_anu.edu.au
F: +61 2 6125 0757
CRICOS Provider # 00120C

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

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Re: [R] RSQLite +textConnection()

2006-11-27 Thread Seth Falcon
Alexander Nervedi [EMAIL PROTECTED] writes:

 Hi !

 I am trying to read in 1000 really small text files.  When on adams, R bails 
 out after reading 125 files with the error message

 Error in textConnection(readLines(f, n = 2)) :
 all connections are in use

Please try updating your version of DBI and RSQLite, I believe this
has been fixed.

+ seth

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Re: [R] Questions about generating samples in R

2006-11-27 Thread Charles C. Berry
On Mon, 27 Nov 2006, Mark Na wrote:

 Further to Alexander's question ... could anyone provide assistance
 with random stratified sampling? Let's say we have Alex's dataframe
 and we want to stratify the random selection by group membership
 (which is contained in one of the eight columns).

 We might want to randomly select:

 1) a constant number (e.g., 5) of rows from each group, or
 2) a percentage (e.g. 10%) of rows from each group resulting in groups
 being represented proportionally in the sample (with respect to the
 population).

 I am aware of stratsrs but this function does not seem to allow the
 second of the above two options.

 Any ideas how to achieve this in R?


Suppose 'grp.numbers' holds the group identitities.

Define wrappers for sample():

sample.just.5 - function(x) sample(x ,size = 5 )

sample.10.pct - function(x) sample(x,size=round(0.10*length(x)))

Then use tapply:

samples.of.5 - tapply(seq(along=grp.numbers),grp.numbers, 
sample.just.5 )

Check this with:

table( grp.numbers[ unlist( samples.of.5 ) ] )

Again use tapply:

samples.of.10.pct - tapply(seq(along=grp.numbers),grp.numbers, 
sample.10.pct )

Check this with:

table( grp.numbers[ unlist( samples.of.10.pct ) ] )


There are loads of variations ...


 Thanks, Mark



 On 11/26/06, Alexander Geisler [EMAIL PROTECTED] wrote:
 Hello!

 I have a data set with 8 columns and in about 5000 rows. What I want to
 do is to generate samples of this data set.

 Samples of a special size, as example 200.

 What is the easiest way to do this? No special things are needed, only
 the random selection of 200 rows of the data set.

 Thanks
 Alex

 --
 Alexander Geisler * Kaltenbach 151 * A-6272 Kaltenbach
 email: [EMAIL PROTECTED] | [EMAIL PROTECTED]
 phone: +43 650 / 811 61 90 | skpye: al1405ex

 __
 R-help@stat.math.ethz.ch mailing list
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 __
 R-help@stat.math.ethz.ch mailing list
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 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Charles C. Berry(858) 534-2098
  Dept of Family/Preventive Medicine
E mailto:[EMAIL PROTECTED]   UC San Diego
http://biostat.ucsd.edu/~cberry/ La Jolla, San Diego 92093-0717

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Re: [R] RSQLite +textConnection()

2006-11-27 Thread Alexander Nervedi

They are uptodate. When I run it on windows the i can load upto 200 files, 
while on Linux it stops after loading 125.

From: Seth Falcon [EMAIL PROTECTED]
To: r-help@stat.math.ethz.ch
Subject: Re: [R] RSQLite +textConnection()
Date: Mon, 27 Nov 2006 17:22:57 -0800

Alexander Nervedi [EMAIL PROTECTED] writes:

  Hi !
 
  I am trying to read in 1000 really small text files.  When on adams, R 
bails
  out after reading 125 files with the error message
 
  Error in textConnection(readLines(f, n = 2)) :
  all connections are in use

Please try updating your version of DBI and RSQLite, I believe this
has been fixed.

+ seth

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_

by Pandora http://radio.msn.com/?icid=T002MSN03A07001

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Re: [R] comments in scan

2006-11-27 Thread Jarrett Byrnes
Right, but what if it is not the first line?  For example

#data block 1
34,54,23
23,53,12
35,23,23
#data block 2
64,24,13
354,24,12
324,13,3

On Nov 27, 2006, at 4:39 PM, Duncan Murdoch wrote:

 On 11/27/2006 7:25 PM, Jarrett Byrnes wrote:
 I had a question about scan in R.  For better code readability, I   
 would like to have lines in the block of data to be scanned that  
 are  commented - not just lines that have a comment at the end.   
 For example
 #age, weight, height
 33,128,65
 34,56,155
 instead of having to do something like
 33,128,65 #age, weight, height
 34,56,155
 Is this at all possible?

 If it's on the first line, it's easy:  just use skip=1 to skip the  
 first line.

 The general case

 #age, weight, height
 33,128,65
 # and now for something completely different
 34,56,155

 probably needs something like this:

  scan(foo, what=list(0,0,0), comment.char=#, sep=,,  
 multi.line=T)

 i.e. you need to tell it how many objects are in a record, and  
 allow records to span multiple lines.  Watch out for typos in the  
 file that put different numbers of entries on each line, because  
 scan() won't complain about it.

 Duncan Murdoch

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[R] Slight discrepancy between predict.lm() and all.effects()

2006-11-27 Thread Michael Kubovy
In the course of exploring response prediction, I stumbled upon a  
small discrepancy between the CIs produced by predict.lm() and  
all.effects()

require(mlmRev)
require(effects)
hsb.lm - lm(mAch ~ minrty * sector, Hsb82)
hsb.new - data.frame(
 minrty = rep(c('No', 'Yes'), 2),
 sector = rep(c('Public', 'Catholic'), each = 2))
hsb.eff - all.effects(hsb.lm)
cbind(
 hsb.new,
 predict(hsb.lm, hsb.new, interval = 'confidence', type =  
'response')
)
# the following lower and upper bounds differ starting with the  
fourth decimal place
data.frame(
 hsb.new,
 fit = hsb.eff[[1]]$fit,
 lwr = hsb.eff[[1]]$lower,
 upr = hsb.eff[[1]]$upper
)

Is this due to rounding or algorithm?
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
 McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
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Re: [R] Fixed zeros in tables

2006-11-27 Thread David Duffy
A.R. Criswell [EMAIL PROTECTED] wrote:

 Hello Andrew Robinson and R-List
 
 Thanks, Andrew, but this does not work. Puttting zero weights on
 structural zeros, one's elsewhere in glm() does not deliver the
 appropriate expected cell counts loglm() provides as one would expect.
 
 If you run the code provided below, you'll see loglm() delivers zero
 cell counts with loglm() but using glm() with the weights you suggest,
 the expected cell counts are not zero.
 
 Still hoping for a resolution.
 Andrew Criswell
 
 Associate Professor
 Hedmark University
 Postboks 104, Rena 2510, NORWAY

If they are structural zeros, I believe you want:

  glm(COUNT ~  CONCERNS + AGE + GENDER, data=health, subset=(WEIGHTS0),
  family=poisson)

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] comments in scan

2006-11-27 Thread Duncan Murdoch
On 11/27/2006 9:23 PM, Jarrett Byrnes wrote:
 Right, but what if it is not the first line?  

If it's not the first line, then you should follow the instructions that 
start on the 4th line of my reply.

Duncan Murdoch


For example
 
 #data block 1
 34,54,23
 23,53,12
 35,23,23
 #data block 2
 64,24,13
 354,24,12
 324,13,3
 
 On Nov 27, 2006, at 4:39 PM, Duncan Murdoch wrote:
 
 On 11/27/2006 7:25 PM, Jarrett Byrnes wrote:
 I had a question about scan in R.  For better code readability, I   
 would like to have lines in the block of data to be scanned that  
 are  commented - not just lines that have a comment at the end.   
 For example
 #age, weight, height
 33,128,65
 34,56,155
 instead of having to do something like
 33,128,65 #age, weight, height
 34,56,155
 Is this at all possible?
 If it's on the first line, it's easy:  just use skip=1 to skip the  
 first line.

 The general case

 #age, weight, height
 33,128,65
 # and now for something completely different
 34,56,155

 probably needs something like this:

  scan(foo, what=list(0,0,0), comment.char=#, sep=,,  
 multi.line=T)

 i.e. you need to tell it how many objects are in a record, and  
 allow records to span multiple lines.  Watch out for typos in the  
 file that put different numbers of entries on each line, because  
 scan() won't complain about it.

 Duncan Murdoch

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[R] Open source electronic lab notebook with R-driven analysis

2006-11-27 Thread John McNeil
All,

I thought you may be interested in hearing about the new web software  
we have developed. LabSynch is a fully integrated:
- Electronic lab notebook
- Web-based collaboration service
- Sample tracking system
- R-based data capture and analysis tool

It is designed to help bench scientists record better information  
with less work and share complete experimental and analytical methods  
and data, in context. Check it out here: http://www.labsynch.com

You can use it hosted on our site for free, or we can set up a  
private work area for you. It is also available as open source and  
runs on LAMP+R servers and OS X.

Please contact me directly with questions etc,

John

email: [EMAIL PROTECTED]
office: (858) 551-0459
skype: johnamcneil
http://www.labsynch.com

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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] RSQLite +textConnection()

2006-11-27 Thread Seth Falcon
Alexander Nervedi [EMAIL PROTECTED] writes:

 They are uptodate. When I run it on windows the i can load upto 200
 files, while on Linux it stops after loading 125.

Could you provide as much of a reproducible example as possible (along
with sessionInfo())?  I will try and have a look.

+ seth

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[R] LP Formulation of Preference Analysis

2006-11-27 Thread Marco LO
Dear All,
   
  I have posted a project on GetAFreelancer.com for a LINMAP (LINear 
programming techniques for multidimensional Analysis of Preference) R package.
   
  http://www.getafreelancer.com/projects/110792.html
   
  See if you are interested to bid.
   
  Redards,
  Marco LO
  USeebi Visual BI
  http://www.geocities.com/useebi
   

 
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