Wayne Aldo Gavioli wrote:
Hello all,
I'm trying to graph a scatterplot of a large (5,000 x,y coordinates) of data
with the caveat that many of the data points overlap with each other (share
the
same x AND y coordinates). In using the usual plot command,
plot(education, xlab=etc,
Wayne Aldo Gavioli wgavioli at fas.harvard.edu writes:
Hello all,
I'm trying to graph a scatterplot of a large (5,000 x,y coordinates) of data
with the caveat that many of the data points overlap with each other (share
the
same x AND y coordinates). In using the usual plot command,
Winkel, David wrote:
All,
I have a question regarding colors in bar plots. I want to stack a
total of 18 cost values in each bar. Basically, it is six cost types and
each cost type has three components- direct, indirect, and induced
costs. I would like to use both solid color bars
Dear R's (most likely Hadley),
I want to build a stacked bar plot where I would like to define which
colours will be used for each of the groups. However, I do not seem
to find a way to do this, even if I've been looking over many places.
I have tried several variations, and my final try was
Dear All,
I need to perform a numerical integration of one dimensional
fucntions. The extrems of integration are both finite and the functions
I'm working on are quite complicated. I have already tried both area()
and integrate(), but they do not perform well: area() is very slow and
Dear Forum,
I have a question about interaction estimate in the Cox model:
why the hazard ratio of the interaction is not produced in the summary of the
model?
(Instead, the estimate of the coefficient is given in the print of the model.)
# Example:
modINT -cph( Surv(T_BASE, T_FIN,STATUS)~
Kunio takezawa wrote:
R-users
E-mail: r-help@r-project.org
I have a quenstion on gam() in gam package.
The help of gam() says:
'gam' uses the _backfitting
algorithm_ to combine different smoothing or fitting methods.
On the other hand, lm.wfit(), which is a routine of
Hi folks,
I am using a data.frame with sediment grain sizes:
grain
sand silt clay
OAT 10.03 56.77 18.25
OAT 10.40 57.40 17.94
WG1 50.03 20.68 12.57
WG1 43.20 25.69 13.41
WG1 33.89 31.10 14.48
WG2 2.84 62.81 20.79
WG2 2.79 60.46 19.16
WG2 16.27 33.04 6.48
WG2 1.39 57.90 9.13
WG3
On Mon, 17 Dec 2007, Moshe Olshansky wrote:
Dear List,
Following the below question I have a question of my
own:
Suppose that I have large matrices which are produced
sequentially and must be used sequentially in the
reverse order. I do not have enough memory to store
them and so I would
?jitter is simpler:
x-rep(1:10,10)
y-x
plot(x,y) #100 points, only 10 show
plot(jitter(x),jitter(y)) #overlap removed.
Milton Cezar Ribeiro [EMAIL PROTECTED] 18/12/2007 04:36
Hi Wayne,
I have two suggestion to you.
1. You add some random noise on both x and y data or
2. You
Hi Thomas,
This looks quite strange. By default, the function use the column names
as labels.
What is grain ? A data.frame ? Why have you duplicated row.names? Please
return the results of class(grain) and names(grain)
Cheers,
PS: If you have questions related to ade4, you can use the adelist
Hiding in the windows faq is the observation that R's computation is
single-threaded, and so it cannot use more than one CPU. So multi-core
should make no difference other than allowing R to run with less
interruption from other tasks. That is often a significant advantage,
though.
Andrew
Gene shaving is implemented in the GeneClust package for R which you can
download from
http://odin.mdacc.tmc.edu/~kim/geneclust/
For more details see The Analysis of Gene Expression Data: Methods and
Software edited by Giovanni Parmiagiani, Elizabeth S. Garett, Rafael A.
Irizarry and Scott L.
I have a matrix y:
dimnames(y)
$x93
[1] 1 2
$x94
[1] 0 1 2
.. so on (there are other dimensions as well)
I need to access a particular dimension, but a random mechanism tells me
which dimension it would. So, sometimes I might need to access
dimnames(y)$x93, some other time
The model here is just a penalised GLM, and the warnings relate to the GLM
fitting process. Fitted probabilities of 0 or 1 can be perfectly appropriate,
but do indicate that the linear predictor is not really uniquely defined, and
that some care may be needed in interpreting results (for
Thanks for this advice.
grain was not a data.frame but a matrix. Now it works:-)
Cheers
Thomas
Stéphane Dray schrieb:
Hi Thomas,
This looks quite strange. By default, the function use the column
names as labels.
What is grain ? A data.frame ? Why have you duplicated row.names?
Please
Hi,
I'm having a bit of problems in creating a new dataframe.
Below you'll find a description of the current dataframe and of the
dataframe that needs to be created.
Can someone help me out on this one?
Thx in advance.
Bert
Current Dataframe
Var1Var2Var3Var4
A Fa W1
On 12/18/07, Bert Jacobs [EMAIL PROTECTED] wrote:
Hi,
I'm having a bit of problems in creating a new dataframe.
Below you'll find a description of the current dataframe and of the
dataframe that needs to be created.
Can someone help me out on this one?
library(reshape)
dfm - melt(df, id =
Dear All,
I continue trying to get several of my plotting functions to use
ggplot, because I really do like the concept of the graphical
objects, and working with them in the abstract.
I am now trying to access the grobs to manipulate using grid.
However, until now all I managed was to get the
Hi Davide,
It is difficult to say what the problem is without knowing more about the
nature of the integrand. So, you should do a couple of preliminary things
before attempting compute the integral.
First, is the integral is finite? You should establish this. Second, plot the
integrand over
On Dec 18, 2007 9:07 AM, Bert Jacobs [EMAIL PROTECTED] wrote:
Hi,
I'm having a bit of problems in creating a new dataframe.
Below you'll find a description of the current dataframe and of the
dataframe that needs to be created.
Can someone help me out on this one?
Thx in advance.
Bert
Duncan Murdoch wrote:
On 18/12/2007 7:31 AM, Antony Unwin wrote:
Wayne,
Try the iplot command in iPlots. You can then vary both the
pointsize and the transparency of your scatterplot interactively and
decide which scatterplot conveys the information best. Sometimes
it's helpful to
On Dec 18, 2007 9:54 AM, Gabor Grothendieck [EMAIL PROTECTED] wrote:
On Dec 18, 2007 9:07 AM, Bert Jacobs [EMAIL PROTECTED] wrote:
Hi,
I'm having a bit of problems in creating a new dataframe.
Below you'll find a description of the current dataframe and of the
dataframe that needs to
On 18 Dec 2007, at 2:42 pm, Duncan Murdoch wrote:
(I must admit to being very surprised that jittering and
sunflower plots have been suggested for a dataset of 5000
points. Do those who mentioned these methods have examples on
that scale where they are effective?)
Sure. The
On 18/12/2007 10:01 AM, Antony Unwin wrote:
On 18 Dec 2007, at 2:42 pm, Duncan Murdoch wrote:
(I must admit to being very surprised that jittering and
sunflower plots have been suggested for a dataset of 5000
points. Do those who mentioned these methods have examples on
that scale
On 18/12/2007 10:02 AM, James W. MacDonald wrote:
Duncan Murdoch wrote:
On 18/12/2007 7:31 AM, Antony Unwin wrote:
Wayne,
Try the iplot command in iPlots. You can then vary both the
pointsize and the transparency of your scatterplot interactively and
decide which scatterplot conveys
Duncan Murdoch wrote:
Yes, I agree. (As an aside, there's actually a capital S in
smoothScatter(), and it's a bit of a pain to install, because
geneplotter depends on something that depends on DBI, which is not so
easily available these days.)
Somehow I always forget the capital S and
I think you're going to find that barchart with that
many values in a bar is going to be pretty well
uninterpretable.
Jim Lemon gives the desired barchart but it is very
difficult to read.
Stealing his code to create the same matrix I'd
suggest may be looking at a dotchart. I'm not sure if
On 18 Dec 2007, at 4:49 pm, Duncan Murdoch wrote:
One good alternative here is the fluctuation diagram variant of a
mosaic plot:
xx-as.factor(x)
yy-as.factor(y)
imosaic(xx,yy, type=f)
That plot is better than jittering, but there's the problem in the
mosaic plot of understanding the
Sorry for using library instead package, but
library() is one command for using packages.
... which is why all efforts to make folks say package instead of
library are doomed to fail, IMHO. Besides, in English, library
also means a collection of software or data usually reflecting a
specific
Dear HelpeRs,
a colleague of mine uses Scientific Workplace to write his LaTeX documents.
I made his mouth water mentioning the advantages of using Sweave.
Not using SW myself I wonder if anyone out there has gathered some
experiences
in using the combination of both.
Thank you in advance
On 12/18/2007 11:21 AM, James W. MacDonald wrote:
Duncan Murdoch wrote:
Yes, I agree. (As an aside, there's actually a capital S in
smoothScatter(), and it's a bit of a pain to install, because
geneplotter depends on something that depends on DBI, which is not so
easily available these
On 12/18/2007 12:44 PM, Antony Unwin wrote:
On 18 Dec 2007, at 4:49 pm, Duncan Murdoch wrote:
One good alternative here is the fluctuation diagram variant of a
mosaic plot:
xx-as.factor(x)
yy-as.factor(y)
imosaic(xx,yy, type=f)
That plot is better than jittering, but there's the
Hello,
I would like to retrieve data stored in MySQL database, so I installed
RMySQL package.
I can successfully connect with the my database using the following code
dvr-dbDriver(MySQL)
con2-dbConnect(dvr,group=exbardiv)
mysqlDescribeConnection(con2)
MySQLConnection:(972,0)
User: mmorag
Is it your use of 'con' rather than 'con2' in dbSendQuery? -Kevin
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Marc Moragues
Sent: Tuesday, December 18, 2007 1:14 PM
To: r-help@r-project.org
Subject: [R] R brakes when submitting a query to MySQL
Another approach which I'm pleased with but was not suggested so far
is jitter + kde2d from MASS:
plot(jitter(x), jitter(y))
if (!exists(kde2d)) require(MASS)
kdesamp - 2 #depending on your RAM
forkde - if (kdesamp length(x)) sample(1:length(x), kdesamp,
replace=FALSE) else 1:length(x)
d -
You are right, it was a mistake copying and pasting the code. There is
no error message from R when I run con2. I get a Windows error message
saying R for windows terminal front-end has encountered a problem and
need to close.
The error signature is:
AppName: rterm.exe AppVer: 2.60.43063.0
The problem is the missing values. The argument na.action is not active
in princomp(), which I think is a bug, even though the help page claims that
factory fresh default is na.omit.
So, you need to either get rid of the rows with any missing values in them,
or use a PCA code that can deal with
I've used the scatterplot3d function to graph some data and had it
graph a smooth fit. Is there a way to actualy find out the function
of the surface? I've looked through the help and figured out how to get
it to report the following:
Family: gaussian
Link function: identity
Formula:
y ~ s(x,
Hello all,
I would like to compare two sets of count data which form
Poisson distributions. I'd like to generate some sort of p-value of the
likely-hood that the distributions are the same. Thanks in advance for
your advice.
Cheers,
Mark
Mark Gosink, Ph.D.
Head of
I am trying to dp a 3d plot.
I tried persp but my data is not a matrix.
the 3dplot function returns this error, (list) object cannot be coerced to
'double'
heres my code,
td-read.csv(td.csv, header=TRUE)
price-read.csv(price.csv, header=TRUE)
contractdate-read.csv(contractdate.csv,
Dear All,
Is it possible to import GAUSS .FMT files into R?
Thanks for your time.
Kind Regards,
Pedro N. Rodriguez
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
60,000
I hope that you actually haven't got any comma to separate the
thousands... it separates fields in a csv files (as the Comma
Separated Values name may suggest). If so, get rid of the commas.
the 3dplot function returns this error,
(list) object cannot be coerced to 'double'
I am using package nlme and would like to specify initial values for a linear
mixed-effects model to help with convergence. I am trying to specify those
initial values using the msScale option under ‘control’ in the lme() function:
lme(Y ~ X1, random= ~ X1|X2, control=list(msScale=lmeScale))
Armin Goralczyk [EMAIL PROTECTED] wrote in
news:[EMAIL PROTECTED]:
On 12/18/07, David Winsemius [EMAIL PROTECTED] wrote:
David Winsemius [EMAIL PROTECTED] wrote in
news:[EMAIL PROTECTED]:
Armin Goralczyk [EMAIL PROTECTED] wrote in
news:[EMAIL PROTECTED]:
I tried the above function
Hi all,
What may be a smart, efficient way to get the following result:
myvector - c(A,B,C,D,E)
myseries - miracle(myvector)
myseries
[1]
[[1]] A
[2]
[[1]] A B
[3]
[[1]] A B
[4]
[[1]] A B C
[5]
[[1]] A B C D
[6]
[[1]] A B C D E
Thanks for any hints,
Joh
Debugged version:
lapply(1:length(myvector), function(.length) {
myvector[1:.length]
})
Thanks for showing the direction!
Joh
[EMAIL PROTECTED] wrote:
From: Johannes Graumann [EMAIL PROTECTED]
Date: 2007/12/18 Tue PM 04:40:37 CST
To: [EMAIL PROTECTED]
Subject: [R] All anchored series from a
On Wed, Dec 19, 2007 at 12:01:25AM +0100, Johannes Graumann wrote:
Debugged version:
lapply(1:length(myvector), function(.length) {
myvector[1:.length]
})
Thanks for showing the direction!
Joh
Note that this fails if length(myvector)==0.
Good to know the corner cases.
Gabor
[EMAIL
Nothing to be sorry about. You suggested a viable solution untested ... my
job to figure it out ;0)
Joh
[EMAIL PROTECTED] wrote:
From: [EMAIL PROTECTED]
Date: 2007/12/18 Tue PM 02:50:52 CST
To: Johannes Graumann [EMAIL PROTECTED]
Cc: r-help@r-project.org
Subject: Re: [R] All anchored series
Dear R users,
An updated version of the np package has recently been uploaded to CRAN
(version 0.14-1).
The package is briefly described in a recent issue of Rnews (October,
2007, http://cran.r-project.org/doc/Rnews/Rnews_2007-2.pdf) for those
who might be interested.
A somewhat more detailed
I am running a series of candidate mixed models using lmer (package lme4)
and I'd like to be able to compile a list of the AIC scores for those
models so that I can quickly summarize and rank the models by AIC. When I
do logistic regression, I can easily generate this kind of list by creating
the
Dear all,
I would like to use a tree regression method to analyze my dataset. I
am interested in the fact that random forests creates in-bag and
out-of-bag datasets, but I also need an estimate of support for each
split. That seems hard to do in random forests since each tree is
grown using a
You can calculate the AIC as follows:
(fm1 - lmer(Reaction ~ Days + (Days|Subject), sleepstudy))
aic1 - AIC(logLik(fm1))
Hope this helps.
Dave
On 12/18/07, Peter H Singleton [EMAIL PROTECTED] wrote:
I am running a series of candidate mixed models using lmer (package lme4)
and I'd like to be
On 19/12/2007, at 6:46 AM, bogdan romocea wrote:
Sorry for using library instead package, but
library() is one command for using packages.
... which is why all efforts to make folks say package instead of
library are doomed to fail, IMHO.
Yes, but it gives so much pleasure to
On Dec 18, 2007 2:06 PM, [EMAIL PROTECTED] wrote:
I am plotting fishing vessel positions and want these points to be
relative in size to the catch at that point. Is this possible? I am just
begining to use R and my search of the help section didnt help in this
area. Heres what Im using so
I am currently designing a clustering algorithm in collaboration with one of
my colleagues. For comparison purposes we would like to contrast it with the
Support Vector Clustering algorithm of (A. Ben-Hur, D. Horn, H.T.
Siegelmann, and V. Vapnik. Support vector clustering. Journal of Machine
Hello,
I am trying to display some harmonic functions in a plot. The kind of
display I have in mind is like the one that cn be obtained by a call
to plot.ts with plot.type = multiple. The only difference is that I
want a single box containing all the plots instead of one box per
plot. I thought
From ?cbind:
Data frame methods
The cbind data frame method is just a wrapper for data.frame(...,
check.names = FALSE). This means that it will split matrix columns in data
frame arguments, and convert character columns to factors unless
stringsAsFactors = TRUE is passed.
(I'm guessing
R-users
E-mail: r-help@r-project.org
This iteration seems to be for iteratively reweighted least squares not
for backfitting. And lm.wfit may solve multiple linear equation using
QR decomposition; but I am not sure.
Let me tell you something about my guess above.
The iteration below is from
To access your dimension idx you could do either
assign(a,paste(dimnames(y)$x,idx,sep=))
or
eval(parse(text=paste(a-dimnames(y)$x,idx,sep=)))
--- [EMAIL PROTECTED] wrote:
I have a matrix y:
dimnames(y)
$x93
[1] 1 2
$x94
[1] 0 1 2
.. so on (there are other
dimensions
Can a simple matrix be used for this or would it be better and more
efficient to create an external database to hold the data. If so,
should the database be created using C and how would I do this (seeing
as that I have never programmed in C)?
You don't want to be down at the C level,
Dear R users,
I am analysing a very large data set and I need to perform several data
manipulations. The dataset is so big that the only way I can play with it
without having memory problems (E.g. cannot allocate vectors of size...)
is to write a batch script to:
1. cut the data into pieces
2.
you want to use:
save(list=paste(data, i, sep=), file=paste(data, i, .Rdata,
sep=))
b
On Dec 18, 2007, at 9:24 PM, Marie Pierre Sylvestre wrote:
Dear R users,
I am analysing a very large data set and I need to perform several
data
manipulations. The dataset is so big that the only way
Thank you for your response!
'write.table' writes up to 15 decimal digits which is
not the machine (double) precision but not far from
that - sorry for the misleading comments!
After all I found a way to do what I needed without
using disk or much memory and doing only twice as much
work as I
On Tue, 18 Dec 2007, Art Owen wrote:
Dear R-ophiles,
I've found something very odd when I apply convolve
to ever larger vectors. Here is an example below
with vectors ranging from 2^11 to 2^17. There is
a funny bump up at 2^12. Then it gets very slow at 2^16.
The time is consumed by
I have the following list of observations of calendar time:
[1] 03-Nov-1997 09-Oct-1991 27-Aug-1992 01-Jul-1994 19-Jan-1990 12-Nov-1993
[7] 08-Oct-1993 10-Nov-1982 08-Dec-1986 23-Dec-1987 02-Aug-1995 20-Oct-1998
[13] 29-Apr-1991 16-Mar-1994 20-May-1991 28-Dec-1987 14-Jul-1999 27-Nov-1998
[19]
Good morning!
I have 4 questions which trouble me:
1. I want to test the hypothesis that the 2 proportions (the mean of a
binomial) which come from 2 different samples are equal. I want to use the
following function
z= (p1-p2)/ sqrt((p1(1-p1)/n1)+(p2(1-p2)/n2)) which is one of the standard
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