Viviana Ruiz vivruiz at gmail.com writes:
I am doing kernel density plots, and am trying to make the lines thicker. I
comparing three groups, in sm.density.compare. I tried changing lwd to make
the line sthicker right on the density compare call, but was not able to do
it. There is not an
Hi Viviana,
I am doing kernel density plots, and am trying to make the lines thicker.
You need to hack the code for sm.density.compare. See the code below. This
uses the same defaults as the original, but you can customize band colour,
line width, and so on using arguments to the function. The
Jani Lobo lobo at grupocomar.com writes:
I want to estimate the survival mean of a few specific teams. I'm trying to
calculate it through a Kaplan Meier estimator. For doing so, I load the
survival package and run the following instructions:
options(survfit.print.mean=TRUE) allows
On Thu, 2009-03-05 at 02:20 +, Ben Bolker wrote:
Sueli Rodrigues srodrigu at esalq.usp.br writes:
Olá. Tenho um arquivo que a cada 6 linhas corresponde uma amostra da qual
preciso dos coeficientes da regressão linear. Como faço para que o
programa distinga a cada 6 linhas como uma
Hi
I am using R scripts which are running remotely. To make debugging
easier, I would like to have the possibility to execute traceback()
automatically when an error occurs. Is this possible?
OS: Linux
Thanks
Rainer
--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Hi
r-help-boun...@r-project.org napsal dne 05.03.2009 15:21:22:
Hello Petr,
In fact spec is data.frame with a column called code (containing
numerical
values) and some other columns called data1, data2, ... containing data
for
each equipment (that is for each code).
But I don't have
Hi all,
I' m trying to figure out if it is appropriate to do a PCA having only
categorical data (not ordinal). I have only find the following quote:
One method to find such relationships is to select appropriate variables and
to view the data using a method like Principle Components Analysis
Hi,
I am using glm().
I'd like to know what the command means.
For example,
glm(family=binomial(link=logit))
means logit model.
Then,
glm(family=gaussian(link=logit)),
does this mean?
Thank you in advance.
Kenji. A
Analysis Manager
SPI - Strategy, Productivity, Insight., Japan
On Fri, 6 Mar 2009, Rainer M Krug wrote:
Hi
I am using R scripts which are running remotely. To make debugging
easier, I would like to have the possibility to execute traceback()
automatically when an error occurs. Is this possible?
See options 'error' and 'showErrorCalls'. The latter is
You might want to look into correspondence analysis, which has several
variants of PCA designed for categorical data.
On Fri, 6 Mar 2009, Galanidis Alexandros wrote:
Hi all,
I' m trying to figure out if it is appropriate to do a PCA having only
categorical data (not ordinal). I have only
On 06-Mar-09 09:25:26, Prof Brian Ripley wrote:
You might want to look into correspondence analysis, which has several
variants of PCA designed for categorical data.
In particular, have a look at the results of
RSiteSearch(correspondence)
Ted.
On Fri, 6 Mar 2009, Galanidis Alexandros
The best encoding depends upon which language you would like to
manipulate
the variable in. In R, genders are most naturally represented as
factors.
That means that in an external data source (like a spreadsheet of
data),
you should ideally have the gender recorded as
Hi Galandis,
dudi.mix() in package ade4 does PCA using categorical and/or quantitative
variables. Ordered cats are replaced by poly(x, deg=2). Squares of
categoricals can also be used. The method is a generalization by Chessel of
the method of Hill and Smith.
Regards, Mark.
Galanidis
John Sorkin jsorkin at grecc.umaryland.edu writes:
R 2.8.1
Windows XP
Fedora Linux.
I would like a suggestion for an editor that will help format my R code that
can be used with Rcmdr. Is there
anything I need to know about running or installing an editor when using
Rcmdr? I run R on
See homals package in R. But also look documents for ade4 package.
Justin BEM
BP 1917 Yaoundé
Tél (237) 76043774
De : Galanidis Alexandros a...@env.aegean.gr
À : r-help@r-project.org r-help@r-project.org
Envoyé le : Vendredi, 6 Mars 2009, 10h09mn 18s
Objet
Hi Maxl18,
error in mo...@fit(data,...) : object var3 not found
What should I do?
Make sure that var3 exists/is available
##
str(datalist$var3) ## is it here?
ls(pattern=var3) ## is it here?
Regards, Mark.
Maxl18 wrote:
Hi,
I have a problem with the function ctree in the
HI,Barry.
Thanks a lot for your details reply. I have already rewritten the programs. Now
it totally works.
Your comment: Note the use of comments and breaking the code up into small
independent, testable functions is really Valuable! Thanks again.
Hi,David,
You are right, My previous
Hello,
If I want to apply some f(x) to such chunks of the the array
dim(A)==c(d1,d2,d3,..,dk,...,dn) which are defined by A[...,ik,...]
(ik belongs to {1,..,dk}), for now I use iteration via 'for (i in
dim(A)[k]) f(A[...,k,...])' . Is there any more elegant approach, e.g
like in 'apply' function
Thanks a lot to everybody that helped me out with this.
Conclusions:
(1)
In order to edit arima in R:
fix(arima)
or alternatively:
arima-edit(arima)
(2)
This is not contained in the Introduction to R manual.
(3)
A productive fix of arima is attached (arma coefficients printed out and
error
well, you can still use apply(), e.g.,
A - array(rnorm(3*4*5), c(3, 4, 5))
f - sum
out - numeric(4)
for (i in 1:4)
out[i] - f(A[, i, ])
out
apply(A, 2, f)
I hope it helps.
Best,
Dimitris
Todor Kondic wrote:
Hello,
If I want to apply some f(x) to such chunks of the the array
Hi,
I have a problem with the function ctree in the package party.
When I launch ctree with weights=NULL it works.
ctree(function~var1+var2, data=datalist, weights=NULL,
controls=ctree_control(mincriterion=0.95, maxdepth=4,
teststat=quad,testtype=Bonferroni))
But when I try
Hi all,
Thanks very much for the suggestions. My experience for the benefit of
others is:
- use addtable2plot if you want a fancier legend or small table *within* a
plot area
- use textplot if you want combinations of tables and text listings in the
graphics device. The help for textplot gives a
If I well understand, maybe you have still apply at your disposal:
arrayA - 1:60
dim(arrayA) - c(3,4,5)
apply(arrayA, 2, sum)
You have the same result of:
res-numeric(4);for (i in 1:4) res[i]-sum(arrayA[,i,])
Ciao,
domenico
PS:
have a look at plyr package for more slicing and applying
Hi,
I have the following dataframe:
IDDates
1 16-07-01 06-10-95
224/01/02 06-10-95
3 16/01/02 16/08/94 12/01/91
And I would like to extract the dates, but couple the ID's to the right
dates, eg:
ID Dates
116-07-01
1
Dear all!
I tried to fit Gompertz growth models to describe cummulative germination rates
using nls. I used the following code:
germ.model-nls(percent.germ~a*exp(-b*exp(-k*day)),data=tab,start=list(a=100,b=10,k=0.5))
My problem is that I want that the fitted model goes through the origin, since
Dear All,
I am going through a worked example provided by Harrell, Lee and Mark
(1996, Stats in Medicine, 15, 361-387). I know that the code provided
is for S-PLUS and R but the languages don't differ enough for this to
be a problem.
I am using the Hmisc and Design libraries and have used the
Hi, every body!
I am a new comer for R, so my question would unavoidablely sounds stupid.
Sorry!
In my experiment, there are two type of soil ( soil F and soil D), each half
of them were subjected to steam sterilize (result in FS and DS soil). A
equal volume of soil from two of the four soil
?is.na
Manli Yan wrote:
I have a 50*50 matrix,some entry are NAs,I want to replace these NA by
0,so can I use some syntax to do so other than using ifelse?
I tried to use replace(a,NA,0),it didnt work~~(a is matrix name)
Thanks~
[[alternative HTML version deleted]]
Dear All,
I have many files in my directory. I want to transfer each data into one which
is readable.
They have so many possibilities, i have collected(manually and visually) all
possibilities and represent them as different numbers.
Try this:
library(gsubfn)
# convert date strings to dd-mm-yy
Dates - gsub(/, -, dat$Dates)
# regular expressiont to match dates
re - \\d\\d-\\d\\d-\\d\\d
# extract dates and convert them to Date class
# giving a list d each of whose components is a vector of dates
d - strapply(Dates, re, ~
On Fri, Mar 6, 2009 at 6:07 AM, Sueli Rodrigues srodr...@esalq.usp.br wrote:
Hi, I have the following file, and I need to work out the linear
regression for each sample. I tried the model(*) and receive the error
message (**):
data=split(mydata,rep(1:(nrow(mydata)/6),each=6))
Uploaded the data and my comparison. Hopefully this will help illustrate and
solve the problem.
http://www.nabble.com/file/p22371555/data.csv data.csv
http://www.nabble.com/file/p22371555/arima%2Bmethods.docx arima+methods.docx
--
View this message in context:
On Thu, Mar 5, 2009 at 7:49 PM, per243 jose.perezsua...@csiro.au wrote:
How can a non-linear regression to calculate the statistical R-square,
R-square adjusted, RMSE, VIF??
It is not clear that these statistics are meaningful for a nonlinear
regression model. For example, an R^2 value is
On 3/6/09, kenji_aoyagi kenji_aoy...@spi-consultants.com wrote:
Hi,
I am using glm().
I'd like to know what the command means.
For example,
glm(family=binomial(link=logit))
means logit model.
Means : binomial response variable transformed with the logit
Then,
Your methods were sent in a docx file. I could be wrong, but it seems
unlikely that very many people will bother to open such a file even if
they do have an M$ product that will allow them to do so. My advice:
First read the posting guide; then learn to sent plain text attachments.
This is
janey ding janeding1 at hotmail.com writes:
Sorry!
In my experiment, there are two type of soil ( soil F and soil D), each half
of them were subjected to steam sterilize (result in FS and DS soil). A
equal volume of soil from two of the four soil types (F, D, FS, DS) were
mixed as follows:
On 06-Mar-09 11:33:21, Swantje Löbel wrote:
Dear all!
I tried to fit Gompertz growth models to describe cummulative
germination rates using nls. I used the following code:
germ.model-nls(percent.germ~a*exp(-b*exp(-k*day)),data=tab,
start=list(a =100,b=10,k=0.5))
My
*** Travel and Accommodation Support ***
Funds from the U.S. National Science Foundation may be available to
provide partial support for travel and accommodation for some graduate
students and junior faculty at U.S. post-secondary institutions to
attend DSC 2009 and useR 2009. If
I have many files in my directory. I want to transfer each data into
one which is readable.
They have so many possibilities, i have collected(manually and
visually) all possibilities and represent them as different numbers.
Rep[grep('context_log',log1$Remain[1:length(log1$Date)]),]-2
Hi,
i am using spatstat package for spatial data analysis and now i have a problem
to create a point pattern. The points are in file points.txt (first column
for Latitude and second column for Longitude ) and I imported them and
separated each columns in two arrays x and y. If I plots x and
Dear Sueli,
Assuming that your data is in a data frame called mydata, something like
the following should work:
# splitting the data by SAMPLE
msp-with(mydata,split(mydata,SAMPLE))
# linear models by sample
models-lapply(msp,function(x) lm(KA ~ PA, data = x))
# linear models by sample
that statistic would be appropriate for non-linear regression?. know how I
can calculate the VIF for a linear model?.
per243 wrote:
How can a non-linear regression to calculate the statistical R-square,
R-square adjusted, RMSE, VIF??
Thanks
jose
--
View this message in context:
Hi,
I know the function LETTERS, but, now I have some letters to convert it in
numbers, like A=1,B=2, etc... Is any function to do that?
Atenciosamente,
Leandro Lins Marino
Centro de Avaliação
Fundação CESGRANRIO
Rua Santa Alexandrina, 1011 - 2º andar
Rio de Janeiro, RJ - CEP: 20261-903
R (21)
try this:
x - c(A, X, F, W, G, V, L)
match(x, LETTERS)
I hope it helps.
Best,
Dimitris
Leandro Marino wrote:
Hi,
I know the function LETTERS, but, now I have some letters to convert it in
numbers, like A=1,B=2, etc... Is any function to do that?
Atenciosamente,
Leandro Lins Marino
Dear Michael,
For what it's worth, I develop the Rcmdr under Eclipse, and it works fine
with Eclipse -- both under Windows and under Mac OS X. Of the IDEs that I've
used with R, I'm most impressed with Eclipse/StatET, but configuration is
non-trivial and documentation is sparse.
I have a little
Hi,
I also use R under Eclipse/StatET. I found the following doc really
useful:
http://www.splusbook.com/Rintro/R_Eclipse_StatET.pdf
Regards
Alain
212-449-4894
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of John Fox
Sent:
### example:start
v - sample(rnorm(200), 100, replace=T)
k - rep.int(c(locA, locB, locC, locD), 25)
tapply(v, k, summary)
### example:end
... (hopefully) produces 4 summaries of v according to k group
membership. How can I transform the output into a nice table with the
croups as columns and
Dear Sören,
How about this?
do.call(cbind,tapply(v, k, summary))
HTH,
Jorge
On Fri, Mar 6, 2009 at 10:48 AM, soeren.vo...@eawag.ch wrote:
### example:start
v - sample(rnorm(200), 100, replace=T)
k - rep.int(c(locA, locB, locC, locD), 25)
tapply(v, k, summary)
### example:end
...
soeren.vo...@eawag.ch wrote:
### example:start
v - sample(rnorm(200), 100, replace=T)
k - rep.int(c(locA, locB, locC, locD), 25)
tapply(v, k, summary)
### example:end
Maybe this could be a solution:
t1 - tapply(v, k, summary)
t2 - sapply(t1, cbind)
rownames(t2) - names(t1[[1]])
t2
Ciao,
soeren.vo...@eawag.ch wrote:
### example:start
v - sample(rnorm(200), 100, replace=T)
k - rep.int(c(locA, locB, locC, locD), 25)
tapply(v, k, summary)
### example:end
This one is better:
do.call(cbind, tapply(v,k,summary))
Ciao,
domenico
... (hopefully) produces 4 summaries of v according to
On 06.03.2009, at 16:48, soeren.vo...@eawag.ch wrote:
### example:start
v - sample(rnorm(200), 100, replace=T)
k - rep.int(c(locA, locB, locC, locD), 25)
tapply(v, k, summary)
### example:end
... (hopefully) produces 4 summaries of v according to k group
membership. How can I transform the
You have pretty much exhausted my expertise on time series, you may want to
reask your question on the sig-finance list (with a more specific subject
line), there seem to be more time series experts hanging out on that list
(though someone please correct me if my impression is wrong).
--
I'd like to report another instance...one of my students has had the exact
same error. I've checked the data, at it is a clean .csv file, with no
quotation marks at all. I am currently at a loss at how to figure out what
might be going wrong.
--
View this message in context:
Hello,
I have been noticing that some of my column headings are missing.
Can you give me a clue as to how to
1] replace Var1 and Var 2 by Region and type ie do it right the first time
x-matrix(c(266, 359, 533, 313, 555, 504, 502, 242),nrow=4)
rownames(x)=c( Northeast, Midwest, South, West )
Dimitris, Domenico,
It seems I was using apply in a wrong way.
Thank you!
TK
2009/3/6 Domenico Vistocco visto...@unicas.it:
If I well understand, maybe you have still apply at your disposal:
arrayA - 1:60
dim(arrayA) - c(3,4,5)
apply(arrayA, 2, sum)
You have the same result of:
Thank you for your reply, Dieter. I will try it.
Looks like a split-block experiment. You should check # 1.6 at the bottom
of library\nlme\scripts\Ch01.R, the package nlme, and the book by Pinheiro/
Bates.
Dieter
__
R-help@r-project.org mailing
Dear Doug,
Can you send me the file, along with information about the versions of the
Rcmdr and R that you're using, and your OS? I suspect that the problem
doesn't have to do with the file, but with the command that the Rcmdr is
generating to read it, so some additional information would also be
Dear Doug,
Here's my guess: the path to your file has an apostrophe in it -- I'm able
to duplicate the error in this case. If that's the case, then a work-around
would be to move the file. Meanwhile, I'll look into fixing the problem.
Regards,
John
-Original Message-
From:
Hello R Help Team,
I have created graph from weighted adjecency matrix .Is there a way I can
find highly connected nodes in Igraph like the Package RBGL does.
nathan
--
View this message in context:
http://www.nabble.com/Highly-Connected-Nodes-in-Igraph-tp22377522p22377522.html
Sent from
Nathan,
if you have a weighted adjacency matrix, then you don't need graph
packages for this, just do
rowSums(data)
or
rowSums(data != 0)
depending you want the sum of the weights of the adjacent edges, or
just the number of adjacent edges. Or optionally colSums instead of
rowSums if your
Answer to your first question:
x-matrix(c(266, 359, 533, 313, 555, 504, 502, 242),nrow=4)
rownames(x)=c( Northeast, Midwest, South, West )
colnames(x)=c(Public, Private)
y - as.data.frame(as.table(x))
names(y)[1:2] - c(Region, Type)
y
RegionType Freq
1 Northeast Public 266
2
Hello,
I know I am forgetting to do something silly. I typed coordinates in
vectors (as below) but when I call them in R they come out as integers,
and I want them to be real numbers. I have tried using as.numeric,
as.real, etc... but they are still read by R as integers.
STX-c(16.0962,
There are real numbers:
STX-c(16.0962, 16.1227, 16.0921, 16.1498)
STY-c(2.0387, 2.0214, 1.9877, 1.9846)
str(STX)
num [1:4] 16.1 16.1 16.1 16.1
str(STY)
num [1:4] 2.04 2.02 1.99 1.98
So what is your question?
On Fri, Mar 6, 2009 at 1:47 PM, John Poulsen jpoul...@zoo.ufl.edu wrote:
Hello,
STX-c(16.0962, 16.1227, 16.0921, 16.1498)
STY-c(2.0387, 2.0214, 1.9877, 1.9846)
STX
[1] 16.0962 16.1227 16.0921 16.1498
STY
[1] 2.0387 2.0214 1.9877 1.9846
Did you perhaps redefine c()?
Or:
options()$digits
If not, then what do these say:
str(STX)
str(STY)
On Mar 6, 2009, at 1:47 PM,
To do that be sure to give each dimension, itself, a name when
the matrix is defined:
mat -matrix(c(266, 359, 533, 313, 555, 504, 502, 242), nrow = 4,
dimnames = list(Region = c(Northeast, Midwest, South, West),
Type = c(Public, Private)))
Dear all -
I do fret this to be a revealing beginner question - fortunately, this
mailing list have been good to me in the paste .-)
I am looking for a good R editor/environment in ubuntu. To that end, I have
decided to dive into gvim as the modality offered here seems to make sense
for editing.
Hello,
I know I am forgetting to do something silly. I typed coordinates in
vectors (as below) but when I call them in R they come out as integers,
and I want them to be real numbers. I have tried using as.numeric,
as.real, etc... but they are still read by R as integers.
STX-c(16.0962,
Thanks! That solved it. I obviously had done something stupid. I just
redefined my options(digits=7) and they are all there. Sorry for the
silly question, and thanks for the suggestion towards options().
Thanks!
John
David Winsemius wrote:
STX-c(16.0962, 16.1227, 16.0921, 16.1498)
Hello,
please post to the list instead of posting me directly.
I am sorry to say, but I don't really know what you want to do. First
you asked about highly connected nodes, and now about clustering.
Perhaps you could give an example with the input and the expected
output.
Btw, if you know how
You might also look at http://www.portableapps.com for a portable version of
several editors, including gVim, Notepad++ and SciTE which all have some level
of support for R
--
I like nonsense, it wakes up the brain cells. Fantasy is a necessary
ingredient in living, it's a way of looking at
Liaw, == Liaw, Andy andy_l...@merck.com writes:
Are you sure that's dual atoms? AFAIK it has a single Atom
N270 (single core) at 1.6GHz. With hyper-threading, you
may see two cpus.
Yep - that is exactly what is going on.
Mike
__
Is there an easy way to add a thousand separator mark on the axis of a
plot? The best solution I've found so far is the following:
y - seq(0, 10, 1)
plot(y, yaxt = n, ylab = )
axis(2, at = y, labels = formatC(y, big.mark = , format = d), las=2)
But that seems like quite a hassle to do
On Fri, Mar 06, 2009 at 09:46:17AM -, Ted Harding wrote:
On 06-Mar-09 09:25:26, Prof Brian Ripley wrote:
You might want to look into correspondence analysis, which has several
variants of PCA designed for categorical data.
In particular, have a look at the results of
Dear all,
I have a dataset where the interaction is more than obvious, but I was asked
to give a p-value, so I ran a logistic regression using glm. Very funny, in
the outcome the interaction term is NOT significant, although that's
completely counterintuitive. There are 3 variables : spot (binary
chaogai chao...@xs4all.nl [Thu, Mar 05, 2009 at 07:04:19PM CET]:
I'm having similar experiences on my Acer Aspire One. Everything will
work good. Only thing that takes a lot of time is compiling R if you are
in the habit of doing so.
On the Fedora version that came with my Acer Aspire One, I
Hello,
The example shows a sequence of songtypes a bird has sang.
The entire list contains several thousand songs which the bird has produced
consecutively.
Is there any convenient way in R to produce a contingency table which shows how
often a special song type was sang after a special other
Hi all,
I´m fitting GLM´s and I can´t interprete the coefficients when I run a
model with interaction terms.
When I run the simpliest model there is no problem:
Model1-glm (Fishes ~ Year + I(Year^2) + Kind.Geographic +
Kind.Fishers + Zone.2 + Hours + Fishers + Month, family =
?lag
?xtabs
songseq - read.table(textConnection(NrSongtype
1 S1
2 S2
3 S3
4 S1
5 S1
6 S2
7 S4), header=TRUE, stringsAsFactors=FALSE)
songseq$precsong -c(NA,lag(songseq$Songtype)[1:6])
# need to drop last entry
xtabs( ~ precsong + Songtype,
Hi everyone,
Although this question is more related to ChIP and ChIP-seq, it could be
probably anchored in a more general statistical context.
The question is : what method is better to assess the significance of the
change in a signal (the signal can be DNA binding, for instance) given the
Hi list,
I have a real problem with plotting US state map. When I try to plot the
northern state, there will be some blank space in the top of graph (see case
1 example), and when I plot southern states, there will be a blank space in
the bottom of plot (see case 2). I spent almost 2 days to
One thing I notice immediately is a number of NA values for your
coefficients. If I were you, I would try a model with less parameters, and
use the anova() function to compare models, to see if the extra terms really
improve the model.
e.g.
fit1 - glm(Y~X1+X2+X3,...)
fit2 -
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
when I try to run an R command eg, x - rnorm(100,10,5) vim returns this
error:
~/.pipe E212: can't open file for wirting
Hi Andreas,
I'd recommend to use this script instead. It uses screen to
communicate R and vim, it works well.
Waldir Leôncio wrote:
Is there an easy way to add a thousand separator mark on the axis of a
plot? The best solution I've found so far is the following:
y - seq(0, 10, 1)
plot(y, yaxt = n, ylab = )
axis(2, at = y, labels = formatC(y, big.mark = , format = d), las=2)
But that seems
To r-help Forum:
I have downloaded R 2.8.1 and stalled it on my WinXP platform in folder:
C:\Program Files\R\R-2.8.1\bin\R.exe
R has worked properly with my data files and packages, which one call, past.
However, this week I decided to move the data files and packages to
different location:
Hi All,
I'll appreciate your help on this. Do you know of any package that can be
used to solve optimization problems subject to general *non-linear* equality
constraints.
Thanks!
Lars.
[[alternative HTML version deleted]]
__
Hello, I'm switching over from SAS to R and am having trouble merging data
frames. The data frames have several columns with the same name, and each has a
different number of rows. Some of the values are missing from cells with the
same column names in each data frame. I had hoped that when I
Could somebody share some tips on implementing multivariate integration and
partial differentiation in R?
For example, for a trivariate joint distribution (cumulative density function)
of F(x,y,z), how to differentiate with respect to x and get the bivariate
distribution (probability density
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