On Wed, 21 Dec 2011, Keith Jewell wrote:
Thanks Uwe,
I was happy that my 2 lines gave what the OP asked for, albeit in a
different order.
My puzzlement arose from Jeff Newmillers comment:
You could read the help for expand.grid very carefully for the answer to
this question.
... which I
I want to take slices of a multi-dimensional table (or array) without
knowing the number of dimensions in advance.
As a test I tried using (in this example a 3d table):
do.call(`[`, list(tbl, x,NULL,NULL)]
where I built the list on the fly. It works great as long as I only want
Dear All,
It is my first time using this mail list to post a question. And I
sincerely hope that this will not bother any subscribers.
So far as I know, there are functions like union( ), which can help to
combine two sets of discrete data. But what if the data sets are with
continuous data. For
Hi All,
I'm trying to run a conditional logistic regression in R (2.14.0) using
clogit from the survival package. The dataset I have is relatively small
(300 observations) with 25 matched strata- there are roughly 2 controls for
each case, and some strata have multiple case/control groups. When I
here is the dump and the code once again, sorry for creating so much noise.
c1-structure(list(HTN = structure(c(2L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L), .Label = c(, Y), class = factor), HTN_FDR = structure(c(2L,
1L, 1L, 1L, 2L, 1L,
Hello,
I am trying to plot means and standard errors conditioned by a factor, using
qplot. I am successful at getting the bar graph I want with a error bar,
however I have tried many things and cannot get the bars to change colors.
Currently showing as red and blue, but need it to be black and
Sorry. I erred somewhere in making the original M1 matrix using sampling call
in the spMatrix function. I still don't really understand why the matrix
values do not match exactly with M1@x. If I regenerate M1 this way...
i=c(1:5,5:1)
j=c(1:5,2:6)
x=rnorm(10,2)
M1 -
From library(diptest):
Shouldn't the following almost always be non-significant for
Hartigan's dip test?
dip(x = rnorm(1000))
I get dip scores of around 0.0008 which based on p values taken from
the table (at N=1000), using the command: qDiptab, are 0.02 p
0.05.
Anyone familiar with
Hi,
My name is Curtis and I'm a 1st year student in Biochemistry at the
University of Geneva. I need some help completing the code for my NEWTON
ALGORITHM. It is a bonus exercice to our autumn semester maths exam and we
can hand it in or not. Usually people copy and paste but I decided to sit
Dear R users,
I am currently attempting to fit logistic regression models in R, where
the slopes should be restricted to positive values. Although I am aware
I guess non-negative, as in the subject line, so there actually is a
solution.
Indeed, I meant non-negative, zero slopes are also
colnames = c(date,price)
data = read.csv(file=data.csv, sep=,, header=F, nrows=261, skip=5,
col.names=colnames)
library(quantmod)
data
date price
1 2011-12-18 13.7825
2 2011-12-11 13.5500
...
...
...
259 2007-01-07 10.8256
260 2006-12-31 10.8531
261 2006-12-24 10.8169
#
Thanks to mrflick on Freenode, I was able to get chartSeries to plot the data.
data$date-strptime(data$date, format=%Y-%m-%d)
dataxts-xts(data$price, order.by=data$date)
chartSeries(dataxts)
chartSeries(dataxts, type=candlesticks) plots the same graph though:
http://i.imgur.com/P0Jh0.png
Why is
Both
barChart(dataxts,bar.type='hlc')
candleChart(dataxts)
give the same results as well.
On Wed, Dec 21, 2011 at 11:15 PM, Adrian Berg adrian.ber...@gmail.com wrote:
Thanks to mrflick on Freenode, I was able to get chartSeries to plot the data.
data$date-strptime(data$date, format=%Y-%m-%d)
Thanks Bill, the output of dput was very similar to your example, I was not
sure so did not put it on the post. however i uploaded the foo.txt file
which contains the part of the data.
sharad
--
View this message in context:
http://r.789695.n4.nabble.com/Help-with-code-tp4218989p4222947.html
On 21.12.2011 22:43, Curtis Moyo wrote:
Hi,
My name is Curtis and I'm a 1st year student in Biochemistry at the
University of Geneva. I need some help completing the code for my NEWTON
ALGORITHM. It is a bonus exercice to our autumn semester maths exam and we
can hand it in or not. Usually
Hello. I'm using as.ffdf(mydataframe) to create ffdf objects inside an lapply
loop and returning that. I then use crbind to combine the lapply results
into allData.
So...simplified flow looks like this.
res - lapply(1:nchunks, function(n)
{
blah blah with nth chunk
Season's Greetings.
I am using 'predict' in a loop, but it is behaving unexpectedly, so I am more
explicit and use 'predict.loess', and R says it can't find it. Even if I
explicitly load the stats library, which is already in the search path.
Any ideas?
This is odd, because if I use RB LB
On 21.12.2011 18:08, Michael Griffiths wrote:
Dear List,
I have the code below, where I am using the constrained optimisation
package, 'constrOptim.nl' to find the values of two values, b0 and b1.
I have no problems when I enter further variable information DIRECTLY into
the functions, fn,
On 21.12.2011 21:16, rachaelohde wrote:
Hello,
I am trying to plot means and standard errors conditioned by a factor, using
qplot. I am successful at getting the bar graph I want with a error bar,
however I have tried many things and cannot get the bars to change colors.
Currently showing as
On 22.12.2011 07:56, khai wrote:
Hello. I'm using as.ffdf(mydataframe) to create ffdf objects inside an lapply
loop and returning that. I then use crbind to combine the lapply results
into allData.
So...simplified flow looks like this.
res- lapply(1:nchunks, function(n)
{
See methods(predict) and find that methods are hidden in the Namespaces
and are ought to be accessed by the generic. If you really want to
access it explicitly (which i not intended by design), see help(:::)
Your code is not reproducible, hence we cannot help in detail.
Uwe Ligges
On
http://santoencanto.com/next2012.php?did=94cyf=55yp=354i=39
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal,
On 22/12/2011 08:55, Uwe Ligges wrote:
See methods(predict) and find that methods are hidden in the Namespaces
and are ought to be accessed by the generic. If you really want to
access it explicitly (which i not intended by design), see help(:::)
Your code is not reproducible, hence we cannot
Here is a snippet to show what i'm trying to do.
library(randomForest)
library(ROCR)
library(caret)
data(iris)
iris - iris[(iris$Species != setosa),]
fit - randomForest(factor(Species) ~ ., data=iris, ntree=50)
train.predict - predict(fit,iris,type=prob)[,2]
On Thu, Dec 22, 2011 at 4:34 AM, David A Vavra dava...@verizon.net wrote:
I want to take slices of a multi-dimensional table (or array) without
knowing the number of dimensions in advance.
As a test I tried using (in this example a 3d table):
do.call(`[`, list(tbl, x,NULL,NULL)]
Hi,
I have a list called spec in which a variable foundOK indicates whether or
not the given element contains data and must be processed. I have to split the
list and process only the good elements, and do something different later on
with the bad elements. The code below works. However, is
I'm manually doing a form of stepwise regression in a mixed model but with
many variables, it is time consuming. I thought I'd try to use an automated
approach. stepAIC gave me false convergence when I used it with my model,
so I thought it can't be hard to set up a basic program to do it based
delongman wrote
Hi,
My name is Curtis and I'm a 1st year student in Biochemistry at the
University of Geneva. I need some help completing the code for my NEWTON
ALGORITHM. It is a bonus exercice to our autumn semester maths exam and we
can hand it in or not. Usually people copy and paste
The byte pixies have rolled up R-2.14.1.tar.gz (codename December Snowflakes)
at 9:00 this morning. This is a maintenance release; see the list below for
details.
You can get it from
http://cran.r-project.org/src/base/R-2/R-2.14.1.tar.gz
or wait for it to be mirrored at a CRAN site nearer to
I have the following data as input, from which I would like to make a lattice
levelplot:
-
x y level
1 m3134 m3134 1.000
2 m3134 m416B 0.4189057
3 m416B m3134 0.2696508
4 m3134 mA20 0.3322170
5 mA20 m3134 0.2454191
6 m3134mB 0.3176792
...
Berend Hasselman wrote
.
g - function(x){
out - (2/(3))*exp(x^2)-(20)*log(x)
return(out)
}
gp - function(x) {
out - (4/3)*exp(x) - 20/x
return(out)
}
function gp is incorrect. It should be
gp - function(x) {
out - (4/3)*x*exp(x^2) - 20/x
Pablo pschatfield at gmail.com writes:
I'm manually doing a form of stepwise regression in a mixed model but with
many variables, it is time consuming. I thought I'd try to use an automated
approach. stepAIC gave me false convergence when I used it with my model,
so I thought it can't be
Stepwise regression without proper penalization is invalid.
Frank
Pablo wrote
I'm manually doing a form of stepwise regression in a mixed model but with
many variables, it is time consuming. I thought I'd try to use an
automated approach. stepAIC gave me false convergence when I used it
I'm trying to make a set of contour plots of bivariate kernel density
estimates, showing three such plots overlaid,
similar to this plot
http://euclid.psych.yorku.ca/SCS/Private/Test/ridge-boot2.pdf
except that I would like to have the contours *filled* (using
transparent colors). To make
On Dec 21, 2011, at 10:34 PM, David A Vavra wrote:
I want to take slices of a multi-dimensional table (or array) without
knowing the number of dimensions in advance.
As a test I tried using (in this example a 3d table):
do.call(`[`, list(tbl, x,NULL,NULL)]
Surely that was meant to be:
I'm working on a logistic regression in R with the car package but keep
getting the following error message.
It's only and warning and not an error, but I'm just not sure how to
resolve the issues.
glm.fit: algorithm did not converge
glm.fit: fitted probabilities numerically 0 or 1 occurred
d1
Hi,
I'm trying to call some of R's statistical functions within my C++
code, developed under VS2005, but I can't seem to find out how to do
it. I tried RInside and Rcpp, but they either don't work on Windows or
with VS. Is there a way to do this?
Appreciate the help.
Regards,
Dear All,
I am trying to finding overlapping regions in two diff datasets for that I
am using IRanges. But I am getting an error in the process of doing the
overlap. Advance thanks
df3.rl-RangedData(IRanges(start=df3$V3,width=1),
+ space=df3$start)
Error in .normargSEW0(start, start) :
'start'
Hi Tal,
Thank you very much! I ran your codes in the example session, but if you see
the output by the codes of wdTable(format(head(mtcars))) and
wdTable(head(mtcars)) in the word file, the two tables have the same kind
of problems. If you drag the bottom line of the first row down to make the
谢一鸣 cutexym at gmail.com writes:
Dear All,
It is my first time using this mail list to post a question. And I
sincerely hope that this will not bother any subscribers.
So far as I know, there are functions like union( ), which can help to
combine two sets of discrete data. But what if the
I believe (unchecked) that you need OHLC data for candlesticks. You can use
to.TTT functions to make some from your daily data.
Michael
On Dec 21, 2011, at 11:52 PM, Adrian Berg adrian.ber...@gmail.com wrote:
Both
barChart(dataxts,bar.type='hlc')
candleChart(dataxts)
give the same results
On 22 December 2011 at 15:25, Jawad Elomari wrote:
| I'm trying to call some of R's statistical functions within my C++
| code, developed under VS2005, but I can't seem to find out how to do
i) As has been stated fairly frequently, R itself does not build under
VS* making the linking of C
I use windows xp. When trying to use the function mtrace from package debug
the window that should open with the function to be debugged do not show
any text at all. It shows only a part of my desktop. Does anyone know why.
Is there any imcompatibility between windows xp and debug package.
Thanks
* peter dalgaard cqn...@tznvy.pbz [2011-12-21 23:59:18 +0100]:
On Dec 21, 2011, at 23:10 , Sam Steingold wrote:
When qqnorm on a vector of length 10M+ I get a huge pdf file which
cannot be loaded by acroread or evince.
Any suggestions? (apart from sampling the data).
Sample intelligently?
On 12/22/2011 05:50 AM, Naveen Thota wrote:
Dear All,
I am trying to finding overlapping regions in two diff datasets for that I
am using IRanges. But I am getting an error in the process of doing the
overlap. Advance thanks
df3.rl-RangedData(IRanges(start=df3$V3,width=1),
+ space=df3$start)
--- begin included message ---
I'm trying to run a conditional logistic regression in R (2.14.0) using
clogit from the survival package. The dataset I have is relatively small
(300 observations) with 25 matched strata- there are roughly 2 controls
for
each case, and some strata have multiple
(This does imply you knew the number of dimensions was 3.)
Yes, at run time.
It looks as though the Nulls became 0's. So if you wanted to use
do.call(`[` then this succeeds:
do.call(`[`, list(tbl, x, 1:dim(tbl)[2], 1:dim(tbl)[3]) )
...
As does this using the empty comma approach:
On Dec 22, 2011, at 18:17 , Sam Steingold wrote:
* peter dalgaard cqn...@tznvy.pbz [2011-12-21 23:59:18 +0100]:
On Dec 21, 2011, at 23:10 , Sam Steingold wrote:
When qqnorm on a vector of length 10M+ I get a huge pdf file which
cannot be loaded by acroread or evince.
Any suggestions? (apart
I ran three logit models in R with the Zelig package and I'm trying to
compute the
predicted probabilities for a number of different values on the independent
variable.
My dep variable was accepted or decline and my indep variable is bid
amount, and varies.
So for a bid amount of 3, what's the
I am trying to use the dmt function in the package {mnormt}. Throughout my
algorithm, the covariance matrix is sometime calculated to be singular.
When attempting to calculate the dmt function with a covariance that is not
positive definite, I would like it to return Inf or NaN instead of an
I just realized that mwin had three levels.
I went ahead and deleted one of them.
summary(mwin)
table(mwin)
mwin = factor(mwin)
levels(mwin)
mwin = mwin
mwin[mwin %in% levels(mwin)[1]] - NA
mwin = factor(mwin)
levels(mwin)
mwin = factor(mwin, levels=c(DECLINED,ACCEPTED))
On Thu, Dec 22, 2011
Hi Thomas,
Using box-constrained optimizer in glm.fit is a good suggestion for finding the
point estimates. However, there is still the issue of making inference, i.e.,
computing the variances and p-values for the estimates. You have to deal with
the issue of MLE possibly being on the
Something like the following may be what you are looking for.
try.out - try(dmt(y[,j],new$mu[,,4],sigij,ceiling(new$nu[4])),silent=TRUE)
if (class(try.out) == 'try-error'} ) {
out - NaN
} else { out - try.out
}
-Don
--
Don MacQueen
Lawrence Livermore National Laboratory
7000 East Ave.,
Em 21/12/2011 11:22, Uwe Ligges escreveu:
On 21.12.2011 14:25, David Winsemius wrote:
There are no restrictions needed. Any of your staff can view the (open)
source code just as any other member of the human race
I do not think the GPL excludes other species ...
Since the null hypothesis
From help([, package=base): An index value of NULL is treated as
if it were integer(0)..
Yeah, I should have read it better.
I don't think there is an easy way to achieve:
y[,2:3,1,drop=FALSE]
using do.call([) without explicitly specify the indices for that
missing dimension, i.e.
...
Hi Joann,
I am not sure I followed you.
My suggestion for you is actually to ask about this here:
http://superuser.com/
Cheers,
Tal
Contact
Details:---
Contact me: tal.gal...@gmail.com | 972-52-7275845
Read me:
I am trying to rename column names in a dataframe within a function. I am
seeing an error (listed below) that I don't understand.
Would be grateful of an explanation of what I am doing wrong and how I
should rewrite the function to allow me to be able to rename my variables.
Thanks.
# Test
Continuing the annnoying tradition of partial quotes:
I don't think there is an easy way to achieve:
y[,2:3,1,drop=FALSE]
, , c1
b2 b3
a1 3 5
a2 4 6
using do.call([) without explicitly specify the indices for that
missing dimension, i.e.
Why do you want to create a variable within the function since it will
disappear after the return. Is there a reason for that? Here is one
way of getting the names by just using them on the cbind.
Also you are create a 'matrix' and 'names' is not appropriate for that
type of object.
# Test
Sam Steingold s...@gnu.org writes:
Hi,
When qqnorm on a vector of length 10M+ I get a huge pdf file which
cannot be loaded by acroread or evince.
Any suggestions? (apart from sampling the data).
Thanks.
Following the other suggestions, I did not notice mention of another
trick for slimming
Chuck:
A bad idea, I think: Rounding to unique values loses data density,
while sampling preserves it (to display resolution -- also a form of
rounding).
-- Bert
On Thu, Dec 22, 2011 at 11:10 AM, cbe...@tajo.ucsd.edu wrote:
Sam Steingold s...@gnu.org writes:
Hi,
When qqnorm on a vector of
On 21/12/2011 3:37 PM, kbrownk wrote:
From library(diptest):
Shouldn't the following almost always be non-significant for
Hartigan's dip test?
dip(x = rnorm(1000))
Well, it should be non-significant about 95% of the time
I get dip scores of around 0.0008 which based on p values taken from
From: William Dunlap [mailto:wdun...@tibco.com]
You can build the 2nd argument to do.call with alist() instead.
alist() produces a list that you can use c() and subscripting on
to add or modify arguments. It is usually better to encapsulate
this sort of thing in a function like extract() that
The error is because you are trying to assign to the result of a get call, and
nobody has programmed that (hence could not find function) because it is
mostly (if not completely) meaningless to do so.
It is not completely clear what you want to accomplish, but there is probably a
better way to
When I use the image() function for a relatively small matrix it works
perfectly, eg.x - 1:100
z - matrix(rnorm(10^4),10^2,10^2)
image(x=x,y=x,z=z,col=rainbow(3))but when I want to plot a larger matrix, it
doesn't really work. Most of the times, it just plot a few intermitent
points.x -
Hello all,
I have a brief IRT related question regarding the ltm package.
I am am using tpm which is part of the ltm package. I am constraining the
item parameters for this package since they have been estimated earlier. I
notice that the difficulty parameter changes, despite the fact that it is
Have made a stacked area plot, but now want to manipulate the x axis: make in
even increments (50) in order to suppress the tick marks (forming solid bar
under plot). However, the plot functions do not seem to work, and I cannot find
documentation for use of xat in stackpoly.
This is a time
Thanks, I found dip.test after posting. I reread the original paper
and found that the probability is that the dip is less than the given
dip score. Less here is ambiguous to me, and it is strange that
dip.test interpolates from the same p value lookup table I was using
(gDiptab), but returns very
Bert Gunter gunter.ber...@gene.com writes:
Chuck:
A bad idea, I think: Rounding to unique values loses data density,
while sampling preserves it (to display resolution -- also a form of
rounding).
Bert,
The subject is qqnorm huge datasets.
Downsampling for qqplots produces unreliable
Hello
Would anyone be able to direct me to information on how to perform a
straightforward Principal Components Analysis in r? Including the data file
set-up?
I'm rather new to r and not having much luck.
I'm pretty certain I have the data entered into the txt file properly but when
I try
I am trying to get mdots^-1 in a x-axis label for a publication ready
graph. I can get ms^-1 with no problem, but I can't get the symbol for
the dot to work. I am have tried the following:
plot(x,y,xlab=expression(paste(Target Velocity
(,ms^-1,))),ylab=Passage Probability,ylim=c(0,1))
which
Hello all:
I'm sure this is quite simple, but I tried several options and I still can't
get I right.
I've got a data.frame and I want to delete all columns of which the sum is
zero.
Any ideas? Thanks,
Frederico Mestre
[[alternative HTML version deleted]]
You'll get more useful answers if you tell us what you did, and provide a
reproducible example.
For instance, a bit of your data using dput(), your sessionInfo(), str() for
your data, and the actual commands you're using to run PCA, as well
as the error messages you're getting.
The clearer you
I'd like to convert a dist into a table/matrix/thingy of the form:
A B value
A C value
B C value
(assuming the dist was over 3 names).
Is there a way to do this without using a for loop?
--
Taral tar...@gmail.com
Please let me know if there's any further trouble I can give you.
-- Unknown
Hi,
I am trying to work with the output of the MINE analysis routine found at
http://www.exploredata.net
Specifically, I am trying to read the results into a matrix (ideally an
n x n x 6 matrix, but I'll settle right now for getting one column into
a matrix.)
The problem I have is not
Hi,
On Thu, Dec 22, 2011 at 4:54 PM, Frederico Mestre
mestre.freder...@gmail.com wrote:
Hello all:
I'm sure this is quite simple, but I tried several options and I still can't
get I right.
I've got a data.frame and I want to delete all columns of which the sum is
zero.
If this, then
I'm not at all sure what you mean with your matrix: is that supposed to
be three columns? What about:
fakedata - data.frame(X=runif(3), Y = runif(3))
rownames(fakedata) - c(A, B, C)
dist(fakedata)
A B
B 0.8617733
C 0.3813032 0.5124284
data.frame(t(combn(rownames(fakedata),
On Dec 22, 2011, at 4:16 PM, tamre wrote:
I am trying to get mdots^-1 in a x-axis label for a publication
ready
graph. I can get ms^-1 with no problem, but I can't get the symbol
for
the dot to work. I am have tried the following:
plot(x,y,xlab=expression(paste(Target Velocity
Tena koe Frederico
Something like
yourDF[, apply(yourDF, 2, sum)!=0]
HTH
Peter Alspach
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Frederico Mestre
Sent: Friday, 23 December 2011 10:55 a.m.
To: r-help@r-project.org
Dear Frederico,
Try
d[, rowSums(d) != 0]
where d is your data.frame().
HTH,
Jorge.-
On Thu, Dec 22, 2011 at 4:54 PM, Frederico Mestre wrote:
Hello all:
I'm sure this is quite simple, but I tried several options and I still
can't
get I right.
I've got a data.frame and I want to
Sorry for the noise, it should have been colSums(d) instead of what I
wrote. My apologies.
HTH,
Jorge.-
On Thu, Dec 22, 2011 at 10:43 PM, Jorge I Velez wrote:
Dear Frederico,
Try
d[, rowSums(d) != 0]
where d is your data.frame().
HTH,
Jorge.-
On Thu, Dec 22, 2011 at 4:54 PM,
On 20/12/11 10:24, Michael Fuller wrote:
TOPIC
My question regards the philosophy behind how R implements corrections to
chi-square statistical tests. At least in recent versions (I'm using 2.13.1
(2011-07-08) on OSX 10.6.8.), the chisq.test function applies the Yates
continuity correction
hi
How to get p-values for lmer funtion other than pvals.fnc(), since it takes
long time for execution
-
Thanks in Advance
Arun
--
View this message in context:
http://r.789695.n4.nabble.com/p-values-in-lmer-tp4227434p4227434.html
Sent from the R help mailing list archive at
On Dec 22, 2011, at 11:13 PM, arunkumar wrote:
hi
How to get p-values for lmer funtion other than pvals.fnc(), since
it takes
long time for execution
http://psy-ed.wikidot.com/glmm
http://glmm.wikidot.com/faq
--
David Winsemius, MD
West Hartford, CT
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