It helps. But it is overly sophisticated.
I have already downloaded and used the Excel file containing the validated
stuff.
Since there are R commands to download gzip as well as FASTA files, I wonder
whether it is possible to
automatically download the Excel file from
Thank you Mr. Lumley and Mr. Greg. That was helpful.
Regards
Utkarsh
Thomas Lumley wrote:
On Fri, 3 Jul 2009, utkarshsinghal wrote:
Hi Sir,
Thanks for making package available to us. I am facing few problems
if you can give some hints:
Problem-1:
The model summary and residual
R Help:
When I look at the object S, I see about half of them are
zeroes.
I've address the object S being zero so often by changing the value of
alpha, which I'm allowed to do according to the author. All values of S are
non zero and should not give Inf.
The expectation of a binomial model
Thanks for your reply! This is what I was looking for!
I'm using
nas1 - apply(data_matrix,1,function(x)sum(is.na(x))/nrow(data_matrix))
nas2 - apply(data_matrix,2,function(x)sum(is.na(x))/ncol(data_matrix))
The thing about significantly more isn't really a helpful as I look at the
data now.
I
On Mon, Jul 6, 2009 at 12:12 AM, nykn...@nyk.ch wrote:
Thanks for your reply! This is what I was looking for!
I'm using
nas1 - apply(data_matrix,1,function(x)sum(is.na(x))/nrow(data_matrix))
nas2 - apply(data_matrix,2,function(x)sum(is.na(x))/ncol(data_matrix))
You can simplify this a
Hi R-users,
I have a data from multi skew t and would like to transform each of the data
to uniform data. I tried using 'pmst' but only got one output:
rr1 - as.vector(r1);rr1
[1] 0.7207582 5.2250906 1.7422237 0.5677233 0.7473555 -0.6020626
-2.1947872 -1.1128313 -0.6587316 -1.1409261
Thanks a lot, this works! The one I used before was wrong:
data_matrix
[,1] [,2] [,3] [,4] [,5]
[1,]11 NA11
[2,]22222
[3,]33333
[4,] NA NA NA NA NA
[5,]55555
[6,] NA66 NA6
[7,] NA NA
Dear R users,
I included 2 internal functions in the package 'dlnm', called 'mkbasis' and
'mklagbasis'.
Despite they are not meant to be called by the users, I included them in the
namespace in order to make them available, keeping the process more transparent
and giving the opportunity to
Hi. As I said in my first email, converting your data into a long
format makes a lot of sense. I'm sorry that you find it hard ... to
understand why this would make plotting easier.
Wide format:
Subject ID, Experiment ID, humidity, light, whatever, T1, T2,T3,T4.
is much better rotated to be
Hi Everyone,
Thank you for all your comments and suggestions.
I determined that I had a full rank model matrix by using the code:
qr(covaeb)$rank
This is 17 which is equal to the number of covariates in the matrix, covaeb.
I cannot invert the model matrix using 'solve' as my matrix is not
If the question is to how download and read into R an Excel file at
a known location into an R data frame then try this:
library(gdata)
URL - http://mirecords.umn.edu/miRecords/download_data.php?v=1;
DF - read.xls(URL)
See ?read.xls for more info.
On Mon, Jul 6, 2009 at 2:27 AM, mau...@alice.it
Laura Bonnett wrote:
Hi Everyone,
Thank you for all your comments and suggestions.
I determined that I had a full rank model matrix by using the code:
qr(covaeb)$rank
This is 17 which is equal to the number of covariates in the matrix, covaeb.
I cannot invert the model matrix using
Dear all,
I am doing my first steps with odfWeave.
After running the r code (see below), I am trying to open the ODF-document
with open office, but I am getting the error message:
The file is damaged, but it can be repaired. If I confirm the question and
repair the file with open office, I can
Dear all,
I am doing my first steps with odfWeave.
After running the r code (see below), I am trying to open the ODF-document
with open office, but I am getting the error message:
The file is damaged, but it can be repaired. If I confirm the question and
repair the file with open office, I can
Hi,
I just got a value for the dip test out of my data of 0.074 for a sample
size of 33. I'm trying to work out what this actually means though?
Could someone help me relate this to a p-value?
Thanks
James
__
R-help@r-project.org mailing list
On 06-Jul-09 12:39:29, James Allsopp wrote:
Hi,
I just got a value for the dip test out of my data of 0.074 for a
sample size of 33. I'm trying to work out what this actually means
though?
Could someone help me relate this to a p-value?
Thanks
James
Have a look at
I'll appreciate the help on the following problem:
I solved many Nonlinear programming problems with nonlinear
constraintsRdonlp is working well but i am unable to get INTEGER data
with nonlinear constraints in Rdonlp. Is it possible to get Integer Values
of parameters in any package of R
James,
I assume that you use package diptest.
Look up
?qDiptab
for a table of quantiles from which you can obtain your p-value.
data(qDiptab)
qDiptab
You then look up your statistic value (0.074) for a suitable n
(n=30, say), and you take one minus the Pr value you find on top of the
table.
On Jul 5, 2009, at 5:15 PM, sjkimble wrote:
R Help:
When I look at the object S, I see about half of them are
zeroes.
I've address the object S being zero so often by changing the value of
alpha, which I'm allowed to do according to the author. All values
of S are
non zero and should
On Jul 5, 2009, at 5:15 PM, sjkimble wrote:
R Help:
When I look at the object S, I see about half of them are
zeroes.
I've address the object S being zero so often by changing the value of
alpha, which I'm allowed to do according to the author. All values
of S are
non zero and should
Hi,
I would like to solve the following equation with R: Cov(A,x)=0.
A is a given matrix, x is the an unknown vector.
Is there any nice solution for this?
Thank you for your help.
Best wishes,
Luba Stein
[[alternative HTML version deleted]]
instrument.input[,6] appears to be a vector of factors. You are putting the
underlying factor number into data. Assuming instrument.input[,6] is supposed
to be numeric you will need to convert from factor.
See the FAQ Part 7 R Miscellanea How do I convert factors to numeric?
for that.
---
WinXP, R-2.9.1
Thanks to Don for the suggestion and especially to Phil for the perfect
and elegant solution! It shows that R is a piece of miracle, when in the
hands of those who really know how to work it.
Since my originally request turned out to be easy to solve, let me move
one step back in
Hi,
Are you looking for variable selection? If this is the case than you
can use LASSO, Elastic net, Sparse PLS regression methods which encourages
variable selection. PCA does not select variables as you get all your
variables in the PCs. You can sparse PCA.
Regards
Alex
On Wed, Jun 24,
It appears to me that you really have no idea what the original author
was doing. I honestly don't either. I never used the sweep operator
and I don't know what his S's represent. I do understand what
offsets represent in the context of glm(), and this set of operations
does not fit my
Hi Laura,
I do think that the problem occurs during the iterations of the Newton's method
for solving the estimating equations in the Fine Gray model. One way to
overcome this would be to use the generalized inverse in the Newton algorithm.
But this would yield non-unique, possibly large,
The AIC of the biglm models is highly dependent on the size of chunks
selected (example provided below). This I can somehow expect because the
model error will increase with the number of chunks.
It will be helpful if you can provide your opinion for comparing
different models in such cases:
I have 2 matrices. One which contains a complete set of row combinations.
Another which contains a subset of the first. What I would like to extract
is the rows which are in the first but not repeated in the second. For
instance if the following were my two matrices,
A
[,1] [,2] [,3] [,4]
Hello dear R-users,
today I have a question that I completely do not know how to solve (R-newbie!).
In a temperature chamber I have measured temperature over time. The result is
shown in the attached eps-file (if attachments are shown): There are two
temperature levels, 150°C and -40°C. A
Thanks again for all the help, now I was able to write the function I need:
namax - function(m,mp) {
# arguments: matrix, maximum percentage of NA values allowed in rows/colums
c1 - 0
c2 - 0
repeat {
nas1 - rowMeans(is.na(m))
nas2 -
Rahul Varshney itsrahulvarshney at gmail.com writes:
I'll appreciate the help on the following problem:
I solved many Nonlinear programming problems with nonlinear
constraintsRdonlp is working well but i am unable to get INTEGER data
with nonlinear constraints in Rdonlp. Is it
Dear McLeod,
I am a PhD student working with the Kendall package in R. I used
this package to make the so-called TauKr matrix correlation analysis
(Hemelrijk, 1990). However, lately I've been getting this warning:
Error exit, tauk2. IFAULT = 12. From the forums I've been looking
into, I
Hi,
We are seeing performance degradation when running the same R script in
multiple instances of R on a multi-processor system. We are a bit surprised
by this because we figured that each instance of R is running in its own
processor, and therefore running a second, third or fourth instance
Hello,
I have written a function in order to analyse gaze paths. It works with the test data but when I try to apply the function to a data frame that stores the real data in columns I receive the error message that the
In if (pp 1) { :
condition has length 1 only the first element will
Hi R Users,
Hopefully a very simple solution, but I am stumped nevertheless. I am
running glmer in which the output is too large so that not all the
correlations are displayed. I expanded the max.print as recommended on this
website. However, this still does not allow me to see the relevant
The below seems like a Fortunes candidate to me.
-- Bert Gunter
Genentech Nonclinical Biostatistics
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Greg Snow
Sent: Friday, July 03, 2009 7:00 PM
To: Kurt Smith; r-help@r-project.org
Hi Mark,
Don't be the least bit sorry that I'm finding any of this hard to
understand. That's my problem. I ordered the Phil Spektor's Data
Manipulation with R (Use R) book last night as I realize I need to go
through some sort of training. Hopefully that will help clear up some
of my questions
I have written a function in order to analyse gaze paths. It works
with the test data but when I try to apply the function to a data
frame that stores the real data in columns I receive the error
message that the
In if (pp 1) { :
condition has length 1 only the first element will
Use 'sink' or 'capture.output' to put the output to a text file that
might be easier to view. You did not indicate what OS you are using
or what interface that appears to be limiting what you are seeing.
On Mon, Jul 6, 2009 at 11:34 AM, Christine
Griffithschristine.griffi...@bristol.ac.uk wrote:
Is it possible to have the dendrogram created by heapmap.2 and as.dendrogram
in the same ordering for the same data? Or will there always be a randomly
different ordering of the equivalent clusters?
--
View this message in context:
On Jul 6, 2009, at 11:34 AM, Christine Griffiths wrote:
Hi R Users,
Hopefully a very simple solution, but I am stumped nevertheless. I
am running glmer in which the output is too large so that not all
the correlations are displayed.
Details? Code?
Guess: I have on more than one
You can count the number of times the values make a transition through
some threshold and average over some short time period because you
probably get multiple transitions in a short time as it is approaching
the threshold. Once you have that, you can count then number of times
it happens.
On
Here is one way of doing it:
set.seed(1)
a - matrix(sample(1:2, 10, TRUE), ncol=2)
b - matrix(sample(1:2, 4, TRUE), ncol=2)
a
[,1] [,2]
[1,]12
[2,]12
[3,]22
[4,]22
[5,]11
b
[,1] [,2]
[1,]12
[2,]11
# create a vector of values
Try this:
subset(merge(as.data.frame(A),
cbind(as.data.frame(B), ID=1), all = T), is.na(ID), select = -ID)
On Mon, Jul 6, 2009 at 8:39 AM, dreamworx andy_wools...@hotmail.com wrote:
I have 2 matrices. One which contains a complete set of row combinations.
Another which contains a
Good day,
Using R-project version 2.9.0 and the latest version of package fGarch you
can extract fitted values by the following commands:
fit - garchFit(~ garch(1,1), residuals_TASI, trace = TRUE, include.mean =
FALSE)
fitted_TASI - f...@fitted
Murilo Eiji Doi
Mohammad Sabr wrote:
Good
Hi,
In the examples from the ReShape package there is a simple example
of using melt followed by cast that produces a smallish amount of
output about the chicks database. Here's the code:
library(reshape)
names(ChickWeight) - tolower(names(ChickWeight))
chick_m - melt(ChickWeight, id=2:4,
Try this:
diet.s - subset(DietResults, diet == 1)
matplot(diet.s[,-(1:2)],
type='l',
col = ifelse(as.numeric(as.character(diet.s$chick)) %% 2, 'red',
'green'))
On Mon, Jul 6, 2009 at 3:22 PM, Mark Knecht markkne...@gmail.com wrote:
Hi,
In the examples from the ReShape
Take a look at the print method for the mer class, class?mer. I believe
setting the correlation argument to FALSE will give you what you want.
See the examples.
Mark Lyman, Statistician
Engineering Systems Integration, ATK
Hi R Users,
Hopefully a very simple solution, but I am stumped
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of mau...@alice.it
Sent: Sunday, July 05, 2009 11:28 PM
To: Martin Morgan
Cc: r-h...@stat.math.ethz.ch
Subject: [R] R: R: Is there a way to extract some fields data
from HTML
Wow Henrique! Close in only 2 lines. Very, very cool.
There seem to be a couple of problems:
1) It seems that none of the chicks are showing up at X=0 on my plot
even though they all have data in column 0.
2) For chicks with NA's it appears that matplot continues their line
to the right. Is
I am clearly doing something extremely stupid here but why is this code not
writing the axis values for this graph?
Any suggestions gratefully received.
structure(list(year = c(1911L, 1921L, 1931L, 1941L, 1951L, 1961L,
1971L, 1981L, 1991L, 2001L, 2006L), total = c(7206643L, 8788483L,
On Mon, Jul 6, 2009 at 8:22 PM, Mark Knechtmarkkne...@gmail.com wrote:
Hi,
In the examples from the ReShape package there is a simple example
of using melt followed by cast that produces a smallish amount of
output about the chicks database. Here's the code:
library(reshape)
I think the offered solution was reading values down the columns
rather than keeping the row values together. I think you need to a)
supply a proper x and b) transpose:
matplot(x = as.numeric(names(diet.s)[3:14]), y= t(diet.s[,-(1:2)]),
type='l', xlab=Days ???, ylab=Weights in (..)
Initializing like this is generally recommended only when the object
sizes get very big. Otherwise it's ok to grow your object as you go
(i.e., append to it on each iteration).
When I want to initialize a list, I do this:
array - list()
length(array) - n
## then,
for (i in 1:n) {
Please show the error message.
At 12:13 PM -0700 7/6/09, John Kane wrote:
I am clearly doing something extremely stupid here but why is this
code not writing the axis values for this graph?
Any suggestions gratefully received.
structure(list(year = c(1911L, 1921L, 1931L, 1941L, 1951L, 1961L,
After your plot command, type
par()$usr
It will show you that your x axis range is 1907 to 2009. But you
tried to put the axis labels at x=1 to 11, which are not within the
range of the data.
-Don
At 12:13 PM -0700 7/6/09, John Kane wrote:
I am clearly doing something extremely stupid
Hello Everyone,
We have recently purchased a server which has 64GB of memory running
a 64bit OS and I have compiled R from source with the following config
./configure --prefix=/usr/local/R-2.9.1 --enable-Rshlib
--enable-BLAS-shlib --enable-shared --with-readline --with-iconv
--with-x
Are you sure that you are fitting all the models on the same total data? A
first glance looks like you may be including more data in some of the chunk
sizes, or be producing an error that update does not know how to deal with.
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Of course. I actually tried that but apparently messed it up.
My thanks to eveyone. I knew it was something relatively obvious but I was
completely blanking out on it.
--- On Mon, 7/6/09, Don MacQueen m...@llnl.gov wrote:
From: Don MacQueen m...@llnl.gov
Subject: Re: [R] drawing an axis
Dear R-users,
Recently, I am facing some problems when converting mlbench data into matrix
format.
library(mlbench)
data(BostonHousing)
X- BostonHousing[,1:13]
y-BostonHousing[,14]
I want to convert X and y into matrix form. I am getting these obvious
errors...
t(X)%*%y
Error in t(X) %*% y :
You could probably just make a big array and watch top usage -- a 5gb
array would do the trick -- if you can break 4gb you are golden.
big_vector=c(1:100) and keep adding zeroes...
--j
Scott Zentz wrote:
Hello Everyone,
We have recently purchased a server which has 64GB of memory
Dear R experts,
I was just wondering why R is not picking up the order that I am putting in.
Total ordering is the first argument of the sinDAG function from the package
'SIN'.
Description of sinDAG
This function computes the matrix of simultaneous p-values for SIN model
selection for acyclic
On Jul 6, 2009, at 4:42 PM, Jonathan Greenberg wrote:
You could probably just make a big array and watch top usage -- a
5gb array would do the trick -- if you can break 4gb you are golden.
big_vector=c(1:100) and keep adding zeroes...
Except the maximum size for a vector (and I wonder
If the structure is your xx variable, then you are creating a plot that goes
from 1911 to 2006 (plus a little to either side), then asking the axis function
to draw and label an axis from 1 to 11, which is very far off the plotting
device to the left. Try giving the axis function a list of
On 7/6/2009 3:52 PM, Scott Zentz wrote:
Hello Everyone,
We have recently purchased a server which has 64GB of memory running
a 64bit OS and I have compiled R from source with the following config
./configure --prefix=/usr/local/R-2.9.1 --enable-Rshlib
--enable-BLAS-shlib --enable-shared
Scott Zentz wrote:
Hello Everyone,
We have recently purchased a server which has 64GB of memory running
a 64bit OS and I have compiled R from source with the following config
./configure --prefix=/usr/local/R-2.9.1 --enable-Rshlib
--enable-BLAS-shlib --enable-shared --with-readline
I am using splint to perform cubic spline interpolation,
but I don't know how this function set up knots?
Does anyone know about this?
Thanks,
jlf
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
Hello,
I'd like to know how R does calculate each component in the decompose()
function?
More precisely, how is calculated the final trend component in this
function?
Thanks for your answer
Myriam
--
View this message in context:
On Jul 6, 2009, at 3:16 PM, spime wrote:
Dear R-users,
Recently, I am facing some problems when converting mlbench data
into matrix
format.
library(mlbench)
data(BostonHousing)
X- BostonHousing[,1:13]
If you look at X with str(), you will see it has a factor variable.
On 7/07/2009, at 2:15 AM, Stein, Luba (AIM SE) wrote:
Hi,
I would like to solve the following equation with R: Cov(A,x)=0.
A is a given matrix, x is the an unknown vector.
Is there any nice solution for this?
What on earth do you mean by ``Cov(A,x)''? This makes no sense
at all.
On Jul 6, 2009, at 5:01 PM, David Winsemius wrote:
On Jul 6, 2009, at 4:42 PM, Jonathan Greenberg wrote:
You could probably just make a big array and watch top usage -- a
5gb array would do the trick -- if you can break 4gb you are golden.
big_vector=c(1:100) and keep adding zeroes...
On Mon, Jul 6, 2009 at 12:37 PM, David Winsemiusdwinsem...@comcast.net wrote:
I think the offered solution was reading values down the columns rather than
keeping the row values together. I think you need to a) supply a proper x
and b) transpose:
matplot(x = as.numeric(names(diet.s)[3:14]),
On Mon, Jul 6, 2009 at 12:28 PM, hadley wickhamh.wick...@gmail.com wrote:
On Mon, Jul 6, 2009 at 8:22 PM, Mark Knechtmarkkne...@gmail.com wrote:
Hi,
In the examples from the ReShape package there is a simple example
of using melt followed by cast that produces a smallish amount of
output
check Memory in R:
?Memory
--- On Mon, 7/6/09, Scott Zentz ze...@email.unc.edu wrote:
From: Scott Zentz ze...@email.unc.edu
Subject: [R] Testing memory limits in R??
To: r-help@r-project.org
Date: Monday, July 6, 2009, 3:52 PM
Hello Everyone,
We have recently purchased a server which has
On Mon, Jul 6, 2009 at 2:45 PM, Mark Knechtmarkkne...@gmail.com wrote:
SNIP
1) I think it's displaying all the chicks, not just the chicks on diet
1. I presume that this is because you chose group=chick from chick_m
but when I went to the qplot help page I didn't find group documented.
Is
On 06/07/2009 4:16 PM, Peter Dalgaard wrote:
Scott Zentz wrote:
Hello Everyone,
We have recently purchased a server which has 64GB of memory running
a 64bit OS and I have compiled R from source with the following config
./configure --prefix=/usr/local/R-2.9.1 --enable-Rshlib
On Jul 6, 2009, at 8:39 PM, Duncan Murdoch wrote:
On 06/07/2009 4:16 PM, Peter Dalgaard wrote:
Scott Zentz wrote:
Hello Everyone,
We have recently purchased a server which has 64GB of memory
running a 64bit OS and I have compiled R from source with the
following config
./configure
Hi Christine,
How about try again?
Cheers
milton
On Mon, Jul 6, 2009 at 11:34 AM, Christine Griffiths
christine.griffi...@bristol.ac.uk wrote:
Hi R Users,
Hopefully a very simple solution, but I am stumped nevertheless. I am
running glmer in which the output is too large so that not
On Jul 6, 2009, at 9:39 PM, Duncan Murdoch wrote:
On 06/07/2009 4:16 PM, Peter Dalgaard wrote:
Scott Zentz wrote:
Hello Everyone,
We have recently purchased a server which has 64GB of memory
running a 64bit OS and I have compiled R from source with the
following config
./configure
79 matches
Mail list logo
