I am working on a gene expression microarray dataset, each sample has been
taking from animal A and animal B on the same type of microarray.
I would like to take the mean of these columns and create a dataset with
columns with data which are means of the corresponding rows of A and B
For
Hi All,
I am using canonical correspondence analysis to compare a community
composition matrix to a matrix of sample spatial relationships and
environmental variables. In order to parse out how much variance is
explained purely by space (S/E) or the environment (E/S) I am using a
conditional
On Mar 26, 2013, at 6:50 PM, Michael Budnick wrote:
I am working on a gene expression microarray dataset, each sample has been
taking from animal A and animal B on the same type of microarray.
I would like to take the mean of these columns and create a dataset with
columns with data
Hi
If you can not share information you need to solve your problems yourself.
you can trace code by some print statements
sn-(S-n);snfact-gamma(sn); print(sn)
or use
?debug
as Sarah pointed out, n is probably greater than 100 and in that case gamma(sn)
results in NaN.
Regards
Petr
Dear all,
1) I have a very large matrix of
str(keep)
num [1:153899, 1:3415] -98.6 -95.8 -96.4 -95.8 -98 ...
that I would like to reduce its size to something like
str(keep)
num [1:1000, 1:3415] -98.6 -95.8 -96.4 -95.8 -98 ...
or anything similar in size as this is a matrix that needs
Hi everyone:
This may be trivial but I just have not been able to figure it out.
Imagine the following dataframe:
a b c d
TRUE TRUE TRUE TRUE
FALSE FALSE FALSE TRUE
FALSE TRUE FALSE FALSE
I would like to create a new dataframe, in which TRUE gets 0 but if
false then add 1
On Tue, 26-Mar-2013 at 05:05PM +0900, Pascal Oettli wrote:
| Hi,
|
| You are right. The following should solve that problem:
|
| plot(0, 0, pch = )
| text(0, .5, expression(Temperature~(degree*C)))
It's not *exactly* the same. It uses a different font family for the
brackets, evidently from
Here's a possible solution.
dd - structure(list(a = c(TRUE, FALSE, FALSE),
b = c(TRUE, FALSE, TRUE),
c = c(TRUE, FALSE, FALSE),
d = c(TRUE, TRUE, FALSE)),
.Names = c(a, b, c, d),
row.names = c(NA,
Hi
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
project.org] On Behalf Of Alaios
Sent: Wednesday, March 27, 2013 9:13 AM
To: R help
Subject: [R] Averaging Out many rows from a column AND funtion to
string
Dear all,
1) I have a very large
see inline
From: PIKAL Petr petr.pi...@precheza.cz
Sent: Wednesday, March 27, 2013 11:24 AM
Subject: RE: [R] Averaging Out many rows from a column AND funtion to string
Hi
-Original Message-
From: r-help-boun...@r-project.org
On Tue, 26 Mar 2013, SHISHIR MATHUR wrote:
Thanks for the reply Achim. The reason I suspect autocorrelation is
because I think that within the same neighborhood, homes sold a few
months back are likely to impact the price of homes sold subsequently.
This may well be spatial
Baer,Thank you for help.huu
Date: Mon, 25 Mar 2013 08:20:28 -0500
From: rb...@atsu.edu
To: petr.pi...@precheza.cz
CC: uddessy2...@hotmail.com; r-h...@stat.math.ethz.ch
Subject: Re: [R] Automatic script for updating packages in R
try,
update.packages(ask='graphics', checkBuilt=TRUE)
Hi
From: Alaios [mailto:ala...@yahoo.com]
Sent: Wednesday, March 27, 2013 11:46 AM
To: PIKAL Petr; R help
Subject: Re: [R] Averaging Out many rows from a column AND funtion to string
see inline
From: PIKAL Petr petr.pi...@precheza.czmailto:petr.pi...@precheza.cz
Hi,
You could try:
dat1- read.table(text=
a b c d
TRUE TRUE TRUE TRUE
FALSE FALSE FALSE TRUE
FALSE TRUE FALSE FALSE
,sep=,header=TRUE)
dat2-dat1
dat2[]-t(apply(1*!dat1,1,function(x)
unlist(lapply(split(x,cumsum(c(0,abs(diff(x),cumsum
dat2
# a b c d
#1 0 0 0 0
#2 1 2 3
HI,
Just a correction:
:
dat2[]-t(apply(!dat1,1,function(x)
unlist(lapply(split(x,cumsum(c(0,abs(diff(x),cumsum #should also work
A.K.
- Original Message -
From: arun smartpink...@yahoo.com
To: Camilo Mora cm...@dal.ca
Cc: R help r-help@r-project.org
Sent: Wednesday, March
Hello all!
I want to create animated chart of temperature variation in last century.
how can I do this with R?
Thank you!
--
---
Catalin-Constantin ROIBU
Forestry engineer, PhD
Forestry Faculty of Suceava
Str. Universitatii no. 13, Suceava, 720229, Romania
office phone +4 0230 52 29 78,
Shane Carey careys...@gmail.com
on Tue, 26 Mar 2013 11:03:20 + writes:
Yup, Ive tried all these things and I think Johns might be
the best approach,
well, :-)
you have not yet seen the following one :
if(!require(sfsmisc)) install.packages(sfsmisc)
require(sfsmisc)
## the
see inline
From: PIKAL Petr petr.pi...@precheza.cz
Sent: Wednesday, March 27, 2013 1:50 PM
Subject: RE: [R] Averaging Out many rows from a column AND funtion to string
Hi
Â
Sent: Wednesday, March 27, 2013 11:46 AM
To: PIKAL Petr; R help
Subject: Re: [R]
Well, I don't think that is what Shane wants either but my suggestion is
clearly wrong. I was reading the question as a dual axis not just a
suplimentary , equivalent value axis. DUH.
What I think he wants is what IIRC Petr orginally suggested which is this..
Create the data to be graphed
maybe try the shiny examples that use googleviz. Have a look at the
following link:
https://code.google.com/p/google-motion-charts-with-r/
I would be interested to know what you decide.
Thanks
On Wed, Mar 27, 2013 at 1:20 PM, catalin roibu catalinro...@gmail.comwrote:
Hello all!
I want to
Yes, what I wanted was the original suggestion and that is what I went
with. John, I found a solution around par also. There is a function called
split.screen that allows you split the screen up, and also use par at the
same time.
Thanks everyone for all your help.
Cheers
On Wed, Mar 27, 2013
Any chance that you made an earlier call to par() resetting cex in your
session? I just had that happen.
John Kane
Kingston ON Canada
-Original Message-
From: tea...@gmail.com
Sent: Tue, 26 Mar 2013 10:15:33 -0400
To: r-help@r-project.org
Subject: [R] Odd graphic device behavior
Glad it worked. Sorry to mislead you so badly.
John Kane
Kingston ON Canada
-Original Message-
From: careys...@gmail.com
Sent: Wed, 27 Mar 2013 14:09:58 +
To: jrkrid...@inbox.com
Subject: Re: [R] How do I show real values on a log10 histogram
Yes, what
Dear Catalin,
If you have an R function that plots a fragment of your data and takes the
specific fragment selection as parameter, you can readily turn this into a
Shiny app. The slider control (see example in
http://rstudio.github.com/shiny/tutorial/#sliders) in Shiny can be animated
(you can
Whether can any R package run Full modified OLS (Phillips and Hansen 1990 ),
DOLS (Stock and Watson 1993) and ADL model (Pesaran and Shin 2001) for
cointegrated VAR model?
I cannot find any useful order in VAR and SVAR package.
Thanks.
Eric Wang
[[alternative HTML version deleted]]
Hi,
I'm using crrstep package to do stepwise covariate selection for the Fine
Gray competing risks regression model. However, I keep getting an error
(please see below). Please help!!
PHstep -
crrstep(years~1+var1+var2+var3+var4+var5,scope.min=~1,censorcmprsk,
data=crisk, direction=c(forward),
HI,
Try this:
dat1- read.csv(DQP.csv,sep=\t)
res- do.call(cbind,lapply(seq_len(nrow(dat1)),function(i)
do.call(rbind,lapply(split(rbind(dat1[i,],dat1[-i,]),1:nrow(rbind(dat1[i,],dat1[-i,]))),
function(x) {x1-rbind(dat1[i,],x);colnames(x1)-gsub([.],,colnames(x1));
if({indx-
Hi
str(as.matrix(keep.ag[,-1]) ) # does look like numeric
num [1:10, 1:30] 75.1 93 79 81.7 76.3 ...
- attr(*, dimnames)=List of 2
..$ : NULL
..$ : chr [1:30] V1 V2 V3 V4 ...
Please read and follow what was recommended.
quote
use as.matrix(data.frame) on numeric part
I have fixed it like that:
keep-matrix(data=rnorm(900,80,20),nrow=30,ncol=30)
ShrinkTo-500
idx-cut(1:nrow(keep), ShrinkTo)
keep.ag-aggregate(keep, list(idx), mean)
PlotMe-data.matrix(keep.ag[2:ShrinkTo])
The only problem is that takes ages to finish. Would it be possible to
convert it to
Hi,
I have a few raster layers and I would like to customized their x and y axis.
I have tried already something like:
require('raster')
keep-matrix(data=rnorm(900,80,20),nrow=30,ncol=30)
xlab-seq(100e6,200e6,length.out=5)
test-raster(keep)
plot(test,ylab=,xaxt=n,yaxt=n)
axis(1,
Hi
system.time({
+ keep-matrix(data=rnorm(900,80,20),nrow=30,ncol=30)
+ ShrinkTo-500
+ idx-cut(1:nrow(keep), ShrinkTo)
+ keep.ag-aggregate(keep, list(idx), mean)
+ PlotMe-as.matrix(keep.ag[,-1])
+ })
user system elapsed
29.230.14 29.37
It takes 30 seconds when using 30
Well my true matrix is
of
num [1:153899, 1:3415]
that I want to convert to something like
num [1:1000, 1:3415] (keeping column number the same).
I only give subsets here to allow others to run the code at their computer
Thanks a lot
Regards
Alex
From:
Hi,
I have a string of text as follows LOI .
How do I replace the dot with (%)
gsub(.,(%),LOI .)
gives
(%)(%)(%)(%)(%)
Thanks
--
Shane
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
John,
Thanks for the suggestion, but no. I have even gone so far as to rebuild R
from source, re-booted my computer, and tried the 'experiment':
require(stats)
plot(cars)
immediately after starting R. Still the same result. I think it must be
related to some default Ubuntu Unity
txt- LOI .
gsub([.],%,txt)
#[1] LOI %
A.K.
From: Shane Carey careys...@gmail.com
To: r-help@r-project.org
Sent: Wednesday, March 27, 2013 12:09 PM
Subject: [R] find and replace characters in a string
Hi,
I have a string of text as follows LOI .
How do I
Hello,
The period is a metacharacter so you have to escape it.
The period is escaped with a '\'. In it's turn, '\' is a metacharacter
so it needs to be escaped. Hence the double'\\'.
x - LOI .
gsub(\\., (%), x)
Hope this helps,
Rui Barradas
Em 27-03-2013 16:09, Shane Carey escreveu:
Hi,
Hi
Such a big matrix is above capability of my computer as it requires about 4GB
(If I compute it correctly) and I have only 2GB.
Maybe you could try package data.table which is designed for fast data
manipulation.
Regards
Petr
From: Alaios [mailto:ala...@yahoo.com]
Sent: Wednesday, March
Although I am not an expert, this is simple.
txt- LOI .
gsub(.,%,txt, fixed=TRUE)
Regards
Petr
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
project.org] On Behalf Of Rui Barradas
Sent: Wednesday, March 27, 2013 5:17 PM
To: Shane Carey
Cc:
Thanks for pointing that out.
Mike
On Tue, Mar 26, 2013 at 6:53 PM, David Winsemius dwinsem...@comcast.netwrote:
On Mar 26, 2013, at 2:51 PM, C W wrote:
Dear list,
I am a little confused as to when to use apply, sapply, tapply, vapply,
replicate. I've encountered this several times,
On Mar 27, 2013, at 9:07 AM, Thomas Adams wrote:
John,
Thanks for the suggestion, but no. I have even gone so far as to rebuild R
from source, re-booted my computer, and tried the 'experiment':
require(stats)
plot(cars)
immediately after starting R. Still the same result. I
Hi all,
I think I've run into an error caused by my computer's having too little
computational power, but I'm not sure. I used the following code to
perform continuous registration on two functional objects:
lambda1 - 10E-2
norder=8
samples-seq(0,780,length=781)
nbasis -
Hello,
I apologize for such a basic question, but I have been trying to do this in
multiple packages without much success. I am trying to set up a state
space model for Kalman filtering. I am using package dlm. The DLM is
specified by:
observation: y(t) = F(t)*theta(t) + v(t)
state: theta(t)
Thanks to all of you for your very helpful comments! As Terry suggested,
svykm is what I was looking for.
While testing that I get the same results with the package survey as with
the package survival, I encountered the issue of how to draw survival
curves. Apparently the implementations in the
On Mar 27, 2013, at 18:11 , David Winsemius wrote:
On Mar 27, 2013, at 9:07 AM, Thomas Adams wrote:
John,
Thanks for the suggestion, but no. I have even gone so far as to rebuild R
from source, re-booted my computer, and tried the 'experiment':
require(stats)
plot(cars)
Hi Elisa,
Try this:
dat1- read.csv(DQV.csv,sep=\t)
res- do.call(cbind,lapply(seq_len(nrow(dat1)),function(i)
do.call(rbind,lapply(split(rbind(dat1[i,],dat1[-i,]),1:nrow(rbind(dat1[i,],dat1[-i,]))),function(x)
{x1- rbind(dat1[i,],x); colnames(x1)- gsub([.],,colnames(x1));
if({indx-
Peter,
Thank you.
When I run: X11(width=7, height=7), I get the same full-screen graphics
device window.
Running dev.list() gives me X11cairo
Running system(xdpyinfo) looks reasonable
I tried running options(device=x11) at the R prompt, but this did not
seem to change anything.
When I started
Thanks.
On Tue, Mar 26, 2013 at 4:45 AM, Simon Wood s.w...@bath.ac.uk wrote:
For 1) see reply just sent to R help...
Re: [R] Use pcls in mgcv package to achieve constrained cubic spline
(I'm assuming you mean to fix the value of the smooth at a particular knot
location - i.e. to impose a
Dear R helpers,
Everyday I do receive many many mails from R forum and after some period of
times, INBOX is filled with numerous mails. At times if for some period of
time, I haven't accessed mails, it becomes difficult to keep track of mails and
many times simply due to the volume (and owing
On Mar 27, 2013, at 1:58 PM, Katherine Gobin katherine_go...@yahoo.com wrote:
Dear R helpers,
Everyday I do receive many many mails from R forum and after some period of
times, INBOX is filled with numerous mails. At times if for some period of
time, I haven't accessed mails, it becomes
http://r-help.markmail.org/ has a nice interface for searching the
archives, too.
On Wed, Mar 27, 2013 at 12:18 PM, Marc Schwartz marc_schwa...@me.comwrote:
On Mar 27, 2013, at 1:58 PM, Katherine Gobin katherine_go...@yahoo.com
wrote:
Dear R helpers,
Everyday I do receive many many
Dear Arun,
Thank you very much for your help with this.I did not know where to
start looking to solve that problem, so I truly appreciate your input.
The line of code you sent seems to work but it duplicates the results.
Do you know why that may happen?
Below is a larger database, to
This completes in about a second on my system and uses the actual matrix
dimensions you quote:
nr - 153899
nc - 3415
keep - rnorm(nr * nc, 80, 20)
dim(keep) - c(nr, nc)
shrink.to - 1000
system.time(
{
idx - rep(1:shrink.to, length.out = nr)
plot.me -
Dear Camilo,
How do you want to deal with the NAs?
If I remove the NAs:
dat1 - structure(list(
w = c(TRUE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE,TRUE),
x = c(NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA),
y =
On Thu, Mar 28, 2013 at 5:07 AM, rm r...@wippies.se wrote:
While testing that I get the same results with the package survey as with
the package survival, I encountered the issue of how to draw survival
curves. Apparently the implementations in the two packages differ, as I
show below.
I
Thanks Arun,
Well that is interesting. My intention was to have a dataframe with
the same number of rows in the original data, and for the rows with
NAs, then return NA (If there are NAs, often the entire row has NAs).
What is interesting is that in your code with NAs, the row that has
This is an old post, but I had the exact problem described here and after
two days of monkeying around in theme, I wanted to provide the non-ggplot
related solution.
In summary, the problem is that in the faceted plots, lines on the right an
bottom in the subplots appear to be thicker than
Dear Camilo,
You can do this:
dat1 - structure(list(
w = c(TRUE,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,TRUE,TRUE),
x = c(NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA),
y = c(FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,TRUE,TRUE,TRUE,FALSE),
z =
Nice!.
Thanks,
Camilo
Camilo Mora, Ph.D.
Department of Geography, University of Hawaii
Currently available in Colombia
Phone: Country code: 57
Provider code: 313
Phone 776 2282
From the USA or Canada you have to dial 011 57 313 776 2282
All,
How come both of these are the same. Both say 1-sample proportions test
without continuity correction. I would suspect one would say without and
one would say with.
prop.test(118,236,.5,correct=FALSE,conf.level=0.95)
1-sample proportions test without continuity correction
data:
Hi Camilo,
No problem.
In case, you wanted to process the partial NA rows, this could help:
datNew- structure(list(a = c(TRUE, NA, FALSE, TRUE, TRUE), b = c(TRUE,
NA, FALSE, TRUE, TRUE), c = c(TRUE, NA, FALSE, TRUE, FALSE),
d = c(TRUE, NA, FALSE, TRUE, FALSE), e = c(TRUE, NA, FALSE,
?prop.test is helpful.
Continuity correction is used only if it does not exceed the
difference between sample and null proportions in absolute value.
albyn
On Wed, Mar 27, 2013 at 02:04:51PM -0700, David Arnold wrote:
All,
How come both of these are the same. Both say 1-sample proportions
Dear Sir,
Thanks a lot for the input. I am sure it will go a long way for me to
understand R.
Thanks again.
Regards
Katherine
--- On Wed, 27/3/13, Mason ma...@verbasoftware.com wrote:
From: Mason ma...@verbasoftware.com
Subject: Re: [R] Archieve of mails from R forum
To: Marc Schwartz
can u explain me, how it works your code??? please. i´m also doing a simple
perceptron for homework on R and i dont know where to start.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
On 27-Mar-2013 21:04:51 David Arnold wrote:
All,
How come both of these are the same. Both say 1-sample proportions
test without continuity correction. I would suspect one would say
without and one would say with.
prop.test(118,236,.5,correct=FALSE,conf.level=0.95)
1-sample
On Mar 27, 2013, at 19:26 , Thomas Adams wrote:
Peter,
Thank you.
When I run: X11(width=7, height=7), I get the same full-screen graphics
device window.
Running dev.list() gives me X11cairo
Running system(xdpyinfo) looks reasonable
I tried running options(device=x11) at the R
http://www.signdesignbooks.com/acsw/df.km?flnu
Man Zhang
3/27/2013 11:31:04 PM
bf
iopo rarv rsh atzwnxfqoijhcwndgcyyyvtllyxaqkmiftoh
Hi R community,
I have a question concerning passing arguments between apply and lapply? Or
maybe, once my problem is explained, the question is really about how to best
transform my nested for loops into list/matrix operations; I am just beginning
this transformation away from nested for
Dear Help:
I am trying to follow Professor Bates' recommendation, quoted by Professor
Crawley in The R Book, p629, to determine whether I should model data using the
'plain old' lm function or the mixed model function lmer by using the syntax
anova(lmModel,lmerModel). Apparently I've not
Hi all,
I was wondering if there was package/ tutorial somewhere so that I can
plot INTERACTIVE networks in R. What I mean by interactive is that you
can zoom in, twist and rotate, and if necessary move nodes around.
Any thoughts?
Thanks,
Sachin
__
After installing updated twitteR and ROAuth, I am still getting the same error
as stated in these links. As there anyone who has been able to solve the
prolem? Suggested solution do not work.
On Mar 27, 2013, at 12:18 PM, Marc Schwartz wrote:
On Mar 27, 2013, at 1:58 PM, Katherine Gobin katherine_go...@yahoo.com
wrote:
Dear R helpers,
Everyday I do receive many many mails from R forum and after some period of
times, INBOX is filled with numerous mails. At times if for
On Mar 27, 2013, at 7:53 PM, David Winsemius dwinsem...@comcast.net wrote:
On Mar 27, 2013, at 12:18 PM, Marc Schwartz wrote:
On Mar 27, 2013, at 1:58 PM, Katherine Gobin katherine_go...@yahoo.com
wrote:
Dear R helpers,
Everyday I do receive many many mails from R forum and after
Michael Grant michael.grant at colorado.edu writes:
Dear Help:
I am trying to follow Professor Bates' recommendation, quoted by
Professor Crawley in The R Book, p629, to determine whether I should
model data using the 'plain old' lm function or the mixed model
function lmer by using
On Mar 27, 2013, at 7:00 PM, Ben Bolker wrote:
Michael Grant michael.grant at colorado.edu writes:
Dear Help:
I am trying to follow Professor Bates' recommendation, quoted by
Professor Crawley in The R Book, p629, to determine whether I should
model data using the 'plain old' lm
i literally just ran one.
when i ran one of mine and the did summary(mod) i get the following:
mod - lmer(dem ~ xbar + cpi + (1 | country), data=wvsAB)
summary(mod)
Linear mixed model fit by REML
Formula: dem ~ xbar + cpi + (1 | country)
Data: wvsAB
AIC BIC logLik deviance REMLdev
i meant to add, i am not sure if an example lmer model woulf be helpful,
since i can't see the OP.
On Mar 27, 2013, at 10:13 PM, Nicole Ford wrote:
i literally just ran one.
when i ran one of mine and the did summary(mod) i get the following:
mod - lmer(dem ~ xbar + cpi + (1 | country),
i did find this for you, down towards the end, they discuss the anova method.
i am on my way to a bayesian analysis/lmer is a step towards that- so i won't
be doing anova. i can't be of much specific help with that question, but here
you go.
On 13-03-27 10:10 PM, David Winsemius wrote:
On Mar 27, 2013, at 7:00 PM, Ben Bolker wrote:
Michael Grant michael.grant at colorado.edu writes:
Dear Help:
I am trying to follow Professor Bates' recommendation, quoted by
Professor Crawley in The R Book, p629, to determine whether I should
Mark Orr mo2259 at columbia.edu writes:
Hi R community,
I have a question concerning passing arguments between apply and lapply?
[snip]
#START CODE SNIPPET
#LIST AND VECTOR
rm(list=ls())
l - list(1:3,2:3,4:10,7:9)
v - 1:3
#USED IN j loop to catch values
catch.mat -
Hi,
I met tough problems when calling R in PHP. I have tried several ways, but none
of them succeed.Â
first of all, I tried Rserve, but I failed to connect to it.
Then, I tried cmd.exe. I get the result when I use R CMD BATCH --vanilla...
in cmd, but I have no idea how to call cmd in php.
I
Dear Katherine,
For your first question:
If you are creating these files in a specific folder, then
list.files()
#[1] Individual_Present_Value_BONDS.csv Individual_Present_Value_Equity.csv
#[3] Individual_Present_Value_FOREX.csv
gives you which files are present. But, suppose you have other
While someone around here might know about PHP (I don't h, the fact that you
don't know how to call system suggests that you should be asking in a PHP help
forum.
Rserve can be used for interactive sessions, but web services usually aren't
designed that way, so you probably want to call R with
Hi,
Regarding the first question:
ListFacGroup- lapply(ListFacGroup,unique)
Spec(ListFacGroup,0.05)
#
# Seq Mod z a2 c2 c3 t2
#1 aAATATAGPR 1-n_acPro/ 2 1 0 0 1
#2 aAAASSPVGVGQR
83 matches
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