I've found a problem when using
categorical variables in lmp() from package lmPerm
According to help(lmp): This function will behave identically to lm()
if the following parameters are set: perm=, seq=TRUE,
center=FALSE.)
But not in the case of including categorical variables:
require(lmPerm)
Dear R-package Folk,
I am pleased to announce the release of a new version of the ndl package (
http://cran.r-project.org/web/packages/ndl/)
What is NDL? It is a simple learning model based on the Rescorla-Wagner
model of discrimination learning.
I have become the new maintainer, replacing Dr.
Thank you very much,
First, sorry for posting on wrong mailing list, I did not know that
there exists a special one for lmer.
Yes, there are collinearities in the data.
Still, I would like to have the variables in one model to compare
explained variability. Is there some option, or it is simply
Hi,
I have been exploring graph dashboards like
http://sematext.com/img/products/spm/spm-solr-overview.png. I use R but
haven't attempted to create a
dashboard like this. I am thinking of parsing logs and showing dynamic
logs - logs that fit into a small window but move left or right
Thanks to Thomas, Martin, Jim and William,
Your input was very informative, and thanks for the reference to Sedgwick.
In the end, it does seem to me that all these algorithms require fast
lookup by ID of nodes to access data, and that conditional on such fast
lookup, algorithms are possible
I have a matrix names test which I want to convert to a data frame. When I
use a command test2-as.data.frame(test) it is executed without a problem.
But when I want to browse the content I receive an error message Error in
data.frame(outcome = c(cardva, respir, cereb, neoplasm, :
duplicate
Hi everybody,
does anyone of you know how to create a (crime) hotspot map using R?
Are there any packages or do you know any ressources?
It should be something like this:
http://www.caliper.com/Maptitude/Crime/MotorVehicleTheft2.png
(but it doesnt necessarely have to be a map)
Many thanks,
sounds like FAQ 7.31
Sent from my iPad
On Nov 7, 2013, at 18:39, Filippo ingf...@gmail.com wrote:
Hi,
I'm having strange differences between the R function prod ad the F90
function product.
Processing the same vector C (see attachment). I get 2 different results:
prod(C) = 1.069678e-307
On 08-11-2013, at 10:40, Kuma Raj pollar...@gmail.com wrote:
I have a matrix names test which I want to convert to a data frame. When I
use a command test2-as.data.frame(test) it is executed without a problem.
But when I want to browse the content I receive an error message Error in
Beend, Thanks for that. Conversion of test to a data frame resulted in a
factor. Is there a possibility to selectively convert to numeric? I have
tried this code and that has not produced the intended result.
test[, c(2:4)] - sapply(test[, c(2:4)], as.numeric)
On 8 November 2013 11:31, Berend
There is indeed a glitch in 'dredge' that prevents you from seeing the
actual error message. It is explained in ?dredge, in section Missing
values. (it's been corrected now in 1.9.14, on R-forge)
kamil
On 2013-11-08 11:00, r-help-requ...@r-project.org wrote:
--
I want to compute the total surface area of an isosurface in 3D space as
approximated with
`computeContour3d' by adding up the areas of the triangles making up the
contour surface.
problem:
the vertex matrix returned by `computeContour3d' in general seems to
provide the vertices
not in the
regarding my previous mail for this topic, I have in the meantime
identified my misconception.
actually, `computeContour3d' returns the vertices just fine in the correct
coordinate frame.
the misconception was caused basically by assuming that the `level'
argument was a fractional
On Fri, Nov 8, 2013 at 1:01 PM, j. van den hoff
veedeeh...@googlemail.com wrote:
ps: it of course would still be nice, if the surface area (or a vector
containing the individual triangle areas)
were returned to the caller as well ...
Does the 'surfaceArea' function in the sp package do what
On Fri, 08 Nov 2013 15:32:00 +0100, Barry Rowlingson
b.rowling...@lancaster.ac.uk wrote:
On Fri, Nov 8, 2013 at 1:01 PM, j. van den hoff
veedeeh...@googlemail.com wrote:
ps: it of course would still be nice, if the surface area (or a vector
containing the individual triangle areas)
were
a_lampei anna.lampei-bucharova at uni-tuebingen.de writes:
Thank you very much,
First, sorry for posting on wrong mailing list, I did not know that
there exists a special one for lmer.
Yes, there are collinearities in the data.
Still, I would like to have the variables in one model to
Hi,
Try:
test2 - as.data.frame(test,stringsAsFactors=FALSE)
test2[,c(2:4)] - lapply(test2[,c(2:4)],as.numeric)
A.K.
On Friday, November 8, 2013 6:24 AM, Kuma Raj pollar...@gmail.com wrote:
Beend, Thanks for that. Conversion of test to a data frame resulted in a
factor. Is there a possibility
Hi,
Following my earlier posts about having problems performing a PCA, I have
worked out what the problem is. The problem lies within the PLINK to gds
conversion.
It seems as though the SNPs are imported as samples and in turn, the
samples are recognised as SNPs:
snpsgdsSummary(chr2L)
Some
Doesn't this belong on Bioconductor rather than here?
-- Bert
On Fri, Nov 8, 2013 at 6:04 AM, Danica Fabrigar danica_...@hotmail.com wrote:
Hi,
Following my earlier posts about having problems performing a PCA, I have
worked out what the problem is. The problem lies within the PLINK to gds
Removing na.action=na.omit solved the problem.
Thanks for the help and thanks Dr. BatoÅ for making such useful package.
Mart
Martin Turcotte, Ph. D.
mart.turco...@gmail.com
[[alternative HTML version deleted]]
__
Stripping down to the bare essentials seems to get it. In
particular making the query just select * instead of select *
where B!='' works. You don't need the processing that the more
complicated Guardian web page requires. After loading the RCurl
package and creating the gsqAPI function:
It does indeed.
Thank you David,
Luca
2013/11/8 David Carlson dcarl...@tamu.edu
Stripping down to the bare essentials seems to get it. In
particular making the query just select * instead of select *
where B!='' works. You don't need the processing that the more
complicated Guardian web
Hi,
I have 300 .txt files in a directory. Out of this 300, I need just 100 of the
files.
I have the names of the 100 .txt files which are also found in the 300 .txt
files.
How can I extract only the 100 .txt files from the 300 ,txt files?
e.g given d1.txt, ds.txt, dx.txt, df.txt...d300.txt, how
Hi Colin,
The GAMLSS package allows modelling of the response variable distribution
using either Exponential family or non-Exponential family distributions.
It also allows modelling of the scale parameter
(and hence the dispersion parameter for Exponential family distributions)
using explanatory
How do you decide which ones you need?
Is there some pattern that lets you distinguish needing df.txt from
not needing ds.txt?
You say you have the names - how do you have them? In a text file?
What are you trying to do with the text files?
Sarah
On Fri, Nov 8, 2013 at 12:33 PM, Zilefac Elvis
I do not understand the question. If you already know the names what is the
problem to select the files by names?
If you have the names but not inside of R you have to find a name pattern to
avoid typing them in. Is there a pattern, e.g. da.txt, db.txt, dc.txt?
On 08 Nov 2013, at 18:33,
1. Please don't post in HTML (see posting guide).
2. What do you mean by extract?
3. Your qiestion sounds very basic. Have you read An Introduction to
R or other online R tutorial? If not please do so before posting
further. All of R's file input functions allow you to specify the
directory path
All files are text files. They are found in a folder on my computer.
Assume that I know the names of some of the files I want to select from the 300
txt files.
How can I do this in R.
Atem.
On Friday, November 8, 2013 11:44 AM, Simon Zehnder szehn...@uni-bonn.de
wrote:
I do not understand
If you want to type in the names by hand, you can simply use read.table to load
them into R … I still don’t get the aim of your text file handling
On 08 Nov 2013, at 18:51, Zilefac Elvis zilefacel...@yahoo.com wrote:
All files are text files. They are found in a folder on my computer.
R-Help Mailing List,
I'm currently working with a user who is actively trying to download install
libraries for 'R' on her office PC. While using install.packages(packageName,
dependencies = TRUE) works without a problem on our home PCs, we use a proxy at
the firm and therefore it doesn't let
Hi,
I have the next script in R:
x=c(8.0,17.5,23.5,32.0,38.5,48.5,58.5,68.5)
y=c(267,246,290,294,302,301,301,298)
gap.plot(x,y,ylim=c(8,310),pch=8,cex=0.5,
xlab=c('Time'),ylab=c('uS'),
gap=c(30,240),gap.axis='y',
ytics=c(10,20,30,270,280,290,300))
abline(h=31,col='white',lwd=20)
Hi Bert,
I thought it was suitable to post the question on the R mailing list first
seeing as the problem/question is related to an R package.
Danica
Date: Fri, 8 Nov 2013 08:14:03 -0800
Subject: Re: [R] SNPRelate: Plink conversion
From: gunter.ber...@gene.com
To:
I have no idea where gap.plot() came from, so I can't reproduce this,
but you almost certainly need
y ~ x
in your formula.
abline(coef(lm(y ~ x)),col=1)
Sarah
On Fri, Nov 8, 2013 at 11:04 AM, Domokos Péter dom...@gmail.com wrote:
Hi,
I have the next script in R:
Hi,
I'm not particularly interested in opening unsolicited binary attachments.
Why don't you use dput() to provide part of your data to the R-help
list (copied on this email; emailing just me not being that useful).
You still haven't told us what you want to do with the named text
files - read
Revolution Analytics staff write about R every weekday at the Revolutions blog:
http://blog.revolutionanalytics.com
and every month I post a summary of articles from the previous month
of particular interest to readers of r-help.
In case you missed them, here are some articles related to R from
Elvis,
first, keep things on the list - so others can learn and comment. Second, as
Sarah already commented: We do not like to open unsolicited binary attachments
on the list. Sarah gives a good hint how to post data to the list.
What I would do so far is use the matching columns to get the
Dear All,
I usually work with time series data. The data may come in AM/PM date
format or on 24 hour time basis. R can not recognize the two differences
automatically - at least for me. I have to specifically tell R in which
time format the data is. It seems that Pandas knows how to handle date
In my role as a moderator I am attempting to bypass the automatic mail filters
that are blocking this posting. Please reply to the list and to:
=
Kevin Shaney kevin.sha...@rosetta.com
C50 Node Assignment
I am using C50 to classify individuals into 5 groups / categories
Hi Jose
I faced the same problem at my workplace too - the solution (at least for
us) was to insert the following function into the Rprofile.ste file in the
etc folder in the R install folder - or, if the .First function already
exists, you could just insert the line beginning Sys.setenv(
.)
Have a look at the lubridate package. It claims to try to make
dealing with dates easier.
-- Bert
On Fri, Nov 8, 2013 at 11:41 AM, Alemu Tadesse alemu.tade...@gmail.com wrote:
Dear All,
I usually work with time series data. The data may come in AM/PM date
format or on 24 hour time basis. R
It is not clear to me what you want/need to do, but it is possible that
the spatstat package (in particular the function density.ppp()) might
help you.
cheers,
Rolf Turner
On 11/08/13 23:10, David Studer wrote:
Hi everybody,
does anyone of you know how to create a (crime) hotspot
On 11/09/2013 03:04 AM, Domokos Péter wrote:
Hi,
I have the next script in R:
x=c(8.0,17.5,23.5,32.0,38.5,48.5,58.5,68.5)
y=c(267,246,290,294,302,301,301,298)
gap.plot(x,y,ylim=c(8,310),pch=8,cex=0.5,
xlab=c('Time'),ylab=c('uS'),
gap=c(30,240),gap.axis='y',
ytics=c(10,20,30,270,280,290,300))
Hi Mihretu,
Can you grep for AM or PM? If so build your format string depending
upon whether one of these exists in the date string.
Jim
On 11/09/2013 06:41 AM, Alemu Tadesse wrote:
Dear All,
I usually work with time series data. The data may come in AM/PM date
format or on 24 hour time
Hi all:
The CODA package provides Geweke Diagnostic method for convergence
checking. The geweke.diag in CODA returns Z-score value but not give a
conclustion that it is convergence or not. So I'd like to know how
small/big the magnitude of Z-score is corresponding to the convergence of
a chain.
Hello,
having a data frame like test with pairs of characters I would like to
create chains. For instance from the pairs A/B and B/I you get the vector A
B I. It is like jumping from one pair to the next related pair. So for my
example test you should get:
A B F G H I
C F I K
D L M N O P
test
You might try to import your data in GenABEL,
use
as.numeric (gtdata (data))
to get a matrix that delivers you 0,1 or 2 for each snp and id (observation)
and then try prcomp.
Also check this
http://gettinggeneticsdone.blogspot.de/2011/10/new-dimension-to-principal-components_27.html
Hi Atem,
It is not clear what you wanted to do. If you want to transfer the subset of
files from the main folder to a new location, then you may try: (make sure you
create a copy of the original .txt folder before doing this)
I created three sub folders and two files
Hi,
Try either:
Ceramic - read.table(ceramic.dat,header=TRUE)
Ceramic1 - Ceramic
Ceramic$indx - ((seq_len(nrow(Ceramic))-1)%/%60)+1
library(plyr)
DF1 - data.frame(M=as.vector(t(ddply(Ceramic,.(indx), colwise(mean))[,-1])),
S=as.vector(t(ddply(Ceramic,.(indx),colwise(sd))[,-1])),Rep = 60)
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