Ali S wrote:
Is there a way to run TukeyHSD with Type III instead of Type I SS?
I am sure Bill Venables will respond, but in the meantime read:
http://r-project.markmail.org/search/?q=type+III+venables
And search google for Venables exegesis. It's one of the unique terms.
Dieter
--
I realize the problem now, and you are right aov is wrong.
It seams that it was completely wrong to use the transect in a fixed formula,
since my Trasects are labeled A to P, and A to D is in one mainplot, E-H in
another, I-L an a third, and M-P in a fourth. In this case lme, with random
Greetings,
My goal is to create a Markov transition matrix (probability of moving from
one state to another) with the 'highest traffic' portion of the matrix
occupying the top-left section. Consider the following sample:
inputData - c(
c(5, 3, 1, 6, 7),
c(9, 7, 3, 10, 11),
c(1, 2, 3,
Hi,
I was wondering if it would be possible to print the counts of common
items in the venneuler() diagrams.
Anybody knows a straightforward idea?
I can always count things from the data matrix, but I have vectors with
50 thousands elements.
thanks
Francesco
--
Hi,
Here is a not so easy way to do your first step, but it works:
MAT2 - cbind(MAT, rowSums(MAT))
MAT[order(MAT2[,6], decreasing=TRUE),]
For the second, I don't know!
HTH,
Ivan
Le 12/2/2010 09:46, Aaron Polhamus a écrit :
Greetings,
My goal is to create a Markov transition matrix
Hello group,
I am experimenting with parallel processing on my quad core Win 7 32
bit machine. Using these packages for the first time.
I can see all my processor running at full performance when I use a
smaller dataset
require(snow)
require(doSNOW)
require(foreach)
#change the 8 to however
Hi Aaron,
Following up on Ivan's suggestion, if you want the column order to
mirror the row order...
mo - order(rowSums(MAT), decreasing=TRUE)
MAT2 - MAT[mo, mo]
Also, you don't need all those extra c() calls when creating
inputData, just the outermost one.
Regarding your second question, your
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On 12/02/2010 10:56 AM, Santosh Srinivas wrote:
Hello group,
Hi
First of all: there is a special interest group for high performance
computing in R, which includes parallel computing, wghich would be more
appropriate to ask. But I will try anyway:
Cheers Bill.
You got me halfway, since:
temp - merge(x=x, y=y[,17, drop=FALSE], by=rownames, sort=FALSE)
Error in fix.by(by.x, x) : 'by' must specify valid column(s)
but, using row.names instead of rownames, like:
temp - merge(x=x, y=y[,17, drop=FALSE], by=row.names, sort=FALSE)
works (but
Hi all,
I am trying to predict a target variable that takes values 0 or 1 using the
rpart command. In my initial dataset I have few positive observations of the
target variable; therefore I have oversampled the rare event by a multiple of 6
(i.e. from 762 to 4572).
However, in my results, I
On Dec 2, 2010, at 5:22 AM, Karl Brand wrote:
Cheers Bill.
You got me halfway, since:
temp - merge(x=x, y=y[,17, drop=FALSE], by=rownames, sort=FALSE)
Error in fix.by(by.x, x) : 'by' must specify valid column(s)
but, using row.names instead of rownames, like:
temp - merge(x=x, y=y[,17,
On 12/2/2010 11:36 AM, David Winsemius wrote:
On Dec 2, 2010, at 5:22 AM, Karl Brand wrote:
Cheers Bill.
You got me halfway, since:
temp - merge(x=x, y=y[,17, drop=FALSE], by=rownames, sort=FALSE)
Error in fix.by(by.x, x) : 'by' must specify valid column(s)
but, using row.names instead
Dear List,
We are using RHmm to cluster data through HMM. We would like to
restrict the transition matrix of HMM, to get hierarchical connections
between clusters. But, RHmm doesn't seem to support these
restrictions. Can any one suggest a library to do that.
Thanks,
Kishor
Date: Thu, 2 Dec 2010 11:06:14 +0100
From: r.m.k...@gmail.com
To: santosh.srini...@gmail.com
CC: r-help@r-project.org
Subject: Re: [R] using foreach (parallel processing)
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On 12/02/2010 10:56 AM,
Thanks. I guess I had to wait long enough to get the threads running
and now they seem be on top gear.
Hope this thing doesn't crash now!
On Thu, Dec 2, 2010 at 3:36 PM, Rainer M Krug r.m.k...@gmail.com wrote:
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On 12/02/2010 10:56 AM, Santosh
I found a very simple way:
you start winbugs from R and state: debug=TRUE, start maybe with few
iterations, like 10.
If everything goes fine, open a new empty odc document in winbugs. Now
scan the log file and find something like this:
update(10)
On Wed, 2010-12-01 at 14:19 -0600, Christine Dolph wrote:
Dear All,
I am using a Procrustes analysis to compare two NMDS ordinations for the
same set of sites. One ordination is based on fish data, the other is based
on invertebrate data. Ordinations were derived using metaMDS() from the
It seems to me that summary for ridge coxph() prints summary but returns NULL.
It is not a big issue because one can calculate statistics directly from a
coxph.object. However, for some reason the score test is not calculated for
ridge coxph(), i.e score nor rscore components are not included
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[[alternative HTML version deleted]]
__
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,
Short answer: Not really.
Slightly longer answer: from what I remember of partitioning methods, a
given split is made at either a single observation or between two
consecutive observations. In your case, I estimate rpart would have split
on that particular point... except that there are 6 of
Hi all (and especially Frank),
I'm trying to use x=T, y=T in order to run a validated stepwise cox
regression in rsm, having multiply imputed using mice. I'm coding
model.max-fit.mult.impute(baseform,cph,miced2,dated.sexrisk2,x=T,y=T)
baseform is
baseform-Surv(si.age,si==Yes)~ peer.press +
Sorry everybody, temporary dyslexia.
Sent from my BlackBerry wireless smartphone
__
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
On 11/30/2010 5:59 PM, David Winsemius wrote:
I'm guessing from this behavior on my system that it may be Matrix.
showMethods(as.array)
Function: as.array (package base)
x=ANY
x=Matrix
I'm still perplexed by this. Running R CMD install gives this warning:
** testing if installed package
On 12/2/2010 8:58 AM, Michael Friendly wrote:
Under ?methods the Note says
Functions can have both S3 and S4 methods, and function showMethods will
list the S4 methods (possibly none).
Does the warning mean that I cannot (or should not) have an S3 as.array
method in a package?
The method works
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I would like to call both p-values and R-squared values from lm's in a
function. I can get the p-values from coef(summary(name.lm))[r,c], however, I
cannot figure out how to call the R-squared values without manually calling the
summary and inserting them in the script - which negates the
Dear all,
For a population of about 200 I have a continuous variable and an ordinal
variable. The question I would like to ask is whether the continuously
increases (or decreases) as the rank of the ordinal variable increases. I was
thinking that a Spearmen's rank correlation or or a chi
On 12/02/2010 03:15 PM, Wegan, Michael (DNRE) wrote:
I would like to call both p-values and R-squared values from lm's in a
function. I can get the p-values from coef(summary(name.lm))[r,c], however, I
cannot figure out how to call the R-squared values without manually calling the
summary
On Dec 2, 2010, at 8:15 AM, Wegan, Michael (DNRE) wrote:
I would like to call both p-values and R-squared values from lm's in a
function. I can get the p-values from coef(summary(name.lm))[r,c], however,
I cannot figure out how to call the R-squared values without manually calling
the
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как
On Dec 2, 2010, at 5:58 AM, Karl Brand wrote:
On 12/2/2010 11:36 AM, David Winsemius wrote:
On Dec 2, 2010, at 5:22 AM, Karl Brand wrote:
Cheers Bill.
Inserting earlier debris:
I don't understand why i get this error message when attempting to
use merge() -
temp - merge(x,
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Hi everyone
I spent hours trying to figure this out but as a newbie I am stuck...
can someone show me the R code for the following:
If I had a tab delimited file called file, containing 3 rows :
9.568.679.288.817.939.858.9210.19 8.63
6.367.296.68
Dear Ingmar,
Thanks a lot.
Regards,
Kishor
On Thu, Dec 2, 2010 at 6:39 PM, Ingmar Visser i.vis...@uva.nl wrote:
depmixS4 enables linear constraints on parameters, best, Ingmar
On Thu, Dec 2, 2010 at 12:01 PM, Kishor Tappita kishor.tapp...@gmail.com
wrote:
Dear List,
We are using RHmm to
Hi,
I typically install new versions of R on windows using the downloadable
executable file rather than the full tar.
I need to now document the success of the installation in addition to my
preferred procedure of running an old dataset against the new build.
I found quickly that this is all
Hello
I am trying to fit a model using glm function with family=Gamma(link=inverse).
Is it possible to give initial values, and how? I tried to search for info but
not managed to get any answer.
Kind regards and thanks in advance.
Rosario
[[alternative HTML version deleted]]
Hi,
I have a dataframe like this:
procedure propertysensor_data sensor_date
| | | |
[1,] PAT_Laser_2 Distance 30.42 2010-09-30T15:00:12+0200
[2,] PAT_Laser_2 Distance 31.22
On Dec 2, 2010, at 10:36 AM, David Lyon wrote:
Hi everyone
I spent hours trying to figure this out but as a newbie I am stuck...
can someone show me the R code for the following:
If I had a tab delimited file called file,
Are you sure that you are not on an OS that hides the file
Hi
r-help-boun...@r-project.org napsal dne 02.12.2010 16:36:09:
Hi everyone
I spent hours trying to figure this out but as a newbie I am stuck...
can someone show me the R code for the following:
If I had a tab delimited file called file, containing 3 rows :
9.56 8.67 9.28 8.81
Thanks David
Do you have the url link that details the worked solution to my problem:
that we have an extensive collection of documentation suitable for beginners
that probably has similar problems worked out:
If not can someone show me how to
How do I import the file, then plot the mean and
On 12/2/2010 3:52 PM, David Winsemius wrote:
On Dec 2, 2010, at 5:58 AM, Karl Brand wrote:
On 12/2/2010 11:36 AM, David Winsemius wrote:
On Dec 2, 2010, at 5:22 AM, Karl Brand wrote:
Cheers Bill.
Inserting earlier debris:
I don't understand why i get this error message when
I am trying to aggregate data in column 2 to identifiers in col 1
eg..
take this
identifier quantity
1 10
1 20
2 30
1 15
2 10
3 20
and make this
identifier
On Dec 2, 2010, at 11:10 AM, David Lyon wrote:
Thanks David
Do you have the url link that details the worked solution to my
problem:
that we have an extensive collection of documentation suitable for
beginners that probably has similar problems worked out:
I've wrote some code to simulate a random walk in 2 dimensions on a lattice.
Basically I want to add something in to make it plot it point by point so
you can see what is going on.
Heres my code for the random walk in 2d
RW2D-function(N)
{
i-0
xdir-0
ydir-0
xpos-vector()
I can say is used as filter Kalman
thanks
Cordialmente,
JAVIER SANTIAGO PARRA RAMOS
INGENIERO DE SISTEMAS
ESP. EN GERENCIA DE SISTEMAS INFORMATICOS
CEL: (57) 313 416 71 21
[[alternative HTML version deleted]]
see ?aggregate, and ?summaryBy (in package doBy)
I think ddply (in package plyr) could also do the job
Ivan
Le 12/2/2010 17:24, chris99 a écrit :
I am trying to aggregate data in column 2 to identifiers in col 1
eg..
take this
identifier quantity
1 10
1
I didn't change your rownames to row.names
because I figured you had the name you wanted
but only forgot to include the quotes. Both rownames
and row.names are valid inputs, but they mean
different things. Howver, without the quotes you were
passing in the contents of the object called
rownames,
see also tapply()
e.g.
a-c(1,1,1,2,2,2,3,3,3)
b-c(10,10,10,15,15,15,20,20,20)
c.dat-data.frame(a,b)
tapply(c.dat[,2],c.dat[,1],sum)
Mike
On Thu, Dec 2, 2010 at 10:33 AM, Ivan Calandra ivan.calan...@uni-hamburg.de
wrote:
see ?aggregate, and ?summaryBy (in package doBy)
I think ddply (in
Here are some examples with tapply, aggregate, ddply:
x - read.table(clipboard, head=TRUE)
with(x, tapply(quantity, identifier, sum))
aggregate(x$quantity, by=list(x$identifier), sum)
aggregate(quantity ~ identifier, data = x, sum)
library(plyr)
ddply(x, .(identifier), summarise,
Hopefully someone has a good suggestion
for your question. I'd just like to
point out that the generation of the
random walk is pretty much optimized for
worst performance.
A 'for' loop is not necessary and growing
the objects could be a very significant
drag. See Circles 2 and 3 of 'The R
Nice thing about R is there are a number of ways to do things:
x
identifier quantity
1 1 10
2 1 20
3 2 30
4 1 15
5 2 10
6 3 20
require(sqldf)
sqldf('select identifier, sum(quantity) as quantity from x
Try this:
with(DF, rowsum(quantity, identifier))
On Thu, Dec 2, 2010 at 2:24 PM, chris99 chea...@hotmail.com wrote:
I am trying to aggregate data in column 2 to identifiers in col 1
eg..
take this
identifier quantity
1 10
1 20
2
Cheers Bill,
Thank you for the clarificaiton. Prabably showing the str() of these
objects would have made it easier for you see exatly where i was going
wrong. Which as David pointed out, was really a lack of ?merge reading...:)
Karl
On 12/2/2010 5:46 PM, William Dunlap wrote:
I didn't
Hi, Thanks very much for your response.
Unfortunately, using the set.seed() call does not seem to solve my problem.
If I do not use set.seed(), I do indeed get some small differences in
protest() results due to the effect of random starts. But with my sites in a
given order in the input files,
Here is a use of color to show what the path is and following up on
Patrick's post to make the code a little more efficient:
# compute path
n - 1
rw - matrix(0, ncol = 2, nrow = n)
# generate the indices to set the deltas
indx - cbind(seq(n), sample(c(1, 2), n, TRUE))
# now set the values
Dear R-group,
I am trying desperately to get this Tukey test working. Its my first time here
so I hope my question is not too stupid, but I couldn't find anything helpful
in the help or in the forum.
I am analysing a dataset of treated grasses. I want to find out, if the grasses
from
Hello,
I'm attempting to create a data frame with correlations between every pair
of variables in a data frame, so that I can then sort by the value of the
correlation coefficient and see which pairs of variables are most strongly
correlated.
The sm2vec function in the corpcor library works very
Hello list,
I seem to have a problem with the openNLP package, I'm actually stuck in
the very beginning. Here's what I did:
install.packages(openNLP)
install.packages(openNLPmodels.de, repos =
http://datacube.wu.ac.at/;, type = source)
library(openNLPmodels.de)
library(openNLP)
So I
Dear R-group,
I am trying desperately to get this Tukey test working. Its my first time
here so I hope my question is not too stupid, but I couldn't find anything
helpful in the help or in the forum.
I am analysing a dataset of treated grasses. I want to find out, if the
grasses from different
There are many possibilities depending on what you are really looking for
(strict increasing, vs. increasing or constant, vs. general trend, etc.)
I would start with a plot of the data, that may result in a significant
interocular concussion test and will at least help you understand what is
Is it possible to use Eclipse (StatET) to connect to an rterm instance
running on another computer? It looks like it should be easy, but when I
select an R Engine it says Connection failed to: hostname everytime. Is
there a guide somewhere?
--
View this message in context:
Dear WanderingWizard,
On 12/02/2010 07:58 PM, WanderingWizard wrote:
Is it possible to use Eclipse (StatET) to connect to an rterm instance
running on another computer?
Yes. You can launch, disconnect and reconnect to a remote R console.
It looks like it should be easy, but when I
select
Greetings to all --
I have a set of ~1300 radon measurements from homes across British
Columbia in Canada. We have split these measurements into five groups
according the the tectonic belt in which they fall, with N ranging
from ~160 to ~600 measurements per group. The values are roughly
Hello,
I understand that question is probably stupid, but ...
I have data (polity IV index)
country,year,democ,autoc,polity,polity2
1,Afghanistan ,1800,1,7,-6,-6
2,Afghanistan ,1801,1,7,-6,-6
3,Afghanistan ,1802,1,7,-6,-6
I need to create new data sets which
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I'm looking for an R method to produce latex versions of tables for
table/array objects of 3 or more dimensions,
which, of necessity is flattened to a 2D display, for example with
ftable(), or vcd::structable, as shown below.
I'd be happy to settle for a flexible solution for the 3D case.
UCB
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
project.org] On Behalf Of Diogenas
Sent: Thursday, December 02, 2010 12:09 PM
To: r-help@r-project.org
Subject: [R] Filter data
Hello,
I understand that question is probably stupid, but ...
I
On Dec 2, 2010, at 3:47 PM, Michael Friendly wrote:
I'm looking for an R method to produce latex versions of tables for
table/array objects of 3 or more dimensions,
which, of necessity is flattened to a 2D display, for example with
ftable(), or vcd::structable, as shown below.
I'd be happy
Simplified version of str(poli): (real dataset includes 36 variables)
$ country : chr [1:15846] Afghanistan Afghanistan
Afghanistan Afghanistan ...
$ year: num [1:15846] 1800 1801 1802 1803 1804 ...
$ democ : num [1:15846] 1 1 1 1 1 1
rms and fit.mult.impute don't necessarily play well with mice.
Note also that you will need a special adjustment for variances for having
done stepwise regression. One approach is to insert a zero for a
coefficient every time that variable is not 'selected', then compute the
sample variance of
How do I get MANOVA results with Type III sums of squares?
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
The integral of any probability density from -Inf to Inf should equal 1,
correct? I don't understand last result below.
integrate(function(x) dnorm(x, 0,1), -Inf, Inf)
1 with absolute error 9.4e-05
integrate(function(x) dnorm(x, 100,10), -Inf, Inf)
1 with absolute error 0.00012
On Dec 2, 2010, at 4:18 PM, Ali S wrote:
How do I get MANOVA results with Type III sums of squares?
First pull on your asbestos underwear, then visit :
Adaikalavan Ramasamy wrote:
Using the info from that website, I can code up the following to give
the two-tailed p-value of difference in correlations:
diff.corr - function( r1, n1, r2, n2 ){
...
William Revelle also mentioned the r.test in the psych package.
I would add here that
Hello everybody,
I've got a bit of a problem with parLapply that's left me scratching my head
today. I've tried this in R 2.11 and the 23 bit Revolution R Enterprise and
gotten the same result, OS in question is Windows XP, the package involved
is the snow package.
I've got a list of 20 rain/no
On 12/2/2010 4:04 PM, David Winsemius wrote:
?latex # yes I know you are aware of this but it seemed as though you
hadn't read its help page.
# Attached is the output on my device from the following command:
latexVerbatim( ftable(UCB))
Perhaps I should have been more explicit. I can
Hi Diogenas,
Try this,
data-subset(poli, poli$year1994)
Best,
M
Diogenas dioge...@gmail.com a écrit :
Hello,
I understand that question is probably stupid, but ...
I have data (polity IV index)
country,year,democ,autoc,polity,polity2
1,Afghanistan ,1800,1,7,-6,-6
2,Afghanistan
Try looking at subset()... I typically use this when I'm trying to isolate
specific cases from a data frame.
Also, Dalgaard's introductory R book has some great examples for parsing
data in the manner you're attempting you might want to look at that.
Mike
On Thu, Dec 2, 2010 at 2:08 PM,
Ivan and Michael,
Many thanks for the tips, those solved my queries. Still interested in how
to force custom functions to work over rows rather than columns when using
apply, but the MAT/rowSums(MAT) technique is definitely the most efficient
way to go for this application.
Cheers,
Aaron
Comments in-line below
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Lilith
Sent: December-02-10 9:39 AM
To: r-help@r-project.org
Subject: [R] Tukey Test, lme, error: less than two groups
Dear R-group,
I am trying
You can dive into the thread puzzle with integrate over infinite range
from September this year. The short answer appears to be: Increase the
error tolerance.
integrate(function(x) dnorm(x, 500,50), -Inf, Inf,
subdivisions=500, rel.tol=1e-11)
# 1 with absolute error
Michael,
I think this is what you are looking for.
Rich
library(Hmisc)
tmp - array(rnorm(60), c(3,4,5),
list(letters[1:3],LETTERS[4:7],letters[8:12]))
## latex(tmp)
ftable(tmp)
dviname - latex(ftable(tmp))
ft - ftable(tmp)
dviname - latex(ft,
colheads=attr(ft,col.vars)[[1]],
To really understaand it you will have to look at the fortran code
underlying integrate. I tracked it back through a couple of layers
(dqagi, dqagie, ... just use google, these are old netlib
subroutines) then decided I ought to get back to grading papers :-)
It looks like the integral is split
Hello
I am trying to fit a model using glm function with family=Gamma(link=inverse).
Is it possible to give initial values, and how? I tried to search for info but
not managed to get any answer.
Kind regards and thanks in advance.
Rosario
[[alternative HTML version deleted]]
You can use trace() to see what is happening
trace(dnorm, quote(print(round(x
integrate(function(x) dnorm(x, 500,50), -Inf, Inf)
Tracing dnorm(x, 500, 50) on entry
[1] 1 233 0 38 0 14 0 7 0 4 0 2 0 2 1
Tracing dnorm(x, 500, 50) on entry
[1] -1 -2330 -38
I believe the R intro manual and R-inferno have some pretty stern
warnings about never using 'c' or 't' as variable names, for obvious
reasons.
Similarly, I nearly crushed some code once by writing a nice little
function to find the mode of a data set and calling the function
mode() .
But that only postpones the misery, Hans Werner! You can always make the
mean large enough to get a wrong answer from `integrate'.
integrate(function(x) dnorm(x, 700,50), -Inf, Inf,
subdivisions=500, rel.tol=1e-11)
integrate(function(x) dnorm(x, -700,50), -Inf, Inf,
Albyn's reply is in line with an hypothesis I was beginning to
formulate (without looking at the underlying FoRTRAN code),
prompted by the hint in '?integrate':
Details:
If one or both limits are infinite, the infinite range
is mapped onto a finite interval.
For a finite
On Thu, Dec 02, 2010 at 01:13:40PM -0800, Aaron Polhamus wrote:
...
Many thanks for the tips, those solved my queries. Still interested in how
to force custom functions to work over rows rather than columns when using
apply,
In the command
TMAT - apply(MAT, 1, function(X) X/sum(X))
the
On Thu, Dec 02, 2010 at 06:23:45PM -0500, Ravi Varadhan wrote:
A simple solution is to locate the mode of the integrand, which should be
quite easy to do, and then do a coordinate shift to that point and then
integrate the mean-shifted integrand using `integrate'.
Ravi.
Translation: think
Hello all,
I've been comparing results from kmeans() in R to PROC FASTCLUS in SAS and
I'm getting drastically different results with a real life data set. Even
with a simulated data set starting with the same seeds with very well
seperated clusters the resulting cluster means are still different.
I have recently been bitten by an aspect of the behaviour of
the read.csv() function.
Some lines in a (fairly large) *.csv file that I read in had
too many entries. I would have hoped that this would cause
read.csv() to throw an error, or at least issue a warning,
but it read the file without
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