Hi everyone, I'm running the following analysis for two meadows and two
periods. I need to get the post hoc comparisons for the combination of the two
factors (meadowA*PeriodA, meadowA*PeriodB, meadowB*PeriodB, meadowB*PeriodA). I
use the function glht glht(model, linfct=mcp(Meadow=Tukey) in
Le mardi 12 février 2013 à 15:41 -0600, Andrew Barr a écrit :
Hi all,
I am searching for a way to recover results from lapply() when one or more
values returns an error. I have a written a function that uses tryCatch()
to recover from errors. Here is a very simple example of such a
HI all,
I am using R (version 2.13.1) in batch mode on a server and I use
trycatch() to handle the exceptions.
When the code run without any exceptions, everything goes fine, however as
soon as trycatch handle an error, my code works fine but R keeps hold on
the folder after quiting.
Therefore
On 13-02-12 11:09 PM, Asis Hallab wrote:
Dear R users,
writing an R package I wonder, if there is a place to put executable R
scripts into. So that when the package is installed one can use the
script from the command line.
Say we have e new package called FunkyR and wanted to deliver with it
Dear all,
I have a data (bellow) and I want to make a correlation test with p-value
structure(list(Name = structure(c(3L, 3L, 3L, 3L, 3L, 3L, 3L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c(CTJ,
PKR, TTK), class = factor), score = c(86.4371428571428,
89.7028571428572,
Nico,
Check https://stat.ethz.ch/pipermail/r-help/2008-May/161725.html for some
alternatives. You might have to change the structure of your data, though.
HTH,
Jorge.-
On Wed, Feb 13, 2013 at 10:13 PM, Nico Met wrote:
Dear all,
I have a data (bellow) and I want to make a correlation test
You can control the width and height of a plot in addPlot(), but you must
use addPageBreak() to control the width and the height of the page. Here
is a modification of the example provided in the help for rtf,
?RTF
library(rtf)
myplot - function() {
par(mar=c(4, 4, 1, 1), cex=2)
plot(rnorm(25),
The documentation for caret::train shows a list of parameters that one can
tune for each method classification/regression method. For example, for
the method randomForest one can tune mtry in the call to train. But the
function call to train random forests in the original package has many
other
You can use package Hmisc. Assuming your data.frame is called dta:
library(Hmisc)
dta2 - do.call(cbind, split(dta[,2], dta$Name))
dta2
CTJ PKR TTK
[1,] 83.99429 88.54571 86.43714
[2,] 86.43714 85.71714 89.70286
[3,] 84.59600 84.90200 87.72800
[4,] 84.74000 89.88286 89.99000
I have two data matrices that I want to make the correlation between each
column from data1 and each column from data 2 and also calculate the p-value
Matrices dont have the same size and I tried such a script.
bg - read.table (file.choose(), header=T, row.names)
bg
Otu00022 Otu00029
Hello,
i want to match a column of one data.frame to another, my problem is, that i
only want to match the data, if 2 columns are equal.
i have a example:
data.frame1
cu.nr. name value
A 1 Evo 100
B
Thanks very much Milan. Your answer makes perfect sense.
Best,
Andrew
On Wed, Feb 13, 2013 at 3:51 AM, Milan Bouchet-Valat nalimi...@club.frwrote:
Le mardi 12 février 2013 à 15:41 -0600, Andrew Barr a écrit :
Hi all,
I am searching for a way to recover results from lapply() when one
I want estimate MIMIC latent variable with R in a Monte Carlo simulation.
The packages plspm and semPLS don't permit to introduce MIMIC variable
but only reflexives or formatives variables.
The only one program which permits to use MIMIC latent variable with
PLSPM seems to be XLSTAT, which can
densityplot(~x+y) does what I expect it to do if x and y have equal length. I
know how to get what I want if x and y have different lengths. But what is
this actually doing if x and y have different lengths?The relevant example
is
x=rnorm(10)
y=rnorm(50,1)
densityplot(~x+y)
Hi,
#data: dat1
mat1-matrix(dat1[,2],ncol=3,nrow=7)
colnames(mat1)-unique(dat1[,1])
library(Hmisc)
rcorr(mat1)$P
# TTK CTJ PKR
#TTK NA 0.0151874 0.6277163
#CTJ 0.0151874 NA 0.5214368
#PKR 0.6277163 0.5214368 NA
A.K.
- Original Message -
From:
Hi Elisa,
Try this:
date1-format(seq.Date(as.Date(1991.1.1,format=%Y.%m.%d),as.Date(1996.12.31,format=%Y.%m.%d),by=day),%Y.%m.%d)
length(date1)
#[1] 2192
mat1-matrix(c(.314,.314,.273,.273,.236,.236,.236,.236,.273,.314,.403,.314),ncol=1)
res1-
Hi,
Just forgot about one thing:
With more matrices with one column:
One way would be to combine them as a single matrix:
date1-format(seq.Date(as.Date(1991.1.1,format=%Y.%m.%d),as.Date(1996.12.31,format=%Y.%m.%d),by=day),%Y.%m.%d)
Hello,
I have submitted a R question to stackoverflow and have not received an answer.
Could anyone help me out?
http://stackoverflow.com/questions/14825443/backtesting-accuracy-of-regression-model-through-rolling-window-regression-with
Best regards,
Pedro
Dear R-helpers:
I am trying to fit a multivariate Cox proportional hazards model,
modelling survival outcome as a function of treatment and receptor
status. The data look like below:
# structure of the data
str(sample.data)
List of 4
$ survobj : Surv [1:129, 1:2] 0.8925+ 1.8836+ 2.1191+
Minor edit
dta2 - unstack(dta, score~Name)
is simpler.
---
David C
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
project.org] On Behalf Of David L Carlson
Sent: Wednesday, February 13, 2013 9:40 AM
To: 'Jorge I Velez'; 'Nico Met'
Cc: 'R
?merge
If I have not reversed the data sets this should work
With data sets called dat1 and dat2
merge(dat1,dat2, all.y = TRUE)
John Kane
Kingston ON Canada
-Original Message-
From: matthias.we...@fnt.de
Sent: Wed, 13 Feb 2013 06:39:57 -0800 (PST)
To: r-help@r-project.org
roxygen2::roxygenize() process an entire package and rd2roxygen can
convert existing Rd
documentation to roxygen format.
But are there equivalents/analogs of prompt() or SoDA::promptAll() for
one or more .R/.RData files that would
create skeleton roxygen documentation of functions or data?
Hello,
Try the following.
data.frame1 - read.table(text =
cu.nr. name value
A 1 Evo 100
B 1 Mer 80
C 2 Ford50
Hello everyone,
Does anyone know what would cause the skewness() function (from
e1071), as well as skew() from psych, to return a value of NaN?
I have a vector of positively-skewed data
(https://docs.google.com/file/d/0B6-m45Jvl3ZmYzlHRVRHRURzbVk/edit?usp=sharing)
which these functions return a
Hi,
thank you for your response. I tried the
A[-1,]-do.call(rbind,lapply(split(A[-1,],((1:nrow(A[-1,])-1)%/%2)+1),function(x){x[4]-max(x[4]);x}))
but somehow my computer got stuck...
I tried the other option using rollapply and that works pretty well, doing
exactly what I wanted to get.
This is
Hi everyone,
Please disregard my last message, I found a 0 in the vector, which is
what was causing problems with the log and reciprocal data.
Best,
Steve
On Wed, Feb 13, 2013 at 10:55 AM, Stephen Politzer-Ahles
politzerahl...@gmail.com wrote:
Hello everyone,
Does anyone know what would
On Feb 13, 2013, at 6:58 AM, James Jong wrote:
The documentation for caret::train shows a list of parameters that one can
tune for each method classification/regression method. For example, for
the method randomForest one can tune mtry in the call to train. But the
function call to train
Hello,
That value means that some values of your data are negative or zero. A
simple inspection shows that
any(dat 0) # FALSE
any(dat == 0) # TRUE
Solution: don't log your data
Hope this helps,
Rui Barradas
Em 13-02-2013 16:55, Stephen Politzer-Ahles escreveu:
Hello everyone,
Does
Hello,
Just remembered, you can see how many values are zero, and since it's
only one value, remove it and log the rest.
sum(dat == 0) # 1
d2 - dat[dat != 0]
library(psych)
skew(log(d2))
[1] 0.6089985
Hope this helps,
Rui Barradas
Em 13-02-2013 17:59, Rui Barradas escreveu:
Hello,
On Feb 13, 2013, at 7:46 AM, Cindy Yao wrote:
Dear R-helpers:
I am trying to fit a multivariate Cox proportional hazards model,
modelling survival outcome as a function of treatment and receptor
status. The data look like below:
# structure of the data
str(sample.data)
List of 4
$
Dear All,
I was wondering whether someone has created a kernel density evaluator that
estimates the density at given specified points.
The regular density() function evaluates the kernel at equidistant points,
but I am interested in doing such evaluation along a list of values
existing in a
Dear all mailing listers,
I failed in install source packages in Windows system. I have installed
Rtools in order to install the source package based on the discussion
available on the following link:
http://r.789695.n4.nabble.com/Installing-a-Package-tar-gz-in-windows-td3411393.html.
By the way,
HI Elisa,
You also mentioned about more than 100 matrices with 1 column each.
Suppose, if the matrices are named from mat1:mat4 (In your case mat1:mat124)
mat1-matrix(c(.314,.314,.273,.273,.236,.236,.236,.236,.273,.314,.403,.314),ncol=1)
Dear Elisa,
When you save it as matrix, if there is atleast one column with character
class, others will be converted to that class. It would be better to store it
as data.frame
res2-lapply(seq_len(ncol(mat3)),function(i)
James,
You really need to read the documentation. Almost every question that you
have has been addressed in the existing material. For this one, there is a
section on custom models here:
http://caret.r-forge.r-project.org/training.html
Max
On Wed, Feb 13, 2013 at 9:58 AM, James Jong
Dear All,
I am using WriteXLS to write tables with multiple sheets with the command:
WriteXLS(tables, ExcelFileName = fileName, SheetNames = tableList, perl =
perl,
verbose = FALSE, Encoding = c(UTF-8, latin1),
row.names = TRUE, col.names = TRUE,
AdjWidth =
Greetings,
I am exploring some random forest analysis methods and have come upon one
aspect I don't fully understand from any manual. The code of interest is
as follows from the randomForest package:
myiris=cbind(iris[1:4], matrix(runif(508*nrow(iris)),nrow(iris),508))
This would be following
Thank you David and Max,
@David - Thanks, I am already aware that I cannot *directly* pass
arguments to train to specify parameters controlling the method, and that
one has to pass those parameters via the tuneGrid argument to caret::train.
My question is about the method parameters that are
@Max - Thanks a lot for your help. I have already been using that website
as a reference, and it's incredibly helpful. I have also been experimenting
with tuneGrid already. My question was specifically if tuneGrid (or caret
in general) supports passing method parameters to the method functions
On Feb 13, 2013, at 12:07 PM, Scott Robinson scott.robin...@glasgow.ac.uk
wrote:
Dear All,
I am using WriteXLS to write tables with multiple sheets with the command:
WriteXLS(tables, ExcelFileName = fileName, SheetNames = tableList, perl =
perl,
verbose = FALSE, Encoding =
Hmmm... is this a (unknown or even a) bug ? Not sure this is what OP was
getting at and I haven't gone through the lattice docs to see if this is
mentioned, but, with unequal sizes the extended formula is not producing
what one (or at least I) might expect:
require(latticeExtra)
set.seed(4321) ;
Hi Irucka,
No problem.
I guess this could be done using:
Sample data:
Dailydo- structure(list(Date = structure(c(11231, 11232, 11233, 11234,
11235, 11236, 11207, 11208, 11209, 11179, 11180, 11181, 11151,
11152, 11123, 11093, 11064, 11065, 11035, 11036, 11008, 11009,
10979, 10980, 11347,
On Feb 13, 2013, at 9:25 AM, Marino David wrote:
Dear all mailing listers,
I failed in install source packages in Windows system. I have installed
Rtools in order to install the source package based on the discussion
available on the following link:
On 13/02/2013 1:26 PM, Charles Determan Jr wrote:
Greetings,
I am exploring some random forest analysis methods and have come upon one
aspect I don't fully understand from any manual. The code of interest is
as follows from the randomForest package:
myiris=cbind(iris[1:4],
On Feb 13, 2013, at 12:09 PM, David Winsemius wrote:
On Feb 13, 2013, at 9:25 AM, Marino David wrote:
Dear all mailing listers,
I failed in install source packages in Windows system. I have installed
Rtools in order to install the source package based on the discussion
available on
On Wed, Feb 13, 2013 at 3:09 PM, David Winsemius dwinsem...@comcast.net wrote:
On Feb 13, 2013, at 9:25 AM, Marino David wrote:
Dear all mailing listers,
I failed in install source packages in Windows system. I have installed
Rtools in order to install the source package based on the
I recently installed OpenBUGS322 and obtained the same error using the
schools example. I suspect that I will run into difficulties with other
examples. I want to download the older version but the BUGS website does not
seem to have OpenBUGS321 available any longer.
Are there patches for
There is an archive link at the bottom of the downloads page from which you
can grab 321.
Dan
On Wed, Feb 13, 2013 at 3:53 PM, Paul J Ossenbruggen [via R]
ml-node+s789695n4658464...@n4.nabble.com wrote:
I recently installed OpenBUGS322 and obtained the same error using the
schools example. I
Please learn to search!
A google search on R density estimation brought up the akj()
function in the quantreg package, which would seem to do what you
requested. However, I didn't look very hard and there are probably
still others in other packages.
-- Bert
On Wed, Feb 13, 2013 at 8:35 AM,
Hi All
I have been struggling with this model for some time now and I just can't
get it to work correctly. The messages I get when running the code is:
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will
summary: I can display a lon-lat map on a lattice::layerplot, and I
can display a Lambert conformal conic (LCC) map on a spam::image, but
I can't display an LCC map on a lattice::layerplot. Example follows.
What am I doing wrong?
details:
I've been using `lattice` (via `rasterVis`) successfully
Joshua,
Thanks for the example, and the explanation. Nice article that you wrote -
the figures alone deserve a deeper dive, I think.
As side note, I found out about profiling on another post and did it - it
appears that my ignorance about how slow dataframes can be was the main
problem. After
Following our successful book: 'A Beginner's Guide to R', we are please to
announce an online R course based on this book.
Video/audio files
Discussion board
Video footage of instructors
Nearly every section of ‘A Beginner’s Guide to R’ is covered. Each
chapter is presented as a powerpoint
Hello,
My name is Craig and I need help plotting a line for a multiple linear
regression in R.
Here is my sample data (filename: convis.txt)
Output of convis.txt is (vis and density being predictors of either
avoidance or entrance):
vis den avoid entrance
1 10 1 0. 0.
2 10
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
project.org] On Behalf Of Mark Leeds
Sent: Wednesday, February 13, 2013 2:59 PM
To: r-help@r-project.org
Subject: [R] sweave question
Hi Everyone: I was having trouble getting the plot size correct
Dear Rhelp,
I would like to have 6 xyplots in the same page. Similar to (par(mfrow=c(3,3))
Found this example on the R archives.
library(lattice)
trellis.par.set(theme = col.whitebg())
xy - xyplot(decrease ~ treatment, OrchardSprays,
groups = rowpos, type = a,
On 02/13/2013 08:48 PM, Ozgul Inceoglu wrote:
I have two data matrices that I want to make the correlation between each
column from data1 and each column from data 2 and also calculate the p-value
Matrices dont have the same size and I tried such a script.
bg- read.table (file.choose(),
Dear Rhelp,
I was able to plot 6 figures in one page. I do need help in reducing the space
between the title and the plot and assigning A,B,C,D,E,F to each figure
library(lattice)
trellis.par.set(theme = col.whitebg())
xy - xyplot(decrease ~ treatment, OrchardSprays,
main=Some plot,
thanks dan. I'll try the double slash on both sides when I get back later
tonight. In the solution on
the net, he only had the backslash on the end quotes ( well there was a
backslash at the beginning but that's a real backslash needed for latex
commands ). I'll let you know how it works out.
Hello,
The first error message says:
Error in model.frame.default(formula = r ~ tm, drop.unused.levels =
TRUE) : variable lengths differ (found for 'tm')
Please compare the size of 'r' and 'tm'.
Regards,
Pascal
Le 14/02/2013 07:14, Craig O'Connell a écrit :
Dear R-Help,
I'm using an
On Feb 13, 2013, at 3:33 PM, Benjamin Caldwell wrote:
Joshua,
Thanks for the example, and the explanation. Nice article that you wrote -
the figures alone deserve a deeper dive, I think.
As side note, I found out about profiling on another post and did it - it
appears that my ignorance
Look at the gsubfn package, it has functionality to do this.
Here is an example from the vignette:
fn$cat(pi = $pi, exp = `exp(1)`\n)
pi = 3.14159265358979, exp = 2.71828182845905
The formula syntax to function conversion in the package may help with the
last part.
On Fri, Feb 8, 2013 at
Hi Lisa
You can use the page function of xyplot to do this
xy -
xyplot(decrease ~ treatment, OrchardSprays,
groups = rowpos, type = a,
page = function(n){
grid.text(LETTERS[j],
y = 0.95,
x = 0.01,
That makes sense David; thanks again everyone for your help.
*Ben Caldwell*
Graduate Fellow
University of California, Berkeley
130 Mulford Hall #3114
Berkeley, CA 94720
Office 223 Mulford Hall
(510)859-3358
On Wed, Feb 13, 2013 at 4:25 PM, David Winsemius dwinsem...@comcast.netwrote:
On Feb
Hi
Dan is correct
The alternative is to use a chunk to create the plot
eg
reg3print, results=hide, echo=FALSE=
pdf(reg_tree-fig3.pdf, width = wid, height = hei)
plot(cal.tree,uniform=TRUE,compress=TRUE,margin=0.0)
text(cal.tree, all=TRUE,fheight=1.0,fwidth=1.0)
dev.off()
@
an call the file in
Mark,
just to be clear, since R uses the backslash character as an escape character
inside strings, then any backslash that you want to appear in your latex code
must be escaped, i.e. it must be doubled. But any backslash character that is
being used as an escape character should remain as a
Hi Lisa
have a look at par.settings in ?xyplot
trellis.par.get() shows the settings
trellis.par.get()[[27]]
$left
$left$tck
[1] 1
$left$pad1
[1] 1
$left$pad2
[1] 1
$top
$top$tck
[1] 1
$top$pad1
[1] 1
$top$pad2
[1] 1
$right
$right$tck
[1] 1
$right$pad1
[1] 1
$right$pad2
[1] 1
I thought it was going to the r-list.
Date: Wed, 13 Feb 2013 11:33:13 -0500
From: bbol...@gmail.com
To: likhonna...@hotmail.com
Subject: Re: [R] standard error very high in maximum liklihood fitting
I can't respond to e-mails off-list. Please follow up on r-help.
cheers
Dear all r-users,
I have this code below to draw two squares, small and big square. I would like
to colour the small square with red and the big square with blue for example.
I tried using polygon but fail. Thank you so much for your help.
par(mar=c(4,4,2,1.2),oma=c(0,0,0,0),xaxs=i,
Other people in this thread have explained the rule of double
backslashes. I just want to add one more comment:
That clever solution was in 2009 when knitr has not come out, and I
have used this picture several times to show how much I dislike it:
Hi,
?rect
par(mar=c(4,4,2,1.2),oma=c(0,0,0,0),xaxs=i, yaxs=i)
plot.new()
plot.window(xlim= c(0,8), ylim=c(0,8),col=blue,lwd=3, bg=5)
axis(1)
axis(2)
title(main=The Overall Title)
title(xlab=An x-axis label)
title(ylab=A y-axis label)
box()
rect(0,0,4,4,col='blue',border=NA)
If you are on windows then there is a task scheduler for windows.
Generally the best solutions are to use the OS tools to schedule your task,
chron or task scheduler.
If you need a solution inside of R then you can use the tclTaskSchedule
function in the tcltk2 package.
On Mon, Feb 11, 2013 at
The thread starting with this post:
https://stat.ethz.ch/pipermail/r-sig-teaching/2013q1/000534.html answers a
similar question and many of the answers there should apply here as well.
On Tue, Feb 12, 2013 at 11:51 AM, David Arnold dwarnol...@suddenlink.netwrote:
All,
If you have any good
See ?commandArgs for a way to access the arguments on the command line.
With that you can write the FunkyCold.R script to grab the command line
arguments and run the proper function (after loading your package). If you
give more detail on what you want to accomplish we may be able to give more
Hello,
Herewith is one approach:
grid1 - rbind(OrchardSprays, OrchardSprays, OrchardSprays,
OrchardSprays, OrchardSprays, OrchardSprays)
grid1$category - rep(c('A','B','C','D','E','F'), each=nrow(OrchardSprays))
trellis.par.set(theme = col.whitebg())
xy - xyplot(decrease ~ treatment |
i'm somehow embarrassed to even ask this, but is there any built-in
method for doing this:
my_list - list()
my_list[[1]] - matrix(1:20, ncol = 5)
my_list[[2]] - matrix(20:1, ncol = 5)
now, knowing that these matrices are identical in dimension, i'd like
to unfold the list to a 2x4x5 (or some
FYI - this is my current method, but somehow i just don't like it ;-)
foo - array(NA, dim = c(4,5,length(my_list)))
for(k in 1:length(my_list)) {
foo[,,k] - my_list[[k]]
}
-m
On Thu, Feb 14, 2013 at 1:03 AM, Murat Tasan mmu...@gmail.com wrote:
i'm somehow embarrassed to even ask this, but is
Hi,
May be this helps:
library(plyr)
res-aaply(laply(my_list, as.matrix),c(2,3),function(x) x)
attr(res,dimnames)- NULL
identical(res,foo)
#[1] TRUE
A.K.
- Original Message -
From: Murat Tasan mmu...@gmail.com
To: r-help@r-project.org
Cc:
Sent: Thursday, February 14, 2013 1:13 AM
HI,
#ag data was created
bg- as.matrix(read.table(text=
Otu00022 Otu00029 Otu00039 Otu00042 Otu00101 Otu00105 Otu00125 Otu00131
Otu00137 Otu00155 Otu00158 Otu00172 Otu00181 Otu00185 Otu00190 Otu00209
Otu00218
Gi20Jun11 0.001217 0 0.001217 0 0.00 0 0
thank you, this code works:
library(plyr)
join(dat1,dat2,by=c(cu.nr.,name),type=right)
but my dat2 frame has a lot of columns, which i don't want to match.
How can i say, that only the column value should be match to dat1 ?
Thank you.
Mat
--
View this message in context:
Dear Duncan,
Thank you. It helped a lot.
I was able to get it correct though I couldn't get it working under
simpleTheme() (for publication purpose).
#this gave me the correct format.
library(grid)
library(lattice)
xy -xyplot(decrease ~ treatment, OrchardSprays,
main= Some plot,
Thank you all for the answers. I really need to learn a lot.
Bu I also discover cor2m(x, y, trim = TRUE, alpha = 0.05)
in ecodist package, which gives an output file with significant correlations.
Özgül
YjHI,
#ag data was created
bg- as.matrix(read.table(text=
Otu00022 Otu00029 Otu00039
Dear Duncan and Pascal,
Thank you for the response.
Duncan:
I was able to fix the space between title and figure. I would also like to
have separate main titles for each row of figures in addition to the individual
titles.
xy -xyplot(decrease ~ treatment, OrchardSprays,
main= Some
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