Hey,
Thank you for your swift responses, both options work great.
Aimee
On Wed, Jun 15, 2011 at 11:30 PM, Rolf Turner rolf.tur...@xtra.co.nzwrote:
On 16/06/11 11:07, Aimee Jones wrote:
Hi all,
My apologies if this message is incredibly inept but I am very new to both
computer programming
Sorry, forgot to mention ncredint is from emdbook.
Thanks,
Tina
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Sent from the R help mailing list archive at Nabble.com.
I will break my query into 2 parts:
1. My main idea is to give some data as an input and if any seasonality is
there in the input, it should be captured automatically and the
corresponding frequency automatically generated. please comment whether this
is possible with auto.arima()
2. If
Use the `xlim` parameter of the `plot` function.
IFor example, if X1 and X2 are the variables that contain the values of your
x-axis,
do xlim1 - range(X1,X2),
than do plot(, xlim = xlim1,...)
Hope this helps.
2011/6/15 bjmjarrett bjmjarr...@gmail.com
Hi all,
I have scoured the
Dear all,
I am estimating a bivariate probit model using the package VGAM:
fit1 = vglm(cbind(y1, y2) ~ x1+x2, binom2.rho, data=dat, trace=TRUE)
I would like to estimate this via the method vglm.fit (in an analogous way
as lm.fit for lm or glm.fit for glm). Unfortunately my trials did
Hello everyone,
I use the following command lines to get important variable from training
dataset.
data.controls - cforest_unbiased(ntree=500, mtry=3)
data.cforest - cforest(V1~.,data=rawinput,controls=data.controls)
data.cforest.varimp - varimp(data.cforest, conditional = TRUE)
I got
I am trying to optimize a simple function, but I want to optimize it for
values of k between 0 and 1.
I read the help file for constrOptim function but it is always giving me
the error
constrOptim((0.4),simulation,NULL,ui=rbind(c(0,0),c(1,1)))
Error in ui %*% theta : non-conformable arguments
Hello,
For one reason or another, I cannot install Rcmdr on my R 2.12.2 ubuntu 11.4
system.
I run R as root When I try to install Rcmdr, then whatever mirror I select, I
get the message:
install.packages('Rcmdr',dependencies=TRUE)
Installing package(s) into /usr/local/lib/R/site-library
(as
Dear Sir,
I would like to ask whether there is any tool in R, developed for the function
of non parametric Anova, where the non parametric analysis is able to compute
the p-value for interaction as well (similar to Anova)? If not, would sir like
to suggest any of the other statistical software
On 06/15/2011 09:51 PM, bjmjarrett wrote:
Hi all,
I have scoured the archives of this forum but nothing quite seems to fit the
bill...
I would like to plot a graph displaying two variables (y axes) that share
date as the x axis. However, the date values for each variable are not the
same - for
Hi everyone,
I retrieved the values of form elements such as radiobuttons, text
area,textbox etc into MySQL database. I retieved the values from MySQL db to
R using RODBC package. If i want to do a corelational analysis using the
values in textarea and radiobutton how is it possible as textarea
On Thu, 16 Jun 2011, Frans Marcelissen wrote:
Hello,
For one reason or another, I cannot install Rcmdr on my R 2.12.2 ubuntu 11.4
system.
I run R as root When I try to install Rcmdr, then whatever mirror I select, I
get the message:
install.packages('Rcmdr',dependencies=TRUE)
Installing
Hi everyone,
I want to do data analysis using the values retrieved from a MySQL
database. Is there a way to save the results of data analysis in R.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
People,
I want to create seven plots on the one graph - each with it's own Y
axis and scale - I want the plots overlaid because it is the shape of
the graphs that I want to compare, not so much the values. I have found
examples where people show how to put two Y axes on the left of the plot
Dear Philip,
If the values are not important, then you don't need different Y-axes. Why not
standardise the seven datasets so they have a common scale?
Best regards,
Thierry
ir. Thierry Onkelinx
Instituut voor
On 06/16/2011 07:12 PM, amrita gs wrote:
Hi everyone,
I want to do data analysis using the values retrieved from a MySQL
database. Is there a way to save the results of data analysis in R.
Hi amrita,
If you mean save the output of an analysis, there are several ways.
1) Enter
On 06/16/2011 07:12 PM, Philip Rhoades wrote:
People,
I want to create seven plots on the one graph - each with it's own Y
axis and scale - I want the plots overlaid because it is the shape of
the graphs that I want to compare, not so much the values. I have found
examples where people show how
On 06/16/2011 09:23 AM, Jim Lemon wrote:
On 06/16/2011 07:12 PM, amrita gs wrote:
Hi everyone,
I want to do data analysis using the values retrieved from a MySQL
database. Is there a way to save the results of data analysis in R.
Hi amrita,
If you mean save the output of an analysis,
get(a)[[b]][[c]]
with
b - 2011-01-02
Sent from my iPad
On Jun 15, 2011, at 9:58, Franc Lucas franc.lu...@web.de wrote:
Hello,
I am wondering how to get the quotation marks into a variable expression. I
can't escape it with the backslash \ ...
Example:
I can access my data
Another update: I ditched the pre-installed version of openmpi and
installed openmpi from source (./configure --without-openib).
Compiling and running your test programme gives me the following error:
unger@zytosrv01dmi:~/R_projects/OS ./mtest
[zytosrv01dmi:6094] *** An error occurred in
On 16.06.2011 10:25, Animesh wrote:
I am trying to optimize a simple function, but I want to optimize it for
values of k between 0 and 1.
I read the help file for constrOptim function but it is always giving me
the error
constrOptim((0.4),simulation,NULL,ui=rbind(c(0,0),c(1,1)))
Your
Try something like:
par(mar=c(4,2,1,12),tcl=0.2,mgp=c(1,0,0))
plot(1:10,1:10)
for (i in 1:7)
{
par(new=TRUE)
plot(1:10,(i+(1:10)+rnorm(10,0,0.4)),yaxt='n',col=i,type='l')
axis(4,line=(i-1)*1.5,col=i-1,col.ticks=i-1)
}
You may need to tweek around the options a bit and check that the
Hi
I got a file that looks like this: (i have shorten it alot the real file is
over 200k rows long)
chr10 rs7909677 101955 A G 0 1 0 1 0 0...
chr10 rs2436025 238506 C G 1 0 0 1 0 0...
chr10 rs11253562 148946 C T 0 1 0 0 1 ...
chr10 rs1105116 230788 G T 0 0 1 0 0 1...
chr10 rs4881551 149076 A G 0
Hi all,
I am trying to re-compile some unmaintained (it seems) packages, namely
rSoNIA
and dynamicnetwork from:
http://csde.washington.edu/~skyebend/rsonia/rsoniaDemo/
These packages predates R 2.10.0 so they need to be recompile.
After split the single big file in /man in each packages into
Found what was wrong with my code
changed:
inFile - file('gwas_data_chr10.gen')
to:
inFile - file('gwas_data_chr10.gen','r')
Dunno why its important but it is :P
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Sent from the R help
The script command coda is not necessary, unless you want to read in in
coda-format output. Necessary are the other commands: history save
(odc). save (txt) lets you read the on-screen output of winbugs later as
a text-file.
Another way is also to take the saved last values of the chains and use
On Thu, 16 Jun 2011, Joel wrote:
Found what was wrong with my code
Please follow the posting guide, and give the context asked for there.
changed:
inFile - file('gwas_data_chr10.gen')
to:
inFile - file('gwas_data_chr10.gen','r')
Dunno why its important but it is :P
You didn't open the
On 16.06.2011 14:46, Ben Rhelp wrote:
Hi all,
I am trying to re-compile some unmaintained (it seems) packages, namely rSoNIA
and dynamicnetwork from:
http://csde.washington.edu/~skyebend/rsonia/rsoniaDemo/
These packages predates R 2.10.0 so they need to be recompile.
After split the single
bbolker wrote:
bialozyt at biologie.uni-marburg.de writes:
you answerd to Nancy Shackelford about Clarks 2Dt function.
Since the thread ended just after your reply,
I would like to ask, if you have an idea how to use this function in R
I got started on your problem, but I didn't finish
bbolker wrote:
bialozyt at biologie.uni-marburg.de writes:
you answerd to Nancy Shackelford about Clarks 2Dt function.
Since the thread ended just after your reply,
I would like to ask, if you have an idea how to use this function in R
I got started on your problem, but I didn't finish
On 15.06.2011 15:58, Franc Lucas wrote:
Hello,
I am wondering how to get the quotation marks into a variable expression. I
can't escape it with the backslash \ ...
Example:
I can access my data frame via
TABLE$2011-01-02$columnD
Now I want to do this
On Thu, 16 Jun 2011, Mr Rhelp wrote:
Hi all,
I am trying to re-compile some unmaintained (it seems) packages, namely rSoNIA
and dynamicnetwork from:
http://csde.washington.edu/~skyebend/rsonia/rsoniaDemo/
These packages predates R 2.10.0 so they need to be recompile.
Well, re-installed.
On 16 June 2011 at 07:17, Frans Marcelissen wrote:
|
| Hello,
| For one reason or another, I cannot install Rcmdr on my R 2.12.2 ubuntu 11.4
system.
| I run R as root When I try to install Rcmdr, then whatever mirror I select, I
get the message:
Rcmd is an Ubuntu package too, so just do
$
Dear R users,
I am using package alphahull version 0.2-0 with R-2.13.0. Here is my problem.
I have produced a 2-D plot of points and need to draw convex hulls around some
subsets of these points. So I just need to add the convex hulls to the already
existing plot. That is why I cannot use the
On 06/16/2011 03:04 AM, siddharth arun wrote:
I will break my query into 2 parts:
1. My main idea is to give some data as an input and if any seasonality
is there in the input, it should be captured automatically and the
corresponding frequency automatically generated. please comment
Hi
Dear R users,
I am using package alphahull version 0.2-0 with R-2.13.0. Here is my
problem.
I have produced a 2-D plot of points and need to draw convex hulls
around
some subsets of these points. So I just need to add the convex hulls to
the already existing plot. That is why I
I am not sure what you actually want to accomplish. If you try to correlate
numeric/rank data with text data, I have no clue how that could be achieved
(other than with text length, or presence/absence of a comment). If you try
to figure out how you prevent the cor() function to fail when it
Those are in fact the coefficients for p and q they are estimating, though
their M is different. Who knows what they did with that.
The data source was:
Title: Diffusion models of mobile telephony in Greece
Source: Telecommunications policy [0308-5961] Michalakelis yr:2008 vol:32
iss:3-4
Greg Snow Greg.Snow at imail.org writes:
The individual tests on coefficients in logistic regression
are generally based on a Wald test statistic.
Unfortunately there is a bit of a paradox possible in this
case where the coefficient is highly
significant, but due to a flattening of the
Hi all,
What is the best package to use to evaluate correlations between events
by time (species co-occurrence).
Chron?
I would like to determine fi there is any solid relationship between the
occurrence of critter A given critter B is present at a given time frame.
Bruce
Hi everybody,
I just tried to run R on one of my projects
but it did not want to run:
R version 2.12.1 (2010-12-16)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-bit)
some lines deleted
Loading required package: utils
Error
I got an array similar to the one below, and want to replace all NAs with the
previous value.
99 8.2 b
NA 8.3 x
NA 7.9 x
98 8.1 b
NA 7.7 x
99 9.3 b
...
i.e. the first two NAs should be replaced to 99, whereas the last one should
be 98.
I would like to apply a function to reach row, checking if
Jannis,
Beautiful! Thanks for the useful responses from others as well.
Regards,
Phil.
On Thu, 16 Jun 2011 12:49:58 +0100 (BST), Jannis wrote:
Try something like:
par(mar=c(4,2,1,12),tcl=0.2,mgp=c(1,0,0))
plot(1:10,1:10)
for (i in 1:7)
{
par(new=TRUE)
Hello
I have a annoying problem with R (which I am running in MAC).
Every time I enter a function and I press enter to run it, I get many
additional ´s, it is really bothering me. I have tried to google to find out
how to fix the problem but I did not succeed. Anyone with similar experience
Dear R.oo package users,
while testing some functionality of the R.oo, I found that during the first
construction of a object from a class, the constructor is twice called, but
only one object is finalized.
In all subsequent creation processes, the constructor is (expectedly) called
once.
Do you mean prompts (the that indicates R is waiting for input)?
Your issue is not clear. Please post a copy/paste of your session, as
well as your sessionInfo().
On Thu, Jun 16, 2011 at 7:16 AM, Rosario Garcia Gil
m.rosario.gar...@slu.se wrote:
Hello
I have a annoying problem with R (which I
Dear list,
I have read several posts on this topic. I would use the same
methodology as proposed
by Simon Wood in this post:
http://r.789695.n4.nabble.com/variance-explained-by-each-term-in-a-GAM-td836513.html
My first question is:
Does anyone know a scientific source (paper, book,...) that
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
On 06/16/2011 01:47 PM, Rob James wrote:
Ben,
Thanks for this. Very helpful and clearly others have tripped over the
same problem
I would have supposed that the solution was to ask lrm (or glm) to use
LR rather than Wald, but I don't see syntax
Hi,
If you truly have an array, this is option that should be much faster
than a loop:
index - which(is.na(dat))
dat[index] - dat[index - 1]
the only catch is that when there previous value is NA, you may have
to go through the process a few times to get them all. One way to
automate this
Petr Savicky-2, thanks you. It seems the code works very well. I use rate=1,
so common is between 0 to 1. Thanks again.
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Sent from the R help mailing list
Non- Parametric equivalent to parametric anova is Kruskal-Wallis test - I am
not sure R has any function for this - I am new to R (I think R should have it
already) - SAS has this option.
Sharif
-Original Message-
From: r-help-boun...@r-project.org
Hi,
I am working under Linux and have an executable R script like this:
#! /usr/bin/env Rscript
script logic
X11()
plot(data, ...) # as placeholder for some wireframe plot
readline(prompt = Hit Return to quit.)
X11() and readline() are only run, if no other device is requested. My problem
now
Dear members,
I'm fitting linear model using lm which has numerous auto-regressive terms as
well as other explanatory variables. In order to calculate prediction
intervals, i've used a for-loop as the auto-regressive parameters need to be
updated each time so that a new forecast and
Hi All - I am using the daisy function from the cluster library to create a
dissimilarity matrix. I'm going to use that matrix to run a cluster
analysis. My participants are identified with the variable, hhid. However,
when I try to keep hhid in the dataset that I use to create the
Bill,
Thank you for the correction; yes, Nevilles' is an algorithm to produce the
same Lagrange interpolating polynomial. And thank you for the polynomF
package!
Don Slowik
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View this message in context:
Hi,
my problem sounds simple but I've been trying and looking for a solution,
but just can not find out how to solve it.
I have a dataset and want to do a GAM with binomial link function, random
effects (for individuals as there are severeal measurements for everyone)
and a time-spline.
For
Kristian,
Another update: I ditched the pre-installed version of openmpi and
installed openmpi from source (./configure --without-openib).
A very reasonable approach. Remembering my own struggles with SuSE years
ago, I did not dare to propose that procedure.
Compiling and running your test
Using a line width 1 results in not only a thicker line but also some fuzz
in the other direction, as shown in this example program. You will see that
the thick vertical black lines extend below the gray scale horizontal lines.
Does anyone know whether this is intended or is it a bug? The
Hi Frank,
It's not inaccuracy, exactly, and it's intentional.
The default behavior is to use a round endcap on a line, and with such
a large linewidth that endcap is arcing below and above the starting
points.
This being R, there's a par for that: putting lend=1 in your lines()
statements will
Hi,
If 100 frames can work but 730 cannot, I think this might be due to
the limit of ImageMagick. If that is the case, I do not have any
solutions from R's aspect, instead, you may want to try
GraphicsMagick, which is similar to ImageMagick. I'm not sure if it is
better than ImageMagick in terms
On Thu, 16 Jun 2011, Sarah Goslee wrote:
Hi Frank,
It's not inaccuracy, exactly, and it's intentional.
The default behavior is to use a round endcap on a line, and with such
a large linewidth that endcap is arcing below and above the starting
points.
This being R, there's a par for that:
On Thu, Jun 16, 2011 at 3:43 PM, Prof Brian Ripley
rip...@stats.ox.ac.uk wrote:
On Thu, 16 Jun 2011, Sarah Goslee wrote:
Hi Frank,
It's not inaccuracy, exactly, and it's intentional.
The default behavior is to use a round endcap on a line, and with such
a large linewidth that endcap is
On Thu, 16-Jun-2011 at 09:19AM -0400, Jinrui Xu wrote:
Thanks for your feedback.
I think the problem is not because of many levels. There is only 1
column with two levels as class labels in my input data.
Below is my code. The commandline data.cforest.varimp -
varimp(data.cforest,
I don't think that this approach is appropriate here. Each iteration after the
1st the lm/predict combination will assume that the new data is exact when in
fact it is an estimate with some error involved. To properly do this you need
to take into account that variability. There is a time
You could do this using permutation tests. If everything is balanced and
orthogonal then you can permute the predictors, otherwise you can follow these
main steps:
1. Formulate the test of interest as a full and reduced model test and find the
F statistic (or other, but I will assume F) for
Dear List,
I wanted to calculate the asymmetrical confidence interval based on the sample
statistic and standard error that available from the published report (complex
survey-based).
The calculation details can be seen from pages 17-18 of the document at the
following link:
Greetings to the help mailing list.
I am in the process of translating a large graphic from xyplot to ggplot2 (13
columns by about rows).
I have been unsuccessful trying to understand how to place the following text
strings after three days of:
* Perusing Wickham's gg2plot book;
* Searching his
Hi,
As far as I know secondary y-axis and multiple pages are not possible
in ggplot2 (there are workarounds for the latter in the ggplot2 list
archives). For the subtitle, you could implement it with grid.text and
grid viewports,
library(gridExtra)
library(ggplot2)
grid.arrange( qplot(1,1), sub
Hi all,
I have the following script which fills the values which are less than
the mean of a given timeseries.
If you look closely, the colored regions are out of line.
Any suggestions how I can rectify this?
Thanks
Muhammad
# -
#rm(list=ls())
x - abs(rnorm(100))
tt - 1:100
m -
Hi all~
I have a bit of stupid question. And I promise, I have struggled through this
and it sort of pains me to post this question...
I have the following vector which is are the estimated parameter values output
from optim.
$Rates
[1] 0.006280048 0.330934659
I want to match the order in
On Jun 16, 2011, at 4:52 PM, Jeremy Beaulieu wrote:
Hi all~
I have a bit of stupid question. And I promise, I have struggled through this
and it sort of pains me to post this question...
I have the following vector which is are the estimated parameter values
output from optim.
Folks:
This is sufficiently tricky that a word of explanation might be
helpful to reveal the magic.
Rates - c(0.006280048, 0.330934659)
Index.Matrix - matrix(c(1, 2, 1, 2), 2, 2)
Rates
[1] 0.006280048 0.330934659
Index.Matrix
[,1] [,2]
[1,] 1 1
[2,] 2 2
Just index
caret has many useful preprocessing facilities for numeric predictors,
such as removing near-zero-variance predictors, removing correlated
predictors, removing linear combinations, centering/scaling, and
Box-Cox transformations. However, these don't work for factor data,
which is common in many
Without seeing the model I'm not clear on the cause. In general it is not
very useful to compute 1 d.f. tests for parameters that represent only part
of a meaningful hypothesis.
Note that anova.lrm computes Wald statistics, which are subject to the
Hauck-Donner effect (which may not be the cause
Dear R People:
Suppose I have the following two character vectors:
xf
[1] W NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
xg
[1] NA k h NA g r j NA v d NA v NA z r r i
I want to end up with
W k h ...
What is the best way to achieve this, please? I was thinking that
Hi,
You did not specify what assumptions you can make about xf and xg
(such as will they have identical lengths and is it possible both
could contain nonmissing values in the same element?), but this seems
a straightforward approach in your little example:
index - is.na(xf)
xf[index] - xg[index]
I made different assumptions than Josh.
xf-c(W,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA)
xg-c(NA,k,h,NA,g,r,j,NA,v,d,NA,v,NA,z,r,r,i)
xf
xg
unlist(apply(cbind(xf,xg), 1, function(x) x[!is.na(x)]))
as.vector(unlist(apply(cbind(xf,xg), 1, function(x) x[!is.na(x)])))
I am still thinking about this problem. The solution could look something
like this (it's net yet working):
k-lapply(h, function (x) x*0) # I keep the same format as h, but set all
values to 0
years-c(1997:1999) # I define the years
for (t in 1:length(years))
{
year =
I am new to R and am having difficulty merging 2 data sets, both of which have
the same 30 variables and about 2,000 records. I've looked high and lowâPaul
Johnson's help page, through some of the 5,420 (yikes!) results for âmergeâ
on the R list archives, and google searchesâand I'm
Dear R-users,
I computed a simple coxph model and plotted survival over time with
associated confidence intervals for 2 covariate levels (males and
females).
M1 - coxph(survobject~sex, data=surv)
M1
survsex - survfit(survobject~sex,data=surv)
summary(survsex)
plot(survsex, conf.int=T,
Sorry, Patrick and other victims. My bad~~
The data file can be accessed at
http://zhanglab.ccmb.med.umich.edu/TM-fold/featureSelection_rec.vectors
The code is attached below. Error happens at data.cforest.varimp -
varimp(data.cforest, conditional = TRUE): Error in
Dear R users,
I hope this email finds you well,
My name is Mariam and I am currently using R in my thesis
project. I is about modeling investors' sentiment.
My R skills are very modest and I am trying to solve a Garch in mean
equation using the rgarch package.
The main issue I am facing is with
the examples work great but it gives me this error on this file
http://r.789695.n4.nabble.com/file/n3603737/il1ra_L.csv il1ra_L.csv
Age.co-c(dat2b$Dr_Age)
Sex.co-as.factor(dat2b$Sex)
casecont.co-as.factor(dat2b$Self_T1D)
stat.co-as.factor(dat2b$status)
m -
Hi R Help list
I'm looking to visualise US foreign aid 1946-2009 and I have the dataset for
this. The trouble is it's a bit too complex and I need to simply it
I want to merge all of the rows with the same country together and add up the
individual totals to make one total figure per country
Hello,
I am working on a project to create some scatter plots. I have syntax
for 26 plots, and 22 of them display as they should. But here, for
example, is a sample of the command syntax I am using:
good - complete.cases(affect1,adh1scr)
plot
Hi,
I am working on a heatmap and clustering all the rows with the method of
'ward'.
But I notice that my rows are in a weird order which is not what I want /
expect.
Could anyone help on this? My questions are with the figure below. Thanks
in advance
To whom it may concern,
I am trying to maximize a log-likelihood function using optim. This is a
simple problem with only 18 parameters. To conserve memory, I am using sparse
matrices (SLAM) for some of the data matrices used in the computation of the
likelihood. However, optim appears to
Something like this could work for you (note that a few other packages would be
faster, such as data.table), but plyr is intuitive.
require(plyr)
# example data set
dat - data.frame(col1 = rep(c(a,b), each=5),
col2 = rep(c(prog1,prog2,prog3,prog4,prog5), 2),
col3 = rnorm(10), col4 =
Dube, Jean-Pierre wrote:
To whom it may concern,
I am trying to maximize a log-likelihood function using optim. This is a
simple problem with only 18 parameters. To conserve memory, I am using
sparse matrices (SLAM) for some of the data matrices used in the
computation of the
Dear R People: (particularly those who have build Rcmdr Plugin packages):
I'm building a new Plugin and keep getting the following error:
Error in if (is.null(where) || where = n) rbind(object1, object2)
else if (where :
missing value where TRUE/FALSE needed
Error in library(RcmdrPlugin
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