Hi,
I just started learning R to do survival analysis using coxphfit and survfit
(to compare to neural network prediction for survival). Currently, I can
generate the Cox model using N cases and then get the estimated survival times
for the same N cases with survfit.cox <- coxph(Surv(time,delta
The typos were just transcription errors I'' report out the session info
On Sat, Aug 14, 2010 at 5:35 PM, Joshua Wiley wrote:
> That worked for me once I properly quoted "test.RData" on
>
> > sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-pc-mingw32
>
> locale:
> [1] LC_COLLATE=English_Un
- Original Message
From: Seth Falcon
To: Stephen Liu
Cc: r-help@r-project.org
Sent: Sun, August 15, 2010 12:56:16 PM
Subject: Re: [R] 64 bit RSQLite
>> Where can I find 64 bit RSQLite?
>>
>> It seems not there;
>> RSQLite: SQLite interface for R
>> http://cran.r-project.org/web/packag
Tal Galili [Thu, Jul 29, 2010 at 03:42:28PM CEST]:
> This is the new and exiting kid on the block:
> http://stats.stackexchange.com/
>
Sorry for being late to this thread, but while looking somewhat exciting,
this does not seem to be a mailing list.
--
Johannes Hüsing There is so
On Saturday 14 August 2010 23:08:31 Peter Dalgaard wrote:
> Johannes Graumann wrote:
> > Hi,
> >
> > can someone point me at material to understand how in
> > http://upload.wikimedia.org/wikipedia/commons/8/89/Boxplot_vs_PDF.png the
> > "fivenum"-corresponding percentages might be calculated?
>
>
Hi Stephen,
On 8/12/10 7:10 PM, Stephen Liu wrote:
> Hi folks,
>
> Ubuntu 10.04 64 bit
>
> Where can I find 64 bit RSQLite?
>
> It seems not there;
> RSQLite: SQLite interface for R
> http://cran.r-project.org/web/packages/RSQLite/index.html
You should be able to install the RSQLite source pac
Try this:
library(sos)
findFn('bandpass')
If necessary, install the package first. I got 24 hits in eight packages.
Hopefully one or more of them will be suitable.
HTH,
Dennis
On Sat, Aug 14, 2010 at 8:52 PM, nuncio m wrote:
> Hello list,
> Is there any way to bandpass filter in
Hello list,
Is there any way to bandpass filter in R
thanks
nuncio
--
Nuncio.M
Research Scientist
National Center for Antarctic and Ocean research
Head land Sada
Vasco da Gamma
Goa-403804
[[alternative HTML version deleted]]
__
R
Your second fit makes no sense, as you can easily tell if you look at the
regression summaries. Fitting with spray as a categorical variable gives you
an overall p-value of less than 2.2e-16, while fitting with
as.numeric(spray) gives an overall p-value of .2118. The fit you've done
with as.numeric
On Aug 14, 2010, at 6:23 PM, Steven C. Bagley wrote:
In R 2.11.1 on Mac OS 10.6.4, the following code works, but if the
print statement is removed or commented out, then an infinite
recursion results. Can someone explain what is going on? Thanks. --
Steve
foo2=function(f1, f2){
print(f1
In R 2.11.1 on Mac OS 10.6.4, the following code works, but if the print
statement is removed or commented out, then an infinite recursion results. Can
someone explain what is going on? Thanks. --Steve
foo2=function(f1, f2){
print(f1)
function(x){
f1(x) + f2(x) } }
foo=function(...) Re
I need to increment cells of a matrix (collusionM). The indexes to increment
are in an index (matchIndex). This is sample code
library(seqinr)
library(Matrix)
x <- "abcabcabc"
mx <- s2c(x)
collisionM <- Matrix(0,nrow=10, ncol=10, sparse=TRUE)
matchIndex <- list()
rows <-
That worked for me once I properly quoted "test.RData" on
> sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-pc-mingw32
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_Unite
In the particular application I have I save "test.Rdata" to a sub directory
dir<-"Example"
dir.create(dir)
test<-data.frame(a=c(1,2,3),b=c(3,4,5)
full<-file.path(dir,"test.Rdata,fsep=.Platform$file.sep)
save(test,file=full)
load(full)
returns NULL
it works fine when the object is saved to the wor
I need to increment cells of a matrix (collusionM). The indexes to increment
are in an index (matchIndex). This is some of the code
for (j in 1:(rows-1)) matchIndex[[j]] <- which(mx[j]==mx)
for (j in 1:(rows-1)) collisionM[j,matchIndex[[j]]] <-
collisionM[j,matchIndex[[j]]] + 1
Hi
I am trying to run an ANOVA on data with unequal variance. I am new to nlme,
but to my understanding I need to use the gls function. I have single response
variable (distance which is continuous) and the explanatory variable is
individual ID (class variable: individuals differ in the varia
Johannes Graumann wrote:
> Hi,
>
> can someone point me at material to understand how in
> http://upload.wikimedia.org/wikipedia/commons/8/89/Boxplot_vs_PDF.png the
> "fivenum"-corresponding percentages might be calculated?
Looks like a pretty straightforward application of pnorm() and qnorm().
Hi,
can someone point me at material to understand how in
http://upload.wikimedia.org/wikipedia/commons/8/89/Boxplot_vs_PDF.png the
"fivenum"-corresponding percentages might be calculated?
Thanks, Joh
__
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https://stat
Hi all,
I've got an xts time series with monthly OHLC Dow Jones industrial index
data from 1980 to present, the data is in stored in x.
I've done an OLS fit on the data in 1982::1994 and stored it in extrapolate1
(x[,4] contains the closing value for the index).
> t3 <- seq(1980,1994,length = le
On 14.08.2010 11:21, anderson nuel wrote:
Dear r-help,
I run R CMD INSTALL :
c:\Rp>R CMD INSTALL namepackage
*installing to library'c:/PROGRA~1/R/R-210~1-1/library'
*installing *source* 'namepackage'...
**R
**preparing package for lazy loading
**help
Avis:./man/namepackage-package.Rd:25:'>'
On 14-Aug-10 16:07:14, Thomas Lumley wrote:
> On Sat, 14 Aug 2010, ted.hard...@manchester.ac.uk wrote:
>> Hi Thomas,
>> I'm not too sure about your interpretation. Consider:
>
> It seems hard to interpret "The formula interface is only applicable
> for the 2-sample tests." any other way
>
>>
>> J
On Aug 14, 2010, at 11:43 AM, Musky Dee wrote:
Dear colleagues/contributors,
I'd be pleased if someone could provide insights on how to plot
impulse response functions in a format that can easily be copied in
a word document just as plotting time-series of variables.
I had followed the o
Le 14/08/10 19:13, baptiste auguie a écrit :
Thank you everyone, I think I'll follow the technique used in Rcpp
(dummy vignettes + Makefile).
Cool. Let us (Rcpp team) know if you find better ways or if something is
too much trickery.
It would be great to have a mechanism to select the dri
Thx, I see my problem. more sleep required
On Sat, Aug 14, 2010 at 9:25 AM, Romain Francois wrote:
>
> Le 14/08/10 18:22, steven mosher a écrit :
>
>
>> Stupid question, but its been a long night.
>>
>> If I have a long vector how can I turn it into a list of the same length
>>
>> x<-rep(seq(1,1
Thank you everyone, I think I'll follow the technique used in Rcpp
(dummy vignettes + Makefile).
It would be great to have a mechanism to select the driver for
vignette generation though.
Also, as a side-note, the choice of a driver has its own shortcoming;
I cannot use the features of highlight a
Dear colleagues/contributors,
I'd be pleased if someone could provide insights on how to plot impulse
response functions in a format that can easily be copied in a word document
just as plotting time-series of variables.
I had followed the outline suggested by Benhard Pfaff [see
http://127.0.
Le 14/08/10 18:22, steven mosher a écrit :
Stupid question, but its been a long night.
If I have a long vector how can I turn it into a list of the same length
x<-rep(seq(1,100,by=1),each=10)
Perhaps as.list ?
--
Romain Francois
Professional R Enthusiast
+33(0) 6 28 91 30 30
http://romainf
Stupid question, but its been a long night.
If I have a long vector how can I turn it into a list of the same length
x<-rep(seq(1,100,by=1),each=10)
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https://stat.ethz.ch
On Sat, 14 Aug 2010, ted.hard...@manchester.ac.uk wrote:
Hi Thomas,
I'm not too sure about your interpretation. Consider:
It seems hard to interpret "The formula interface is only applicable for the
2-sample tests." any other way
Johannes' original query was about differences when there
ar
Frank E Harrell Jr Professor and ChairmanSchool of Medicine
Department of Biostatistics Vanderbilt University
On Sat, 14 Aug 2010, David Winsemius wrote:
On Aug 14, 2010, at 9:59 AM, Frank Harrell wrote:
Once you guys figure all this out, I'm glad to modif
install.packages('rms')
require(rms)
?Gls
?plot.Predict
Frank E Harrell Jr Professor and ChairmanSchool of Medicine
Department of Biostatistics Vanderbilt University
On Sat, 14 Aug 2010, Camilo Mora wrote:
Hi everyone:
Is there a function in R to calculate th
On Aug 14, 2010, at 9:59 AM, Frank Harrell wrote:
Once you guys figure all this out, I'm glad to modify bplot to pass
more arguments lattice if needed.
As always, Frank, I appreciate your support. In this case I think it's
not needed. What seems to be needed is simply the correct use of
Hi everyone:
Is there a function in R to calculate the confidence intervals for the
predictions of a GLS(Generalized Least Square) model?
The function "predict" gives confidence intervals for the predictions
of other types of models (lm, glm, etc) but not gls.
Any input will be much appre
Emilie Chary wrote:
> Hello,
> Any idea?
Different test statistic (chi^2 vs. table probability).
>
>
>
>
> À : r-help@r-project.org
> Envoyé le : Jeu 12 août 2010, 12h 17min 10s
> Objet : [R] Difference in Monte Carlo calculation between chisq.test and
> fishe
Shubha Vishwanath Karanth wrote:
> Hi R,
>
>
>
> Does the "step" function used to perform stepwise regression has the
> option to specify the entry/exit significance levels for the independent
> variables? (This is similar to the 'slentry' and 'slstay' option in
> 'Proc reg' of SAS.). Or do we
Saji Ren wrote:
> Hello, Mr Dalgaard:
>
> you're right about the problem.
>
> "Works for me, so there's something you're not telling us Possibly
> that x is not a vector (a data frame, maybe?)."
>
> the mistake message is below:
> Error in if (track01[i] > 1) track01[i] <- 1 :
> missing v
Once you guys figure all this out, I'm glad to modify bplot to pass
more arguments lattice if needed.
Frank E Harrell Jr Professor and ChairmanSchool of Medicine
Department of Biostatistics Vanderbilt University
On Fri, 13 Aug 2010, David Winsemius wrote:
O
The values of slentry and slstay that will avoid ruining the
statistical properties of the result are slentry=1.0 and slstay=1.0.
Frank
Frank E Harrell Jr Professor and ChairmanSchool of Medicine
Department of Biostatistics Vanderbilt University
On Sat, 14 Aug
Hello, Mr Dalgaard:
you're right about the problem.
"Works for me, so there's something you're not telling us Possibly
that x is not a vector (a data frame, maybe?)."
the mistake message is below:
Error in if (track01[i] > 1) track01[i] <- 1 :
missing value where TRUE/FALSE needed
the t
Thanks
I wanna to add the species labels in a cca biplot
based on species and environment conditions (maybe sites are of less
relevance here).
1.
Gavin's suggestion worked but the dots previously displayed
using plot(birdrich.cca, scaling = -1) were gone. Pls advise how to retain
the dots.
2.
Take a look in RColorBrewer package.
On Sat, Aug 14, 2010 at 9:13 AM, elaine kuo wrote:
> Dear list,
>
> I am plotting dots using distinct colors according to the species.
> Like the style of topo.colors(18), please kindly advise if any color vector
> exists for green, red, and blue.
>
> Thank y
If you only have seven species, why not draw the label for the species
(the names() component of your data) at the species score, rather than a
colour?
plot(OBJ, display = c("sites","species"), scaling = 3, type = "n")
points(OBJ, display = "sites", scaling = 3, type = "p")
points(OBJ, display = "
In an ordination such as this, you have two sets of scores; i) one
pertaining to the (dis)similarity of your samples in terms of species
composition, and ii) one pertaining to the species and which species
co-occur. You can't display both sets of information and retain the
meaning of the scores on
Dear list,
I am plotting dots using distinct colors according to the species.
Like the style of topo.colors(18), please kindly advise if any color vector
exists for green, red, and blue.
Thank you
Elaine
[[alternative HTML version deleted]]
_
Hello,
Thanks for the response.
matplot was tried for its function to distinguish assigned parts of a matrix
by letters,
for I wanna differentiate the dissimilar columns in a matrix.
Any suggestion based on the idea above will be highly appreciated, such as
points.
Elaine
On Sat, Aug 14, 2010
Hello,
Any idea?
À : r-help@r-project.org
Envoyé le : Jeu 12 août 2010, 12h 17min 10s
Objet : [R] Difference in Monte Carlo calculation between chisq.test and
fisher.test
Hello all,
I would like to know what the difference is between chisq.test and
fisher.te
Hi R,
Does the "step" function used to perform stepwise regression has the
option to specify the entry/exit significance levels for the independent
variables? (This is similar to the 'slentry' and 'slstay' option in
'Proc reg' of SAS.). Or do we have any other package which does the
above? Than
> Dear List,
>
> I am trying to plot the result of cca using matplot but failed.
> Pls kindly help and thanks.
There is no 'matplot' method for "cca" objects. Where did you get the idea
that there was one? If you want to plot the cca object, then ?plot.cca and
?ordiplot should help. Also look at t
Dear r-help,
I run R CMD INSTALL :
c:\Rp>R CMD INSTALL namepackage
*installing to library'c:/PROGRA~1/R/R-210~1-1/library'
*installing *source* 'namepackage'...
**R
**preparing package for lazy loading
**help
Avis:./man/namepackage-package.Rd:25:'>' inatttendu
**installing help indices
**buildin
Dear List,
I am trying to plot the result of cca using matplot but failed.
Pls kindly help and thanks.
Elaine
The error message was
error in xy.coords(x, y, xlabel, ylabel, log = log) :
(list) object cannot be coerced to type 'double'
code
rm(list=ls())
library(vegan)
library(MASS)
#
On Aug 14, 2010, at 4:05 AM, Saji Ren wrote:
In response to JesperHybel, saji wrote:
that's not a problem of {}.
Correct, as indicated by the continuation "+"
By using {} you can put the command in one line.
Actually the curly brackets are more often used to put a series of
commands
On Aug 14, 2010, at 3:38 AM, JesperHybel wrote:
JH .how to plot 4 graphs simultaneously?
Depends on what graphs were talking about: A Side-by-side boxplot
containing
fx 4 boxplots can be generated by a single plot() command. However
often you
use a primary command that activivates
the
code
rm(list=ls())
library(vegan)
library(MASS)
data(varespec)
print(varespec)
str(varespec)
#PCA
vare.pca <- rda(varespec)
vare.pca
plot(vare.pca)
sum(apply(varespec, 2, var))
biplot(vare.pca, scaling = -1)
Elaine
On Sat, Aug 14, 2010 at 10:48 AM, Ben Bolker wrote:
> elaine kuo gmail
Hi:
Your example doesn't make much sense as stated, but is this what you had in
mind?
d <- ggplot (mtcars, aes(qsec, wt)
d + geom_point() + stat_smooth(aes(colour = factor(cyl)),
fill="darkgrey", size=2, alpha = 0.2) +
scale_colour_discrete("No. cylinders")
In this case, the multiple plots
that's not a problem of {}.
By using {} you can put the command in one line.
Still you can put the command in several lines as well by pur "enter".
That's why in the second line, the ">" becomes "+"
thank you for your reply though.
saji
-
You need {}
for (i in 1:500){ ...commands...}
Like:
x<-rep(c(0.8,1.2),250)
for (i in 1:500) {
if (x[i]>1) x[i]=1
}
BR
JEsper
--
View this message in context:
http://r.789695.n4.nabble.com/How-to-perform-a-substitution-in-a-loop-tp2325048p2325073.html
Sent from the R help mailin
Saji Ren wrote:
> Hello all:
>
> I have a data series of 500 data, and I want to limit the value of it to be
> less than 1.
> Below is my code:
>
>> for (i in 1:500)
> +if( x[i] > 1)
> +x[i] = 1
>
> but the system told me it's wrong. Can anyone told me the reason?
Works for me, so there's somet
Saji Ren wrote:
>
> ...
> I have a data series of 500 data, and I want to limit the value of it to
> be less than 1.
> Below is my code:
>
>>for (i in 1:500)
> +if( x[i] > 1)
> +x[i] = 1
>
> but the system told me it's wrong. Can anyone told me the reason?
>
You don't show the error message.
how to plot 4 graphs simultaneously?
Depends on what graphs were talking about: A Side-by-side boxplot containing
fx 4 boxplots can be generated by a single plot() command. However often you
use a primary command that activivates
the plot window and plots one graph, then afterwards you use s
Hello all:
I have a data series of 500 data, and I want to limit the value of it to be
less than 1.
Below is my code:
>for (i in 1:500)
+if( x[i] > 1)
+x[i] = 1
but the system told me it's wrong. Can anyone told me the reason?
-
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