Hello all,
I have been trying to figure out how to replace non-zero values of a matrix
with non-zero values from corresponding rows from another matrix. More
specifically, let say we have the following original matrix:
original -
Hi,
I am a researcher in chemistry. I have to do pls-da for some of my samples.
The number of variables for my sample is 4000 . The categorical variable
has two classes. Some of the values are missing (cant find out).
I s there any package for R (or any illustration that would be helpful) to
On Jul 14, 2013, at 8:24 PM, L S wrote:
Thanks Jim and David for your helpful feedback. I still have not terminated
RStudio (and it still has not gone to completion). A few observations I
forgot to mention is that the red stop icon is showing in RStudio so I am
unable to enter any new
For small matrix you could use a for-loop.
for (i in 1:nrow(randomized)){
randomized[i,randomized[i,]!=0] - sample(original[i,original[i,]!=0])
}
randomized
If you have a larger matrix sapply is probably faster
randomized - t(sapply(1:nrow(randomized), function(i) {
Hi
Most methods can somehow deal with NA values. You can find many packages
regarding discriminant analysis by simply searching CRAN.
discriminant analysis site:r-project.org
Or you can look to CRAN task view Multivariate statistics
maybe package pls or DiscriMiner does what you want.
You
Thanks for this guidance.
In light of your advice I have reduced the titanic to a dingy by reducing the
size of my sample to just 100 instances, making this an optimisation of 100
parameters. I am, however, seeing similar output when I output the function
value at each evaluation. This is the
The CRAN master machines are being moved to the new WU campus in Vienna
today. The services will be partially or completely unavailable,
including www.r-project.org, ftp uploads for packages and the web
submission form. We expect services to be available again this evening
European time.
Hi,
What should I do if I want to use non-default R-options for the
functions inside a package, but not affect the options of the rest of
the session? Specifically, I'm thinking of using sum contrasts instead
of the default, in functions like lm, etc. when they are called by
other functions in a
a 'split' function should not take hours to complete. I will not even wait a
couple of minutes for one until I look at other approaches. Can you at least
show what the command looks like and what the structure of the data is. Are
you trying to split a dataframe on multiple criteria? I tend
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Alok Jadhav
updated code pasted here. So I guess CC is not an option at
all? In that case is there any other package that would be useful?
I'm guessing here (based on experience of PHP's sendmail
Hi all,
several packages print messages during loading. How do I avoid to see
them when the packages are in the defaultPackages?
Here is an example.
With this in ~/.Rprofile
,[ ~/.Rprofile ]
| old - getOption(defaultPackages)
| options(defaultPackages = c(old, filehash))
| rm(old)
`
I
Look at the package chemometrics, it can certainly handle your number of
variables (p n is what that's called and it requires special considerations).
I don't recall about missing values. The authors of that package also have a
very helpful text. Good Luck. Bryan
On Jul 14, 2013, at 10:50
On 13-07-15 5:27 AM, Helios de Rosario wrote:
Hi,
What should I do if I want to use non-default R-options for the
functions inside a package, but not affect the options of the rest of
the session? Specifically, I'm thinking of using sum contrasts instead
of the default, in functions like lm,
Dear list,
I have got a weird encoding problem with the xmlEventParse() function
from the 'XML' package.
I tried finding an answer on the web for several hours and a Stack
Exchange question came back without success :(
So here's the problem. I created a small XML test file, which looks
Hello,
You should Cc the list.
What I meant is that, at an R prompt you should type
install.packages(pkgname)
substituting 'pkgname' by the name of the package you're using.
Rui Barradas
Em 15-07-2013 12:01, waqas shafqat escreveu:
Sorry sir
i could not find the install.packages(pkgname)
El día 15/07/2013 a las 13:30, Duncan Murdoch
murdoch.dun...@gmail.com escribió:
On 13-07-15 5:27 AM, Helios de Rosario wrote:
Hi,
What should I do if I want to use non-default R-options for the
functions inside a package, but not affect the options of the rest
of
the session? Specifically,
Hi all,
several packages print messages during loading. How do I avoid to
see
them when the packages are in the defaultPackages?
Here is an example.
With this in ~/.Rprofile
,[ ~/.Rprofile ]
| old - getOption(defaultPackages)
| options(defaultPackages = c(old, filehash))
|
Hi Helios,
Helios de Rosario helios.derosa...@ibv.upv.es writes:
Hi all,
several packages print messages during loading. How do I avoid to
see
them when the packages are in the defaultPackages?
Here is an example.
With this in ~/.Rprofile
,[ ~/.Rprofile ]
| old -
With minor corrections, the original problem can be solved with nlxb
from nlmrt package.
coef(modeln)
a b
-0.8470857 409.5190808
ssquares = 145585533
but since
svd(modeln$jacobian)$d
[1] 5.128345e+04 6.049076e-14
I may have made nlmrt too robust.
JN
On 13-07-15
Hi
I am trying to use ANOVA for mixture experiment.
The data can be seen below
Run Blend X1 X2 X3 Response
1 Pure 0.0 0.0 1.0 43.6
2 Pure 0.0 0.0 1.0 42.0
3 Pure 0.0 0.0 1.0 43.0
4 Binary 0.0 0.5 0.5 30.0
5 Binary 0.0 0.5 0.5 29.4
6 Binary 0.0 0.5 0.5 33.6
7 Pure 0.0 1.0 0.0 17.6
8
Arun, thanks for clearing that up. I was making assumptions about R that I
shouldnât have when it comes to column(variable) assignments. Hope everyone
has a good Monday. BNC
From: arun kirshna [via R] [mailto:ml-node+s789695n4671473...@n4.nabble.com]
Sent: Friday, July 12, 2013 11:59 PM
On 15/07/2013 8:49 AM, Andreas Leha wrote:
Hi Helios,
Helios de Rosario helios.derosa...@ibv.upv.es writes:
Hi all,
several packages print messages during loading. How do I avoid to
see
them when the packages are in the defaultPackages?
Here is an example.
With this in ~/.Rprofile
Great! Thank you, Nello. It works on my larger matrices.
On Mon, Jul 15, 2013 at 2:40 AM, Blaser Nello nbla...@ispm.unibe.ch wrote:
For small matrix you could use a for-loop.
for (i in 1:nrow(randomized)){
randomized[i,randomized[i,]!=0] - sample(original[i,original[i,]!=0])
}
On 07/15/2013 06:25 AM, Duncan Murdoch wrote:
On 15/07/2013 8:49 AM, Andreas Leha wrote:
Hi Helios,
Helios de Rosario helios.derosa...@ibv.upv.es writes:
Hi all,
several packages print messages during loading. How do I avoid to
see
them when the packages are in the defaultPackages?
But the ANOVA results is incorrect when I use
aov.out = aov(Response~-1+x1*x2*x3).
First, this doesn't work at all. Your variables are in upper case and your data
environment is not specified, so you must have done something else. I can get
an answer using something like
Looking for a function which returns the stem of the filename given a path.
i.e.
file.stem(/the/path/to/afile.txt)
afile
regards
--
Witold Eryk Wolski
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
Dear Petr,
Sorry for the delay. I've been out.
Unfortunately, your code doesn't work either even when using fromLast = T.
Thank you for your help and your time.
Santi
From: PIKAL Petr petr.pi...@precheza.cz
To: Santiago Guallar sgual...@yahoo.com
Cc: r-help
Read the Posting Guide... use plain text email.
help.search(file)
---
Jeff NewmillerThe . . Go Live...
DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go...
Hello,
You can use ?basename to write a file.stem function:
basename(/the/path/to/afile.txt)
file.stem - function(x){
bn - basename(x)
gsub(\\..*$, , bn)
}
file.stem(/the/path/to/afile.txt)
Hope this helps,
Rui Barradas
Em 15-07-2013 15:23, Witold E Wolski escreveu:
Hello everyone on the list
I want to run a FindU function on as many files as in a directory. Due of my
limitations on data management I am calling the function, wait until finish the
process, call for the next file and so on. I have almost 120 CSV files on the
same directory. This the example
Rui, Thank you
On 15 July 2013 16:32, Rui Barradas ruipbarra...@sapo.pt wrote:
Hello,
You can use ?basename to write a file.stem function:
basename(/the/path/to/afile.txt)
file.stem - function(x){
bn - basename(x)
gsub(\\..*$, , bn)
}
file.stem(/the/path/to/afile.txt)
This should also work:
mask - randomized 0
mask
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] FALSE FALSE TRUE FALSE FALSE TRUE
[2,] TRUE TRUE FALSE TRUE TRUE TRUE
[3,] FALSE TRUE TRUE FALSE FALSE TRUE
[4,] TRUE TRUE FALSE TRUE FALSE TRUE
randomized[mask] - original[mask]
randomized
Hm, so you probably ask to get something what you actually do not want.
AFAIK what I called âfinalâ is the same as you asked for with your toy
data except of column âactâ which you can easily get rid of.
If what I suggested does not work with your real data you shall prepare better
Dear all,
I would like to do t-test across two columns name with different cat
with overall mean (val).
(Removing if there is a single observation)
And finally, make a matrix with t-value and p-value associated with a name
(in rows) and cat (in columns)
dput(x)
structure(list(name =
Dear all,
I am having problem on plots in R for some cases.
For example:
plot( 1:10 )
text( 1:10, letters[1:10], cex = 1)
works well but :
plot(1:10)
text(1:10, letters[1:10], cex = 0.9)
returns :
Erreur dans text.default(1:10, letters[1:10], cex = 0.9) :
impossible de charger la
Bill,
Thanks so much for the tips. For the project that I'm doing now, I don't
need to worry about bullet-proofing it too much, but this is definitely
educational and will help tons when the next one comes around.
Cheers,
eric
On Sun, Jul 7, 2013 at 10:22 AM, William Dunlap wdun...@tibco.com
I was not clear on exactly what you want to do. I assume that you want to
automate the process given 120 file names. Here is part of a script that
will parse the file names and give you the output file you want. If it is
something different, then clarify your request:
input -
On 15/07/2013 15:59, Alice Julien-Laferrière wrote:
Dear all,
I am having problem on plots in R for some cases.
Your machine has Cairo: Cairo-based X11 devices do not use those fonts.
So it seems you have done something you have not shown us.
The fix is to use the Cairo-based X11 devices.
It is a (very) large marked point process object that is being split (see
original post), and that is some other kind of structure. So I think all
bets are off, in terms of what kind of duration to expect.
The folks on r-sig-geo might be able to help with suggestions for faster
approaches.
In
Hi,
Not sure about the format for the 2nd part.
df1- ##data
library(plyr)
df2-ddply(df1,.(name,cat),summarize,
cbind(t.test(val,df1$val)$statistic,t.test(val,df1$val)$p.value))
df3-cbind(df2[,1:2],data.frame(df2[,3]))
colnames(df3)[3:4]- c(t-val,p.val)
library(reshape2)
df3m-
Dear all,
Is there a possibility to remove a geom from a ggplot? Background suppose I
have a function which returns a ggplot object after some data re-formatting and
aggregation. While this ggplot object is fine in 90% of the cases it turns out
that for some cases I want to suppress one of the
This may be close to what you want:
t.val - by(x, x$cat, function(y) if (min(table(y$name)1)) {
+ t.test(val~name, y)})
t.out - do.call(rbind, sapply(t.val, function(y) c(y$statistic,
+ p.value=y$p.value)))
t.out
t p.value
p178266580 -0.1156475 0.9144054453
On Mon, Jul 15, 2013 at 1:08 PM, Thaler,Thorn,LAUSANNE,Applied
Mathematics thorn.tha...@rdls.nestle.com wrote:
Dear all,
Is there a possibility to remove a geom from a ggplot? Background suppose I
have a function which returns a ggplot object after some data re-formatting
and aggregation.
On 2013-07-15, at 4:00 AM, r-help-requ...@r-project.org wrote:
On 7/14/2013 3:05 PM, Rolf Turner wrote:
On 15/07/13 08:57, Spencer Graves wrote:
SNIP
You may know that mixed effects is another term for repeated
measurements.
SNIP
I must of course preface this comment with an
On Jul 15, 2013, at 4:11 AM, Andreas Leha wrote:
Hi all,
several packages print messages during loading. How do I avoid to see
them when the packages are in the defaultPackages?
I'm pretty sure this has been asked before (although the wrinkle of adding a
package to default packages may
Hello again,
Let say I have following data-frame:
MyData - data.frame(Names1 = paste(XXX, 1:150), Values1 = 1:150 + 10,
Values2 = 1:150)
Now I want to plot this data-frame with googleVis. Therefore I run
following codes:
library(googleVis)
plot(gvisBarChart(MyData, xvar=Names1, yvar=c(Values1,
Hi,
May be I misunderstood ur question.
The output David got could be also obtained by:
#df1 dataset
library(plyr)
df2-ddply(df1,.(cat),function(x) if(min(table(x$name))1){x1-
t.test(val~name,x);cbind(t=x1$statistic,p.value=x1$p.value)})
df2
# cat t p.value
#1 p178266580
The plantbreeding package is on R-forge. See this link for install
instructions:
http://rplantbreeding.blogspot.com/
Kevin
On Sun, Jul 14, 2013 at 12:49 AM, waqas shafqat waqas1...@gmail.com wrote:
sir i could not find the plant breeding libraray in Rgui3.0.0
[[alternative HTML
Hi,
May be this also works.
basename(file_path_sans_ext(/the/path/to/afile.txt))
#[1] afile
A.K.
- Original Message -
From: Rui Barradas ruipbarra...@sapo.pt
To: Witold E Wolski wewol...@gmail.com
Cc: r-help@r-project.org
Sent: Monday, July 15, 2013 10:32 AM
Subject: Re: [R] file.stem?
HI Irucka,
May be this is what you wanted:
pat-paste(paste0(http://www.,siter[,1],..rdb;),collapse=|)
pat
[1]
http://www.02437100..rdb|http://www.02439500..rdb|http://www.02441500..rdb|http://www.02446500..rdb|http://www.02467000..rdb|
#or
pat1-paste(http://www.;, siter[,1], ..rdb, sep=, collapse = |)
identical(pat,pat1)
#[1] TRUE
A.K.
- Original Message -
From: arun smartpink...@yahoo.com
To: Irucka Embry iruc...@mail2world.com
Cc: R help r-help@r-project.org
Sent: Monday, July 15, 2013 2:47 PM
Subject: Re:
Hello,
I use glm within a function testing for the appearence of the coexistence
of (minor allels in a subset of) snps. And then I extract the
Pr(|z|)-value for the interaction. Principally it works but sometimes the
function stops because this value for the interaction is NA. For
instance,
I think what you want is
?try ##or
?tryCatch
## The second is more flexible but slightly more complicated.
to trap the error and perhaps refit the model without interaction?
Cheers,
Bert
On Mon, Jul 15, 2013 at 10:45 AM, Hermann Norpois hnorp...@gmail.com wrote:
Hello,
I use glm within a
Hi David,
David Winsemius dwinsem...@comcast.net writes:
On Jul 15, 2013, at 4:11 AM, Andreas Leha wrote:
Hi all,
several packages print messages during loading. How do I avoid to see
them when the packages are in the defaultPackages?
I'm pretty sure this has been asked before
Hi Martin,
Martin Morgan mtmor...@fhcrc.org writes:
On 07/15/2013 06:25 AM, Duncan Murdoch wrote:
On 15/07/2013 8:49 AM, Andreas Leha wrote:
Hi Helios,
Helios de Rosario helios.derosa...@ibv.upv.es writes:
Hi all,
several packages print messages during loading. How do I avoid to
Dear Jari,
Thanks a lot for your reply.
Let me describe more about my dataset: it consists of count data for samples,
and shows how many copies of a certain bacteria are in a sample. There are 92
samples (rows), and about 3500 kinds of bacteria (columns). Variable 1 (Var1)
is a factor
Hellos,
I am looking for a package that can scrub values from flow cytometry data
file keywords that have either the $ or @ keyword prefix. Are their any
options out there? The options from WEHI, TreeStar, and whoever made File
Sanitizer aren't working.
thanks for any help on this,
--
-
Dear R-Users,
I need a very fast and reliable database solution so I try to serialize a
data.frame (to binary data) and to store this data to an SQLite database.
This is what I tried to do:
library(RSQLite)
con - dbDriver(SQLite)
db - dbConnect(con, test)
dbSendQuery(db, 'CREATE TABLE
Group - I'm having problems with the 'cluster' package. Installation
appears successful but attempts to load it with either library() or
require() result in the error message
Error in library(cluster) : there is no package called ‘cluster’
All that appears to be installed is cluster.dll in
On 15.07.2013 23:51, David Stevens wrote:
Group - I'm having problems with the 'cluster' package. Installation
appears successful but attempts to load it with either library() or
require() result in the error message
Error in library(cluster) : there is no package called ‘cluster’
All that
dear R experts: I am curious again about R memory allocation strategies.
Consider an intentionally inefficient program:
ranmatme - function( lx, rx ) {
m - matrix(NA, nrow=lx, ncol=rx)
for (li in 1:rx) {
cat(\tLag i=, li, object size=, object.size(m), \n)
m[,li] -
Dear R users,
I'm currently using the Graphics package to display several hundred of
matrix objects, using a layout and the image() function.
It works well except for large matrices ( 1000*1000) or for a large
number of matrices (there is a limitation around 400 if I remember well)
To solve
I can give you the answer to #1. If you had put a print(str(m)) you
would have seen that initially the matrix was setup as logical which
requires 4 bytes per element. On the first assignment of a numeric, the
mode of 'm' is changed to numeric which requires 8 bytes per element; that
is the
Hi,
I am currently working with the package JGL.
I tried to run JGL function JGL(Y,penalty=fused,...) over my data, but
there is the following error which makes it stop:
Error in while ((iter==0)|| (iter maxiter diff_valuetol))
missing value where TRUE/FALSE needed.
I would appreciate it if
I could be wrong, but I would guess that doing what you are describing is very
unusual. Most of the time the data frame is mapped to a table in the database
so the rows can be searched. Storing data frames as BLOBs really seems odd.
Note that there is an R-sig-db mailing list for questions of
I have a data frame like shown below
sample1 sample2 sample3 sample4 sample5 a P P I P P b P A P P A c P P P
P P d P P P P P e M P M A P f P P P P P g P P P A P h P P P P P
I want to keep only those rows which have all P across all the columns.
Since the matrix is large (about 20,000
Hi,
If I understand it correctly,
df1- read.table(text=
sample1 sample2 sample3 sample4 sample5
a P P I P P
b P A P P A
c P P P P P
d P P P P P
e M P M A P
f P P P P P
g P P P A P
h P P P P P
,sep=,header=TRUE,stringsAsFactors=FALSE)
df1[rowSums(df1==P)==ncol(df1),]
# sample1 sample2
thx, jim. makes perfect sense now.
I guess a logical in R has a few million possible values ;-).
(Joke. I realize that 4 bytes is to keep the code convenient and faster.)
regards,
/iaw
Ivo Welch (ivo.we...@gmail.com)
On Mon, Jul 15, 2013 at 4:26 PM, jim holtman jholt...@gmail.com
You mentioned data.frame at one place and matrix at another. Matrix would be
faster.
#Speed comparison
#Speed
set.seed(1454)
dfTest- as.data.frame(matrix(sample(LETTERS[15:18],5*1e6,replace=TRUE),ncol=5))
system.time(res-dfTest[rowSums(dfTest==P)==ncol(dfTest),])
# user system elapsed
#
There was a small typo in my sendmail command. I was passing header=header
instead of headers=header. This argument was accepted because of `...`
argument which is not the last argument as one would except. A minor mistake
caused me a bit of frustration. This issue is resolved now. Thanks
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