[R] possible bug in ggplot2 v0.5.2???
Dear R-Users, I recently gave a try to the nice package ggplot2. Everything went well until I tried to add a smoother (using lm method for instance). On the graphic device the regression line is displayed but not confidence intervals as it should be (at least on ggplot website). I tried to do the job on both MS winXP and Linux i586: same result. Did anyone encountered this problem? Did I miss something? My R version is 2.4.1. Thanks, Stéphane. -- == Stephane CRUVEILLER Ph. D. Genoscope - Centre National de Sequencage Atelier de Genomique Comparative 2, Rue Gaston Cremieux CP 5706 91057 Evry Cedex - France Phone: +33 (0)1 60 87 84 58 Fax: +33 (0)1 60 87 25 14 EMails: [EMAIL PROTECTED] ,[EMAIL PROTECTED] === __ R-help@stat.math.ethz.ch 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, self-contained, reproducible code.
[R] .C interface and Strings...
Dear R users,
I am trying to include C code into R via the .C interface. I have read
that arguments passed to a C function have to be correctly DEreferenced.
This is something that can be easily done for numbers (integers or
float) by adding
a * before the reference like for instance:
#includeR.h
void hellofct(int *n)
{
int i;
for (i=0;i*n;i++)
{
Rprintf(Hello, world!\n);
}
}
However, I can not figure out how that can be achieved for strings.
My prototype function would be something like:
#includeR.h
void displaystring(char *str)
{
Rprintf(String displayed:%s\n, );
}
any hints?
Thx.
Stéphane.
--
==
Stephane CRUVEILLER Ph. D.
Genoscope - Centre National de Sequencage
Atelier de Genomique Comparative
2, Rue Gaston Cremieux CP 5706
91057 Evry Cedex - France
Phone: +33 (0)1 60 87 84 58
Fax: +33 (0)1 60 87 25 14
EMails: [EMAIL PROTECTED] ,[EMAIL PROTECTED]
===
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] RMySQL...Can't initialize driver??? Solved!!!
Hi, I have finally made it working. I do not if that was the problem but the libraries (DBI and RMySQL) were installed in a non-standard location (of course specified in a .Renviron file). Reinstalling both of them at R root did the trick... thanks to you all for your help... Stephane. Rainer M Krug wrote: Stephane Cruveiller wrote: Rainer M Krug wrote: I followed your instruction. Here is my .my.cnf: --- [client] user=steff password=XX database=justforfun --- with it, I can connect to my MYSQL server without problem and then I try to connect through R: --- library(RMySQL) Loading required package: DBI m - dbDriver(MySQL) Error in new(MySQLDriver, Id = drvId) : unused argument(s) (Id ...) --- It still produces the error. I really do not know what is going on here... Sorry - no idea. I guess you are using Linux? And all packages are up to date? Rainer Then you do: library(RMySQL) m - dbDriver(MySQL) con - dbConnect(m, group = renpatch) q - TheSQLQuery rs - dbSendQuery(con, q) TheResults - fetch(rs, n = -1) dbDisconnect(con) rm(con) and it should work - at least that is what it is doing for me. Rainer Stephane. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] RMySQL...Can't initialize driver???
Dear R users, I would like to query a MySQL database through R. I have installed the latest required packages (RMySQL and DBI) in R (v2.3.1). A MySQL server (v5.0.22) is running on my local machine but I can't initialize MYSQL driver: library(RMySQL) Loading required package: DBI MySQL(max.con = 10, fetch.default.rec = 500, force.reload = F) Error in new(MySQLDriver, Id = drvId) : unused argument(s) (Id ...) - Could somebody tell me what I have missed? Thx Stéphane. -- == Stephane CRUVEILLER Ph. D. Genoscope - Centre National de Sequencage Atelier de Genomique Comparative 2, Rue Gaston Cremieux CP 5706 91057 Evry Cedex - France Phone: +33 (0)1 60 87 84 58 Fax: +33 (0)1 60 87 25 14 EMails: [EMAIL PROTECTED] ,[EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] RMySQL...Can't initialize driver???
Dear R users, I would like to query a MySQL database through R. I have installed the latest required packages (RMySQL and DBI) in R (v2.3.1). A MySQL server (v5.0.22) is running on my local machine but I can't initialize MYSQL driver: library(RMySQL) Loading required package: DBI MySQL(max.con = 10, fetch.default.rec = 500, force.reload = F) Error in new(MySQLDriver, Id = drvId) : unused argument(s) (Id ...) - Could somebody tell me what I have missed? Thx Stéphane. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] RMySQL...Can't initialize driver???
Duncan Murdoch wrote: On 6/27/2006 8:51 AM, Stephane Cruveiller wrote: Dear R users, I would like to query a MySQL database through R. I have installed the latest required packages (RMySQL and DBI) in R (v2.3.1). A MySQL server (v5.0.22) is running on my local machine but I can't initialize MYSQL driver: library(RMySQL) Loading required package: DBI MySQL(max.con = 10, fetch.default.rec = 500, force.reload = F) Error in new(MySQLDriver, Id = drvId) : unused argument(s) (Id ...) - Could somebody tell me what I have missed? I have never used RMySQL, but from the error message, this looks like an incompatibility between it and DBI, presumably because one is newer than the other. I have always found it easier to use RODBC. Because it uses the more general ODBC interface, it may be slower than a package that is tuned to a particular database, but it works, which is a substantial advantage. thanks for the hint... I will give it a try very soon. Duncan Murdoch Stephane. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] RMySQL...Can't initialize driver???
Rainer M Krug wrote: Stephane Cruveiller wrote: Duncan Murdoch wrote: On 6/27/2006 8:51 AM, Stephane Cruveiller wrote: Dear R users, I would like to query a MySQL database through R. I have installed the latest required packages (RMySQL and DBI) in R (v2.3.1). A MySQL server (v5.0.22) is running on my local machine but I can't initialize MYSQL driver: library(RMySQL) Loading required package: DBI MySQL(max.con = 10, fetch.default.rec = 500, force.reload = F) Error in new(MySQLDriver, Id = drvId) : unused argument(s) (Id ...) - Could somebody tell me what I have missed? I am running R 2.3.0 under Linux and connect to a MySQl 4.1 server. You have to create a file in your home directory which has the connection infos. It should look like that: [renpatch] user = UserName password = PassWord database = ... host = ... [renpatch_renosterbos] user = UserName password = PassWord database = ... host = .. and be called .my.conf I followed your instruction. Here is my .my.cnf: --- [client] user=steff password=XX database=justforfun --- with it, I can connect to my MYSQL server without problem and then I try to connect through R: --- library(RMySQL) Loading required package: DBI m - dbDriver(MySQL) Error in new(MySQLDriver, Id = drvId) : unused argument(s) (Id ...) --- It still produces the error. I really do not know what is going on here... Then you do: library(RMySQL) m - dbDriver(MySQL) con - dbConnect(m, group = renpatch) q - TheSQLQuery rs - dbSendQuery(con, q) TheResults - fetch(rs, n = -1) dbDisconnect(con) rm(con) and it should work - at least that is what it is doing for me. Rainer Stephane. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] aggregate function....
Nice trick, thx...
Stéphane.
On Wed, 2006-03-29 at 11:17 -0500, jim holtman wrote:
try 'by':
x
S_id AF_Class count... R_gc_percent S_length
5 82644971 30 0.4835678
6 826449737 0.4835678
8 82645541 31 0.5138894
9 82645542 11 0.5138894
10 826455431 0.5138894
do.call('rbind', by(x, x$S_id, function(y) y[which.max(y
$AF_Class),]))
S_id AF_Class count... R_gc_percent S_length
8264497 826449737 0.4835678
8264554 826455431 0.5138894
On 3/29/06, Stephane CRUVEILLER [EMAIL PROTECTED] wrote:
Dear R users,
I have some trouble with the aggregate function. Here are my
data
daf
S_id AF_Class count... R_gc_percent S_length
5 82644971 30 0.4835678
6 826449737 0.4835678
8 82645541 31 0.5138894
9 82645542 11 0.5138894
10 826455431 0.5138894
for a given S_id, I would like to select the line
corresponding to the
max count. To perform this, I used:
aggregate(daf,list(daf$S_id),max)
Group.1S_id AF_Class count... R_gc_percent S_length
1 8264497 82644973 30 0.4835678
2 8264554 82645543 31 0.5138894
which is ok for the count. But I realized that max function is
also
applied
to AF_class (should be 1 and 1 instead of 3 and 3), so it
seems that
aggregate is not the appropriate function for that I want to
do. Is
there any other function I could use instead?
Best whishes,
Stéphane.
--
==
Stephane CRUVEILLER Ph. D.
Genoscope - Centre National de Sequencage
Atelier de Genomique Comparative
2, Rue Gaston Cremieux CP 5706
91057 Evry Cedex - France
Phone: +33 (0)1 60 87 84 58
Fax: +33 (0)1 60 87 25 14
EMails: [EMAIL PROTECTED] ,[EMAIL PROTECTED]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390 (Cell)
+1 513 247 0281 (Home)
What the problem you are trying to solve?
--
==
Stephane CRUVEILLER Ph. D.
Genoscope - Centre National de Sequencage
Atelier de Genomique Comparative
2, Rue Gaston Cremieux CP 5706
91057 Evry Cedex - France
Phone: +33 (0)1 60 87 84 58
Fax: +33 (0)1 60 87 25 14
EMails: [EMAIL PROTECTED] ,[EMAIL PROTECTED]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] kmeans: did not converge in 10 iterations
On Thu, 2006-03-30 at 11:56 -0800, Linda Lei wrote: Hi All, I run function kmeans to cluster a matrix. But when the matrix size is big enough, it keeps saying did not converge in 10 iterations. Could you explain what it means and if the result is wrong? It means that the partition obtained is not stable (i.e. the algorithm did not converge toward an optimal solution). Indeed, a supplementary iteration will modify it significantly. try to increase iter.max parameter (default set to 10) $ x.kmeans-kmeans(x,centers=3,iter.max=30) Stéphane. And the interesting thing is sometimes this warning happens when the sample size is around 51200 x 6, sometimes it happens around 3 x 6. Does the warning related to sample size or not? This also happens in bclust. Thank you! [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- == Stephane CRUVEILLER Ph. D. Genoscope - Centre National de Sequencage Atelier de Genomique Comparative 2, Rue Gaston Cremieux CP 5706 91057 Evry Cedex - France Phone: +33 (0)1 60 87 84 58 Fax: +33 (0)1 60 87 25 14 EMails: [EMAIL PROTECTED] ,[EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] aggregate function....
Dear R users, I have some trouble with the aggregate function. Here are my data daf S_id AF_Class count... R_gc_percent S_length 5 82644971 30 0.4835678 6 826449737 0.4835678 8 82645541 31 0.5138894 9 82645542 11 0.5138894 10 826455431 0.5138894 for a given S_id, I would like to select the line corresponding to the max count. To perform this, I used: aggregate(daf,list(daf$S_id),max) Group.1S_id AF_Class count... R_gc_percent S_length 1 8264497 82644973 30 0.4835678 2 8264554 82645543 31 0.5138894 which is ok for the count. But I realized that max function is also applied to AF_class (should be 1 and 1 instead of 3 and 3), so it seems that aggregate is not the appropriate function for that I want to do. Is there any other function I could use instead? Best whishes, Stéphane. -- == Stephane CRUVEILLER Ph. D. Genoscope - Centre National de Sequencage Atelier de Genomique Comparative 2, Rue Gaston Cremieux CP 5706 91057 Evry Cedex - France Phone: +33 (0)1 60 87 84 58 Fax: +33 (0)1 60 87 25 14 EMails: [EMAIL PROTECTED] ,[EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] List of lists???
Thx for the hint... the div - factor(c(1,1,1,2,2)) did exactly what I was expecting... Stéphane. Le Mardi 31 Janvier 2006 15:50, Gabor Grothendieck a écrit : Your post seems to be messed up but I will assume you have a 5 column data frame and the questino is how to run f on the first three columns and separately on the last two. I think the easiest is just the following where I have used the builtin iris data set where I have assumed that the operation you want to perform is summary for purposes of example: summary(iris[,1:3]) summary(iris[,4:5]) If this is not your real problem and the real problem has many more divisions then try this where div is a factor that defines the division of columns into sets: div - factor(c(1,1,1,2,2)) lapply(split(names(iris), div), function(n) summary(iris[n])) On 1/31/06, Stephane CRUVEILLER [EMAIL PROTECTED] wrote: Hi, I would like to perform computations on some variables belonging to the same dataframe. For instance my data frame has the following shape: toto1toto2toto3toto4toto5 1 12345 2678910 I would like to perform the calculation on c(toto1,toto2,toto3) and then the same calculation on c(toto4,toto5). Is there a way to tell R to do it using 3 loop (a list of lists)?? Stephane. -- == Stephane CRUVEILLER Ph. D. Genoscope - Centre National de Sequencage Atelier de Genomique Comparative 2, Rue Gaston Cremieux CP 5706 91057 Evry Cedex - France Phone: +33 (0)1 60 87 84 58 Fax: +33 (0)1 60 87 25 14 EMails: [EMAIL PROTECTED] ,[EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- == Stephane CRUVEILLER Ph. D. Genoscope - Centre National de Sequencage Atelier de Genomique Comparative 2, Rue Gaston Cremieux CP 5706 91057 Evry Cedex - France Phone: +33 (0)1 60 87 84 58 Fax: +33 (0)1 60 87 25 14 EMails: [EMAIL PROTECTED] ,[EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] List of lists???
Hi, I would like to perform computations on some variables belonging to the same dataframe. For instance my data frame has the following shape: toto1 toto2 toto3 toto4 toto5 1 1 2 3 4 5 2 6 7 8 9 10 I would like to perform the calculation on c(toto1,toto2,toto3) and then the same calculation on c(toto4,toto5). Is there a way to tell R to do it using a loop (a list of lists)?? Stephane. -- == Stephane CRUVEILLER Ph. D. Genoscope - Centre National de Sequencage Atelier de Genomique Comparative 2, Rue Gaston Cremieux CP 5706 91057 Evry Cedex - France Phone: +33 (0)1 60 87 84 58 Fax: +33 (0)1 60 87 25 14 EMails: [EMAIL PROTECTED] ,[EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
