[R] Gamma
Hey, I am having trouble graphing the following function â2Î(n/2)/[ân â 1Î((n â 1)/2 for the values of n between 2 and 50. i know that Î(n) = (n-1)!, which in R is factorial(n-1) When i type that into R, using y - function(n). and then plot(y,2,50), it doesnt give me anything meaningful, in fact, it comes up with a message saying something like in gamma(n+1) ploted or something along those lines. Can anyone please help? thank you _ Looking to move somewhere new this winter? Let ninemsn property help http://a.ninemsn.com.au/b.aspx?URL=http%3A%2F%2Fninemsn%2Edomain%2Ecom%2Eau%2F%3Fs%5Fcid%3DFDMedia%3ANineMSN%5FHotmail%5FTagline_t=774152450_r=Domain_tagline_m=EXT [[alternative HTML version deleted]] __ R-help@r-project.org 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] How to turn the xyplot graphics upside-down?
Hi everyone, I'm learning to use R. The below script works well, but i want to turn the y-axis and the graphics upside-down, how should i do? Appreciate if any tips! library(lattice) xyplot(P3+PZ+P4+C3+CZ+C4+F3+FZ+F4~Time,groups=Cond,data=data,type=l,auto.key=list(space=top,points=FALSE,lines=TRUE),layout=c(3,3)) Liam [[alternative HTML version deleted]] __ R-help@r-project.org 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] Gamma function
Hi Guy, I am having trouble graphing the following function â2Î(n/2)/[ân â 1Î((n â 1)/2 for the values of n between 2 and 50. i know that Î(n) = (n-1)!, which in R is factorial(n-1) When i type that into R, using y - function(n). and then plot(y,2,50), it doesnt give me anything meaningful, in fact, it comes up with a message saying something like in gamma(n+1) ploted or something along those lines. Can anyone please help? thanks you _ Looking to change your car this year? Find car news, reviews and more http://a.ninemsn.com.au/b.aspx?URL=http%3A%2F%2Fsecure%2Dau%2Eimrworldwide%2Ecom%2Fcgi%2Dbin%2Fa%2Fci%5F450304%2Fet%5F2%2Fcg%5F801459%2Fpi%5F1004813%2Fai%5F859641_t=762955845_r=tig_OCT07_m=EXT [[alternative HTML version deleted]] __ R-help@r-project.org 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] Fwd: Cannot allocate a new database connection error
-- Forwarded message --
From: Moumita Das das.moumita.onl...@gmail.com
Date: Sat, May 16, 2009 at 2:26 PM
Subject: Cannot allocate a new database connection error
To: r-help-requ...@r-project.org
Hi friends,
why do i keep getting this error?The program runs, twice and every third
time i get this error.I have to quit.Again get teh R-prompt and then run the
script.
*Error in mysqlNewConnection(drv, ...) :
RS-DBI driver: (�...@`qe@°
°
cannot allocate a new connection -- maximum of 16 connections already
opened)
Error in is(object, Cl) :
error in evaluating the argument 'conn' in selecting a method for function
'dbSendQuery'
Error in is(object, Cl) :
error in evaluating the argument 'res' in selecting a method for function
'fetch'*
*this is my DB connection function*
*myDbConnect - function (dbName, hostName) {
drv-MySQL()
con - dbConnect(drv, user=xyz, password=xyz,dbname = dbName, host
= hostName)
return(con)
}*
everytime i need ,Db connection , i used in this way:
This is the structure of my code:--
main - function ()
{
#Looping through subgroups
for(sub_group_num_loopcounter in 1:sub_group_num_data_size[1])
{
#Fetching the where clause for the particular subgroup
*sub_group_where_condition -
fetch(dbSendQuery(myDbConnect(dbName,hostName), paste(c(SELECT where_clause
FROM sub_grp where
num=,sub_group_num_data[sub_group_num_loopcounter,1]),collapse=)), n =
-1) *
}
dbDisconnect(con)
dbListConnections(MySQL())
l-list()
}
Where should i close the DB connection or use one single connection
throughout the prograam.
--
Thanks
Moumita
--
Thanks
Moumita
[[alternative HTML version deleted]]
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Re: [R] Gamma
Kon Knafelman konk2...@hotmail.com [Sat, May 16, 2009 at 08:49:44AM CEST]: Hey, I am having trouble graphing the following function ???2??(n/2)/[???n ??? 1??((n ??? 1)/2 for the values of n between 2 and 50. i know that ??(n) = (n-1)!, which in R is factorial(n-1) When i type that into R, using y - function(n). and then plot(y,2,50), it doesnt give me anything meaningful, in fact, it comes up with a message saying something like in gamma(n+1) ploted or something along those lines. Please send us the actual code, and the actual lines, not something along them. For me, both plot(gamma, 1, 4) and plot(factorial, 0, 3) give meaningful results without warnings or errors. I am using the following: R.Version() $platform [1] i486-pc-linux-gnu $arch [1] i486 $os [1] linux-gnu $system [1] i486, linux-gnu $status [1] $major [1] 2 $minor [1] 7.2 $year [1] 2008 $month [1] 08 $day [1] 25 $`svn rev` [1] 46428 $language [1] R $version.string [1] R version 2.7.2 (2008-08-25) -- Johannes Hüsing There is something fascinating about science. One gets such wholesale returns of conjecture mailto:johan...@huesing.name from such a trifling investment of fact. http://derwisch.wikidot.com (Mark Twain, Life on the Mississippi) __ R-help@r-project.org 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] Installing R on Ubuntu 8.10
Hi, I am trying to install R on Ubuntu 8.10. I have added this line: deb http://cran.at.r-project.org/bin/linux/ubuntu intrepid/ in my /etc/apt/sources.list file. However when I Reload, I get the following error message: W: GPG error: http://cran.at.r-project.org intrepid/ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY D67FC6EAE2A11821 I have tried different mirror sites, but the result is the same. There is nothing written about public keys on the download page: http://cran.at.r-project.org/ Then, I have tried (after I added the line to the /etc/apt/sources/list file) not pressing Reload, but Close, and I have written in the console: sudo apt-get update but I received similar message again: Reading package lists... Done W: GPG error: http://cran.rakanu.com intrepid/ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY D67FC6EAE2A11821 W: You may want to run apt-get update to correct these problems Do you know what the problem is, and what should I do? Thanks in advance. Maria __ R-help@r-project.org 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.
Re: [R] Installing R on Ubuntu 8.10
-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Maria I. Tchalakova Sent: Saturday, May 16, 2009 2:37 AM To: R-help Forum Subject: [R] Installing R on Ubuntu 8.10 Hi, I am trying to install R on Ubuntu 8.10. I have added this line: deb http://cran.at.r-project.org/bin/linux/ubuntu intrepid/ in my /etc/apt/sources.list file. However when I Reload, I get the following error message: W: GPG error: http://cran.at.r-project.org intrepid/ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY D67FC6EAE2A11821 I have tried different mirror sites, but the result is the same. There is nothing written about public keys on the download page: http://cran.at.r-project.org/ Then, I have tried (after I added the line to the /etc/apt/sources/list file) not pressing Reload, but Close, and I have written in the console: sudo apt-get update but I received similar message again: Reading package lists... Done W: GPG error: http://cran.rakanu.com intrepid/ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY D67FC6EAE2A11821 W: You may want to run apt-get update to correct these problems Do you know what the problem is, and what should I do? Thanks in advance. Maria Maria, Go to the CRAN website (or your preferred mirror), select Linux under the download and install section, then select Ubuntu, and read what it says about installation. http://cran.r-project.org/ Hope this is helpful, Dan Daniel J. Nordlund Washington State Department of Social and Health Services Planning, Performance, and Accountability Research and Data Analysis Division Olympia, WA 98504-5204 __ R-help@r-project.org 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.
Re: [R] drawing arrows
christophe dutang wrote: Hi, I would like to draw arrows in a classic 2D plot. Which package should I use? is there R base functions that do job? On google, I could not find any useful discussion about this topic, except a link to the function 'grid.arrows' of the grid package. My problem is I would like to draw arrows at the edge of circles drawn by the 'symbols' function. Maybe there is already a dedicated function for this? Any help is appreciated. Christophe Hi Christophe, If you are trying to do what I think you are trying to do, consider drawing the arrow first, with the starting point at the center of the circle, then draw the circle with a fill color the same as the background. This should give you a circle with a nice radial arrow emerging from the edge. Jim __ R-help@r-project.org 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.
Re: [R] Installing R on Ubuntu 8.10
Hi Dan, thanks for the reply. Yes, I have read everything there, but it didn't help. I've written to the Ubuntu forums as well, from where I was told to type first: gpg --keyserver keyserver.ubuntu.com --recv D67FC6EAE2A11821 gpg --export --armor D67FC6EAE2A11821 | sudo apt-key add - before sudo apt-get update sudo apt-get install r-base and it worked. Best, Maria On Sat, May 16, 2009 at 11:52 AM, Nordlund, Dan (DSHS/RDA) nord...@dshs.wa.gov wrote: -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Maria I. Tchalakova Sent: Saturday, May 16, 2009 2:37 AM To: R-help Forum Subject: [R] Installing R on Ubuntu 8.10 Hi, I am trying to install R on Ubuntu 8.10. I have added this line: deb http://cran.at.r-project.org/bin/linux/ubuntu intrepid/ in my /etc/apt/sources.list file. However when I Reload, I get the following error message: W: GPG error: http://cran.at.r-project.org intrepid/ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY D67FC6EAE2A11821 I have tried different mirror sites, but the result is the same. There is nothing written about public keys on the download page: http://cran.at.r-project.org/ Then, I have tried (after I added the line to the /etc/apt/sources/list file) not pressing Reload, but Close, and I have written in the console: sudo apt-get update but I received similar message again: Reading package lists... Done W: GPG error: http://cran.rakanu.com intrepid/ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY D67FC6EAE2A11821 W: You may want to run apt-get update to correct these problems Do you know what the problem is, and what should I do? Thanks in advance. Maria Maria, Go to the CRAN website (or your preferred mirror), select Linux under the download and install section, then select Ubuntu, and read what it says about installation. http://cran.r-project.org/ Hope this is helpful, Dan Daniel J. Nordlund Washington State Department of Social and Health Services Planning, Performance, and Accountability Research and Data Analysis Division Olympia, WA 98504-5204 __ R-help@r-project.org 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] newbie: closing unused connection + readline
Hello;
I am new to R and trying to read a line from socket connection at a
time but at the end of script I am getting closing unused connection
warning. I am not able to understand how to solve this. I want to read
a line from socket and then use read.table/scan on that line but it
looks like I am opening multiple connections instead of just one. I
think I am doing something wrong or not able to understand correct
method of doing this.
---code
# Create a socket from which to read lines - one at a time (record)
reader.socket - socketConnection( host = 'localhost', 5000,
server = TRUE, blocking = TRUE,
open = r, encoding =
getOption(encoding) );
# now read each record and split/validate it using read.table
repeat {
# here for each line I am opening new connection! how to avoid it?
line.raw - textConnection(readLines( reader.socket, n = 1, ok = TRUE));
line.raw - read.table(line.raw, sep=,);
if ( length(line.raw) 1)
break;
print (showConnections());
print(warnings());
}
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Re: [R] newbie: closing unused connection + readline
Try explicitly closing it:
close(reader.socket)
or
closeAllConnections()
On Sat, May 16, 2009 at 8:34 AM, Aval Sarri aval.sa...@gmail.com wrote:
Hello;
I am new to R and trying to read a line from socket connection at a
time but at the end of script I am getting closing unused connection
warning. I am not able to understand how to solve this. I want to read
a line from socket and then use read.table/scan on that line but it
looks like I am opening multiple connections instead of just one. I
think I am doing something wrong or not able to understand correct
method of doing this.
---code
# Create a socket from which to read lines - one at a time (record)
reader.socket - socketConnection( host = 'localhost', 5000,
server = TRUE, blocking = TRUE,
open = r, encoding =
getOption(encoding) );
# now read each record and split/validate it using read.table
repeat {
# here for each line I am opening new connection! how to avoid it?
line.raw - textConnection(readLines( reader.socket, n = 1, ok = TRUE));
line.raw - read.table(line.raw, sep=,);
if ( length(line.raw) 1)
break;
print (showConnections());
print(warnings());
}
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and provide commented, minimal, self-contained, reproducible code.
[R] barplot in a loop not printing out to directory
Hello!
I am experiencing a problem with section 3 of the code below. I want
to generate barplots (based on data generated in Sections 1 and 2) in
a loop - for each variable in data - and save them as .emf files in
my current directory. But it's not working - it's printing values to
be plotted to the screen but does not print the plots themselves
anywhere (and not in the directory).
Thank you very much for your help!
Dimitri
### Section 1. This section generates my data set data - no problems there:
N-100
myset1-c(1,2,3,4,5)
probs1-c(.05,.10,.15,.40,.30)
myset2-c(0,1)
probs2-c(.65,.30)
myset3-c(1,2,3,4,5,6,7)
probs3-c(.02,.03,.10,.15,.20,.30,.20)
group-as.factor(sapply(1:4,function(x){
out-rep(x,25)
out
}))
set.seed(1)
a-sample(myset1, N, replace = TRUE,probs1)
a[which(rbinom(100,2,.01)==1)]-NA
set.seed(12)
b-sample(myset1, N, replace = TRUE,probs1)
b[which(rbinom(100,2,.01)==1)]-NA
set.seed(123)
c-sample(myset2, N, replace = TRUE,probs2)
set.seed(1234)
d-sample(myset2, N, replace = TRUE,probs2)
set.seed(12345)
e-sample(myset3, N, replace = TRUE,probs3)
e[which(rbinom(100,2,.01)==1)]-NA
set.seed(123456)
f-sample(myset3, N, replace = TRUE,probs3)
f[which(rbinom(100,2,.01)==1)]-NA
data-data.frame(group,a=a,b=b,c=c,d=d,e=e,f=f)
### Section 2. Generating tables with percentages for barplot:
tables-lapply(data,function(x){
out-table(x)
out-prop.table(out)
out-round(out,3)*100
out.df-data.frame(matrix(nrow=length(out),ncol=2))
names(out.df)-c(Value,Percentages)
out.df[1]-dimnames(out)[1]
out.df[2]-out
return(out.df)
})
(tables)
### Section 3. I want to generate a barplot based on each and every
table I produced above and put it in my current directory. But it's
not working.
for(i in 1:length(tables)) {
chart.name-names(data)[i]
filename=paste(i,chart.name,emf,sep=.)
win.metafile(file=filename)
chart-barplot(tables[[i]][[2]],xlab = Values, ylab =
Percentages,ylim=c(0,100))
print(chart)
dev.off()
}
Thank you very much!
--
Dimitri Liakhovitski
MarketTools, Inc.
dimitri.liakhovit...@markettools.com
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Re: [R] fitdistr for t distribution
l == lagreene lagreene...@gmail.com
on Fri, 15 May 2009 04:22:59 -0700 (PDT) writes:
l Thanks Jorge,
l but I still don't understand where they come from. when I use:
l fitdistr(mydata, t, df = 9) and get values for m and s, and the
variance
l of my data should be the df/s?
definitely *not*; How did you get to this completely wrong formula?
l I jsut want to be able to confirm how m and s are calculated
by maximum likelihood.
And, of course, only for the normal (aka Gaussian) are the ML
estimates of mu the artithmetic mean and of sigma (n-1)/n * sd(x)
{i.e. even *there* the ML estimate of s is *not* the SD}
As you can read on ?dt,
the variance of a (0,1)-t-distribution is df / (df - 2)
and hence only defined for df 2.
Consequently, the variance of a (mu,sigma)-t-distribution is
sigma^2 * df / (df - 2)
l mydt - function(x, m, s, df) dt((x-m)/s, df)/s
l fitdistr(x2, mydt, list(m = 0, s = 1), df = 9, lower = c(-Inf, 0))
{this is copy-pasted from example(dt);
the examples have nice comments there}
l Jorge Ivan Velez wrote:
Dear lagreene,
See the second example in
require(MASS)
?fitdistr
HTH,
Jorge
On Thu, May 14, 2009 at 7:15 PM, lagreene lagreene...@gmail.com wrote:
Hi,
I was wondering if anyone could tell me how m and s are calculated for a
t
distribution?
I thought m was the sample mean and s the standard deviation- but
obviously
I'm wrong as this doesn'y give the same answer.
Thank you
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Re: [R] ggplot2: annotating plot with mathematical formulae
Hi Stephen,
The problem is that the label on the graph doesn't get rendered with a
superscript. I want the label on the graph to be rendered the same way
as the label you have put on the axis.
I am plotting a piecewise function and I wanted to label each section of it.
Paul
stephen sefick wrote:
how about this
a - 1:10
b - 1:10
d - paste(x,^,{n-1})
qplot(a,b, xlab=expression(x^{n-1}))+geom_text(aes(4,8, label=d))
On Fri, May 15, 2009 at 10:02 PM, Paul Emberson em...@calidasoft.co.uk
wrote:
Hi,
Is there a way of annotating a ggplot plot with mathematical formulae?
I can do
geom_text(aes(label=some text, ...
but I can't do
geom_text(aes(label=expression(x^{n-1}), ...
It gives the error
Error: geom_text requires the following missing aesthetics: label
Is there a convenient equivalent?
Cheers,
Paul
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Re: [R] barplot in a loop not printing out to directory
Dimitri Liakhovitski wrote:
Hello!
I am experiencing a problem with section 3 of the code below. I want
to generate barplots (based on data generated in Sections 1 and 2) in
a loop - for each variable in data - and save them as .emf files in
my current directory. But it's not working - it's printing values to
be plotted to the screen but does not print the plots themselves
anywhere (and not in the directory).
Thank you very much for your help!
Dimitri
...
I would insert a line just after filename=...
cat(filename,\n)
and see what the filenames are.
Jim
### Section 3. I want to generate a barplot based on each and every
table I produced above and put it in my current directory. But it's
not working.
for(i in 1:length(tables)) {
chart.name-names(data)[i]
filename=paste(i,chart.name,emf,sep=.)
win.metafile(file=filename)
chart-barplot(tables[[i]][[2]],xlab = Values, ylab =
Percentages,ylim=c(0,100))
print(chart)
dev.off()
}
Thank you very much!
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Re: [R] newbie: closing unused connection + readline
On Sat, May 16, 2009 at 6:12 PM, Gabor Grothendieck
ggrothendi...@gmail.com wrote:
Try explicitly closing it:
close(reader.socket)
or
closeAllConnections()
Thank you Sir but is there a way that it does not get open each time?
I mean following line creates a new text connection each time so how
to avoid it or reuse an open connection?
line.raw - textConnection(readLines( reader.socket, n = 1, ok = TRUE));
I tried something line this also:
mydataframe - read.table (socket, sep=,);
but does not work says no input lines.
this also.
mydataframe - read.table (readLine(socket), sep=,);
what is the best method of doing something like this? I am getting
totally lost between textConnection, socket and getConnection. Now I
am trying to get the connection that was opened and reuse it but then
how do I get connection that was previously opened when running code -
since getConnection() requires a number and for that I need to know
the number of my previously opened connection. So how do I get the
number of textConnection that I open?
Sir any pointers would greatly help.
Thanks and regards
-Aval
On Sat, May 16, 2009 at 8:34 AM, Aval Sarri aval.sa...@gmail.com wrote:
Hello;
I am new to R and trying to read a line from socket connection at a
time but at the end of script I am getting closing unused connection
warning. I am not able to understand how to solve this. I want to read
a line from socket and then use read.table/scan on that line but it
looks like I am opening multiple connections instead of just one. I
think I am doing something wrong or not able to understand correct
method of doing this.
---code
# Create a socket from which to read lines - one at a time (record)
reader.socket - socketConnection( host = 'localhost', 5000,
server = TRUE, blocking = TRUE,
open = r, encoding =
getOption(encoding) );
# now read each record and split/validate it using read.table
repeat {
# here for each line I am opening new connection! how to avoid it?
line.raw - textConnection(readLines( reader.socket, n = 1, ok = TRUE));
line.raw - read.table(line.raw, sep=,);
if ( length(line.raw) 1)
break;
print (showConnections());
print(warnings());
}
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and provide commented, minimal, self-contained, reproducible code.
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Re: [R] anova(cph(..) output
pompon wrote:
Hello,
I am a beginner in R and statistics, so my question may be trivial. Sorry in
advance.
I performed a Cox proportion hazard regression with 2 categorical variables
with cph{design}. Then an anova on the results.
the output is
anova(cph(surv(survival, censor) ~ plant + leaf.age + plant*leaf.age,
Mpnymph)
Wald Statistics Response: Surv(survival, censored)
FactorChi-Square d.f. P
plant (Factor+Higher Order Factors) 96.96 12 .0001
All Interactions 10.58
6 0.1022
leaf.age (Factor+Higher Order Factors) 29.11 7 0.0001
All Interactions 10.58
6 0.1022
plant * leaf.age (Factor+Higher Order Factors) 10.58 6 0.1022
TOTAL 106.63 13 .0001
What do All interaction stand for?
The real df of for plant is 6 and 1 for leaf.age. Then, which chi square is
one for my main factors anf their interaction.
thank you,
Julien.
Julien,
I know what you mean when you say 'real df' but that's not the whole
story as plant has 6 more df by interacting with a single df variable.
There is no such thing as 'the' main effect test for plant. The 12 df
test is unique and tests whether plant is associated with Y for any
level of leaf.age.
You can see exactly what is being tested by using various print options
for anova.Design, as described in the help file. The dots option is
easy on the eyes.
Frank
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
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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] Fwd: Cannot allocate a new database connection error
Open a connection as in
con - myDbConnect(dbName,hostName)
before the loop starts and afterwards just work on con.
Uwe Ligges
Moumita Das wrote:
-- Forwarded message --
From: Moumita Das das.moumita.onl...@gmail.com
Date: Sat, May 16, 2009 at 2:26 PM
Subject: Cannot allocate a new database connection error
To: r-help-requ...@r-project.org
Hi friends,
why do i keep getting this error?The program runs, twice and every third
time i get this error.I have to quit.Again get teh R-prompt and then run the
script.
*Error in mysqlNewConnection(drv, ...) :
RS-DBI driver: (�...@`qe@°
°
cannot allocate a new connection -- maximum of 16 connections already
opened)
Error in is(object, Cl) :
error in evaluating the argument 'conn' in selecting a method for function
'dbSendQuery'
Error in is(object, Cl) :
error in evaluating the argument 'res' in selecting a method for function
'fetch'*
*this is my DB connection function*
*myDbConnect - function (dbName, hostName) {
drv-MySQL()
con - dbConnect(drv, user=xyz, password=xyz,dbname = dbName, host
= hostName)
return(con)
}*
everytime i need ,Db connection , i used in this way:
This is the structure of my code:--
main - function ()
{
#Looping through subgroups
for(sub_group_num_loopcounter in 1:sub_group_num_data_size[1])
{
#Fetching the where clause for the particular subgroup
*sub_group_where_condition -
fetch(dbSendQuery(myDbConnect(dbName,hostName), paste(c(SELECT where_clause
FROM sub_grp where
num=,sub_group_num_data[sub_group_num_loopcounter,1]),collapse=)), n =
-1) *
}
dbDisconnect(con)
dbListConnections(MySQL())
l-list()
}
Where should i close the DB connection or use one single connection
throughout the prograam.
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Re: [R] Matrix package,solve() errors and crashes Please help
SS == Surendar Swaminathan surendar.swaminat...@gmail.com
on Fri, 15 May 2009 15:55:23 -0700 writes:
Hello All,
SS Please help me with this problem.I have been having this problem for
over a
SS month now and I could not find any information.I later realised that
error
SS is with MATRIX package.
[...]
SS This is my graph object.
SS The file 'Bonacich Power.RData' (1.5 MB) is available for download at
SS
SS
http://dropbox.unl.edu/uploads/20090522/7a0d0313f21fd6a8/Bonacich%20Power.RData
[...]
and you have asked almost the idetnical question 4 weeks ago,
and got a first answer, but then not a *real* answer.
I'm sorry for that, since I had started answering you,
and even more as I *did* solve the problem back then.. (April 22).
more below ...
SS computer Configuration
SS *WIndows XP service Pack 3 .0 GB RAM*
SS I am using SPARSE matrix to solve the problem
SS This is the code I use to obtain bonpower using Sparse Matrix
SS alternatively the code is in the following website
SS http://igraph.wikidot.com/r-recipes#toc6
I'm really appaled that R-recipes on such a website give
such an unprofessional advice
{the following is so grabled because of your (implicit)
insistence on using HTML-ified e-mail .. }
SS *bonpow.sparse - function(graph, nodes=V(graph), loops=FALSE,
SS exponent=1, rescale=TRUE, tol=1e-07) {*
SS * ## remove loops if requested
SS *
SS * ## sparse adjacency matrix
SS d - get.adjacency(graph, sparse=TRUE)*
SS * ## sparse identity matrix
SS id - spMatrix(vcount(graph), vcount(graph),
SS i=1:vcount(graph), j=1:vcount(graph),
SS x=rep(1, vcount(graph)))
SS id - as(id, dgCMatrix)*
SS * ## solve it
SS ev - solve(id - exponent * d, tol=tol) %*% degree(graph, mode=all)*
SS * if (rescale) {
SS ev - ev/sum(ev)
SS } else {
SS ev - ev * sqrt(vcount(graph)/sum((ev)^2))
SS }*
SS * ev[as.numeric(nodes) + 1]
SS }*
SS **
SS I realised that the error is in Matrix Package
SS *Error: cannot allocate vector of size 3.3 Gb
SS In addition: Warning messages:
SS 1: In solve(id - exponent * d, tol = tol) :
SS Reached total allocation of 1535Mb: see help(memory.size)
SS 2: In solve(id - exponent * d, tol = tol) :
SS Reached total allocation of 1535Mb: see help(memory.size)
SS 3: In solve(id - exponent * d, tol = tol) :
SS Reached total allocation of 1535Mb: see help(memory.size)
SS 4: In solve(id - exponent * d, tol = tol) :
SS Reached total allocation of 1535Mb: see help(memory.size)*
SS **
SS sessionInfo()
SS R version 2.9.0 (2009-04-17)
[ . ] {irrelevant here}
SS Please help Matrix Experts
Well, I've marked the one line above
ev - solve(id - exponent * d, tol=tol) %*% degree(graph, mode=all)*
begin abusive language; excuse in advance ..
which really contains stupid advice.
Yes, this is strongly put, but I think people who tell you to
solve
A x = b (A [n x n] matrix)
in R by x - solve(A) %*% b
should not give advice on programming at all.
end abusive language
One of the proper advices would use
x - solve(A, b)
and indeed that's even more crucial in the case where A is
sparse matrix: solve(A) is never sparse for sparse A (*),
but solve(A, b) can happen with a fast (and memory-efficient)
algorithm, and that's what happens also when you use the Matrix package.
I append a version of your function that is also slightly
improved in other places.
(*) and that's why your memory blows up when A is large and sparse !
SS Thanks in advance
SS Nathan
SS [[alternative HTML version deleted]]
(still It would *really* help if you used a more sensible e-mail
configuration }
Regards,
Martin Maechler
---
Here's the corrected bonpow.sparse() function , actually with
extra code for diagnostic output, etc.
You should probably simplify it again :
## I got help from IGRAPH community to use sparse Matrix
##
## http://igraph.wikidot.com/r-recipes#toc6
##
### Enhanced by Martin Maechler:
bonpow.sparse - function(graph, nodes = V(graph), loops = FALSE,
exponent = 1, adj.type = both,
trace = TRUE,
rescale=FALSE, tol=1e-07)
{
stopifnot(require(igraph),
require(Matrix))
if(trace) {
c.width - 30
C1 - function(s) cat(sprintf(%-*s .. , c.width, s))
C2 - function() cat([Ok]\n)
} else { C1 - C2 - function(...) {} }
## remove loops if requested
if (!loops) {
C1(simplify()ing graph)
graph - simplify(graph, remove.multiple=FALSE, remove.loops=TRUE)
C2()
}
## sparse adjacency matrix
C1(d - get.adjacency(., sparse))
d - get.adjacency(graph, type = adj.type, sparse=TRUE); C2()
if(trace = 2)
cat(class(d): , class(d),\n)
Re: [R] Memory size problems in R
Fernando José Nascimento Sebastião wrote: Dear all, I have some problems how to increase memory in R. I tried to start R by calling e.g. :(in the Properties, Shortcut tab, Target field) Rgui.exe --max-mem-size=2Gb (Is this correct?) But the error message still continue: X-princomp(MAT2D.AltGeop61.90) Error: cannot allocate vector of size 445.4 Mb Note, this just means that the next chunk to be allocated is 445.4 Mb, it does not mean the amount will be sufficient for your problem . memory.size() [1] 456.01 memory.limit() [1] 4095 That's strange, because you have not asked for 4Gb. Do you have some other setting (perhaps in your startup code) that increases memory size to 4Gb after you started R? dim(MAT2D.AltGeop61.90) [1] 10957 5328 I use R 2.9.0 in Windows XP, with 40 GB on the disk and 7 GB of RAM. 64-bit version of Windows XP, I guess? What can I do? Use a 64-bit version of R [i.e. something on a LInux machine or perhaps the recently available commercial 64-bit version for Windows] or rephrase/-code your problem. Uwe Ligges I would appreciate somebody to help with any ideia. [[alternative HTML version deleted]] __ R-help@r-project.org 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-help@r-project.org 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.
Re: [R] Plotting question re. cuminc
K F Pearce wrote: Hello everyone, (This is my second question posted today on the R list). and you have still not read the posting guide? It asks you to provide commented, minimal, self-contained, reproducible code which also means that you need to tell which packages you are using. I get, e.g.: cuminc(ftime,fstatus,group) Error: could not find function cuminc ftime Error: object 'ftime' not found fstatus Error: object 'fstatus' not found group Error: object 'group' not found Best, Uwe Ligges I am carrying out a competing risks analysis using the cuminc function...this takes the form: cuminc(ftime,fstatus,group) In my study, fstatus has 3 different causes of failure (1,2,3) there are also censored cases (0). group has two levels (0 and 1). I therefore have 6 different cumulative incidence curves: cause 1, group=0; cause 1 group=1 cause 2, group=0; cause 2 group=1 cause 3, group=0; cause 3 group=1 If I type the following commands: xx-cuminc(ftime,fstatus,group) plot(xx,lty=1,color=1:6) I end up with the 6 curves plotted on the same graph. Is there a way that I can plot a selection of these curves? (say only curves for cause 1, group=0 and cause 1 group=1). Thank you so much, Kind Regards, Kim Dr Kim Pearce CStat Industrial Statistics Research Unit (ISRU) School of Mathematics and Statistics Herschel Building University of Newcastle Newcastle upon Tyne United Kingdom NE1 7RU Tel. 0044 (0)191 222 6244 (direct) Fax. 0044 (0)191 222 8020 Email: k.f.pea...@ncl.ac.uk __ R-help@r-project.org 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-help@r-project.org 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.
Re: [R] data summary and some automated t.tests.
stephen sefick wrote: I would like to preform a t.test to each of the measured variables (sand.silt etc.) I am a big fan of applying t.test()s, but in this case: Are you really sure? The integers and particularly boxplot(x) do not indicate very well that the variables are somehow close to Gaussian ... with a mean and sd for each of the treatments And what is the treatment??? Best, Uwe Ligges (up or down), and out put this as a table I am having a hard time starting- maybe it is to close to lunch. Any suggestions would be greatly appreciated. Stephen Sefick x - (structure(list(sample. = structure(c(1L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 2L, 3L, 4L, 5L, 6L, 1L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 2L, 3L, 4L, 5L, 6L, 25L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 26L, 25L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 26L, 27L, 25L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 26L, 15L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 16L, 15L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 16L, 36L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 37L, 36L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 37L, 38L), .Label = c(0805-r1, 0805-r10, 0805-r11, 0805-r12, 0805-r13, 0805-r14, 0805-r2, 0805-r3, 0805-r4, 0805-r5, 0805-r6, 0805-r7, 0805-r8, 0805-r9, 0805-u1, 0805-u10, 0805-u2, 0805-u3, 0805-u4, 0805-u5, 0805-u6, 0805-u7, 0805-u8, 0805-u9, 1005-r1, 1005-r10, 1005-r11, 1005-r2, 1005-r3, 1005-r4, 1005-r5, 1005-r6, 1005-r7, 1005-r8, 1005-r9, 1005-u1, 1005-u10, 1005-u11, 1005-u2, 1005-u3, 1005-u4, 1005-u5, 1005-u6, 1005-u7, 1005-u8, 1005-u9 ), class = factor), date = structure(c(2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = c(10/1/05, 8/29/05), class = factor), Replicate = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L ), site = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c(dn, up ), class = factor), sand.silt = c(20L, 45L, 90L, 21L, 80L, 77L, 30L, 80L, 36L, 9L, 62L, 71L, 20L, 65L, 10L, 70L, 50L, 80L, 90L, 97L, 94L, 82L, 30L, 10L, 65L, 80L, 90L, 70L, 10L, 50L, 60L, 40L, 10L, 45L, 10L, 10L, 15L, 10L, 8L, 35L, 10L, 40L, 10L, 10L, 28L, 5L, 45L, 35L, 2L, 10L, 40L, 2L, 70L, 40L, 20L, 30L, 50L, 60L, 10L, 100L, 98L, 98L, 90L, 87L, 87L, 40L, 97L, 92L, 70L, 50L, 81L, 35L, 70L, 89L, 28L, 28L, 82L, 81L, 33L, 80L, 40L, 40L, 60L, 30L, 5L, 50L, 70L, 75L, 85L, 95L, 93L, 80L, 80L, 60L, 82L, 60L, 5L, 70L, 80L, 40L), gravel = c(8L, 45L, 7L, 5L, 10L, 5L, 35L, 7L, 45L, 60L, 0L, 0L, 5L, 8L, 25L, 0L, 45L, 15L, 0L, 1L, 2L, 5L, 6L, 15L, 10L, 5L, 3L, 10L, 20L, 0L, 20L, 31L, 20L, 35L, 70L, 30L, 60L, 60L, 70L, 50L, 70L, 40L, 50L, 30L, 48L, 85L, 20L, 30L, 20L, 60L, 30L, 8L, 10L, 30L, 30L, 10L, 0L, 0L, 10L, 0L, 0L, 0L, 2L, 8L, 8L, 30L, 0L, 3L, 15L, 29L, 11L, 60L, 15L, 8L, 60L, 25L, 8L, 9L, 42L, 1L, 50L, 40L, 10L, 60L, 60L, 30L, 10L, 10L, 0L, 0L, 0L, 2L, 2L, 0L, 1L, 25L, 10L, 10L, 10L, 50L), cobble = c(5L, 2L, 1L, 5L, 0L, 3L, 10L, 2L, 4L, 3L, 1L, 0L, 3L, 14L, 50L, 0L, 1L, 1L, 0L, 0L, 0L, 2L, 0L, 5L, 0L, 0L, 2L, 5L, 3L, 0L, 0L, 0L, 0L, 0L, 0L, 30L, 5L, 2L, 1L, 0L, 0L, 0L, 5L, 35L, 3L, 0L, 0L, 0L, 40L, 0L, 0L, 5L, 0L, 0L, 10L, 5L, 0L, 0L, 10L, 0L, 0L, 0L, 0L, 1L, 1L, 30L, 0L, 0L, 0L, 10L, 4L, 3L, 2L, 0L, 2L, 0L, 0L, 0L, 20L, 0L, 0L, 0L, 0L, 0L, 20L, 0L, 10L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 10L, 0L, 0L, 0L), boulder.bedrock = c(60L, 0L, 0L, 45L, 0L, 0L, 0L, 0L, 0L, 8L, 10L, 0L, 35L, 5L, 8L, 0L, 0L, 0L, 0L, 0L, 0L, 10L, 60L, 70L, 0L, 0L, 0L, 5L, 55L, 0L, 0L, 0L, 40L, 0L, 0L, 0L, 0L, 15L, 0L, 0L, 10L, 0L, 20L, 10L, 0L, 0L, 0L, 0L, 20L, 0L, 0L, 60L, 0L, 0L, 20L, 0L, 10L, 0L, 50L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 10L, 0L, 0L, 0L, 0L, 0L, 4L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 5L, 0L, 0L, 5L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 75L, 10L, 0L, 0L), fine.root = c(5L, 7L, 0L, 10L, 2L, 6L, 5L, 4L, 3L, 7L, 0L, 0L, 7L, 4L, 6L, 1L, 4L, 2L, 2L, 2L, 3L, 1L, 0L, 1L, 20L, 5L, 3L, 5L, 10L, 2L, 0L, 6L, 10L, 10L, 15L, 0L, 0L, 5L, 15L, 0L, 10L, 10L, 0L, 5L, 8L, 5L, 0L, 20L, 0L, 8L, 0L, 0L, 7L, 0L,
Re: [R] (no subject)
On Sat, May 16, 2009 at 12:05 PM, Debbie Zhang debbie0...@hotmail.com wrote:
Dear R users,
Does anyone know how to write a function involving derivative?
i.e. I want to implementing Newton's method in R, so my function is something
like
x- x-y/y'
I am not sure how to write y' in my function. Can anyone help?
In addition, if I want to implementing newton's method several times, what
code should I use?
Currently, I use the following code.
-1
Is this line x - 1?
for (i in 1:20){
+ x-x-(x^3-2*x^2+3*x-5)/(3*x^2-4*x+3)}
x
[1] 1.843734
However, when I typed in the following code, I would yield the same answer.
-1
And is this line x - 1, too?
for (i in 1:1){
+ x-x-(x^3-2*x^2+3*x-5)/(3*x^2-4*x+3)}
x
[1] 1.843734
Are you sure about this result?
What I got is like this:
x - 1; for (i in 1:20) { x - x-(x^3-2*x^2+3*x-5)/(3*x^2-4*x+3); }; x
[1] 1.843734
x - 1; for (i in 1:1) { x - x-(x^3-2*x^2+3*x-5)/(3*x^2-4*x+3); }; x
[1] 2.5
There are different!
Can anyone suggest me what the problem is?
Please help.
Thanks so much.
Debbie
_
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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.
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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] Fw: Help with loops(corrected question)
Amit Patel wrote:
--- On Fri, 15/5/09, Amit Patel amitrh...@yahoo.co.uk wrote:
From: Amit Patel amitrh...@yahoo.co.uk
Subject: Help with loops
To: r-help@r-project.org
Date: Friday, 15 May, 2009, 12:17 PM
Hi
I am trying to create a loop which averages replicates in
my data.
The original data has many rows. and consists of 40 column
zz[,2:41] plus row headings in zz[,1]
I am trying to average each set of values (i.e. zz[1,2:3]
averaged and placed in average_value[1,2] and so on.
below is my script but it seems to be stuck in an endless
loop
Any suggestions??
If you want row-wise means, rowMeans does it without any loop, but
instead you could loop over the column indices or go without any
explicit loop as in:
averaged_value - zz[,1:21]
temp - as.matrix(zz[,2:41])
dim(temp) - c(nrow(temp),2,20)
# and then either:
temp - aperm(temp, c(1,3,2))
averaged_value[,2:21] - rowMeans(temp, dim=2)
#
averaged_value[,2:21] - apply(temp, c(1,3), mean)
Uwe Ligges
for (i in 1:length(zz[,1])) {
#calculates Meanss
#Sample A
average_value[i,2] - rowMeans(zz[i,2:3])
average_value[i,3] - rowMeans(zz[i,4:5])
average_value[i,4] - rowMeans(zz[i,6:7])
average_value[i,5] - rowMeans(zz[i,8:9])
average_value[i,6] - rowMeans(zz[i,10:11])
#Sample B
average_value[i,7] - rowMeans(zz[i,12:13])
average_value[i,8] - rowMeans(zz[i,14:15])
average_value[i,9] - rowMeans(zz[i,16:17])
average_value[i,10] - rowMeans(zz[i,18:19])
average_value[i,11] - rowMeans(zz[i,20:21])
#Sample C
average_value[i,12] - rowMeans(zz[i,22:23])
average_value[i,13] - rowMeans(zz[i,24:25])
average_value[i,14] - rowMeans(zz[i,26:27])
average_value[i,15] - rowMeans(zz[i,28:29])
average_value[i,16] - rowMeans(zz[i,30:31])
#Sample D
average_value[i,17] - rowMeans(zz[i,32:33])
average_value[i,18] - rowMeans(zz[i,34:35])
average_value[i,19] - rowMeans(zz[i,36:37])
average_value[i,20] - rowMeans(zz[i,38:39])
average_value[i,21] - rowMeans(zz[i,40:41])
}
thanks
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[R] maxLik pakage
Hi all;
I recently have been used 'maxLik' function for maximizing G2StNV178 function
with gradient function gradlik; for receiving this goal, I write the following
program; but I have been seen an error in calling gradient function;
The maxLik function can't enter gradlik function (definition of gradient
function); I guess my mistake is in line ,that the vector  âhâ is
defined.
Â
I need your advices for resolve the error;
Sincerely yours
A. Kheradmandi
##data vector
x=c(0,0,14,7,0,22,2,18,10,29,
16,11,59,6,33,5,1,0,28,17,
28,19,10,43,9,17,42,2,22,6,
14,0,59,9,11,5,11,37,15,26,
57,8,16,22,5,13,19,12,34,8,28,35,13,11,59,
8,7,20,36,39,14,31,18,32,30,
29,9,2,5,3,19,27,76,4,32,
24,13,3,13,24,41,20,0,13,26,
0,23,19,10,14,14,13,15,18,29,
29,0,20,0,22,13,17,12,29,0,
0,16,55,11,19,9,2,9,32,16,
55,10,59,8,65,39,1,8,2,7,
37,8,0,5,8,0,7,0,20,10,
11,3,0,7,31,14,18,3,4,34,
32,4,9,9,8,36,44,0,9,27,28,55,72,12,1,
9,0,32,0,0,2,15,5,6,17,
63,61,9,15,15,0,2)
#goal is found unique maximum for 5-parameter function with usingÂ
maxLik function
#the function in latex commands is as following:
 \begin{eqnarray*}
\ell(\xi,\omega,\nu,\lambda_1,\lambda_2)=n\log2-n\log\omega+n\log\Gamma(\frac{\nu+1}{2})-\frac{n}{2}\log(\nu\pi)\\
-n\log\Gamma(\frac{\nu}{2})-\frac{\nu+1}{2}\sum_{i=1}^{n}\log(1+\frac{(x_i-\xi)^2}{\omega^2\nu})+\sum_{i=1}^{n}\log\Phi(\lambda_1\frac{(x_i-\xi)}{\sqrt{\omega^2+\lambda_2(x_i-\xi)^2}})
\end{eqnarray*}
##
G2StNV178-function(a){
require(maxLik)
II=0
nu-(a[1])
lambda1-a[2]
lambda2-a[3]
ksi-a[4]
omega-a[5]
II-log(prod((2*dt((x-ksi)/omega,nu)*pnorm((lambda1*(x-ksi)/omega)/sqrt(1+lambda2*((x-ksi)/omega)^2)))/omega))
II
}
definition of gradient function
gradlik- function(a){
nu-a[1]
lambda1-a[2]
lambda2-a[3]
ksi-a[4]
omega-a[5]Â
#***#
h-c(f1=n*digamma((nu+1)/2)-n/(2*nu)-n*digamma(nu/2)-1/2*sum(log(1+(x-ksi)^2/(omega^2nu)))+(nu+1)/2*sum((x-ksi)^2/(omege^2*nu^2+nu*(x-ksi)^2)),
f2=sum((x-ksi)*dnorm(lambda1*(x-ksi)/sqrt(omega^2+lambda2*(x-ksi)^2))/(sqrt(omega^2+lambda2*(x-ksi)^2)*pnorm(lambda1*(x-ksi)/sqrt(omega^2+lambda2*(x-ksi),
f3=sum((lambda1*(x-ksi)^3*dnorm(lambda1*(x-ksi)/sqrt(omega^2+lambda2*(x-ksi)^2)))/(
2*omega^3*pnorm(lambda1*(x-ksi)/sqrt(omega^2+lambda2*(x-ksi)^2))
*sqrt((1+lambda2*(x-ksi)^2/omega^2 )^3))),
f4=(nu+1)*sum((x-ksi)/(omega^2*nu+(x-ksi)^2))-sum((lambda1*dnorm((lambda1*(x-ksi))/(omega^2+lambda2*(x-ksi)^2)))/(omega*sqrt(1+lambda2*(x-ksi)^2/(omega^2))
*pnorm(lambda1*(x-ksi)/(sqrt(omega^2+lambda2*(x-ksi)^2),
f5=-n/omega+(nu+1)*n*sum((x-ksi)^2/(nu*omega^3+omega*(x-ksi)^2))-sum((lambda1*(x-ksi)*omega*dnorm(lambda1*(x-ksi)/(sqrt(omega^2+lambda2*(x-ksi)^2))
/(pnorm(lambda1*(x-ksi)/(sqrt(omega^2+lambda2*(x-ksi)^2))*sqrt((omega^2+lambda2*(x-ksi)^2)^3)))
}
n- length(x) # the final command is :
res- maxLik(G2StNV178,grad=gradlik,start=c(4.666484 ,4603.399055 ,
4603.399055Â Â ,-0.016674 ,19.055865),tol=1e-16,iterlim =3000)
summary(res)
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[R] MANOVA
Dear Sir,
I am Davide Floriello and I am a student in mathematics. I have got a problem
with the MANOVA commands. I write here what I have done:
PV - read.table('PV.txt')
PV - data.frame(PV)
g - 12
p - 2
REL - factor(PV$REL)
HPV - factor(PV$HPV)
fit - manova(as.matrix(PV) ~ REL + HPV + REL:HPV)
After this last line, an error message is shown:
Errore in `[[-.data.frame`(`*tmp*`, i, value = c(17L, 19L, 16L, 14L, 15L, :
replacement has 48 rows, data has 12
Inoltre: Warning message:
In storage.mode(v) - double : si è prodotto un NA per coercizione
I don't know how to solve this problem.
Thank you.
Davide Floriello
_
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[R] vector fragment
Dear R users: I have got a simple question that has been bothering me for a while. Given a certain character vector, I would like to get in a separate vector a fragment of text, in this case the 3rd and 4th letters of each element. So, if: v- c(stratosphere, mesosphere, troposphere) I want to obtain a different vector like this: c(ra, so, op) Thanks in advance for your help Jonas [[alternative HTML version deleted]] __ R-help@r-project.org 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.
Re: [R] vector fragment
Dear Jonas,
Try this:
v- c('stratosphere', 'mesosphere', 'troposphere')
substr(v,3,4)
[1] ra so op
See ?substr for more information.
HTH,
Jorge
On Sat, May 16, 2009 at 9:52 AM, jonas garcia garcia.jona...@googlemail.com
wrote:
Dear R users:
I have got a simple question that has been bothering me for a while.
Given a certain character vector, I would like to get in a separate vector
a
fragment of text, in this case the 3rd and 4th letters of each element.
So, if:
v- c(stratosphere, mesosphere, troposphere)
I want to obtain a different vector like this:
c(ra, so, op)
Thanks in advance for your help
Jonas
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Re: [R] maxLik pakage
1. Have you worked through the examples in the maxLik help page? Your
example is sufficiently complicated that I hesitate to try it myself,
especially since I see characters in your email that are not simple
ASCII. If you can get the examples in the maxLik help page to work,
identify the differences between your example and those on the help
page, then generate intermediate examples to test your understanding
until you either solve your problem or you find a simpler example that
you don't understand and then post that to this list.
2. Have you checked your gradient with the compareDerivatives function
in the maxLik package? If your gradient function is not correct, this
should help you understand and hopefully fix the problem.
Hope this helps.
Spencer
amene kheradmandi wrote:
Hi all;
I recently have been used 'maxLik' function for maximizing G2StNV178 function
with gradient function gradlik; for receiving this goal, I write the following
program; but I have been seen an error in calling gradient function;
The maxLik function can't enter gradlik function (definition of gradient
function); I guess my mistake is in line ,that the vector  ‘h’ is
defined.
Â
I need your advices for resolve the error;
Sincerely yours
A. Kheradmandi
##data vector
x=c(0,0,14,7,0,22,2,18,10,29,
16,11,59,6,33,5,1,0,28,17,
28,19,10,43,9,17,42,2,22,6,
14,0,59,9,11,5,11,37,15,26,
57,8,16,22,5,13,19,12,34,8,28,35,13,11,59,
8,7,20,36,39,14,31,18,32,30,
29,9,2,5,3,19,27,76,4,32,
24,13,3,13,24,41,20,0,13,26,
0,23,19,10,14,14,13,15,18,29,
29,0,20,0,22,13,17,12,29,0,
0,16,55,11,19,9,2,9,32,16,
55,10,59,8,65,39,1,8,2,7,
37,8,0,5,8,0,7,0,20,10,
11,3,0,7,31,14,18,3,4,34,
32,4,9,9,8,36,44,0,9,27,28,55,72,12,1,
9,0,32,0,0,2,15,5,6,17,
63,61,9,15,15,0,2)
#goal is found unique maximum for 5-parameter function with usingÂ
maxLik function
#the function in latex commands is as following:
 \begin{eqnarray*}
\ell(\xi,\omega,\nu,\lambda_1,\lambda_2)=n\log2-n\log\omega+n\log\Gamma(\frac{\nu+1}{2})-\frac{n}{2}\log(\nu\pi)\\
-n\log\Gamma(\frac{\nu}{2})-\frac{\nu+1}{2}\sum_{i=1}^{n}\log(1+\frac{(x_i-\xi)^2}{\omega^2\nu})+\sum_{i=1}^{n}\log\Phi(\lambda_1\frac{(x_i-\xi)}{\sqrt{\omega^2+\lambda_2(x_i-\xi)^2}})
\end{eqnarray*}
##
G2StNV178-function(a){
require(maxLik)
II=0
nu-(a[1])
lambda1-a[2]
lambda2-a[3]
ksi-a[4]
omega-a[5]
II-log(prod((2*dt((x-ksi)/omega,nu)*pnorm((lambda1*(x-ksi)/omega)/sqrt(1+lambda2*((x-ksi)/omega)^2)))/omega))
II
}
definition of gradient function
gradlik- function(a){
nu-a[1]
lambda1-a[2]
lambda2-a[3]
ksi-a[4]
omega-a[5]Â
#***#
h-c(f1=n*digamma((nu+1)/2)-n/(2*nu)-n*digamma(nu/2)-1/2*sum(log(1+(x-ksi)^2/(omega^2nu)))+(nu+1)/2*sum((x-ksi)^2/(omege^2*nu^2+nu*(x-ksi)^2)),
f2=sum((x-ksi)*dnorm(lambda1*(x-ksi)/sqrt(omega^2+lambda2*(x-ksi)^2))/(sqrt(omega^2+lambda2*(x-ksi)^2)*pnorm(lambda1*(x-ksi)/sqrt(omega^2+lambda2*(x-ksi),
f3=sum((lambda1*(x-ksi)^3*dnorm(lambda1*(x-ksi)/sqrt(omega^2+lambda2*(x-ksi)^2)))/( 2*omega^3*pnorm(lambda1*(x-ksi)/sqrt(omega^2+lambda2*(x-ksi)^2))
*sqrt((1+lambda2*(x-ksi)^2/omega^2 )^3))),
f4=(nu+1)*sum((x-ksi)/(omega^2*nu+(x-ksi)^2))-sum((lambda1*dnorm((lambda1*(x-ksi))/(omega^2+lambda2*(x-ksi)^2)))/(omega*sqrt(1+lambda2*(x-ksi)^2/(omega^2))
*pnorm(lambda1*(x-ksi)/(sqrt(omega^2+lambda2*(x-ksi)^2),
f5=-n/omega+(nu+1)*n*sum((x-ksi)^2/(nu*omega^3+omega*(x-ksi)^2))-sum((lambda1*(x-ksi)*omega*dnorm(lambda1*(x-ksi)/(sqrt(omega^2+lambda2*(x-ksi)^2))
/(pnorm(lambda1*(x-ksi)/(sqrt(omega^2+lambda2*(x-ksi)^2))*sqrt((omega^2+lambda2*(x-ksi)^2)^3)))
}
n- length(x) # the final command is :
res- maxLik(G2StNV178,grad=gradlik,start=c(4.666484 ,4603.399055 ,
4603.399055Â Â ,-0.016674 ,19.055865),tol=1e-16,iterlim =3000)
summary(res)
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[R] bagged importance estimates in earth problem
I was trying to produced bagged importance estimates of attributes in earth using the caret package with the following commands: fit2 - bagEarth(loyalty ~ ., data=model1, B = 10) bagImpGCV - varImp(fit2,value=gcv) My bootstrap estimates are produced however the second command varImp produces the following error: Error in UseMethod(varImp) : no applicable method for varImp Not sure what is going on, any advice would be appreciated, Thanks, Joe Retzer [[alternative HTML version deleted]] __ R-help@r-project.org 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.
Re: [R] barplot in a loop not printing out to directory
Thanks a lot.
The problem was that I was naming my files illegally. I was starting
them with a number. As soon as I changed that, everything worked.
Dimitri
On Sat, May 16, 2009 at 9:12 AM, Jim Lemon j...@bitwrit.com.au wrote:
Dimitri Liakhovitski wrote:
Hello!
I am experiencing a problem with section 3 of the code below. I want
to generate barplots (based on data generated in Sections 1 and 2) in
a loop - for each variable in data - and save them as .emf files in
my current directory. But it's not working - it's printing values to
be plotted to the screen but does not print the plots themselves
anywhere (and not in the directory).
Thank you very much for your help!
Dimitri
...
I would insert a line just after filename=...
cat(filename,\n)
and see what the filenames are.
Jim
### Section 3. I want to generate a barplot based on each and every
table I produced above and put it in my current directory. But it's
not working.
for(i in 1:length(tables)) {
chart.name-names(data)[i]
filename=paste(i,chart.name,emf,sep=.)
win.metafile(file=filename)
chart-barplot(tables[[i]][[2]],xlab = Values, ylab =
Percentages,ylim=c(0,100))
print(chart)
dev.off()
}
Thank you very much!
--
Dimitri Liakhovitski
MarketTools, Inc.
dimitri.liakhovit...@markettools.com
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Re: [R] ggplot2: annotating plot with mathematical formulae
Hi Paul,
Unfortunately that's not something that's currently possible with
ggplot2, but I am thinking about how to make it possible.
Hadley
On Sat, May 16, 2009 at 7:48 AM, Paul Emberson em...@calidasoft.co.uk wrote:
Hi Stephen,
The problem is that the label on the graph doesn't get rendered with a
superscript. I want the label on the graph to be rendered the same way
as the label you have put on the axis.
I am plotting a piecewise function and I wanted to label each section of it.
Paul
stephen sefick wrote:
how about this
a - 1:10
b - 1:10
d - paste(x,^,{n-1})
qplot(a,b, xlab=expression(x^{n-1}))+geom_text(aes(4,8, label=d))
On Fri, May 15, 2009 at 10:02 PM, Paul Emberson em...@calidasoft.co.uk
wrote:
Hi,
Is there a way of annotating a ggplot plot with mathematical formulae?
I can do
geom_text(aes(label=some text, ...
but I can't do
geom_text(aes(label=expression(x^{n-1}), ...
It gives the error
Error: geom_text requires the following missing aesthetics: label
Is there a convenient equivalent?
Cheers,
Paul
__
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__
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--
http://had.co.nz/
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Re: [R] Checking a (new) package - examples require other package functions
After adding the right functions to the NAMESPACE file, I am now getting a different error: Error: package/namespace load failed for 'REEMtree' Call sequence: 2: stop(gettextf(package/namespace load failed for '%s', libraryPkgName(package)), call. = FALSE, domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Execution halted I have attached the NAMESPACE file in case that is where the problem is. Thanks again for your help! Rebecca - Original Message - From: Duncan Murdoch murd...@stats.uwo.ca To: Rebecca Sela rs...@stern.nyu.edu Cc: r-help r-help@r-project.org Sent: Thursday, May 14, 2009 6:57:21 AM GMT -05:00 US/Canada Eastern Subject: Re: [R] Checking a (new) package - examples require other package functions On 13/05/2009 2:38 PM, Rebecca Sela wrote: I am creating an R package. I ran R CMD check on the package, and everything passed until it tried to run the examples. Then, the result was: * checking examples ... ERROR Running examples in REEMtree-Ex.R failed. The error most likely occurred in: ### * AutoCorrelationLRtest flush(stderr()); flush(stdout()) ### Name: AutoCorrelationLRtest ### Title: Test for autocorrelation in the residuals of a RE-EM tree ### Aliases: AutoCorrelationLRtest ### Keywords: htest tree models ### ** Examples # Estimation without autocorrelation simpleEMresult-RandomEffectsTree(Y~D+t+X, data=simpleREEMdata, random=~1|ID, simpleREEMdata$ID) Error: couldn't find function RandomEffectsTree Execution halted The function RandomEffectsTree is defined in the R code for the package. How can I refer to other functions from the package in examples? (I have the Writing R-extensions PDF, so it would be enough to point me to the right page, if the answer is in there and I just missed it.) You should not need to do anything special to make package functions visible, as long as they would be visible to a normal user. (Functions not exported in the NAMESPACE file won't be visible in the examples.) Are you sure you have a function with that exact name? It could be a typo somewhere, e.g. RandomEffectTree or RandomeffectsTree. Duncan Murdoch __ R-help@r-project.org 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] MEXVAL
Greetings: I would like to kindly ask help with obtaining mexval statistics (marginal explanatory value - percentage increase in SEE if the variable were left out of the regression model) for a logit (glm) model with several continuous independent variables. I believe I can do it manually for each variable, but I really hope there might be somebody who has a function already written. Writing one is still a little over my skills (I am working on it though). Thanks, mike [[alternative HTML version deleted]] __ R-help@r-project.org 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.
Re: [R] ggplot2: annotating plot with mathematical formulae
If you're desperate for a workaround, you might want to try this
example using pgfSweave,
http://ggplot2.wik.is/Mathematical_annotations
On a similar vein, you could try psfrag replacements with a postscript
device (there is some code for this on the list archives).
Feel free to comment / edit on the wiki page.
HTH,
baptiste
On 16 May 2009, at 14:48, Paul Emberson wrote:
Hi Stephen,
The problem is that the label on the graph doesn't get rendered with a
superscript. I want the label on the graph to be rendered the same
way
as the label you have put on the axis.
I am plotting a piecewise function and I wanted to label each
section of it.
Paul
stephen sefick wrote:
how about this
a - 1:10
b - 1:10
d - paste(x,^,{n-1})
qplot(a,b, xlab=expression(x^{n-1}))+geom_text(aes(4,8, label=d))
On Fri, May 15, 2009 at 10:02 PM, Paul Emberson em...@calidasoft.co.uk
wrote:
Hi,
Is there a way of annotating a ggplot plot with mathematical
formulae?
I can do
geom_text(aes(label=some text, ...
but I can't do
geom_text(aes(label=expression(x^{n-1}), ...
It gives the error
Error: geom_text requires the following missing aesthetics: label
Is there a convenient equivalent?
Cheers,
Paul
__
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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.
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_
Baptiste Auguié
School of Physics
University of Exeter
Stocker Road,
Exeter, Devon,
EX4 4QL, UK
Phone: +44 1392 264187
http://newton.ex.ac.uk/research/emag
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] fitdistr for t distribution
On Fri, May 15, 2009 at 6:22 AM, lagreene lagreene...@gmail.com wrote: Thanks Jorge, but I still don't understand where they come from. when I use: fitdistr(mydata, t, df = 9) and get values for m and s, and the variance of my data should be the df/s? I jsut want to be able to confirm how m and s are calculated I've wondered the same kind of thing and I've learned the answer is easy! It is not so easy for all R functions, but did you try this with fitdistr? library (MASS) fitdistr the output that follows is the ACTUAL FORMULA that is used to make the calculations! I've not yet mastered the art of getting code for some functions. predict function (object, ...) UseMethod(predict) environment: namespace:stats But I know there is a way to get that code if you know the correct way to run getS3method(). But I usually just go read the R source code rather than puzzle over that. mydt - function(x, m, s, df) dt((x-m)/s, df)/s fitdistr(x2, mydt, list(m = 0, s = 1), df = 9, lower = c(-Inf, 0)) Thanks anyway for the help! -- Paul E. Johnson Professor, Political Science 1541 Lilac Lane, Room 504 University of Kansas __ R-help@r-project.org 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.
Re: [R] MANOVA
Dear Davide,
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On
Behalf Of Davide Floriello
Sent: May-16-09 8:51 AM
To: r-help@r-project.org
Subject: [R] MANOVA
Dear Sir,
I am Davide Floriello and I am a student in mathematics. I have got a
problem
with the MANOVA commands. I write here what I have done:
PV - read.table('PV.txt')
PV - data.frame(PV)
The second command is redundant, since read.table() produces a data frame.
g - 12
p - 2
These commands are unnecessary, since you're not referencing g or p.
REL - factor(PV$REL)
HPV - factor(PV$HPV)
Whether these commands are necessary depends upon whether REL and HPV are
already factors; if they are character data in the file PV.txt, then by
default read.table() will make factors.
fit - manova(as.matrix(PV) ~ REL + HPV + REL:HPV)
This really doesn't make sense: Since REL and HPV are among the variables in
PV (although not necessarily factors), these variables are both on the
left-hand and right-hand side of the model.
After this last line, an error message is shown:
Errore in `[[-.data.frame`(`*tmp*`, i, value = c(17L, 19L, 16L, 14L, 15L,
:
replacement has 48 rows, data has 12
Inoltre: Warning message:
In storage.mode(v) - double : si h prodotto un NA per coercizione
My guess is that REL and HPV are non-numeric. I wouldn't have to guess if
you had provided the data.
I hope this helps,
John
I don't know how to solve this problem.
Thank you.
Davide Floriello
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[R] converting numeric to integer
Hello, Suppose I have x, which is a variable of class numeric. The calculations performed to yield x imply that mathematically it should be an integer , but due to round-off errors, it might not be (and so in either direction). The error is however small, so round(x) will yield the appropriate integer value. Moreover, this integer values is guaranteed to be representable by an 'integer' class, that is -2^31 x 2^31, and logically it is an integer anyway. So I want to convert x from class 'numeric' to 'integer'. What is the most elegant, but always correct way, to achieve this conversion ? What comes to mind is of course something along: x = as.integer(round(x)) I am, however, not sure if this always works, because I do not know if the round-function is guaranteed to return a numeric value which, in finite binary representation, is always = the underlying mathematical integer. If that is however guaranteed, that would of course be a simple + elegant one. An alternative I came up with is: x = as.integer(round(x) + ifelse(x = 0, 0.5, -0.5)) Where I explicitly add a bit to ensure the finite binary representation must be = the underlying integer, and then truncate the decimal digits. IMO, this one is always guaranteed to work, at least within the numerical range of what integers are limited to anyway. What's your opinion on the issue ? Any other solution ? Thanks a lot in advance and cheers, Thomas __ R-help@r-project.org 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] Question about barplot: gridlines value labels
Hello!
I promise I looked into help files before asking. Still cannot figure
it out. I think it's because I am totally confused what packages use
lettice, which use trellis, etc.
Sections 1 and 2 below produce the data and the data to plot. My
question is about barplot in Section 3. I am trying to:
1. add only horizontal gridlines and manipulate the type and color of
that line. tck = 1 is not flexible enough to do it.
2. make the legend come on top of gridlines and not under them
3. add plotted Y values above the bars
Thank you very much for any pointers!
Dimitri
### Section 1: generates my data set data:
N-100
myset1-c(1,2,3,4,5)
probs1-c(.05,.10,.15,.40,.30)
group-unlist(lapply(1:4,function(x){
out-rep(x,25)
return(out)
}))
set.seed(1)
a-sample(myset1, N, replace = TRUE,probs1)
a[which(rbinom(100,2,.01)==1)]-NA
set.seed(12)
b-sample(myset1, N, replace = TRUE,probs1)
b[which(rbinom(100,2,.01)==1)]-NA
set.seed(123)
data-data.frame(group,a=a,b=b)
data[group]-lapply(data[group],function(x) {
x[x %in% 1]-Group 1
x[x %in% 2]-Group 2
x[x %in% 3]-Group 3
x[x %in% 4]-Group 4
return(x)
})
data$group-as.factor(data$group)
lapply(data,table,exclude=NULL)
### Section 2. Creating data to plot:
table.a-with(data,table(group,a))
table.a.percents-apply(table.a,2,function(x){
out-round(x*100/sum(x),1)
return(out)
})
### Section 3. Creating a plot:
barplot(table.a.percents,xlab = Values, ylab =
Percentages,ylim=c(0,100),axis.lty=1,legend=T,beside=T,tck = 1)
--
Dimitri Liakhovitski
MarketTools, Inc.
dimitri.liakhovit...@markettools.com
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[R] How to draw a R plot in Java frame ?
Hi guys, I am new to R and would like to display a R plot inside my Java app. Is there a possibility to do that? If so, what library do I need? May the force be with you [[alternative HTML version deleted]] __ R-help@r-project.org 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.
Re: [R] data summary and some automated t.tests.
Up and down are the treatments. These are replicates within date for percent cover of habiat. This is habitat data for a stream restoration - up is the unrestored and dn is the restored. I have looked at the density plots and they do not look gaussian - you are absolutely right. Even log(n+1) transformed they do not look Gaussian. Is there some other way that I would test for a difference that you can think of? My thoughts were to run a Permutation t.test, but I am very new to permutations, and don't know if this applies. The other thing that I was thinking was to use a npmanova (adonis in vegan) to test if the centroids of the habitat classifications were different. I am in the process of working up my thesis data for publication in a journal (there are other very interesting pieces to the data set that I am working with, and this is one of the last things that I need to wrap up before I can start editing/rewriting my masters work). Any thoughts would be greatly appreciated. thanks, Stephen Sefick 2009/5/16 Uwe Ligges lig...@statistik.tu-dortmund.de: stephen sefick wrote: I would like to preform a t.test to each of the measured variables (sand.silt etc.) I am a big fan of applying t.test()s, but in this case: Are you really sure? The integers and particularly boxplot(x) do not indicate very well that the variables are somehow close to Gaussian ... with a mean and sd for each of the treatments And what is the treatment??? Best, Uwe Ligges (up or down), and out put this as a table I am having a hard time starting- maybe it is to close to lunch. Any suggestions would be greatly appreciated. Stephen Sefick x - (structure(list(sample. = structure(c(1L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 2L, 3L, 4L, 5L, 6L, 1L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 2L, 3L, 4L, 5L, 6L, 25L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 26L, 25L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 26L, 27L, 25L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 26L, 15L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 16L, 15L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 16L, 36L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 37L, 36L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 37L, 38L), .Label = c(0805-r1, 0805-r10, 0805-r11, 0805-r12, 0805-r13, 0805-r14, 0805-r2, 0805-r3, 0805-r4, 0805-r5, 0805-r6, 0805-r7, 0805-r8, 0805-r9, 0805-u1, 0805-u10, 0805-u2, 0805-u3, 0805-u4, 0805-u5, 0805-u6, 0805-u7, 0805-u8, 0805-u9, 1005-r1, 1005-r10, 1005-r11, 1005-r2, 1005-r3, 1005-r4, 1005-r5, 1005-r6, 1005-r7, 1005-r8, 1005-r9, 1005-u1, 1005-u10, 1005-u11, 1005-u2, 1005-u3, 1005-u4, 1005-u5, 1005-u6, 1005-u7, 1005-u8, 1005-u9 ), class = factor), date = structure(c(2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = c(10/1/05, 8/29/05), class = factor), Replicate = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L ), site = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c(dn, up ), class = factor), sand.silt = c(20L, 45L, 90L, 21L, 80L, 77L, 30L, 80L, 36L, 9L, 62L, 71L, 20L, 65L, 10L, 70L, 50L, 80L, 90L, 97L, 94L, 82L, 30L, 10L, 65L, 80L, 90L, 70L, 10L, 50L, 60L, 40L, 10L, 45L, 10L, 10L, 15L, 10L, 8L, 35L, 10L, 40L, 10L, 10L, 28L, 5L, 45L, 35L, 2L, 10L, 40L, 2L, 70L, 40L, 20L, 30L, 50L, 60L, 10L, 100L, 98L, 98L, 90L, 87L, 87L, 40L, 97L, 92L, 70L, 50L, 81L, 35L, 70L, 89L, 28L, 28L, 82L, 81L, 33L, 80L, 40L, 40L, 60L, 30L, 5L, 50L, 70L, 75L, 85L, 95L, 93L, 80L, 80L, 60L, 82L, 60L, 5L, 70L, 80L, 40L), gravel = c(8L, 45L, 7L, 5L, 10L, 5L, 35L, 7L, 45L, 60L, 0L, 0L, 5L, 8L, 25L, 0L, 45L, 15L, 0L, 1L, 2L, 5L, 6L, 15L, 10L, 5L, 3L, 10L, 20L, 0L, 20L, 31L, 20L, 35L, 70L, 30L, 60L, 60L, 70L, 50L, 70L, 40L, 50L, 30L, 48L, 85L, 20L, 30L, 20L, 60L, 30L, 8L, 10L, 30L, 30L, 10L, 0L, 0L, 10L, 0L, 0L, 0L, 2L, 8L, 8L, 30L, 0L, 3L, 15L, 29L, 11L, 60L, 15L, 8L, 60L, 25L, 8L, 9L, 42L, 1L, 50L, 40L, 10L, 60L, 60L, 30L, 10L, 10L, 0L, 0L, 0L, 2L, 2L, 0L,
Re: [R] newbie: closing unused connection + readline
On Sat, May 16, 2009 at 8:34 AM, Aval Sarri aval.sa...@gmail.com wrote:
# Create a socket from which to read lines - one at a time (record)
reader.socket - socketConnection( host = 'localhost', 5000,
server = TRUE, blocking = TRUE,
open = r, encoding =
getOption(encoding) );
# now read each record and split/validate it using read.table
repeat {
# here for each line I am opening new connection! how to avoid it?
line.raw - textConnection(readLines( reader.socket, n = 1, ok = TRUE));
What is the function of textConnection here? Is read.table
incompatible with socketConnection for some reason?
line.raw - read.table(line.raw, sep=,);
...at the end of script I am getting closing unused connection warning
This is not a problem in itself. For some reason, R gives a warning
when connections are garbage collected. Of course, that can be a
symptom of poor connection management, but not necessarily.
In the present case, you are creating many unnecessary
textConnections, and R correctly garbage collects them.
-s
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Re: [R] newbie: closing unused connection + readline
On Sat, May 16, 2009 at 9:11 AM, Aval Sarri aval.sa...@gmail.com wrote: ...I tried something line this also: mydataframe - read.table (socket, sep=,); but does not work says no input lines. this also. mydataframe - read.table (readLine(socket), sep=,); Sorry, I didn't see this before my last email. This seems to be the real problem I don't understand why read.table would have a problem reading directly from a socket instead of a textConnection. Is this a bug? Some subtlety in the semantics of socketConnection as opposed to textConnection? Incorrect parameters when opening the socketConnection? -s __ R-help@r-project.org 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.
Re: [R] Gamma function
What exactly is the R code you wrote for your function f? Without that, it will be hard to help you. -s On Sat, May 16, 2009 at 2:48 AM, Kon Knafelman konk2...@hotmail.com wrote: Hi Guy, I am having trouble graphing the following function √2Γ(n/2)/[√n - 1Γ((n - 1)/2 for the values of n between 2 and 50. i know that Γ(n) = (n-1)!, which in R is factorial(n-1) When i type that into R, using y - function(n). and then plot(y,2,50), it doesnt give me anything meaningful, in fact, it comes up with a message saying something like in gamma(n+1) ploted or something along those lines. Can anyone please help? thanks you _ Looking to change your car this year? Find car news, reviews and more http://a.ninemsn.com.au/b.aspx?URL=http%3A%2F%2Fsecure%2Dau%2Eimrworldwide%2Ecom%2Fcgi%2Dbin%2Fa%2Fci%5F450304%2Fet%5F2%2Fcg%5F801459%2Fpi%5F1004813%2Fai%5F859641_t=762955845_r=tig_OCT07_m=EXT [[alternative HTML version deleted]] __ R-help@r-project.org 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-help@r-project.org 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] Lattice scales question: using at when log = TRUE
All, I have a simple lattice plot where I have set log = TRUE for the y scale. When I attempt to change the tick locations via the at argument within scales, the supplied numeric vector is not followed. Any suggestions much appreciated for the example below: y = c(10^1.5, 10^2, 10^3, 10^2) t = c(1,2,3,4) xyplot(y ~ t, type = b, scales = list(y = list(log = TRUE))) ## tick marks not followed for supplied marks below: xyplot(y ~ t, type = b, scales = list(y = list(log = TRUE), at = c(10^1, 10^2, 10^2.5, 10^3))) Cheers, David PS - Another thing is that the scale is no longer in scientific notations, but that is okay since this can be fixed via the labels argument within scales: e.g., labels = c(expression(10^1), expression(10^2), ...) An example of fancy labels for log axes is on p.147 of Deepayan's Lattice book. __ R-help@r-project.org 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] I can't update
To whom it concenrt I am trying to update the R program 2.9 This is the message that the program give is: update.packages(ask='graphics') Warning in install.packages(update[instlib == l, Package], l, contriburl = contriburl, : 'lib = C:/PROGRA~1/R/R-29~1.0/library' is not writable Erro em install.packages(update[instlib == l, Package], l, contriburl = contriburl, : unable to install packages I will wait for answer about this. Sicerelly -- MSc. Gilson Sánchez Chia Doutorando do curso Agronomia Tropical - AT Universidade Federal do Amazonas, UFAM Av. General Rodrigo Otávio Jordão Ramos 3000 Campus Universitário - Setor Sul, Bloco X. CEP 69077-000 Manaus, Amazonas, Brasil E-mails: gilson...@gmail.com gilson.c...@cpaa.embrapa.br +92-9170-1825 [[alternative HTML version deleted]] __ R-help@r-project.org 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] How to save R clean sessions in BATCH mode?
Thanks a lot for all of you that have reply me about opening and ending R workspaces in BATCH mode. However replies were a king general and Im afraid I could not take the entire message from them. Therefore I chose to expose here a representative fraction of my work. I have 50 Rdata files (F1,F2,F3,F4, ,F50) with objects inside. I need to: open F1: - perform some simple operations with the objects - export the solution with write.table - end F1 session open F2 repeat procedures as F1 open F50 repeat procedures as F1 My difficulty here is to end a workspace and open one from the scratch to avoid mixing files from consecutive worksessions, and thus using R memory unnecessarily. I could use rm() to delete objects from the previous sessions but it seems not an efficient task. Any suggestions on how to perform this in Batch Mode? An examplified help would be nice! Diogo André Alagador http://www.biochange-lab.eu/people/diogo-alagador Biodiversity and Global Change Lab, Museo Nacional de Ciencias Naturales, CSIC, Madrid, España Forest Research Centre, Instituto Superior de Agronomia, UTL, Lisboa, Portugal __ R-help@r-project.org 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.
Re: [R] I can't update
To whom it concenrt I am trying to update the R program 2.9 This is the message that the program give is: update.packages(ask='graphics') Warning in install.packages(update[instlib == l, Package], l, contriburl = contriburl, : 'lib = C:/PROGRA~1/R/R-29~1.0/library' is not writable Erro em install.packages(update[instlib == l, Package], l, contriburl = contriburl, : unable to install packages I will wait for answer about this. Sicerelly -- MSc. Gilson Sánchez Chia Doutorando do curso Agronomia Tropical - AT Universidade Federal do Amazonas, UFAM Av. General Rodrigo Otávio Jordão Ramos 3000 Campus Universitário - Setor Sul, Bloco X. CEP 69077-000 Manaus, Amazonas, Brasil E-mails: gilson...@gmail.com gilson.c...@cpaa.embrapa.br +92-9170-1825 [[alternative HTML version deleted]] __ R-help@r-project.org 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.
Re: [R] How to save R clean sessions in BATCH mode?
Would rm(list=ls()) not be an easier solution, if I understand your question correctly? Sarah On Sat, May 16, 2009 at 11:21 AM, mcnda...@mncn.csic.es wrote: Thanks a lot for all of you that have reply me about opening and ending R workspaces in BATCH mode. However replies were a king general and I’m afraid I could not take the entire message from them. Therefore I chose to expose here a representative fraction of my work. I have 50 Rdata files (F1,F2,F3,F4,…,F50) with objects inside. I need to: open F1: - perform some simple operations with the objects - export the solution with write.table - end F1 session open F2 repeat procedures as F1 … open F50 repeat procedures as F1 … My difficulty here is to end a workspace and open one from the scratch to avoid mixing files from consecutive worksessions, and thus using R memory unnecessarily. I could use rm() to delete objects from the previous sessions but it seems not an efficient task. Any suggestions on how to perform this in Batch Mode? An examplified help would be nice! Diogo André Alagador http://www.biochange-lab.eu/people/diogo-alagador Biodiversity and Global Change Lab, Museo Nacional de Ciencias Naturales, CSIC, Madrid, España Forest Research Centre, Instituto Superior de Agronomia, UTL, Lisboa, Portugal -- Sarah Goslee http://www.functionaldiversity.org __ R-help@r-project.org 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.
Re: [R] How to draw a R plot in Java frame ?
On Sat, May 16, 2009 at 9:18 PM, Obi Wan wan_...@ymail.com wrote: I am new to R and would like to display a R plot inside my Java app. Is there a possibility to do that? If so, what library do I need? Perhaps library(JavaGD) is an option. It is currently used in JGR. Liviu __ R-help@r-project.org 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.
Re: [R] Lattice scales question: using at when log = TRUE
Your parentheses are wrong. It should be y = list(log = TRUE, at = ...) On Sat, May 16, 2009 at 5:11 PM, Afshartous, David dafshart...@med.miami.edu wrote: All, I have a simple lattice plot where I have set log = TRUE for the y scale. When I attempt to change the tick locations via the at argument within scales, the supplied numeric vector is not followed. Any suggestions much appreciated for the example below: y = c(10^1.5, 10^2, 10^3, 10^2) t = c(1,2,3,4) xyplot(y ~ t, type = b, scales = list(y = list(log = TRUE))) ## tick marks not followed for supplied marks below: xyplot(y ~ t, type = b, scales = list(y = list(log = TRUE), at = c(10^1, 10^2, 10^2.5, 10^3))) Cheers, David PS - Another thing is that the scale is no longer in scientific notations, but that is okay since this can be fixed via the labels argument within scales: e.g., labels = c(expression(10^1), expression(10^2), ...) An example of fancy labels for log axes is on p.147 of Deepayan's Lattice book. __ R-help@r-project.org 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-help@r-project.org 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.
Re: [R] bagged importance estimates in earth problem
On Sat, 2009-05-16 at 08:57 -0700, Joseph Retzer wrote: I was trying to produced bagged importance estimates of attributes in earth using the caret package with the following commands: fit2 - bagEarth(loyalty ~ ., data=model1, B = 10) bagImpGCV - varImp(fit2,value=gcv) My bootstrap estimates are produced however the second command varImp produces the following error: Error in UseMethod(varImp) : no applicable method for varImp Not sure what is going on, any advice would be appreciated, The example in ?bagEarth works for me with caret and earth loaded library(earth) data(trees) fit1 - earth(trees[,-3], trees[,3]) fit2 - bagEarth(trees[,-3], trees[,3], B = 10) varImp(fit2) Overall Girth 100.00 Height 2.387985 packageDescription(earth)$Version [1] 2.3-2 packageDescription(caret)$Version [1] 4.15 Have you loaded the relevant packages and are they up-to-date? Can you run the example above? If the example works, then you'll probably need to supply data and code that fails for you or contact the package maintainer for expert help. HTH G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-help@r-project.org 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] Updating to 2.9 - ' no slot call in the result'
I updated R (to R-patched) and Zelig and the problem went away. Raghu [[alternative HTML version deleted]] __ R-help@r-project.org 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.
Re: [R] How to save R clean sessions in BATCH mode?
On Sat, May 16, 2009 at 10:21 AM, mcnda...@mncn.csic.es wrote: Thanks a lot for all of you that have reply me about opening and ending R workspaces in BATCH mode. However replies were a king general and I’m afraid I could not take the entire message from them. Therefore I chose to expose here a representative fraction of my work. I have 50 Rdata files (F1,F2,F3,F4,…,F50) with objects inside. I need to: open F1: - perform some simple operations with the objects - export the solution with write.table - end F1 session open F2 repeat procedures as F1 … open F50 repeat procedures as F1 … My difficulty here is to end a workspace and open one from the scratch to avoid mixing files from consecutive worksessions, and thus using R memory unnecessarily. I could use rm() to delete objects from the previous sessions but it seems not an efficient task. Any suggestions on how to perform this in Batch Mode? An examplified help would be nice! First try either Rcmd BATCH --help # for Windows or R CMD BATCH --help # for Mac OS X or for Linux and note that there are optional arguments --no-save and --no-restore. Use them. Diogo André Alagador http://www.biochange-lab.eu/people/diogo-alagador Biodiversity and Global Change Lab, Museo Nacional de Ciencias Naturales, CSIC, Madrid, España Forest Research Centre, Instituto Superior de Agronomia, UTL, Lisboa, Portugal __ R-help@r-project.org 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-help@r-project.org 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.
Re: [R] fitdistr for t distribution
In addition to seeing the code by typing the name of the function (and copying it from there into a file), you can also enter debug(fitdistr), for example. Then the next time you use fitdistr, either directly or indirectly, it puts you in the environment of that function, and you can walk through it line by line, examining objects, changing them, etc. To get the code for an S3 generic function like predict, use the methods function, followed, e.g., by getAnywhere. Hope this helps. Spencer Graves Paul Johnson wrote: On Fri, May 15, 2009 at 6:22 AM, lagreene lagreene...@gmail.com wrote: Thanks Jorge, but I still don't understand where they come from. when I use: fitdistr(mydata, t, df = 9) and get values for m and s, and the variance of my data should be the df/s? I jsut want to be able to confirm how m and s are calculated I've wondered the same kind of thing and I've learned the answer is easy! It is not so easy for all R functions, but did you try this with fitdistr? library (MASS) fitdistr the output that follows is the ACTUAL FORMULA that is used to make the calculations! I've not yet mastered the art of getting code for some functions. predict function (object, ...) UseMethod(predict) environment: namespace:stats But I know there is a way to get that code if you know the correct way to run getS3method(). But I usually just go read the R source code rather than puzzle over that. mydt - function(x, m, s, df) dt((x-m)/s, df)/s fitdistr(x2, mydt, list(m = 0, s = 1), df = 9, lower = c(-Inf, 0)) Thanks anyway for the help! __ R-help@r-project.org 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.
Re: [R] Lattice scales question: using at when log = TRUE
Thanks, but even with typo corrected as below the supplied marks are not followed: xyplot(y ~ t, type = b, scales = list(y = list(log = TRUE, at = c(10^1,10^2, 10^2.5, 10^3 From: Gabor Grothendieck [ggrothendi...@gmail.com] Sent: Saturday, May 16, 2009 6:11 PM To: Afshartous, David Cc: r-help@r-project.org Subject: Re: [R] Lattice scales question: using at when log = TRUE Your parentheses are wrong. It should be y = list(log = TRUE, at = ...) On Sat, May 16, 2009 at 5:11 PM, Afshartous, David dafshart...@med.miami.edu wrote: All, I have a simple lattice plot where I have set log = TRUE for the y scale. When I attempt to change the tick locations via the at argument within scales, the supplied numeric vector is not followed. Any suggestions much appreciated for the example below: y = c(10^1.5, 10^2, 10^3, 10^2) t = c(1,2,3,4) xyplot(y ~ t, type = b, scales = list(y = list(log = TRUE))) ## tick marks not followed for supplied marks below: xyplot(y ~ t, type = b, scales = list(y = list(log = TRUE), at = c(10^1, 10^2, 10^2.5, 10^3))) Cheers, David PS - Another thing is that the scale is no longer in scientific notations, but that is okay since this can be fixed via the labels argument within scales: e.g., labels = c(expression(10^1), expression(10^2), ...) An example of fancy labels for log axes is on p.147 of Deepayan's Lattice book. __ R-help@r-project.org 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-help@r-project.org 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.
Re: [R] Lattice scales question: using at when log = TRUE
On 5/16/09, Afshartous, David dafshart...@med.miami.edu wrote: Thanks, but even with typo corrected as below the supplied marks are not followed: xyplot(y ~ t, type = b, scales = list(y = list(log = TRUE, at = c(10^1,10^2, 10^2.5, 10^3 How so? Looks OK to me. -Deepayan From: Gabor Grothendieck [ggrothendi...@gmail.com] Sent: Saturday, May 16, 2009 6:11 PM To: Afshartous, David Cc: r-help@r-project.org Subject: Re: [R] Lattice scales question: using at when log = TRUE Your parentheses are wrong. It should be y = list(log = TRUE, at = ...) On Sat, May 16, 2009 at 5:11 PM, Afshartous, David dafshart...@med.miami.edu wrote: All, I have a simple lattice plot where I have set log = TRUE for the y scale. When I attempt to change the tick locations via the at argument within scales, the supplied numeric vector is not followed. Any suggestions much appreciated for the example below: y = c(10^1.5, 10^2, 10^3, 10^2) t = c(1,2,3,4) xyplot(y ~ t, type = b, scales = list(y = list(log = TRUE))) ## tick marks not followed for supplied marks below: xyplot(y ~ t, type = b, scales = list(y = list(log = TRUE), at = c(10^1, 10^2, 10^2.5, 10^3))) Cheers, David PS - Another thing is that the scale is no longer in scientific notations, but that is okay since this can be fixed via the labels argument within scales: e.g., labels = c(expression(10^1), expression(10^2), ...) An example of fancy labels for log axes is on p.147 of Deepayan's Lattice book. __ R-help@r-project.org 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-help@r-project.org 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-help@r-project.org 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.
Re: [R] Lattice scales question: using at when log = TRUE
It works for me on both of these (Windows Vista): R.version.string [1] R version 2.8.1 Patched (2008-12-26 r47350) packageDescription(lattice)$Version [1] 0.17-22 R.version.string [1] R version 2.9.0 Patched (2009-05-03 r48460) packageDescription(lattice)$Version [1] 0.17-22 On Sat, May 16, 2009 at 8:46 PM, Afshartous, David dafshart...@med.miami.edu wrote: Thanks, but even with typo corrected as below the supplied marks are not followed: xyplot(y ~ t, type = b, scales = list(y = list(log = TRUE, at = c(10^1,10^2, 10^2.5, 10^3 From: Gabor Grothendieck [ggrothendi...@gmail.com] Sent: Saturday, May 16, 2009 6:11 PM To: Afshartous, David Cc: r-help@r-project.org Subject: Re: [R] Lattice scales question: using at when log = TRUE Your parentheses are wrong. It should be y = list(log = TRUE, at = ...) On Sat, May 16, 2009 at 5:11 PM, Afshartous, David dafshart...@med.miami.edu wrote: All, I have a simple lattice plot where I have set log = TRUE for the y scale. When I attempt to change the tick locations via the at argument within scales, the supplied numeric vector is not followed. Any suggestions much appreciated for the example below: y = c(10^1.5, 10^2, 10^3, 10^2) t = c(1,2,3,4) xyplot(y ~ t, type = b, scales = list(y = list(log = TRUE))) ## tick marks not followed for supplied marks below: xyplot(y ~ t, type = b, scales = list(y = list(log = TRUE), at = c(10^1, 10^2, 10^2.5, 10^3))) Cheers, David PS - Another thing is that the scale is no longer in scientific notations, but that is okay since this can be fixed via the labels argument within scales: e.g., labels = c(expression(10^1), expression(10^2), ...) An example of fancy labels for log axes is on p.147 of Deepayan's Lattice book. __ R-help@r-project.org 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-help@r-project.org 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] Newton's method for finding roots
Hey guys, i have a relatively simple problem. I need to use netwon's method to find the root of a polynomial, lets say x^3-2x-1 i start off with p - function(x) x^3-2*x-1 My method, which im sure is very amateur, is to type another function, which is the derivative of p, and after picking an initial value to start off with, i follow the steps of newton's method manually, but i dont think that is what the question is asking. I've done some research on wikipedia, but i cant seem to find any code that will help me. Can someone help? Thanks a lot _ [[alternative HTML version deleted]] __ R-help@r-project.org 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.
Re: [R] Using column length in plot gives error
Is spectra.wavelength a factor? If so, plot will treat it as categorical and not draw a line. Try the following modification. plot(as.numeric(spectra.wavelength), cormat, type = l, ylim=c(-1,1), xlab=Wavelength (nm), ylab=Correlation) Quoting MikSmith m...@hsm.org.uk: Hi I'm trying to write a generic script for processing some data which finishes off with some plots. Given Im never sure how many columns will be in my dataframe I wanted to using the following plot(spectra.wavelength, cormat, type = l, ylim=c(-1,1), xlab=Wavelength (nm), ylab=Correlation) however even if I specify as type=l it appears plot as points (right hand plot). If I specify a range such as plot(650:700, cormat, type = l, ylim=c(-1,1), xlab=Wavelength (nm), ylab=Correlation) it looks good (left hand plot). If I try something like: plot(spectra.wavelength[1]:spectra.wavelength[length(spectra.wavelength)], cormat, type = l, ylim=c(-1,1), xlab=Wavelength (nm), ylab=Correlation) it fails with variable lengths differ and when I look at spectra.wavelength[1] it gives me the value but then states there are 53 levels. What does this mean and how can I get the result I want??! many thanks mike http://www.nabble.com/file/p23562717/1.pdf 1.pdf -- View this message in context: http://www.nabble.com/Using-column-length-in-plot-gives-error-tp23562717p23562717.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org 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-help@r-project.org 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.
Re: [R] converting numeric to integer
How about ceiling(x), which return the smallest integer not less than x? On Sun, May 17, 2009 at 2:49 AM, Thomas Mang thomas.m...@fiwi.at wrote: Hello, Suppose I have x, which is a variable of class numeric. The calculations performed to yield x imply that mathematically it should be an integer , but due to round-off errors, it might not be (and so in either direction). The error is however small, so round(x) will yield the appropriate integer value. Moreover, this integer values is guaranteed to be representable by an 'integer' class, that is -2^31 x 2^31, and logically it is an integer anyway. So I want to convert x from class 'numeric' to 'integer'. What is the most elegant, but always correct way, to achieve this conversion ? What comes to mind is of course something along: x = as.integer(round(x)) I am, however, not sure if this always works, because I do not know if the round-function is guaranteed to return a numeric value which, in finite binary representation, is always = the underlying mathematical integer. If that is however guaranteed, that would of course be a simple + elegant one. An alternative I came up with is: x = as.integer(round(x) + ifelse(x = 0, 0.5, -0.5)) Where I explicitly add a bit to ensure the finite binary representation must be = the underlying integer, and then truncate the decimal digits. IMO, this one is always guaranteed to work, at least within the numerical range of what integers are limited to anyway. What's your opinion on the issue ? Any other solution ? Thanks a lot in advance and cheers, Thomas __ R-help@r-project.org 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-help@r-project.org 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.
Re: [R] Question about barplot: gridlines value labels
Dimitri
You mentioned lattice so I presumed that you tried a barchart in lattice
if you found the class of table.a.percents will it comply with the lattice
requirements of the data type ?
class(table.a.percents)
[1] matrix
Using the lattice package and converting to a data.frame
x - data.frame(Group = rep(paste(Group, 1:4), 5), a =
rep(1:5,each=4),percentage = as.vector(table.a.percents))
barchart(percentage~a,x,groups = Group, horizontal = F, auto.key = T,
ylim = c(0,60))
will get you started in lattice, and customize as required
see also ?make.groups
PS ?sweep may be of interest in your data manipulation
Regards
Duncan Mackay
Department of Agronomy and Soil Science
University of New
At 04:57 17/05/2009, you wrote:
Hello!
I promise I looked into help files before asking. Still cannot figure
it out. I think it's because I am totally confused what packages use
lettice, which use trellis, etc.
Sections 1 and 2 below produce the data and the data to plot. My
question is about barplot in Section 3. I am trying to:
1. add only horizontal gridlines and manipulate the type and color of
that line. tck = 1 is not flexible enough to do it.
2. make the legend come on top of gridlines and not under them
3. add plotted Y values above the bars
Thank you very much for any pointers!
Dimitri
### Section 1: generates my data set data:
N-100
myset1-c(1,2,3,4,5)
probs1-c(.05,.10,.15,.40,.30)
group-unlist(lapply(1:4,function(x){
out-rep(x,25)
return(out)
}))
set.seed(1)
a-sample(myset1, N, replace = TRUE,probs1)
a[which(rbinom(100,2,.01)==1)]-NA
set.seed(12)
b-sample(myset1, N, replace = TRUE,probs1)
b[which(rbinom(100,2,.01)==1)]-NA
set.seed(123)
data-data.frame(group,a=a,b=b)
data[group]-lapply(data[group],function(x) {
x[x %in% 1]-Group 1
x[x %in% 2]-Group 2
x[x %in% 3]-Group 3
x[x %in% 4]-Group 4
return(x)
})
data$group-as.factor(data$group)
lapply(data,table,exclude=NULL)
### Section 2. Creating data to plot:
table.a-with(data,table(group,a))
table.a.percents-apply(table.a,2,function(x){
out-round(x*100/sum(x),1)
return(out)
})
### Section 3. Creating a plot:
barplot(table.a.percents,xlab = Values, ylab =
Percentages,ylim=c(0,100),axis.lty=1,legend=T,beside=T,tck = 1)
--
Dimitri Liakhovitski
MarketTools, Inc.
dimitri.liakhovit...@markettools.com
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Re: [R] ggplot2: annotating plot with mathematical formulae
Hi Baptiste,
I think on this occasion I'll edit manually in inkscape with the textext
plugin which is a somewhat clumsy but simple option. Thanks for the
link to the wiki which I wasn't aware of until now.
Paul
baptiste auguie wrote:
If you're desperate for a workaround, you might want to try this
example using pgfSweave,
http://ggplot2.wik.is/Mathematical_annotations
On a similar vein, you could try psfrag replacements with a postscript
device (there is some code for this on the list archives).
Feel free to comment / edit on the wiki page.
HTH,
baptiste
On 16 May 2009, at 14:48, Paul Emberson wrote:
Hi Stephen,
The problem is that the label on the graph doesn't get rendered with a
superscript. I want the label on the graph to be rendered the same way
as the label you have put on the axis.
I am plotting a piecewise function and I wanted to label each section
of it.
Paul
stephen sefick wrote:
how about this
a - 1:10
b - 1:10
d - paste(x,^,{n-1})
qplot(a,b, xlab=expression(x^{n-1}))+geom_text(aes(4,8, label=d))
On Fri, May 15, 2009 at 10:02 PM, Paul Emberson
em...@calidasoft.co.uk wrote:
Hi,
Is there a way of annotating a ggplot plot with mathematical formulae?
I can do
geom_text(aes(label=some text, ...
but I can't do
geom_text(aes(label=expression(x^{n-1}), ...
It gives the error
Error: geom_text requires the following missing aesthetics: label
Is there a convenient equivalent?
Cheers,
Paul
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http://www.R-project.org/posting-guide.html
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__
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PLEASE do read the posting guide
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_
Baptiste Auguié
School of Physics
University of Exeter
Stocker Road,
Exeter, Devon,
EX4 4QL, UK
Phone: +44 1392 264187
http://newton.ex.ac.uk/research/emag
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[R] projecting onto 2d *integer* grid?
I have a bunch of data points in R^2 (Euclidean plane). But I want to project these onto a 2d integer grid -- that is, there's at most one data point for each integer (x, y) coordinate, and points near each other in the integer grid should also be near each other in the original R^2 space. Is there some method to do this? I'm not necessarily looking for an R function (though that would be nice). For example, I tried a kind of simulated annealing approach (basically, I threw all the data points onto a rectangular integer grid, and tried to minimize the distances between points), but is there any other method? I'm not too familiar with self-organizing maps, but would using an SOM with # of clusters = # of original data points give me what I want? Any pointers are appreciated! -- View this message in context: http://www.nabble.com/projecting-onto-2d-*integer*-grid--tp23579946p23579946.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org 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.
Re: [R] How to turn the xyplot graphics upside-down?
lau kue wrote: Hi everyone, I'm learning to use R. The below script works well, but i want to turn the y-axis and the graphics upside-down, how should i do? Appreciate if any tips! Your example isn't reproducible (i.e. we don't have the data), so can't be sure, but try giving an explicit ylim argument with low and high limits reversed. For example: d - data.frame(x=runif(100),y=runif(100)) xyplot(y~x,data=d) xyplot(y~x,data=d,ylim=c(1,0)) or perhaps xyplot(y~x,data=d,ylim=rev(range(d$y))) -- View this message in context: http://www.nabble.com/How-to-turn-the-xyplot-graphics-upside-down--tp23571346p23579970.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org 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.
Re: [R] Row number of minimum value?
MikSmith wrote: This *must* be an insanely easy thing to work out, but I'm not too familiar with R syntax. So how do I work out the row number (if I pass a column) of the minimum value?? I can get the value itself from min(), but where can I get the row?? ?which ?which.min Ben Bolker -- View this message in context: http://www.nabble.com/Row-number-of-minimum-value--tp23578215p23579979.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org 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] wireframe 3-D problems
Dear All R Users, I am trying to graph a 3-D graph of simulated data for logit models using the powerful wireframe command, but I got stuck. Here are the codes: x - seq(-4, 4, by=0.01) y - seq(-4, 4, by=0.01) p - 1/(1+exp(-0.12*x + 0.35*y)) mydata - cbind(x, y, p) require(lattice) wireframe(p~x*y, data=mydata) and I received the following message: Error in eval(substitute(groups), data, environment(formula)) : numeric 'envir' arg not of length one Can anyone here point me to the right direction? Thanks! Jun Xu, PhD Assistant Professor Department of Sociology Ball State University [[alternative HTML version deleted]] __ R-help@r-project.org 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.
