Re: [R] R Book Advice Needed
Cody, I plan to use it in life sciences. We use of course basic descriptive statistics but also classification using ACP and CAH (French abbreviation for Principal Component Analysis and Hierarchical Cluster Analysis). We also use logistic regression for classifying some results of clinical laboratory analyses. In fact, I have been a user of SPSS for - quite - a long time. The price of the licences are increasing and it becomes a problem for us (many thousand of euros). I am the only user and don't work with the programs on a daily basis. So - I confess - I am investigating R. And I am more and more convinced by the possibilities it offers. Regards. Alain [EMAIL PROTECTED] a écrit : Alain, Can you tell us what you plan to use R for? Regards, -Cody [EMAIL PROTECTED] a écrit : I am new to using R and would appreciate some advice on which books to start with to get up to speed on using R. ...cut... -- Alain Reymond CEIA Bruxelles __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Annotating trellis graphics
I'm using xyplot to generate a trellis plot with each panel containing a scatterplot and a best fit line. Is it possible to write the slope of the best fit line in each panel? -- Alan S Barnett [EMAIL PROTECTED] NIMH/CBDB __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Panel data
Panel data is that you have e.g. several subjects (=individuals,firms,households) being tracked over a certain time (meaning there are repeated observations). One could roughly say that it is a collection of (quite similiar) time series. This makes the analysis better than pooling the whole set but it needs certain econometric tools. An example would be estimating wage elasticities. Time series analysis usually just involves one subject (interest rates, share prices etc.) over some time. Standard books on panel data analysis are also Baltagi: econometric analysis of panel data and Wooldridge: econometric analysis of cross sectional and panel data. Both are not introductionary texts since you do not know the difference between time series and panel data maybe you should start with an introductionary econometrics book like Wooldridge introductory econometrics or Verbeek: modern econometrics. Stefan on Thursday 14 June 2007 07:33:05 Megh Dal wrote: MD Then what is the difference between panel data and time series data? You said panel data is data on same subject being tracked over time. But time series data also do the same. Please correct me if I am wrong. MD __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Panel data
On Wed, 13 Jun 2007, Megh Dal wrote:
Then what is the difference between panel data and time series data? You
said panel data is data on same subject being tracked over time. But
time series data also do the same. Please correct me if I am wrong.
Panel data is about several subjects being tracked over time, so gives a
series of related time series. It also known as 'longitudinal data' or
'repeated measures' (perhaps with slightly different emphases).
If the observation times were the same for all subjects a vector AR
(presumably the one of several senses of 'VAR' being used) could be used,
but conventional analyses are via mixed/GEE models (and in simple cases
these reduce to a nested anova).
There are examples in MASS and in Diggle, Hegarty, Liang and Zeger (cited
there).
- Original Message
From: Leeds, Mark (IED) [EMAIL PROTECTED]
To: Megh Dal [EMAIL PROTECTED]
Sent: Wednesday, June 13, 2007 8:30:18 PM
Subject: RE: [R] Panel data
not as far as I know. Panel data is quite specific in that it's the
same subject being tracked over time.
A VAR doesn't take advantage of this and doesn't make that assumption
and I don't think it's applicable to
Your problem. I think there is a book by
Hsaio on panel data and possibly another one by Arellano ( spelling )
but I'm not sure what's available in R for doing panel
data estimation. I've never done it. Maybe do a search for panel data
on the search engine and something may come up ?
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Megh Dal
Sent: Tuesday, June 12, 2007 12:12 PM
To: r-help@stat.math.ethz.ch
Subject: [R] Panel data
Dear all R users,
I have a small doubt about panel data analysis. My basic understanding
on Panel data is a type of data that is collected over time and
subjects. Vector Autoregressive Model (VAR) model used on this type of
data. Therefore can I say that, one of statistical tools used for
analysis of panel data is VAR model? If you clarify my doubt I will be
very grateful.
Thanks and regards,
Megh
Looking for earth-friendly autos?
Browse Top Cars by Green Rating at Yahoo! Autos' Green Center.
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Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
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Re: [R] extractor rows from a matrix
thanks for the answer..but i don't find what i'm looking for! now i'm trying to expose better my problem: i have: ht= a 1096rows x 3 columns matrix i'd like a function like this: d[i]=rbind(ht[i,]) for (i in 1:length(ht)) but this don't work :( can anyone seriously help me? -- View this message in context: http://www.nabble.com/extractor-rows-from-a-matrix-tf3913088.html#a4923 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Responding to a posting in the digest
Is there a convenient way to respond to a particular posting which is a part of the digest? I mean something that will automatically quote the original message, subject, etc. Thank you! Moshe Olshansky [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Formatted Data File Question for Clustering -Quickie Project
The R Data Import/Export guide was mentioned already, it contains everything you should know about data exchange between R and other software. In case it says nothing about dates, try as.Date() and strftime(). For your example below, as.Date(1/31/1994,format=%m/%d/%Y) works. ngottlieb wrote: I am trying to learn how to format Ascii data files for scan or read into R. Precisely for a quickie project, I found some code (at end of this email) to do exactly what I need: To cluster and graph a dendrogram from package (stats). I am stuck on how to format a text file to run the script. I looked at the dataset USArrests (which would be replaced by my data and labels) using UltraEdit. That data appears to be in binary format and I would simply like a readable ASCII text file. How can I: A) format this data to a file for the script below? B) I would like to use squared Euclidean distance, can hclust support this? Thanks, Neil Gottlieb Here is sub-set example of my data set, return series to cluster: 13 cases by 36 observations): Month Convertible Arbitrage Dedicated Short BiasEmerging Markets 1/31/1994 0.004 -0.016 0.105 2/28/1994 0.002 0.020 -0.011 3/31/1994 -0.010 0.072 -0.046 [skip] -- View this message in context: http://www.nabble.com/Formatted-Data-File-Question-for-Clustering--Quickie-Project-tf3915926.html#a5436 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Read Windows-like .INI files into R data structure?
On 6/14/07, Gabor Grothendieck [EMAIL PROTECTED] wrote:
Here is yet another solution. This is the simplest so far.
Lines.raw is as before and the output is a 3 column character
matrix.
section -
f - function(x) {
if (length(x) == 1) section - gsub([\\[\\]], , x)
if (length(x) = 1) return()
return(c(x, section))
}
# Lines - readLines(myfile.ini)
Lines - readLines(textConnection(Lines.raw))
do.call(rbind, lapply(strsplit(Lines, =), f))
The corresponding awk code fits in one line '/\[/{a=$1;next}{print
$1,$2,a}'.
With the example.ini:
$ awk -F= '/\[/{a=$1;next}{print $1,$2,a}' example.ini
var1 value1 [Section1]
var2 value2 [Section1]
A value3 [Section2]
B value4 [Section2]
The output can then be imported in R with read.table.
I know, I am not playing by the rules here... :)
But with programming languages, like with human languages, it pays to be bi
or tri-lingual (or polyglot, if one can).
I also realise that under Windows, it means using the command line,
something that not so many people are comfortable with nowadays.
One reason people insist on using only one language to do everything may be
due to the awkwardness and limitations of the default scripting language
under Windows (DOS). Having everything done inside one single R script can
seem simpler. But a divide-and-conquer approach, with a few small scripts,
can actually work better in some complex cases.
I tend to do as much as possible in R but for all serious data analysis
tasks, I use Makefile to glue the various stages of processing. Data
preprocessing stages (performed with R or other tools) create files that are
then processed with R. One advantage is that preprocessing is performed only
when raw input data change; but the most important, is that when I come back
years later, I can follow the exact flow of transformations.
Again, make (like awk or R) is not without limits and idiosyncrasies. If
someone has a simpler solution, I am interested to hear about it.
Christophe
--
Christophe Pallier (http://www.pallier.org)
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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] Read Windows-like .INI files into R data structure?
Ah! I forgot to mention that it is possible to call awk from R:
a - system(awk -F'=' '/\\[/{a=$1;next}{print $1,$2,a}' example.ini,
intern=T)
z - textConnection(a)
read.table(z)
Christophe
On 6/14/07, Christophe Pallier [EMAIL PROTECTED] wrote:
On 6/14/07, Gabor Grothendieck [EMAIL PROTECTED] wrote:
Here is yet another solution. This is the simplest so far.
Lines.raw is as before and the output is a 3 column character
matrix.
section -
f - function(x) {
if (length(x) == 1) section - gsub([\\[\\]], , x)
if (length(x) = 1) return()
return(c(x, section))
}
# Lines - readLines(myfile.ini)
Lines - readLines(textConnection(Lines.raw))
do.call(rbind, lapply(strsplit(Lines, =), f))
The corresponding awk code fits in one line '/\[/{a=$1;next}{print
$1,$2,a}'.
With the example.ini:
$ awk -F= '/\[/{a=$1;next}{print $1,$2,a}' example.ini
var1 value1 [Section1]
var2 value2 [Section1]
A value3 [Section2]
B value4 [Section2]
The output can then be imported in R with read.table.
I know, I am not playing by the rules here... :)
But with programming languages, like with human languages, it pays to be
bi or tri-lingual (or polyglot, if one can).
I also realise that under Windows, it means using the command line,
something that not so many people are comfortable with nowadays.
One reason people insist on using only one language to do everything may
be due to the awkwardness and limitations of the default scripting language
under Windows (DOS). Having everything done inside one single R script can
seem simpler. But a divide-and-conquer approach, with a few small scripts,
can actually work better in some complex cases.
I tend to do as much as possible in R but for all serious data analysis
tasks, I use Makefile to glue the various stages of processing. Data
preprocessing stages (performed with R or other tools) create files that are
then processed with R. One advantage is that preprocessing is performed only
when raw input data change; but the most important, is that when I come back
years later, I can follow the exact flow of transformations.
Again, make (like awk or R) is not without limits and idiosyncrasies.
If someone has a simpler solution, I am interested to hear about it.
Christophe
--
Christophe Pallier ( http://www.pallier.org)
--
Christophe Pallier (http://www.pallier.org)
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[R] ARIMA with more than one seasonality period
Dear R community, I have a project with electricity load forecasting, and I got hourly data for system load. If you haven't worked with electricity before, seasonality comes in many flavors: a daily pattern, with a peak at around 7pm; a weekly pattern, in which we use more electricity on weekdays in comparison to weekends; a winter-summer pattern, with air conditioning and heaters playing an important role, etc. In SAS, I could specify an ARIMA with multiple seasonality terms, say (1,0,1) with period=24, and (1,0,1) with period=168 (I don't remember the orders I was using). This is how many studies I found on IEEE were modeling electricity load and it worked pretty well with the data I have. However, I can't seem to find how to do that in R. I've read the help files a few times, but to no avail. Is it possible? I hope I'm missing something straightforward. Thank you, Paulo Tanimoto University of Arizona __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] extractor rows from a matrix
billycorg napsal(a): thanks for the answer..but i don't find what i'm looking for! now i'm trying to expose better my problem: i have: ht= a 1096rows x 3 columns matrix i'd like a function like this: d[i]=rbind(ht[i,]) for (i in 1:length(ht)) but this don't work :( can anyone seriously help me? The problem is that people actually are trying to seriously help you, but it is really difficult from your queries... Please specify what you expect to be your output - a vector where you just paste the rows of of the original matrix one by one? If so, you can do d - t(ht) dim(d) - NULL or (a 'dirty' way) d - c(t(ht)) It is not at all clear what your statement should do. For example, what is length(ht) with ht being a matrix? For R it is the total number of elements, but did you mean this or the number of rows/columns?? The suggestion to read R-Intro is the best advice you got here. Petr -- Petr Klasterecky Dept. of Probability and Statistics Charles University in Prague Czech Republic __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] make sample() faster
Hi I have a simulation which is relatively slow. I used Rprofile() and identified the calls to sample() as the culprit is sample(): summaryRprof(Documents/PostDoc/Aloe_Pillansii/R/create.out) $by.self self.time self.pct total.time total.pct sample 1.30 44.2 1.52 51.7 ifelse 0.46 15.6 2.44 83.0 . . . I am using sample() as follow: result - sample( x=d.growth.seedling$growth, size=1, prob=d.growth.seedling$p, replace ) d.growth.seedling$p and d.growth.seedling$growth have a length of 1024 and are calculated initially by using density(). My question: is there any way to make this faster, i.e. replace sample() as I use it with another faster algorithm (if necessary implemented in C)? Thanks in advance, Rainer -- NEW EMAIL ADDRESS AND ADDRESS: [EMAIL PROTECTED] [EMAIL PROTECTED] WILL BE DISCONTINUED END OF MARCH Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Leslie Hill Institute for Plant Conservation University of Cape Town Rondebosch 7701 South Africa Fax:+27 - (0)86 516 2782 Fax:+27 - (0)21 650 2440 (w) Cell: +27 - (0)83 9479 042 Skype: RMkrug email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Difference between prcomp and cmdscale
I'm looking for someone to explain the difference between these
procedures. The function prcomp() does principal components anaylsis,
and the function cmdscale() does classical multi-dimensional scaling
(also called principal coordinates analysis).
My confusion stems from the fact that they give very similar results:
my.d - matrix(rnorm(50), ncol=5)
rownames(my.d) - paste(c, 1:10, sep=)
# prcomp
prc - prcomp(my.d)
# cmdscale
mds - cmdscale(dist(my.d))
cor(prc$x[,1], mds[,1]) # produces 1 or -1
cor(prc$x[,2], mds[,2]) # produces 1 or -1
Presumably, under the defaults for these commands in R, they carry out
the same (or very similar) procedures?
Thanks
Mick
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[R] How to set degrees of freedom in cor.test?
Hello, I want to compute a correlation test but I do not want to use the degrees of freedom that are calculated by default but I want to set a particular number of degrees of freedom. I looked in the manual, different other functions but I did not found how to do it Thanks in advance for your answers Yours Florence Dufour PhD Student AZTI Tecnalia - Spain __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Responding to a posting in the digest
On 14-Jun-07 07:26:26, Moshe Olshansky wrote: Is there a convenient way to respond to a particular posting which is a part of the digest? I mean something that will automatically quote the original message, subject, etc. Thank you! Moshe Olshansky [EMAIL PROTECTED] This will depend on two things. 1. Whether the mail software you use has the capability; 2. Whether the digest format would permit it anyway. Regarding (2), if you are receiving R-help in traditional digest format (all the messages, each with its principal headers, as one single long message-body), then the only way to respond to a particular message is to start to compose a new message and copy what you need from the digest. While I've never reveived R-help in digest format myself, according to Martin Maechler: http://finzi.psych.upenn.edu/R/Rhelp02a/archive/59429.html Please open the URL at the end of every message https://stat.ethz.ch/mailman/listinfo/r-help go to the bottom and log in -- clicking the [Unsubscribe or Edit Options] field. You need your mailing list password sooner or later. The one you get sent every 1st of the month; or you can have it sent to you again. Then you are in a page entitled R-help Membership Configuration for foo@bar Scroll down to the section Your R-help Subscription where the 3rd entry is entitled Get MIME or Plain Text Digests? and now you want MIME. In MIME digest format, each message with its own main headers is a separate MIME attachment, and suitable mail software can bring any message up on its own, You can then reply in the normal way. However (and here is where I'm ignorant as a result of never having received R-help as digest), your reply may not continue the thread -- since this depends on message-identifier headers being present which allow threading software to trace which messages are replies to which message. The JISCMAIL MIME digest for the AllStat mailing list only includes a Message-ID for the digest as a whole, i.e. the ID for the entire digest message. Message-IDs for the individual messages in the digest (as would be seen by people who received them singly) are absent: you only get the likes of Date:DoW, DD Mon HH:MM:SS TZ From:Sender (person who sent the message to the list) Subject: Subject of individual message MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable and no Message ID for the original message from Sender. So any reply to this component message is not identifiable as belonging to its thread. I don't know whether R-help's 'mailman' provides such headers (Martin??). If it does, then your reply could include an In-Reply-To: which identifies the thread. Otherwise it can't. As to (1), you will probably get several suggestions for suitable mail software. My own (see below) opens an AllStat digest in a window with attachment tags displayed, one for Tablf of Contents, one for each message. Clicking on one of these opens a new window with the message attached to that tag displayed, and now the usual reply/forward etc mail sunctions can be applied to that message. But it will reply only to the address given in the From: header (i.e. the original sender, as above), not to the AllStat list (so you have to enter that address by hand, if you want to reply to the list). In principle, mailer software could also identify the address of the list from which the digest has been sent, as well as the sender of the original message, so you could get the option to reply to either or both. But my XFMail does not, and only offers the original sender. Whether other mailer software can do this is for others to comment on! Hoping this helps, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 14-Jun-07 Time: 09:53:58 -- XFMail -- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] A Question about R
Hi, This might help you: https://stat.ethz.ch/pipermail/r-help/2000-February/009984.html Martin On 11 Jun 2007, at 20:50, [EMAIL PROTECTED] wrote: Hi Sir/Madam, I'm a researcher in university of Guelph, Canada and now considering using R to do some data analysis. I'm wondering whether there is a library available in R that includes algorithms for archetypal analysis? This is a method quite similar to principal components analysis that is designed to find archetypes or pure types from multidimensional data. Any help from you is greatly appreciated. Thanks Juan __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using odesolve to produce non-negative solutions
Dear Jeremy, a few notes about your model: The equations of your derivatives are designed in a way that can lead to negative state variables with certain parameter combinations. In order to avoid this, you are using if constructions which are intended to correct this. This method is however (as far as I have learned from theory and own experience ;-) a bad idea and should be strictly avoided. This trick may violate assumptions of the ODE solvers and in many cases also mass-balances (or similar). Instead of this, processes should be modeled in a way that avoids crossing zero, e.g. exponential decay (x, k 0): dx = - k * x (1) and not a linear decay like dx = -k (2) which by its nature can lead to negative state values. Case (1) can be managed almost perfectly by lsoda with his automatic internal time step algorithm. hmax is intended for non-autonomous models to ensure that external signals are not skipped by the automatism, which may be appropriate in your case because p seems to contain time dependent functions. As far as I can see, your equations belong to type (1) and should not need any of the if and for constructs, as long as your parameters (which are not given in your post) do have the correct sign and range (for example, vax = 1, death = 0 etc.). If you perform optimization, you must ensure that parameters stay in the plausible range is met using transformations of the parameters or constraints in the optimization procedure. Thomas PS: another question, what is the purpose of the state variable N? I guess it can be derived from the other states. Jeremy Goldhaber-Fiebert wrote: Hello, I am using odesolve to simulate a group of people moving through time and transmitting infections to one another. In Matlab, there is a NonNegative option which tells the Matlab solver to keep the vector elements of the ODE solution non-negative at all times. What is the right way to do this in R? Thanks, Jeremy [... code deleted, see original post ...] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ML, REML and several random effects
Arnaud Mosnier arnaud_mosnier at UQAR.QC.CA writes: Hello everyone, Hope that my question could have interest for more than one people here. I know that in order to compare mixed models with different fixed effect I need to use ML method. But ... what about comparing models with the same fixed effects and different random effects ? Likelihood ratio test on REML likelihood Gregor __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] extractor rows from a matrix
Well, you cannot have a vector of vectors, you need a list of vectors.
With mean() and sum() it worked probably because these produce a single
number as their output. Also, the rbind() function won't help here, that
is for merging vector into a matrix. Once again, reading R-Intro is the
best advice I can give you.
# creating an ampty list of length 1096:
d - list()
length(d) - 1096
# Filling the list with rows
for(i in (1:1096)){
d[[i]] - ht[i,]
}
Note the double bracketing when indexing lists: d[[1]]
Please respond to the entire list next time, I only read these messages
occasionally.
Petr
vincenzo napsal(a):
thank you a lot for the answer
i don't expect one vector..
but 1096 vector.
example: ht=
123
1 345
2 458
3
4
.
.
.
1096
i'd like 1096 vector like these:
d[1]= 345
d[2]= 458
...
i'm trying now with this:
for(i in 1:1096) d[i]=(rbind(ht[i,]))
but it doesn't work :(
it works with function like mean,sum.. but not with rbind
what can i do?
/---Messaggio originale---/
/*Da:*/ Petr Klasterecky mailto:[EMAIL PROTECTED]
/*Data:*/ 06/14/07 10:07:33
/*A:*/ billycorg mailto:[EMAIL PROTECTED]
/*Cc:*/ r-help@stat.math.ethz.ch mailto:r-help@stat.math.ethz.ch
/*Oggetto:*/ Re: [R] extractor rows from a matrix
billycorg napsal(a):
thanks for the answer..but i don't find what i'm looking for!
now i'm trying to expose better my problem:
i have:
ht= a 1096rows x 3 columns matrix
i'd like a function like this:
d[i]=rbind(ht[i,]) for (i in 1:length(ht))
but this don't work :(
can anyone seriously help me?
The problem is that people actually are trying to seriously help you,
but it is really difficult from your queries...
Please specify what you expect to be your output - a vector where you
just paste the rows of of the original matrix one by one?
If so, you can do
d - t(ht)
dim(d) - NULL
or (a 'dirty' way)
d - c(t(ht))
It is not at all clear what your statement should do. For example, what
is length(ht) with ht being a matrix? For R it is the total number of
elements, but did you mean this or the number of rows/columns??
The suggestion to read R-Intro is the best advice you got here.
Petr
--
Petr Klasterecky
Dept. of Probability and Statistics
Charles University in Prague
Czech Republic
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Charles University in Prague
Czech Republic
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] installing packages
hie how do l install R packages .L'm using windows xp.plus is there a dipository for the packages that one can browse to find out what packages are available. thanks. - Be a PS3 game guru. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] besselK
Assistance, besselK- complex number problem Im a student intrested in using R in my learning and research work in option pricing however i have a problem with besselK function In R. Would you assit me in computing the besselK of third kind of a complex number in R. Any code or suggestion will be highly appriceiated eg besselK(2,10) works well.. but besselK(2,10i) doesnt work !! im supprised it works in MATLAB but NOT in R. rgds ivivi mwaniki student kenya - Don't pick lemons. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Research assistant in biostatistics in Copenhagen
The Statistics Group at the Department of Natural Sciences, Faculty of Life Sciences, University of Copenhagen, is looking for a research assistant with R skills. For details see: http://www.matfys.kvl.dk/~torbenm/eu Please note that the deadline for applications is June 22 2007. Christian __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] pretty report
At 5:01 PM -0400 6/12/07, Weiwei Shi wrote:
Dear Listers:
I have a couple of data frames to report and each corresponds to
different condtions, e.g. conditions=c(10, 15, 20, 25). In this
examples, four data frames need to be exported in a pretty report.
I knew Perl has some module for exporting data to Excel and after
googling, I found R does not.
Weiwei,
If you (or the users who are opening your reports) are going to using
a version of excel that supports the new Office XML formats, you can
write multi-sheeted workbooks as below: simply give spreadsheetML a
named list of dataframes. You can add attributes to the components to
add things such as comments, subheadings that span multiple columns,
hyperlinks and named data-ranges.
If you can't guarantee that the opener won't have a modern Excel (I
don't believe Mac versions are yet at this stage), then you will need
to have a windows box to open the file, and save as 'proper' excel.
Below is a visual basic macro I have set up in a watched directory to
do this on the fly. I use the program filenotify to watch the
directory.
If any of the package developers want to incorporate this function,
then please do get in touch. It's probably not worth a package of
it's own, but I think the ability to have multi-sheeted excel books,
with the extra bits of formatting mentioned above might be useful.
I'ts fairly straightforward to add extra styling (colours, typefaces,
etc).
Regards - Gavin
### The R function, and a demo
spreadsheetML - function(dat, fname, style=NULL) {
if (is.data.frame(dat))
dat - list(Sheet1=dat)
if (is.null(names(dat)))
names(dat) - paste(Sheet,1:length(dat), sep=)
names(dat)[names(dat)==] - paste(Sheet,1:length(dat),
sep=)[names(dat)==]
x - xmlOutputDOM(Workbook, nameSpace=ss,
nsURI=list(
o=urn:schemas-microsoft-com:office:office,
x=urn:schemas-microsoft-com:office:excel,
ss=urn:schemas-microsoft-com:office:spreadsheet,
html=http://www.w3.org/TR/REC-html40;))
if (!is.null(style))
x$addNode(style)
### Annotate any named Ranges
if (any(!is.null(lapply(dat, attr, range {
x$addTag(Names, close=FALSE)
for (sheet in names(dat)) {
rngs - attr(dat[[sheet]],range)
offset - ifelse(is.null(attr(dat[[sheet]],subhead)), 1, 2)
for (i in names(rngs)) {
refersTo - sprintf(=%s!R%iC%i:R%iC%i,
sheet,
rngs[[i]]$rowStart+offset,
rngs[[i]]$colStart,
rngs[[i]]$rowEnd+offset,
rngs[[i]]$colEnd)
x$addTag(NamedRange, attrs=c(ss:Name=i,
ss:RefersTo=refersTo))
}
}
x$closeTag() #Names
}
for (sheet in 1:length(dat)) {
## For each dataframe, construct a worksheet
x$addTag(Worksheet, attrs=c(ss:Name=names(dat)[[sheet]]), close=FALSE)
x$addTag(Table,close=FALSE)
x$addTag(Row, close=FALSE)
## If there's a subheader, expand it, and remove entries from
relevant header
headRow - colnames(dat[[sheet]])
if (!is.null(subhead - attr(dat[[sheet]],subhead))) {
subHeadRow - rep(, length(headRow))
for (i in names(subhead)) {
start - match(i, headRow)
subHeadRow[start:(start+length(subhead[[i]])-1)] -
subhead[[i]]
headRow[(start+1):(start+length(subhead[[i]])-1)] -
}
}
## Create Header Row, with comments
for (i in headRow) {
x$addTag(Cell, close=FALSE)
x$addTag(Data,i , attrs=c(ss:Type=String))
if (!is.null(comment - attr(dat[[sheet]],xlComment)[[i]])) {
if (is.character(comment)) {
x$addTag(Comment, attrs=c(ss:Author=BaBS), close=FALSE)
x$addTag(Data, comment)
x$closeTag() #Comment
}
}
x$closeTag() # Header entry
}
x$closeTag() # Header Row
## Create Sub-Header row, with comments
if (!is.null(subhead)) {
x$addTag(Row, close=FALSE)
for (i in 1:length(subHeadRow)) {
x$addTag(Cell, close=FALSE)
x$addTag(Data,subHeadRow[i] , attrs=c(ss:Type=String))
if (is.list(comment - attr(dat[[sheet]],xlComment)[[headRow[i]]])) {
if (!is.null(comment - comment[[subHeadRow[i]]])) {
x$addTag(Comment, attrs=c(ss:Author=BaBS), close=FALSE)
x$addTag(Data, comment)
x$closeTag() #Comment
}
}
x$closeTag()
}
x$closeTag() # subHeader Row
}
coltypes - rep(String, ncol(dat[[sheet]]))
coltypes[sapply(dat[[sheet]], is.numeric)] - Number
href - attributes(dat[[sheet]])$href
## Enter the data row-wise
for (i in 1:nrow(dat[[sheet]])) {
x$addTag(Row, close=FALSE)
for (j in 1:ncol(dat[[sheet]])) {
## Go through the row, expanding any hyperlinks
cellAttr - NULL
if (!is.na(ind -
Re: [R] installing packages
Menu Packages Install Packages works well for me. --- raymond chiruka [EMAIL PROTECTED] wrote: hie how do l install R packages .L'm using windows xp.plus is there a dipository for the packages that one can browse to find out what packages are available. thanks. - Be a PS3 game guru. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] extractor rows from a matrix
I think I understand what you want. Try htt data.frame(ht) unlist (htt) --- billycorg [EMAIL PROTECTED] wrote: thanks for the answer..but i don't find what i'm looking for! now i'm trying to expose better my problem: i have: ht= a 1096rows x 3 columns matrix i'd like a function like this: d[i]=rbind(ht[i,]) for (i in 1:length(ht)) but this don't work :( can anyone seriously help me? -- View this message in context: http://www.nabble.com/extractor-rows-from-a-matrix-tf3913088.html#a4923 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Dates in Windows
Hi everyone, When using R on Linux I can do the following: x - as.Date(01/04/2007, %d/%m/%Y); x [1] 2007-04-01 print(format(x, %s)); [1] 1175385600 When using R in Windows XP though the format %s does nothing but return a blank string. How can I convert a date to the number of seconds since 1970 in Windows? Cheers Tom __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Responding to a posting in the digest
At 08:26 14/06/2007, Moshe Olshansky wrote: Is there a convenient way to respond to a particular posting which is a part of the digest? I mean something that will automatically quote the original message, subject, etc. Yes, if you use appropriate mailing software. I use Eudora, receive the emails in MIME format and the responses do get properly threaded as far as I can see from the mailing list archives. Thank you! Moshe Olshansky [EMAIL PROTECTED] Michael Dewey http://www.aghmed.fsnet.co.uk __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] make sample() faster
I think the problem is not sample (which is written in C), but that you are calling it with size=1. Taking one sample with probabilities from a large discrete distribution is necessarily slow, but you can take a large sample for little more cost. On Thu, 14 Jun 2007, Rainer M. Krug wrote: Hi I have a simulation which is relatively slow. I used Rprofile() and identified the calls to sample() as the culprit is sample(): summaryRprof(Documents/PostDoc/Aloe_Pillansii/R/create.out) $by.self self.time self.pct total.time total.pct sample 1.30 44.2 1.52 51.7 ifelse 0.46 15.6 2.44 83.0 . . . I am using sample() as follow: result - sample( x=d.growth.seedling$growth, size=1, prob=d.growth.seedling$p, replace ) d.growth.seedling$p and d.growth.seedling$growth have a length of 1024 and are calculated initially by using density(). My question: is there any way to make this faster, i.e. replace sample() as I use it with another faster algorithm (if necessary implemented in C)? Thanks in advance, Rainer -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Dates in Windows
%s is of course not documented on ?strftime: it is a glibc extension and marked as such on my Linux man page. But as.numeric(x) gives you the number of days, and as.numeric(as.POSIXct(x)) gives you the number of seconds, equal to 86400*as.numeric(x). [Why are you including empty commands at the end of every R line? It is not necessary and makes the code harder to read.] On Thu, 14 Jun 2007, Tom McCallum wrote: Hi everyone, When using R on Linux I can do the following: x - as.Date(01/04/2007, %d/%m/%Y); x [1] 2007-04-01 print(format(x, %s)); [1] 1175385600 When using R in Windows XP though the format %s does nothing but return a blank string. How can I convert a date to the number of seconds since 1970 in Windows? Cheers Tom __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] extractor rows from a matrix
Petr, it works!!!
thank you a lot!!!
Vincenzo
Petr Klasterecky wrote:
Well, you cannot have a vector of vectors, you need a list of vectors.
With mean() and sum() it worked probably because these produce a single
number as their output. Also, the rbind() function won't help here, that
is for merging vector into a matrix. Once again, reading R-Intro is the
best advice I can give you.
# creating an ampty list of length 1096:
d - list()
length(d) - 1096
# Filling the list with rows
for(i in (1:1096)){
d[[i]] - ht[i,]
}
Note the double bracketing when indexing lists: d[[1]]
Please respond to the entire list next time, I only read these messages
occasionally.
Petr
vincenzo napsal(a):
thank you a lot for the answer
i don't expect one vector..
but 1096 vector.
example: ht=
123
1 345
2 458
3
4
.
.
.
1096
i'd like 1096 vector like these:
d[1]= 345
d[2]= 458
...
i'm trying now with this:
for(i in 1:1096) d[i]=(rbind(ht[i,]))
but it doesn't work :(
it works with function like mean,sum.. but not with rbind
what can i do?
/---Messaggio originale---/
/*Da:*/ Petr Klasterecky mailto:[EMAIL PROTECTED]
/*Data:*/ 06/14/07 10:07:33
/*A:*/ billycorg mailto:[EMAIL PROTECTED]
/*Cc:*/ r-help@stat.math.ethz.ch mailto:r-help@stat.math.ethz.ch
/*Oggetto:*/ Re: [R] extractor rows from a matrix
billycorg napsal(a):
thanks for the answer..but i don't find what i'm looking for!
now i'm trying to expose better my problem:
i have:
ht= a 1096rows x 3 columns matrix
i'd like a function like this:
d[i]=rbind(ht[i,]) for (i in 1:length(ht))
but this don't work :(
can anyone seriously help me?
The problem is that people actually are trying to seriously help you,
but it is really difficult from your queries...
Please specify what you expect to be your output - a vector where you
just paste the rows of of the original matrix one by one?
If so, you can do
d - t(ht)
dim(d) - NULL
or (a 'dirty' way)
d - c(t(ht))
It is not at all clear what your statement should do. For example, what
is length(ht) with ht being a matrix? For R it is the total number of
elements, but did you mean this or the number of rows/columns??
The suggestion to read R-Intro is the best advice you got here.
Petr
--
Petr Klasterecky
Dept. of Probability and Statistics
Charles University in Prague
Czech Republic
__ Informazione NOD32 2328 (20070613) __
Questo messaggio è stato controllato dal Sistema Antivirus NOD32
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--
Petr Klasterecky
Dept. of Probability and Statistics
Charles University in Prague
Czech Republic
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PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproducible code.
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View this message in context:
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Re: [R] besselK
Hello AFAIK, R has no capability for evaluating Bessel functions for complex arguments. Bessel functions for complex arguments are difficult to evaluate numerically. Some Bessel functions require cut lines or consideration of Riemann surfaces. The GSL library (for which the gsl package is an R wrapper) does not include such functionality although the issue has arisen on the GSL email list a couple of times over the last few years. Writing R functionality for Bessel functions (and in particular the Airy function) is on my List of Things To Do, but don't hold your breath . . . best wishes Robin On 14 Jun 2007, at 10:31, ivivi mwaniki wrote: Assistance, besselK- complex number problem Im a student intrested in using R in my learning and research work in option pricing however i have a problem with besselK function In R. Would you assit me in computing the besselK of third kind of a complex number in R. Any code or suggestion will be highly appriceiated eg besselK(2,10) works well.. but besselK(2,10i) doesnt work !! im supprised it works in MATLAB but NOT in R. rgds ivivi mwaniki student kenya - Don't pick lemons. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. -- Robin Hankin Uncertainty Analyst National Oceanography Centre, Southampton European Way, Southampton SO14 3ZH, UK tel 023-8059-7743 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] function with xyplot
Hi,
I'm a new user trying to switch from SAS, so sorry for the beginner's
question: Suppose I have a dataframe DF that contains variables X,Y,Z. I am
trying to write a function like this:
myplot - function(varname){xyplot(varname ~ Y, group = Z, data = DF)}.
The problem is then how to enter X into my function. If I write myplot(X)
I get an error because the argument is a string and xyplot can make nothing
out of it. If I write myplot(X) I also get an error that tells me the object
X does not exist.
Thanks for your help,
Diego
[[alternative HTML version deleted]]
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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.
[R] Wilcoxon test on data matrix
Dear everyone,
I am trying to do a Wilcoxon one-sided test on my gene expression data.
These are the data i have in R:
data.matrix (matrix, numeric) containing all gene expression data (42
rows=genes, 42 columns=tumors), no column header or row names
data.cl (vector, numeric) consisting of 42 0's and 1's to indicate class 0 or
class 1 for each column in data.matrix
I want to do a Wilcoxon one-sided test on the data from class 0 versus the data
from class 1, for each row (gene) of the data set.
My first try:
#to make separate matrices for both classes:
data.matrix.0 - data.matrix[,data.cl==0]
data.matrix.1 - data.matrix[,data.cl==1]
# to run the wilcox.test function for each row:
rawp - apply(data.matrix.0, 1, wilcox.test, y=data.matrix.1,
alternative=less)
The result of printing rawp is:
$`1`
Wilcoxon rank sum test with continuity correction
data: newX[, i] and data.matrix.1
W = 7585, p-value = 1
alternative hypothesis: true location shift is less than 0
$`2`
Wilcoxon rank sum test with continuity correction
data: newX[, i] and data.matrix.1
W = 6700, p-value = 0.9983
alternative hypothesis: true location shift is less than 0
Etcetera for each row of the data matrix.
I can get the p value for one row (gene) using:
rawp.1 - rawp$'1'$p.value
But how can I get these p-values in one list? I have tried:
rawp - NULL
for (i in 1:42) {
a - paste(', i, ', sep=)
rawp - rbind(rawp, test$a$p.value)
}
but that doesn't work (no errors but rawp stays NULL)
There must be an easier way to do a wilcoxon analysis on a matrix!
I'd appreciate your help with this...
Marije
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Re: [R] Generating artificial datasets with a specific correlation coefficient.
Thanks to all who responded to my request. I'll probably use the corgen function in ecodist, as suggested by Sarah Goslee (below), as I just need examples of correlated vectors. Thanks again. Jim Milks Graduate Student Environmental Sciences Ph.D. Program 136 Biological Sciences Wright State University 3640 Colonel Glenn Hwy Dayton, OH 45435 Begin forwarded message: From: Sarah Goslee [EMAIL PROTECTED] Date: June 12, 2007 5:37:36 PM EDT To: James Milks [EMAIL PROTECTED] Subject: Re: [R] Generating artificial datasets with a specific correlation coefficient. If you don't need anything fancy, just two vectors x and y such that cor(x, y) = 0.30 then the corgen function in ecodist (current version available from CRAN) does just that. Sarah On 6/12/07, James Milks [EMAIL PROTECTED] wrote: I need to create artificial datasets with specific correlation coefficients (i.e. a dataset that returns r = 0.30, etc.) as examples for a lab I am teaching this summer. Is there a way to do that in R? Thanks. Jim Milks Graduate Student Environmental Sciences Ph.D. Program 136 Biological Sciences Wright State University 3640 Colonel Glenn Hwy Dayton, OH 45435 -- Sarah Goslee http://www.functionaldiversity.org [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] function with xyplot
You need to reference the data.frame or append it.
myplot(DF$X) should work
or
append(DF)
myplot(X)
--- Diego Gruber [EMAIL PROTECTED] wrote:
Hi,
I'm a new user trying to switch from SAS, so sorry
for the beginner's
question: Suppose I have a dataframe DF that
contains variables X,Y,Z. I am
trying to write a function like this:
myplot - function(varname){xyplot(varname ~ Y,
group = Z, data = DF)}.
The problem is then how to enter X into my function.
If I write myplot(X)
I get an error because the argument is a string and
xyplot can make nothing
out of it. If I write myplot(X) I also get an error
that tells me the object
X does not exist.
Thanks for your help,
Diego
[[alternative HTML version deleted]]
__
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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
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Re: [R] test if files in current folder
runner wrote:
I want to test if the files are already in my current folder before I
download or copy from somewhere else. What's in my mind is to check if a
file is open-able in current folder. Is there a way to do this, like in
Perl:
if (open()) { do sth}?
To put it another way, how to extract all file names in a folder to an
array or list?
?files
?dir
BTW, Perl has nice -X functions, which allow file testing without explicit
opening:
http://perldoc.perl.org/functions/-X.html
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Re: [R] Wilcoxon test on data matrix
wilcox.test(data.matrix[i,] ~ data.cl)$p.value
will return the p.value for row 'i'.
With a loop:
pv = rep(0,42)
for (i in 1:42) { pv[i]=wilcox.test(data.matrix[i,] ~ data.cl)$p.value }
Is this what you wanted?
Christophe
On 6/14/07, Booman, M [EMAIL PROTECTED] wrote:
Dear everyone,
I am trying to do a Wilcoxon one-sided test on my gene expression data.
These are the data i have in R:
data.matrix (matrix, numeric) containing all gene expression data (42
rows=genes, 42 columns=tumors), no column header or row names
data.cl (vector, numeric) consisting of 42 0's and 1's to indicate class 0
or class 1 for each column in data.matrix
I want to do a Wilcoxon one-sided test on the data from class 0 versus the
data from class 1, for each row (gene) of the data set.
My first try:
#to make separate matrices for both classes:
data.matrix.0 - data.matrix[,data.cl==0]
data.matrix.1 - data.matrix[,data.cl==1]
# to run the wilcox.test function for each row:
rawp - apply(data.matrix.0, 1, wilcox.test, y=data.matrix.1,
alternative=less)
The result of printing rawp is:
$`1`
Wilcoxon rank sum test with continuity correction
data: newX[, i] and data.matrix.1
W = 7585, p-value = 1
alternative hypothesis: true location shift is less than 0
$`2`
Wilcoxon rank sum test with continuity correction
data: newX[, i] and data.matrix.1
W = 6700, p-value = 0.9983
alternative hypothesis: true location shift is less than 0
Etcetera for each row of the data matrix.
I can get the p value for one row (gene) using:
rawp.1 - rawp$'1'$p.value
But how can I get these p-values in one list? I have tried:
rawp - NULL
for (i in 1:42) {
a - paste(', i, ', sep=)
rawp - rbind(rawp, test$a$p.value)
}
but that doesn't work (no errors but rawp stays NULL)
There must be an easier way to do a wilcoxon analysis on a matrix!
I'd appreciate your help with this...
Marije
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Re: [R] Tools For Preparing Data For Analysis
As a tangent to this thread, there is a very relevant article in the latest issue of the RSS magazine Significance, which I have just received: Dr Fisher's Casebook The trouble with data Significance, Vol 4 (2007) Issue 2. Full current contents at http://www.blackwell-synergy.com/toc/sign/4/2 but unfortunately you can only read any of it by paying money to Blackwell (unless you're an RSS member). Best wishes to all, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 14-Jun-07 Time: 12:24:46 -- XFMail -- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] building packages under windows
I tried to check or build a package under windows xp but I got the error the package can not be installed (without any details in the install.out file) I work with R-2.5.0, Miktex 2.5.0, and I have installed the unix tools.zip, Perl and Microsoft HTML Workshop. The path environment is ok. Have someone else encountered the same problem? Thank you, Cinzia Cinzia Viroli Dipartimento di Scienze Statistiche Paolo Fortunati Via delle Belle Arti 41 40126 Bologna Italy Ph. +39 051 2098250 Fax +39 051 232153 home: www2.stat.unibo.it/viroli [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Difference between prcomp and cmdscale
Michael,
Why should that confuse you? Have you tried reading some of the literature
on these methods? There's plenty about them on the Net (Wiki's often a
goodish place to start)---and even in R, if you're prepared to look ;).
BestR,
Mark.
michael watson (IAH-C) wrote:
I'm looking for someone to explain the difference between these
procedures. The function prcomp() does principal components anaylsis,
and the function cmdscale() does classical multi-dimensional scaling
(also called principal coordinates analysis).
My confusion stems from the fact that they give very similar results:
my.d - matrix(rnorm(50), ncol=5)
rownames(my.d) - paste(c, 1:10, sep=)
# prcomp
prc - prcomp(my.d)
# cmdscale
mds - cmdscale(dist(my.d))
cor(prc$x[,1], mds[,1]) # produces 1 or -1
cor(prc$x[,2], mds[,2]) # produces 1 or -1
Presumably, under the defaults for these commands in R, they carry out
the same (or very similar) procedures?
Thanks
Mick
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Re: [R] Difference between prcomp and cmdscale
On Thu, 14 Jun 2007, michael watson (IAH-C) wrote: I'm looking for someone to explain the difference between these procedures. The function prcomp() does principal components anaylsis, and the function cmdscale() does classical multi-dimensional scaling (also called principal coordinates analysis). My confusion stems from the fact that they give very similar results: my.d - matrix(rnorm(50), ncol=5) rownames(my.d) - paste(c, 1:10, sep=) # prcomp prc - prcomp(my.d) # cmdscale mds - cmdscale(dist(my.d)) cor(prc$x[,1], mds[,1]) # produces 1 or -1 cor(prc$x[,2], mds[,2]) # produces 1 or -1 Presumably, under the defaults for these commands in R, they carry out the same (or very similar) procedures? For Eucldean distance, the same. The point being that classical MDS on Euclidean distances is just PCA on the reconstucted configuration, but that MDS is not restricted to a data matrix. The relationship is explained in MASS, for example. Thanks Mick -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] building packages under windows
If you try Rcmd INSTALL mypackage you will get the error messages on the terminal. I've never not seen them in the mypackage.Rcheck/00install.out file, but then I used the correct name. On Thu, 14 Jun 2007, Cinzia Viroli wrote: I tried to check or build a package under windows xp but I got the error the package can not be installed (without any details in the install.out file) I work with R-2.5.0, Miktex 2.5.0, and I have installed the unix tools.zip, Perl and Microsoft HTML Workshop. The path environment is ok. Have someone else encountered the same problem? Thank you, Cinzia Cinzia Viroli Dipartimento di Scienze Statistiche Paolo Fortunati Via delle Belle Arti 41 40126 Bologna Italy Ph. +39 051 2098250 Fax +39 051 232153 home: www2.stat.unibo.it/viroli [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] make sample() faster
Thanks for the info - so the solution would (likely) be to draw several samples and use these whenever I need a new one. tHANKS, i'LL TRY IT OUT, rAINER P.S: somebody said once that the caps-lock key is the most useless key on the keyboard and he is right... Prof Brian Ripley wrote: I think the problem is not sample (which is written in C), but that you are calling it with size=1. Taking one sample with probabilities from a large discrete distribution is necessarily slow, but you can take a large sample for little more cost. On Thu, 14 Jun 2007, Rainer M. Krug wrote: Hi I have a simulation which is relatively slow. I used Rprofile() and identified the calls to sample() as the culprit is sample(): summaryRprof(Documents/PostDoc/Aloe_Pillansii/R/create.out) $by.self self.time self.pct total.time total.pct sample 1.30 44.2 1.52 51.7 ifelse 0.46 15.6 2.44 83.0 . . . I am using sample() as follow: result - sample( x=d.growth.seedling$growth, size=1, prob=d.growth.seedling$p, replace ) d.growth.seedling$p and d.growth.seedling$growth have a length of 1024 and are calculated initially by using density(). My question: is there any way to make this faster, i.e. replace sample() as I use it with another faster algorithm (if necessary implemented in C)? Thanks in advance, Rainer -- NEW EMAIL ADDRESS AND ADDRESS: [EMAIL PROTECTED] [EMAIL PROTECTED] WILL BE DISCONTINUED END OF MARCH Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Leslie Hill Institute for Plant Conservation University of Cape Town Rondebosch 7701 South Africa Fax:+27 - (0)86 516 2782 Fax:+27 - (0)21 650 2440 (w) Cell: +27 - (0)83 9479 042 Skype: RMkrug email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] test if files in current folder
On Thu, 14 Jun 2007, Vladimir Eremeev wrote:
runner wrote:
I want to test if the files are already in my current folder before I
download or copy from somewhere else. What's in my mind is to check if a
file is open-able in current folder. Is there a way to do this, like in
Perl:
if (open()) { do sth}?
To put it another way, how to extract all file names in a folder to an
array or list?
?files
?dir
BTW, Perl has nice -X functions, which allow file testing without explicit
opening:
http://perldoc.perl.org/functions/-X.html
which are based on those in 'test' and most Unix shells, as is R's
file.test() in package 'utils'.
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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[R] Preserving dates in Excel.
Hi, Quick question: Say I have a date variable in a data frame or matrix, and I'd like to preserve the date format when using write.table. However, when I export the data, I get the generic number underlying the date, not the date per se, and a number such as 11323, 11324, etc are not meaningful in Excel. Is there any way I can preserve the format of a date on writing into a text-file? TIA and best, -Tir __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fitted Value Pareto Distribution
Thank you very much and that is exactly what I am looking for. Another question would be how can I test the goodness of fit for the Pareto distribution? J. Hosking wrote: livia wrote: I would like to fit a Pareto Distribution and I am using the following codes. I thought the fitted (fit1) should be the fitted value for the data, is it correct? As the result of the fitted turns out to be a single value for all. fit=vglm(ycf1 ~ 1, pareto1(location=alpha), trace=TRUE, crit=c) fitted(fit) The result is fitted(fit) [,1] [1,] 0.07752694 [2,] 0.07752694 [3,] 0.07752694 [4,] 0.07752694 [5,] 0.07752694 [6,] 0.07752694 [7,] 0.07752694 [8,] 0.07752694 [9,] 0.07752694 [10,] 0.07752694 [11,] 0.07752694 [12,] 0.07752694 [13,] 0.07752694 Could anybody give me some advice? I don't have whatever package function 'vglm' comes from (did you follow the instructions in the last two lines of your post?), but you can fit a GPD and get fitted values for it by some such approach as this: library(POT) threshold - 0 # probably para - fitgpd(ycf1, threshold, method=pwmu)$param ycf1.fit - qgpd( ppoints(ycf1, a=0.44), threshold, para[1], para[2]) Note that the above code contains my own preferences for fitting method and plotting positions: yours may differ. J. R. M. Hosking __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://www.nabble.com/Fitted-Value-Pareto-Distribution-tf3914151.html#a9224 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] problem with hist()
Hey everybody, I try to make a graph with two different plots. First I make a boxplot of my data. It is a collection off correlation values of different pictures. For example: 0.23445 pica 0.34456 pica 0.45663 pica 0.98822 picb 0.12223 picc 0.34443 picc etc. Ok, I make this boxplot and I get for every picture the boxes. After this I want to know, how many correlations per picture exist. So I make a new vector y - as.numeric(data$picture) So I get for my example something like this: y [1] 1 1 1 1 1 1 1 1 1 1 [11] 1 1 1 1 1 1 1 1 2 2 ... [16881] 59 59 59 60 60 60 60 60 60 60 After this I make something like this boxplot(cor ~ pic) par(new = TRUE) hist(y, nclass = 60) But there is my problem. I have 60 pictures, so I get 60 different boxplots, and I want the hist behind the boxes. But it makes only 59 histbars. What can I do? I tried also hist(y, 1:60) # same effect and hist(y, 1:61) this give me 60 places, but only 59 bars. the last bar is 0. I hope anyone can help me. Regards Mario __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Preserving dates in Excel.
Patnaik, Tirthankar wrote: Hi, Quick question: Say I have a date variable in a data frame or matrix, and I'd like to preserve the date format when using write.table. However, when I export the data, I get the generic number underlying the date, not the date per se, and a number such as 11323, 11324, etc are not meaningful in Excel. Is there any way I can preserve the format of a date on writing into a text-file? Er, what is exactly the problem here? d - data.frame(date=as.Date(2007-6-1)+1:5, x=rnorm(5)) d date x 1 2007-06-02 0.7987635130 2 2007-06-03 -0.7381623316 3 2007-06-04 -1.3626708691 4 2007-06-05 0.0007668082 5 2007-06-06 0.6719088533 write.table(d) date x 1 2007-06-02 0.798763513018864 2 2007-06-03 -0.738162331606612 3 2007-06-04 -1.36267086906438 4 2007-06-05 0.000766808196322155 5 2007-06-06 0.671908853312511 write.csv(d) ,date,x 1,2007-06-02,0.798763513018864 2,2007-06-03,-0.738162331606612 3,2007-06-04,-1.36267086906438 4,2007-06-05,0.000766808196322155 5,2007-06-06,0.671908853312511 -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] function with xyplot
Thanks a lot for your suggestions. Referencing the dataset solved the problem. I had actually tried it before but since I was also subsetting the datset within the function (something I didn't mention in my question) the objects were not of the same length and that caused me trouble. Your comment made me realize that. Thanks Hadley for pointing me out to ggplot2, looks like a very complete graphics package and if it simplifies the programming it must be extremely useful. I'll make sure to take a closer look at it. Best regards, Diego [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Preserving dates in Excel.
On Thu, 14 Jun 2007, Patnaik, Tirthankar wrote: Hi, Quick question: Say I have a date variable in a data frame or matrix, Which? It matters: see the help page. and I'd like to preserve the date format when using write.table. However, when I export the data, I get the generic number underlying the date, not the date per se, and a number such as 11323, 11324, etc are not meaningful in Excel. Is there any way I can preserve the format of a date on writing into a text-file? Yes, see the help page and use a data frame. E.g. write.table(data.frame(x=.leap.seconds[1:3]), ) x 1 1972-07-01 01:00:00 2 1973-01-01 00:00:00 3 1974-01-01 00:00:00 -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Difference between prcomp and cmdscale
Hi Mark
I think Brian Ripley answered this most effectively and succinctly. I
did actually do quite a bit of googling and searching of the R help
before posting, and whilst there is quite a lot on each topic
individually, I failed to find articles that compare and contrast PCA
and MDS. If you know of any, of course I would be happy to read them.
Many thanks
Mick
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Mark Difford
Sent: 14 June 2007 12:49
To: r-help@stat.math.ethz.ch
Subject: Re: [R] Difference between prcomp and cmdscale
Michael,
Why should that confuse you? Have you tried reading some of the
literature
on these methods? There's plenty about them on the Net (Wiki's often a
goodish place to start)---and even in R, if you're prepared to look ;).
BestR,
Mark.
michael watson (IAH-C) wrote:
I'm looking for someone to explain the difference between these
procedures. The function prcomp() does principal components anaylsis,
and the function cmdscale() does classical multi-dimensional scaling
(also called principal coordinates analysis).
My confusion stems from the fact that they give very similar results:
my.d - matrix(rnorm(50), ncol=5)
rownames(my.d) - paste(c, 1:10, sep=)
# prcomp
prc - prcomp(my.d)
# cmdscale
mds - cmdscale(dist(my.d))
cor(prc$x[,1], mds[,1]) # produces 1 or -1
cor(prc$x[,2], mds[,2]) # produces 1 or -1
Presumably, under the defaults for these commands in R, they carry out
the same (or very similar) procedures?
Thanks
Mick
The information contained in this message may be\ confiden...{{dropped}}
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and provide commented, minimal, self-contained, reproducible code.
[R] scatterplots: (equal axes and overlay)
Hi, I am doing lots of scatterplots for my dissertation and to make the comparable, I would like to have equal x- amd - y axis. Can I specify their scale? Another question adresses overlay scatterplots. Having prae and post measures for each case, is it possible to have them in one graph with symbols or colors for prae and post. So scatterplot(bdiprae,mocoprae) and scatterplot(bdipost,mocopost) in one graph (for example green for prae and red for post?) thanks a lot in advance Matthias __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] building packages under windows
Thank you for your suggestion. I tried WITH different packages and also I tried to INSTALL the package OC from CRAN and I got the message installing to 'c:PROGRA~1/r/R-25~1.0/library' *** Installation of oc failed *** Removing 'c:/PROGRA~1/r/R-25~1.0/library/oc' my path for R is 'c:/program files/R/R-2.5.0' Is space allowed? Thanks Cinzia At 13.56 14/06/2007, you wrote: If you try Rcmd INSTALL mypackage you will get the error messages on the terminal. I've never not seen them in the mypackage.Rcheck/00install.out file, but then I used the correct name. On Thu, 14 Jun 2007, Cinzia Viroli wrote: I tried to check or build a package under windows xp but I got the error the package can not be installed (without any details in the install.out file) I work with R-2.5.0, Miktex 2.5.0, and I have installed the unix tools.zip, Perl and Microsoft HTML Workshop. The path environment is ok. Have someone else encountered the same problem? Thank you, Cinzia Cinzia Viroli Dipartimento di Scienze Statistiche Paolo Fortunati Via delle Belle Arti 41 40126 Bologna Italy Ph. +39 051 2098250 Fax +39 051 232153 home: www2.stat.unibo.it/viroli [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 Cinzia Viroli Dipartimento di Scienze Statistiche Paolo Fortunati Via delle Belle Arti 41 40126 Bologna Italy Ph. +39 051 2098250 Fax +39 051 232153 home: www2.stat.unibo.it/viroli [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Preserving dates in Excel.
Hi Peter, Prof. Ripley, You're right--I just realized I was exporting a matrix, after converting the data-frame using data.matrix, where the date characteristics are lost. Basically a function I was running converted the dataframe to a matrix first--something I'd forgotten. z1 - data.matrix(head(Banks.Index.daily[,1:5])) Warning message: class information lost from one or more columns in: data.matrix(head(Banks.Index.daily[, 1:5])) z1 Date SBI.BO HDFC.BO KTKM.BO YESB.BO 2001-01-01 11323 102944.3 64134.8 3576.4 NA 2001-01-02 11324 108812.5 64390.9 3606.2 NA 2001-01-03 11325 114101.8 65909.5 3528.2 NA 2001-01-04 11326 112180.8 65266.3 3691.2 NA 2001-01-05 11327 113365.0 69286.3 3700.3 NA 2001-01-08 11330 112180.8 70292.8 3682.0 NA write.table(z1) Date SBI.BO HDFC.BO KTKM.BO YESB.BO 2001-01-01 11323 102944.3 64134.8 3576.4 NA 2001-01-02 11324 108812.5 64390.9 3606.2 NA 2001-01-03 11325 114101.8 65909.5 3528.2 NA 2001-01-04 11326 112180.8 65266.3 3691.2 NA 2001-01-05 11327 113365 69286.3 3700.3 NA 2001-01-08 11330 112180.8 70292.8 3682 NA Apologies for the inconvenience. Best, -Tir -Original Message- From: Peter Dalgaard [mailto:[EMAIL PROTECTED] Sent: Thursday, June 14, 2007 6:07 PM To: Patnaik, Tirthankar [GWM-CIR] Cc: r-help@stat.math.ethz.ch Subject: Re: [R] Preserving dates in Excel. Patnaik, Tirthankar wrote: Hi, Quick question: Say I have a date variable in a data frame or matrix, and I'd like to preserve the date format when using write.table. However, when I export the data, I get the generic number underlying the date, not the date per se, and a number such as 11323, 11324, etc are not meaningful in Excel. Is there any way I can preserve the format of a date on writing into a text-file? Er, what is exactly the problem here? d - data.frame(date=as.Date(2007-6-1)+1:5, x=rnorm(5)) d date x 1 2007-06-02 0.7987635130 2 2007-06-03 -0.7381623316 3 2007-06-04 -1.3626708691 4 2007-06-05 0.0007668082 5 2007-06-06 0.6719088533 write.table(d) date x 1 2007-06-02 0.798763513018864 2 2007-06-03 -0.738162331606612 3 2007-06-04 -1.36267086906438 4 2007-06-05 0.000766808196322155 5 2007-06-06 0.671908853312511 write.csv(d) ,date,x 1,2007-06-02,0.798763513018864 2,2007-06-03,-0.738162331606612 3,2007-06-04,-1.36267086906438 4,2007-06-05,0.000766808196322155 5,2007-06-06,0.671908853312511 -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] nlsList problems: control option does not effect output and strange environment search
Dear R-helpers,
I'm using R 2.5.0 under Windows and am trying to use nlsList from nlme
3.1-80 with the selfstart function for the four parametric logistic
function. My first test went well, but now I'm trying to do some more
sophisticated things and it does not work anymore.
I simulate my data from a five parametric logistic function like this:
Y-as.data.frame(apply(params,1,function(x){
Y-x[1]+(x[2]/(1+x[3]*exp(-1*x[4]*(1:240-x[5])))^(1/x[3]))+rnorm(240,0,s
derror)
return(Y)}))
params contains different parameters for 200 persons in 4 groups. Next I
sample for each person five observations one at the start, one at the
end and three randomly in between. Now I get the following error
messages:
testnlslist2-nlsList(SSfpl,groupedData(Y~Time|group, datset))
Error in nls(y ~ cbind(1, 1/(1 + exp((xmid - x)/exp(lscal, data =
xy, :
step factor 0.000488281 reduced below 'minFactor' of 0.000976562
Error in nls(formula = formula, data = data, control = control) :
singular gradient
For the first error it could be that this is due to the fact that this
group is simulated as a kind of placebo and therefore it may be hard to
fit. To solve this I tried to specify controls like this:
testnlslist2-nlsList(SSfpl,groupedData(Y~Time|group,
datset),control=nls.control(minFactor=1/4096))
but it led to the same error as the first. So it looks like the control
parameter is not evaluated. Any other ideas how to get the function
running?
The second strange thing I encountered is that nlsList does not seem to
analyse the environment from which it is called. I did try to use it
within a function in apply and I got the error that the dataset I gave
was not found, but the function grouped.data worked well within the
function. Any idea what I could have done wrong?
Regards,
Winfried Theis
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Re: [R] Difference between prcomp and cmdscale
On 6/14/07, michael watson (IAH-C) [EMAIL PROTECTED] wrote: ... I failed to find articles that compare and contrast PCA and MDS. If you know of any, of course I would be happy to read them. There's an excellent non-R discussion of a wide range of ordination methods at http://ordination.okstate.edu/ (Mike Palmer's work). If you look under distance-based ordination (like MDS/PCO), you find: Special case: for Euclidean distance, PCoA = PCA. and much other useful information. He also gives an extensive list of references from the literature, if you'd like something more rigorous. For an overview text, I'm partial to _Numerical Ecology_ by Legendre and Legendre (1998) because of its readability, but there are many more good texts. Sarah -- Sarah Goslee http://www.functionaldiversity.org __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Using subset() in a user-defined function
Hello,
I'm having a problem with using subset() inside a function I'm writing.
Ignoring everything else in the function, the problem can be illustrated
by (where master.frame is the data frame I'm using):
function1 - function(arg1=, arg2=, arg3=){
temp.frame - subset(master.frame, a == arg1 b == arg2 c ==
arg3)
}
This works fine if the user specifies all arguments, but if any one or
more of the arguments isn't specified, say arg1 for example, the subset
is empty because subset() goes looking for values of a == in
master.frame, and there are none. I want it to work such that if an
argument is not specified, it is not included in what subset() goes
looking for. So if I were to input:
function1(arg2=5, arg3=6)
then in function1, the subset command will look like
temp.frame - subset(master.frame, b == 5 c == 6)
Any suggestions would be much appreciated.
Thanks,
--
jared tobin, student research assistant
dept. of fisheries and oceans
[EMAIL PROTECTED]
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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] Difference between prcomp and cmdscale
Hi Michael,
Doubtless Professor Ripley did; but it helps to put your back into it. Long
ago Gower (1966) drew attention to the links between PCA and classical
scaling. It took me a few seconds to find this:
http://www.garfield.library.upenn.edu/classics1980/A1980JJ0821.pdf
Of course, I knew about Gower. But I knew about Gower because I had done
the _basic_ research on these methods. And that was my point. In a later
paper Gower argued that classical scaling extended, and was more powerful
than, PCA.
However, classical scaling operates on [a matrix of] similarities between
observations/individuals/rows, whereas PCA operates on [a matrix of]
similarities between variables/descriptors/columns. This means that in
classical scaling the axes cannot be interpreted; often one does a PCA to
get at these.
HTH, bestR,
Mark.
michael watson (IAH-C) wrote:
Hi Mark
I think Brian Ripley answered this most effectively and succinctly. I
did actually do quite a bit of googling and searching of the R help
before posting, and whilst there is quite a lot on each topic
individually, I failed to find articles that compare and contrast PCA
and MDS. If you know of any, of course I would be happy to read them.
Many thanks
Mick
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Mark Difford
Sent: 14 June 2007 12:49
To: r-help@stat.math.ethz.ch
Subject: Re: [R] Difference between prcomp and cmdscale
Michael,
Why should that confuse you? Have you tried reading some of the
literature
on these methods? There's plenty about them on the Net (Wiki's often a
goodish place to start)---and even in R, if you're prepared to look ;).
BestR,
Mark.
michael watson (IAH-C) wrote:
I'm looking for someone to explain the difference between these
procedures. The function prcomp() does principal components anaylsis,
and the function cmdscale() does classical multi-dimensional scaling
(also called principal coordinates analysis).
My confusion stems from the fact that they give very similar results:
my.d - matrix(rnorm(50), ncol=5)
rownames(my.d) - paste(c, 1:10, sep=)
# prcomp
prc - prcomp(my.d)
# cmdscale
mds - cmdscale(dist(my.d))
cor(prc$x[,1], mds[,1]) # produces 1 or -1
cor(prc$x[,2], mds[,2]) # produces 1 or -1
Presumably, under the defaults for these commands in R, they carry out
the same (or very similar) procedures?
Thanks
Mick
The information contained in this message may be\ confiden...{{dropped}}
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--
View this message in context:
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[R] Confidence interval for coefficient of variation
This is a function I coded a few years ago to calculate a confidence
interval for a coefficient of variation. The code is based on a paper
by Mark Vangel in The American Statistician. I have not used the
function much, but it could be useful for comparing cv's from
different groups.
Kevin Wright
confint.cv - function(x,alpha=.05, method=modmckay){
# Calculate the confidence interval of the cv of the vector x
# Author: Kevin Wright
# See: Vangel, Mark. Confidence Intervals for a Normal Coefficient
# of Variation. American Statistician, Vol 15, No1, p. 21--26.
# x - c(326,302,307,299,329)
# confint.cv(x,.05,modmckay)
x - na.omit(x)
v - length(x)-1
mu - mean(x)
sigma - sqrt(var(x))
k - sigma/mu
# CV .33 may give poor results, so warn the user
if(k.33) warning(Confidence interval may be very approximate.)
method - casefold(method) # In case we see McKay
if(method==mckay){
# McKay method. See equation 15.
t1 - qchisq(1-alpha/2,v)/v
t2 - qchisq(alpha/2,v)/v
u1 - v*t1
u2 - v*t2
lower - k/sqrt(( u1/(v+1) -1)*k*k + u1/v)
upper - k/sqrt(( u2/(v+1) -1)*k*k + u2/v)
} else if (method==naive){
# Naive method. See equation 17.
t1 - qchisq(1-alpha/2,v)/v
t2 - qchisq(alpha/2,v)/v
lower - k/sqrt(t1)
upper - k/sqrt(t2)
} else {
# Modified McKay method. See equation 16.
u1 - qchisq(1-alpha/2,v)
u2 - qchisq(alpha/2,v)
lower - k/sqrt(( (u1+2)/(v+1) -1)*k*k + u1/v)
upper - k/sqrt(( (u2+2)/(v+1) -1)*k*k + u2/v)
}
ci - c(lower,upper)
attr(ci,CV) - k
attr(ci,alpha) - alpha
return(ci)
}
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Re: [R] besselK
Robin Hankin r.hankin at noc.soton.ac.uk writes: Hello AFAIK, R has no capability for evaluating Bessel functions for complex arguments. Bessel functions for complex arguments are difficult to evaluate numerically. Some Bessel functions require cut lines or consideration of Riemann surfaces. The GSL library (for which the gsl package is an R wrapper) does not include such functionality although the issue has arisen on the GSL email list a couple of times over the last few years. Writing R functionality for Bessel functions (and in particular the Airy function) is on my List of Things To Do, but don't hold your breath . . . best wishes Robin On 14 Jun 2007, at 10:31, ivivi mwaniki wrote: Assistance, besselK- complex number problem Im a student intrested in using R in my learning and research work in option pricing however i have a problem with besselK function In R. Would you assit me in computing the besselK of third kind of a complex number in R. Any code or suggestion will be highly appriceiated eg besselK(2,10) works well.. but besselK(2,10i) doesnt work !! im supprised it works in MATLAB but NOT in R. rgds ivivi mwaniki student kenya I have some code for complex Bessel functions which consists of R wrappers for C++ code: the licensing a little obscure -- the code is ultimately from Computation of Special Functions, Zhang and Jin, John Wiley and Sons, 1996. The FORTRAN routines are available from http://jin.ece.uiuc.edu/routines/routines.html ; Chris Bond http://www.crbond.com/math.htm has made a C++ translation available. Both versions are copyrighted: Zhang and Jin say we give permission to the user who downloads these routines to incorporate any of these routines into his or her programs provided that the copyright is acknowledged. The code seems to work for my purposes, but hasn't been thoroughly tested. I can send my crude versions to anyone who would like it. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using subset() in a user-defined function
On 6/14/2007 9:38 AM, Tobin, Jared wrote:
Hello,
I'm having a problem with using subset() inside a function I'm writing.
Ignoring everything else in the function, the problem can be illustrated
by (where master.frame is the data frame I'm using):
function1 - function(arg1=, arg2=, arg3=){
temp.frame - subset(master.frame, a == arg1 b == arg2 c ==
arg3)
}
This works fine if the user specifies all arguments, but if any one or
more of the arguments isn't specified, say arg1 for example, the subset
is empty because subset() goes looking for values of a == in
master.frame, and there are none. I want it to work such that if an
argument is not specified, it is not included in what subset() goes
looking for. So if I were to input:
function1(arg2=5, arg3=6)
then in function1, the subset command will look like
temp.frame - subset(master.frame, b == 5 c == 6)
Any suggestions would be much appreciated.
Code it like this:
subset(master.frame, (missing(arg1) | a == arg1)
(missing(arg2) | b == arg2)
(missing(arg3) | c == arg3))
I haven't tried this, and I forget what happens in subset() if you pass
it a subset of the wrong length, so it might fail if all args are
missing, but otherwise I think it should work. It does depend on
defaults for the args existing and not causing errors in the equality
tests (it's not using shortcut evaluation).
Duncan Murdoch
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Re: [R] problem with hist()
Mario Dejung wrote: Hey everybody, I try to make a graph with two different plots. First I make a boxplot of my data. It is a collection off correlation values of different pictures. For example: 0.23445 pica 0.34456 pica 0.45663 pica 0.98822 picb 0.12223 picc 0.34443 picc etc. Ok, I make this boxplot and I get for every picture the boxes. After this I want to know, how many correlations per picture exist. So I make a new vector y - as.numeric(data$picture) So I get for my example something like this: y [1] 1 1 1 1 1 1 1 1 1 1 [11] 1 1 1 1 1 1 1 1 2 2 ... [16881] 59 59 59 60 60 60 60 60 60 60 After this I make something like this boxplot(cor ~ pic) par(new = TRUE) hist(y, nclass = 60) But there is my problem. I have 60 pictures, so I get 60 different boxplots, and I want the hist behind the boxes. But it makes only 59 histbars. What can I do? I tried also hist(y, 1:60) # same effect and hist(y, 1:61) this give me 60 places, but only 59 bars. the last bar is 0. In fact, I am pretty sure you really want to have a barplot() rather than a histogram. If you really want to use hist(), then perhaps hist(y, 0:60). Uwe Ligges I hope anyone can help me. Regards Mario __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] scatterplots: (equal axes and overlay)
Hi Matthias, please see below for some code example. Matthias von Rad wrote: Hi, I am doing lots of scatterplots for my dissertation and to make the comparable, I would like to have equal x- amd - y axis. Can I specify their scale? Another question adresses overlay scatterplots. Having prae and post measures for each case, is it possible to have them in one graph with symbols or colors for prae and post. ### first we create some hypothetical data pre.x - runif(n=100, min=0, max=10) pre.y - 1.5+2*pre.x+rnorm(n=length(pre.x), mean=pre.x, sd=1) post.x - runif(n=100, min=0, max=10) post.y - 20-3*post.x+rnorm(n=length(post.x), mean=post.x, sd=1) ## let's construct a plot from scratch, using type=n to have an ## empty plotting area plot(x=1,y=1, type=n, xlim=c(0,10), ylim=c(0,20), axes=FALSE, xlab=My X-Labels, ylab=My Y-Labels) axis(side=1, at=seq(from=0, to=10, by=2.5)) axis(side=2, at=seq(from=0, to=20, by=5)) points(x=pre.x, y=pre.y, col=green, pch=19) points(x=post.x, y=post.y, col=red, pch=19) ### and this makes it easy to find out which 'pch'-number plots which ### symbol: plot(x=0:25, y=0:25, pch=0:25) I hope this helps. Best, Roland __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] names() after library(RDCOMClient) problem(?)
Hello, Try example(names) in R 2.5.0 after library(RDCOMClient) and you get example(names) names # print the names attribute of the islands data set names names(islands) Error in names(islands) : no applicable method for names Is this normal? Any way round it??? Best regards, Costas -- Costas Vorlow Research Economist Eurobank EFG Division of Research Forecasting --- ( tel: +30-210-3337273 (ext 17273) 7 fax: +30-210-3337687 P Think before you print. Disclaimer: This e-mail is confidential. If you are not the intended recipient, you should not copy it, re-transmit it, use it or disclose its contents, but should return it to the sender immediately and delete the copy from your system. EFG Eurobank Ergasias S.A. is not responsible for, nor endorses, any opinion, recommendation, conclusion, solicitation, offer or agreement or any information contained in this communication. EFG Eurobank Ergasias S.A. cannot accept any responsibility for the accuracy or completeness of this message as it has been transmitted over a public network. If you suspect that the message may have been intercepted or amended, please call the sender. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] system(R CMD BATCH ...) on UNIX-alikes
If I start from R (in emacs) a new R batch job using system(R CMD BATCH --no-save --quiet Rin.txt Rout.txt, intern=FALSE, ignore.stderr=TRUE, wait=FALSE, input=NULL) the job runs fine and smooth. However, when, for any reason, I press later ctrl+C in the calling R, it not only kills the loop or whatever in the emacs/R, but it kills me the called batch job, too. Why? Can I avoid that? Best regards Meinhard PS system : MacOS 10.4.9 Intel, R 2.5.0 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Problems with na.rm=T
Suddenly (e.g. yesterday) all my functions that have na.rm= as a parameter (e.g., mean(), sd(), range(), etc.) have been reporting warnings with na.rm=T. The message is Warning message: the condition has length 1 and only the first element will be used in: if (na.rm) x - x[!is.na(x)] . This has never happened before. I don't recall having done anything that might generate this message. How do I fix this? Joe Joseph F. Lucke, PhD Biostatistician Center for Clinical Research and Evidence-based Medicine Department of Pediatrics School of Medicine University of Texas Health Science Center at Houston Voice: 713-500-5651 Email: [EMAIL PROTECTED] Postal Mail: PO Box 20708, Houston, TX 77225-0708 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using subset() in a user-defined function
Thanks for the quick response, Duncan.
The given code doesn't seem to work, and possibly due to this reason I
found in the online help for missing() (if I understand it correctly):
Currently missing() can only be used in the immediate body of the
function that defines the argument, not in the body of a nested function
or a local call. This may change in the future.
So as I understand it, missing() cannot refer to the arguments of
function1 if it is used in an argument of subset()? It seems to remain
a promising function for this situation regardless, but I'm not sure how
I could implement it into the subset() arguments offhand.
--
jared tobin, student research assistant
dept. of fisheries and oceans
[EMAIL PROTECTED]
-Original Message-
From: Duncan Murdoch [mailto:[EMAIL PROTECTED]
Sent: Thursday, June 14, 2007 11:28 AM
To: Tobin, Jared
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] Using subset() in a user-defined function
On 6/14/2007 9:38 AM, Tobin, Jared wrote:
Hello,
I'm having a problem with using subset() inside a function I'm
writing.
Ignoring everything else in the function, the problem can be
illustrated by (where master.frame is the data frame I'm using):
function1 - function(arg1=, arg2=, arg3=){
temp.frame - subset(master.frame, a == arg1 b == arg2 c ==
arg3)
}
This works fine if the user specifies all arguments, but if any one or
more of the arguments isn't specified, say arg1 for example, the
subset is empty because subset() goes looking for values of a == in
master.frame, and there are none. I want it to work such that if an
argument is not specified, it is not included in what subset() goes
looking for. So if I were to input:
function1(arg2=5, arg3=6)
then in function1, the subset command will look like
temp.frame - subset(master.frame, b == 5 c == 6)
Any suggestions would be much appreciated.
Code it like this:
subset(master.frame, (missing(arg1) | a == arg1)
(missing(arg2) | b == arg2)
(missing(arg3) | c == arg3))
I haven't tried this, and I forget what happens in subset() if you pass
it a subset of the wrong length, so it might fail if all args are
missing, but otherwise I think it should work. It does depend on
defaults for the args existing and not causing errors in the equality
tests (it's not using shortcut evaluation).
Duncan Murdoch
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problems with na.rm=T
On 6/14/2007 10:32 AM, Lucke, Joseph F wrote: Suddenly (e.g. yesterday) all my functions that have na.rm= as a parameter (e.g., mean(), sd(), range(), etc.) have been reporting warnings with na.rm=T. The message is Warning message: the condition has length 1 and only the first element will be used in: if (na.rm) x - x[!is.na(x)] . This has never happened before. I don't recall having done anything that might generate this message. How do I fix this? I imagine you have created a variable T of length greater than 1. Use TRUE (which is a reserved word, so you can't create such a variable). Don't keep big workspaces full of stuff you don't know about, create a new empty one in each session. Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R programming question
Dear All., I've created R-code for which a user will be asked to choose between 2 analyses. I've written one function for each type of analysis. Within each function, the users is prompted to enter information. An example is: cat(Enter value for lower Linf :\n) L1-scan(n=1) cat(Enter value for upper Linf :\n) L2-scan(n=1) cat(Enter Linf interval :\n) int_L-scan(n=1) cat(Enter value for lower K :\n) K1-scan(n=1) cat(Enter value for upper K :\n) K2-scan(n=1) cat(Enter K interval :\n) int_K-scan(n=1) I thought I could evaluate and run the appropriate function at the end of the program by: if(event==1) explore() else evaluate() If I run the whole program and either explore() or evaluate() is run, the first four prompted entries are skipped over. The console output for event==1 is TRUE looks like: if(event==1) explore() else evaluate() Enter value for lower Linf : 1: Read 0 items Enter value for upper Linf : 1: Read 0 items Enter Linf interval : 1: Read 0 items Enter value for lower K : 1: Read 0 items Enter value for upper K : 1: I then tried another way. I created runcase-ifelse(event==1,explore,evaluate) At the bottom of the program I used: eval(call(x=runcase)) But I still get the same problem. Any suggestions? Thanks for your help Gary A. Nelson, Ph.D Massachusetts Division of Marine Fisheries 30 Emerson Avenue Gloucester, MA 01930 Phone: (978) 282-0308 x114 Fax: (617) 727-3337 Email: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problems with na.rm=T
Lucke, Joseph F wrote: Suddenly (e.g. yesterday) all my functions that have na.rm= as a parameter (e.g., mean(), sd(), range(), etc.) have been reporting warnings with na.rm=T. The message is Warning message: the condition has length 1 and only the first element will be used in: if (na.rm) x - x[!is.na(x)] . This has never happened before. I don't recall having done anything that might generate this message. How do I fix this? Rename the object that you suddenly called T... (And notice that some people will advise you to use na.rm=TRUE to avoid this) -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] simulate null hypothesis
Hi, there: This is a bit off-topic but I try to do it in R so I put it here: I have 31 samples from a population of genes, and each sample contains a pair of gene lists, with different lengths and the intersection between the two lists also varies. I want to test my hypothesis by creating a null hypothesis for this population. Since the distribution for the length and the distribution for the intersection size do not follow any known distribution, I think I need to use sample with replacement to simulate those parameters. And use the parameters to permutate genes; but I am not very sure if it is alll right. BTW, is there any general package or I just need sample() to do that? (just tried to make my question on-topic:) thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ARIMA with more than one seasonality period
Paulo, I have run into similar problems when wanting to work with multiple seasonality. You are probably already familiar with the work by James Taylor in this area. I contacted him and he was kind enough to share some of his (Gauss) code, and I have tried to implement it in R, but due to my lack of programming skill I don't really trust the results and it is very slow. I will try to get it to the point where it could be useful for others. best, Spencer On 6/14/07, Paulo Tanimoto [EMAIL PROTECTED] wrote: Dear R community, I have a project with electricity load forecasting, and I got hourly data for system load. If you haven't worked with electricity before, seasonality comes in many flavors: a daily pattern, with a peak at around 7pm; a weekly pattern, in which we use more electricity on weekdays in comparison to weekends; a winter-summer pattern, with air conditioning and heaters playing an important role, etc. In SAS, I could specify an ARIMA with multiple seasonality terms, say (1,0,1) with period=24, and (1,0,1) with period=168 (I don't remember the orders I was using). This is how many studies I found on IEEE were modeling electricity load and it worked pretty well with the data I have. However, I can't seem to find how to do that in R. I've read the help files a few times, but to no avail. Is it possible? I hope I'm missing something straightforward. Thank you, Paulo Tanimoto University of Arizona __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problems with na.rm=T
Brilliant! Yesterday, I created a table called T. Dumb. Removing it solves the problem. Thanks. -Original Message- From: Duncan Murdoch [mailto:[EMAIL PROTECTED] Sent: Thursday, June 14, 2007 10:01 AM To: Lucke, Joseph F Cc: r-help@stat.math.ethz.ch Subject: Re: [R] Problems with na.rm=T On 6/14/2007 10:32 AM, Lucke, Joseph F wrote: Suddenly (e.g. yesterday) all my functions that have na.rm= as a parameter (e.g., mean(), sd(), range(), etc.) have been reporting warnings with na.rm=T. The message is Warning message: the condition has length 1 and only the first element will be used in: if (na.rm) x - x[!is.na(x)] . This has never happened before. I don't recall having done anything that might generate this message. How do I fix this? I imagine you have created a variable T of length greater than 1. Use TRUE (which is a reserved word, so you can't create such a variable). Don't keep big workspaces full of stuff you don't know about, create a new empty one in each session. Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] [OT]Web-Based Data Brushing
There is the TkBrush function in the TeachingDemos package for R. It is not web based. -Original Message- From: Roy Mendelssohn [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch r-help@stat.math.ethz.ch Sent: 6/12/07 10:26 AM Subject: [R] [OT]Web-Based Data Brushing I apologize for the off-topic post, but my Google search did not turn up much and I thought people on this list my have knowledge of this. I am looking for examples of data brushing (i.e. dynmaic linked plots) either on a web site, or in a web-based application, such as an AJAX app. Even better if there is a way to do this in R. Thanks for any help. -Roy M. ** The contents of this message do not reflect any position of the U.S. Government or NOAA. ** Roy Mendelssohn Supervisory Operations Research Analyst NOAA/NMFS Environmental Research Division Southwest Fisheries Science Center 1352 Lighthouse Avenue Pacific Grove, CA 93950-2097 e-mail: [EMAIL PROTECTED] (Note new e-mail address) voice: (831)-648-9029 fax: (831)-648-8440 www: http://www.pfeg.noaa.gov/ Old age and treachery will overcome youth and skill. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problems with na.rm=T
Lucke, Joseph F wrote: Suddenly (e.g. yesterday) all my functions that have na.rm= as a parameter (e.g., mean(), sd(), range(), etc.) have been reporting warnings with na.rm=T. The message is Warning message: the condition has length 1 and only the first element will be used in: if (na.rm) x - x[!is.na(x)] . This has never happened before. I don't recall having done anything that might generate this message. How do I fix Do you have something called 'T': T=c(1,2,3,4) mean(x,na.rm=T) [1] 2 Warning message: the condition has length 1 and only the first element will be used in: if (na.rm) x - x[!is.na(x)] You should always use 'TRUE' for true and 'FALSE' for false. R makes it harder to shoot yourself in the foot that way: TRUE=c(1,2,3) Error in TRUE = c(1, 2, 3) : invalid (do_set) left-hand side to assignment help(TRUE) helps: Details: 'TRUE' and 'FALSE' are part of the R language, where 'T' and 'F' are global variables set to these. All four are 'logical(1)' vectors. Barry __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using subset() in a user-defined function
I should mention the idea I worked on yesterday was cat()ing together
the appropriate condition strings and then ideally printing that entire
concatenated string into the subset argument. However, as far as I
know, cat() only prints directly on the console and cannot be used to
substitute input text into a function, so I scrapped that idea.
Just figured I'd mention that in case there does happen to be a way to
do such a thing, and someone knows of a way offhand.
--
jared tobin, student research assistant
dept. of fisheries and oceans
[EMAIL PROTECTED]
-Original Message-
From: Tobin, Jared
Sent: Thursday, June 14, 2007 12:28 PM
To: 'Duncan Murdoch'
Cc: r-help@stat.math.ethz.ch
Subject: RE: [R] Using subset() in a user-defined function
Thanks for the quick response, Duncan.
The given code doesn't seem to work, and possibly due to this reason I
found in the online help for missing() (if I understand it correctly):
Currently missing() can only be used in the immediate body of the
function that defines the argument, not in the body of a nested function
or a local call. This may change in the future.
So as I understand it, missing() cannot refer to the arguments of
function1 if it is used in an argument of subset()? It seems to remain
a promising function for this situation regardless, but I'm not sure how
I could implement it into the subset() arguments offhand.
--
jared tobin, student research assistant
dept. of fisheries and oceans
[EMAIL PROTECTED]
-Original Message-
From: Duncan Murdoch [mailto:[EMAIL PROTECTED]
Sent: Thursday, June 14, 2007 11:28 AM
To: Tobin, Jared
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] Using subset() in a user-defined function
On 6/14/2007 9:38 AM, Tobin, Jared wrote:
Hello,
I'm having a problem with using subset() inside a function I'm
writing.
Ignoring everything else in the function, the problem can be
illustrated by (where master.frame is the data frame I'm using):
function1 - function(arg1=, arg2=, arg3=){
temp.frame - subset(master.frame, a == arg1 b == arg2 c ==
arg3)
}
This works fine if the user specifies all arguments, but if any one or
more of the arguments isn't specified, say arg1 for example, the
subset is empty because subset() goes looking for values of a == in
master.frame, and there are none. I want it to work such that if an
argument is not specified, it is not included in what subset() goes
looking for. So if I were to input:
function1(arg2=5, arg3=6)
then in function1, the subset command will look like
temp.frame - subset(master.frame, b == 5 c == 6)
Any suggestions would be much appreciated.
Code it like this:
subset(master.frame, (missing(arg1) | a == arg1)
(missing(arg2) | b == arg2)
(missing(arg3) | c == arg3))
I haven't tried this, and I forget what happens in subset() if you pass
it a subset of the wrong length, so it might fail if all args are
missing, but otherwise I think it should work. It does depend on
defaults for the args existing and not causing errors in the equality
tests (it's not using shortcut evaluation).
Duncan Murdoch
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using subset() in a user-defined function
On 6/14/2007 10:57 AM, Tobin, Jared wrote:
Thanks for the quick response, Duncan.
The given code doesn't seem to work, and possibly due to this reason I
found in the online help for missing() (if I understand it correctly):
Currently missing() can only be used in the immediate body of the
function that defines the argument, not in the body of a nested function
or a local call. This may change in the future.
So as I understand it, missing() cannot refer to the arguments of
function1 if it is used in an argument of subset()? It seems to remain
a promising function for this situation regardless, but I'm not sure how
I could implement it into the subset() arguments offhand.
Right, I had forgotten that subset uses nonstandard evaluation. You
could evaluate add some variables to hold it, e.g.
mysubset - function(arg1=, arg2=, arg3=) {
miss1 - missing(arg1)
miss2 - missing(arg2)
miss3 - missing(arg3)
subset(master.frame, (miss1 | a == arg1)
(miss2 | b == arg2)
(miss3 | c == arg3))
}
This time I did test it as I should have last time, so I can tell you
that if all args are missing you'll get the full master.frame.
Duncan Murdoch
--
jared tobin, student research assistant
dept. of fisheries and oceans
[EMAIL PROTECTED]
-Original Message-
From: Duncan Murdoch [mailto:[EMAIL PROTECTED]
Sent: Thursday, June 14, 2007 11:28 AM
To: Tobin, Jared
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] Using subset() in a user-defined function
On 6/14/2007 9:38 AM, Tobin, Jared wrote:
Hello,
I'm having a problem with using subset() inside a function I'm
writing.
Ignoring everything else in the function, the problem can be
illustrated by (where master.frame is the data frame I'm using):
function1 - function(arg1=, arg2=, arg3=){
temp.frame - subset(master.frame, a == arg1 b == arg2 c ==
arg3)
}
This works fine if the user specifies all arguments, but if any one or
more of the arguments isn't specified, say arg1 for example, the
subset is empty because subset() goes looking for values of a == in
master.frame, and there are none. I want it to work such that if an
argument is not specified, it is not included in what subset() goes
looking for. So if I were to input:
function1(arg2=5, arg3=6)
then in function1, the subset command will look like
temp.frame - subset(master.frame, b == 5 c == 6)
Any suggestions would be much appreciated.
Code it like this:
subset(master.frame, (missing(arg1) | a == arg1)
(missing(arg2) | b == arg2)
(missing(arg3) | c == arg3))
I haven't tried this, and I forget what happens in subset() if you pass
it a subset of the wrong length, so it might fail if all args are
missing, but otherwise I think it should work. It does depend on
defaults for the args existing and not causing errors in the equality
tests (it's not using shortcut evaluation).
Duncan Murdoch
__
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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.
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Goodness of fit- Pareto distribution
Hello, I have fitted a Pareto Distribution for some data, I would appreciate if anyone can tell me how to evaluate the goodness of fit for the distribution. What I do now is rather subjective. I just compare the emprcical density distribution and the fitted density distribution. -- View this message in context: http://www.nabble.com/Goodness-of-fit--Pareto-distribution-tf3922663.html#a11123100 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ievent.wait
I don't know iPlot well enough to tell about that. I was not sure if you needed to use iPlot, or just wanted to connect the points and thought that iPlot might be an answer. I suggested locator with type='l' as a possibility if traditional graphics would work for you. If you have other reasons that require you to use iPlot, then someone with more knowledge of iPlot will need to help you. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of ryestone Sent: Wednesday, June 13, 2007 12:09 PM To: r-help@stat.math.ethz.ch Subject: Re: [R] ievent.wait With locator( ) does it only work in a regular R plot or can I use it with iPlot? I am having difficulty getting it to be used with Iplots, it just calls up a new screen when the function is called. Stone. Sundar Dorai-Raj wrote: Hi, Greg, type = 'b' won't work according to ?locator. Try type = 'o'. HTH,x --sundar Greg Snow said the following on 6/13/2007 7:27 AM: Does locator(type='l') (or type ='b') Work for you? -Original Message- From: ryestone [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch r-help@stat.math.ethz.ch Sent: 6/8/07 10:19 AM Subject: [R] ievent.wait I am working on a plot and would be like to click on a few points and then have a line connect them. Could anyone help me with this or advise me in a direction that would suit this. I know I would be using ievent.wait in iplot but not sure about this. thank you. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://www.nabble.com/ievent.wait-tf3891095.html#a11105384 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R vs. Splus in Pharma/Devices Industry
But sweave is expanding. There is a driver for HTML sweaving in the R2HTML package and the odfWeave package allows you to sweave with open office docs (which can be converted to/from MS word). I personally like using LaTeX and the original sweave, but I work with people who want everything in MS word or similar, so for them I will create a template file in open office, odfWeave that, convert to MS word and send that to them. I think the offset is more that S-PLUS 8 is supposed to implement many of the things that R does now (I don't know which, I'm waiting for my copy of 8), so soon it may be possible to sweave in both. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Wednesday, June 13, 2007 4:07 PM To: r-help@stat.math.ethz.ch Subject: Re: [R] R vs. Splus in Pharma/Devices Industry I should have also noted that Sweave is available for use with R. This is offset, however, by the fact that I will probably never be able to convince anyone to use Latex. This is a pity as I often find myself admiring reports done in Latex as opposed to the ones I have worked on in MS Word. Cody Hamilton, PhD Edwards Lifesciences As always, I am speaking for myself and not necessarily for Edwards Lifesciences. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] connecting to DB2 database
Hi,
i am trying to connect to a DB2 server using the DBI library.
getData - function()
{
driver - dbDriver(DB2)
conn - dbConnect(driver,server,uname,pword)
data - dbSendquery(conn, select etc.)
}
When I run the function, i get the error
data - getData()
Error in do.call(as.character(drvName), list(...)) :
could not find function DB2
Can anyone help me here?
Thank you
Zava
This is not an offer (or solicitation of an offer) to buy/se...{{dropped}}
__
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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] names() after library(RDCOMClient) problem(?)
Hi Costas. On my Windows setup, I don't get this error message. What version of RDCOMClient are you using - i.e. the output of packageDescription(RDCOMClient) and also what else is loaded into the R session, i.e. sessionInfo() D. Vorlow Constantinos wrote: Hello, Try example(names) in R 2.5.0 after library(RDCOMClient) and you get example(names) names # print the names attribute of the islands data set names names(islands) Error in names(islands) : no applicable method for names Is this normal? Any way round it??? Best regards, Costas -- Costas Vorlow Research Economist Eurobank EFG Division of Research Forecasting --- ( tel: +30-210-3337273 (ext 17273) 7 fax: +30-210-3337687 P Think before you print. Disclaimer: This e-mail is confidential. If you are not the intended recipient, you should not copy it, re-transmit it, use it or disclose its contents, but should return it to the sender immediately and delete the copy from your system. EFG Eurobank Ergasias S.A. is not responsible for, nor endorses, any opinion, recommendation, conclusion, solicitation, offer or agreement or any information contained in this communication. EFG Eurobank Ergasias S.A. cannot accept any responsibility for the accuracy or completeness of this message as it has been transmitted over a public network. If you suspect that the message may have been intercepted or amended, please call the sender. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R programming question
Gary,
You are asked to
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
when posting.
You have not provided such code, and until you do I doubt we can help.
When I wrap your lines in a dummy function:
foo - function(){
cat(Enter value for lower Linf :\n)
L1-scan(n=1)
cat(Enter value for upper Linf :\n)
L2-scan(n=1)
cat(Enter Linf interval :\n)
int_L-scan(n=1)
cat(Enter value for lower K :\n)
K1-scan(n=1)
cat(Enter value for upper K :\n)
K2-scan(n=1)
cat(Enter K interval :\n)
int_K-scan(n=1)
list(L1,L2,int_L,K1,K2,int_K)
}
and run it as you claim
event - 1
if (event == 1 ) foo() else bar()
it prompts for all input and prints the expected result.
sessionInfo()
R version 2.5.0 (2007-04-23)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
Chuck
On Thu, 14 Jun 2007, Nelson, Gary (FWE) wrote:
Dear All.,
I've created R-code for which a user will be asked to choose between 2
analyses. I've written one function for each type of analysis. Within
each function, the users is prompted to enter information. An example
is:
cat(Enter value for lower Linf :\n)
L1-scan(n=1)
cat(Enter value for upper Linf :\n)
L2-scan(n=1)
cat(Enter Linf interval :\n)
int_L-scan(n=1)
cat(Enter value for lower K :\n)
K1-scan(n=1)
cat(Enter value for upper K :\n)
K2-scan(n=1)
cat(Enter K interval :\n)
int_K-scan(n=1)
I thought I could evaluate and run the appropriate function at the end
of the program by:
if(event==1) explore() else evaluate()
If I run the whole program and either explore() or evaluate() is run,
the first four prompted entries are skipped over. The console output
for event==1 is TRUE looks like:
if(event==1) explore() else evaluate()
Enter value for lower Linf :
1:
Read 0 items
Enter value for upper Linf :
1:
Read 0 items
Enter Linf interval :
1:
Read 0 items
Enter value for lower K :
1:
Read 0 items
Enter value for upper K :
1:
I then tried another way. I created
runcase-ifelse(event==1,explore,evaluate)
At the bottom of the program I used:
eval(call(x=runcase))
But I still get the same problem.
Any suggestions?
Thanks for your help
Gary A. Nelson, Ph.D
Massachusetts Division of Marine Fisheries
30 Emerson Avenue
Gloucester, MA 01930
Phone: (978) 282-0308 x114
Fax: (617) 727-3337
Email: [EMAIL PROTECTED]
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Charles C. Berry(858) 534-2098
Dept of Family/Preventive Medicine
E mailto:[EMAIL PROTECTED] UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
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Re: [R] Confusion with sapply
Thanks Gabor, this is cool!
Best,
-Tir
-Original Message-
From: Gabor Grothendieck [mailto:[EMAIL PROTECTED]
Sent: Wednesday, June 13, 2007 6:53 PM
To: Patnaik, Tirthankar [GWM-CIR]
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] Confusion with sapply
Try this. It takes a Date class date and in the first line
month.day.year converts unclass(x) to chron. In the last
line of the function we convert back to Date class. Its
already vectorized so sapply is unneeded:
library(chron)
f - function(x) with(month.day.year(unclass(x)), {
month - ifelse(month == 6 | month == 9, 3, month)
year - ifelse(month == 12, year + 1, year)
as.Date(paste(year, month, day, sep = -))
})
Running the last line gives:
# test
f(seq(Sys.Date(), length = 12, by = month))
[1] 2007-03-13 2007-07-13 2007-08-13 2007-03-13 2007-10-13
[6] 2007-11-13 2008-12-13 2008-01-13 2008-02-13 2008-03-13
[11] 2008-04-13 2008-05-13
On 6/13/07, Patnaik, Tirthankar [EMAIL PROTECTED] wrote:
Hi,
I have some confusion in applying a function over a column.
Here's my function. I just need to shift non-March
month-ends to March
month-ends. Initially I tried seq.dates, but one cannot give a
negative increment (decrement) here.
return(as.Date(seq.dates(format(xdate,%m/%d/%Y),by=months,len=4)[4
])
)
Hence this simple function:
mydate - as.Date(2006-01-01)
# Function to shift non-March company-reporting dates to March.
Set2March - function(xdate){
+ # Combines non-March months into March months:
+ # Dec2006 - Mar2007
+ # Mar2006 - Mar2006
+ # Jun2006 - Mar2006
+ # Sep2006 - Mar2006
+ # VERY Specific code.
+ Month - format(xdate,%m)
+ wDate - month.day.year(julian(xdate))
+ if (Month==12){
+ wDate$year - wDate$year + 1
+ wDate$month - 3
+ }else
+ if (Month==06){
+ wDate$month - 3
+ }else
+ if (Month==09){
+ wDate$month - 3
+ wDate$day - wDate$day + 1
+ }else warning (No Changes made to the month, since
month is not
one of (6,9,12))
+ cDate -
chron(paste(wDate$month,wDate$day,wDate$year,sep=/))
+ return(as.Date(as.yearmon(as.Date(cDate,%m/%d/%y)),frac=1))
+ }
Set2March(as.Date(2006-06-30))
[1] 2006-03-31
Set2March(mydate)
[1] 2006-01-31
Warning message:
No Changes made to the month, since month is not one of (6,9,12) in:
Set2March(mydate)
Works well when I use it on a single date. Then I try it on
a vector:
dc - seq(as.Date(2006-01-01),len=10, by=month) dc
[1] 2006-01-01 2006-02-01 2006-03-01 2006-04-01
2006-05-01
2006-06-01 2006-07-01 2006-08-01
[9] 2006-09-01 2006-10-01
sapply(as.vector(dc),Set2March)
Error in prettyNum(.Internal(format(x, trim, digits,
nsmall, width, 3,
:
unimplemented type 'character' in 'asLogical'
What am I missing here? Shouldn't the function work with the sapply
working on each entry?
TIA and best,
-Tir
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Re: [R] connecting to DB2 database
On Thu, 14 Jun 2007, Aydemir, Zava (FID) wrote:
i am trying to connect to a DB2 server using the DBI library.
The DBI *package* does not allow you to connect to anything by itself.
For that you need a driver package, currently available for MySQL, ORACLE
and SQLite (only, AFAIK).
There are ODBC drivers for DB2 (on several platforms) so perhaps
you could use RODBC: perhaps also RJDBC.
getData - function()
{
driver - dbDriver(DB2)
conn - dbConnect(driver,server,uname,pword)
data - dbSendquery(conn, select etc.)
}
When I run the function, i get the error
data - getData()
Error in do.call(as.character(drvName), list(...)) :
could not find function DB2
Can anyone help me here?
Thank you
Zava
This is not an offer (or solicitation of an offer) to buy/se...{{dropped}}
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--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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[R] clustalW
Hello, I try to make directly with R a multiple alignment querying CLUSTAL W, do you know how can I do this? Thanks Jérémy Mazet [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] besselK- complex number problem any help is welcome
Assistance, Im a student intrested in using R in my learning and research work in option pricing however i have a problem with besselK function In R. Would you assit me in computing the besselK of third kind of a complex number in R. Any code or suggestion will be highly appriceiated eg besselK(2,10) works well.. but besselK(2,10i) doesnt work !! im supprised it works in MATLAB but NOT in R. rgds ivivi mwaniki student school of mathematics nairobi university kenya - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] JGR, Java and Kubuntu 7.04 ...
R-ists
Yet again Java rears its ugly head.
I have Kubuntu 7.04 running the Kubuntu-repository version of R 2.4.1-1.
Yes it isn't the very latest version but this is not the issue here.
I want a Windows-like environment and everyone is talking about JGR.
I downloaded it and installed it along with rJava. Both compile and install
satisfactorily.
But when I come to run it:
library('JGR')
Loading required package: rJava
Error in dyn.load(x, as.logical(local), as.logical(now)) :
unable to load shared library
'/usr/local/lib/R/site-library/rJava/libs/rJava.so':
/usr/local/lib/R/site-library/rJava/libs/rJava.so: undefined symbol:
JNI_GetCreatedJavaVMs Error: .onLoad failed in 'loadNamespace' for 'rJava'
Error: package 'rJava' could not be loaded
When I first tried to run it without Java being installed, I got a message
saying that JDK wasn't installed but mentioned 1.4.2. The version of Java
actually installed as the latest from the Ubuntu repository is Sun 1.5.0.11.
I don't see the point in installing old versions of Java just for one
application because the language, or at least the writing, should be
backwards compatible.
In all aspects I have seen Kubuntu is a very impressive in checking
compatibility. Unfortunately this is frequently not the case with Java. I
steer clear of Java as much as possible.
Can anyone suggest what I should do? Use Windows perhaps? Run Windows in a
kvm virtual machine just to run R? Put my head in a bucket of cold water?
Is there an alternative IDE? Is there a later JGR somewhere that is not yet
on CRAN?
TIA
--
Best wishes
John
John Logsdon Try to make things as simple
Quantex Research Ltd, Manchester UK as possible but not simpler
[EMAIL PROTECTED] [EMAIL PROTECTED]
+44(0)161 445 4951/G:+44(0)7717758675 www.quantex-research.com
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Re: [R] Normal and Poisson tail area expectations in R
Ravi,
This looks simple to me.
km_G - function(lambda,k)
lambda*ppois(k-1,lambda,lower=FALSE) -
k*ppois(k,lambda,lower=FALSE)
Am I confused here?
Chuck
On Wed, 13 Jun 2007, Ravi Varadhan wrote:
More interesting is the Poisson convolution. I don't know if there is an
analytic solution to this. I looked at Jolley's Summation of Series and
Abramowitz and Stegun, but no help there. It seems that discrete FFT
technique should work. Does anyone know the answer?
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of kavindra malik
Sent: Wednesday, June 13, 2007 5:45 PM
To: Charles C. Berry
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] Normal and Poisson tail area expectations in R
Thank you very much. This solves the problem I was trying to solve. I am new
to R and am learning. A great lesson in the power of R...
Charles C. Berry [EMAIL PROTECTED] wrote: On Wed, 13 Jun 2007,
kavindra malik wrote:
I am interested in R functions for the following integrals / sums
(expressed best I can in text) -
Normal: G_u(k) = Integration_{Lower limit=k}^{Upper limit=infinity} [(u
-k) f(u) d(u)], where where u is N(0,1), and f(u) is the density function.
Poisson: G(lambda,k) = Sum_{Lower limit=k}^{Upper limit=infinity} [(x-k)
p(x, lambda)] where P(x,lambda) is the Poisson prob function with parameter
lambda.
The Normal expression is very commonly used in inventory management to
determine safety stocks (and its tabular values can be found in some
texts) - and I am also looking for Poisson and/or Gamma as that'd fit
the situation better.
I am wondering if there are standard functions in R that might allow me to
get these values, instead of needing to do the numerical integration, etc.
myself.
Not that I know of, but it is not difficult to do the integration:
k - 1.1 # for example
integrate(function(x) (x-k)*dnorm(x),lower=k,upper=Inf)
0.06861951 with absolute error 5.5e-07
see
?integrate
?qnorm
?qpois
?qgamma
Thank you very much.
-
Sucker-punch spam with award-winning protection.
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Charles C. Berry(858) 534-2098
Dept of Family/Preventive
Medicine
E mailto:[EMAIL PROTECTED] UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
-
[[alternative HTML version deleted]]
__
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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.
Charles C. Berry(858) 534-2098
Dept of Family/Preventive Medicine
E mailto:[EMAIL PROTECTED] UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
__
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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.
[R] random effects in logistic regression (lmer)-- identification question
Hello R users! I've been experimenting with lmer to estimate a mixed model with a dichotomous dependent variable. The goal is to fit a hierarchical model in which we compare the effect of individual and city-level variables. I've run up against a conceptual problem that I expect one of you can clear up for me. The question is about random effects in the context of a model fit with a binomial family and logit link. Unlike an ordinary linear regression, there is no way to estimate an individual level random error in the linear predictor z_i = a + b*x_i + e_i because the variance of e_i is unidentified. The standard deviation of the logistic is pi*s/3, and we assume s=1, so the standard deviation is assumed to be pi/3 (just a bit bigger than 1, if you are comparing against the Standard Normal). The logistic fitting process sets the variance of the error and the parameters a and b are rescaled accordingly. As a result, there is an implicit individual-level random effect within a logistic model. There is a good explanation of this issue in Tony Lancaster's textbook An Introduction to Modern Bayesian Econometrics. So we usually end up thinking about a linear predictor in a logistic regression like so z_i = a + b*x_i Random effects can be estimated for groups or clusters of observations. If j is a grouping variable, then we estimate z_i = a + b*x_i + u_j The variance component here is, as far as I understand, measured on the same scale as the logistic distribution's standard deviation. Currently, I'm working on a project in which there are observations collected in many cities, represented by a variable PLACE. We are comparing the effect of several variables on a response for each of the values of a RACE variable. RACE is dichotomized into White and Nonwhite by the people who collect the data. For Nonwhites only, we can estimate the effect of individual level predictors (x) on the output (y). fm1 - lmer( y ~ x + (1 | PLACE), data=dat, , family=binomial, subset= Race %in% c(Nonwhite)) The random effect in this model indicates the variance caused by a Nonwhite's location on the response variable. Random effects: Groups NameVariance Std.Dev. PLACE (Intercept) 0.047326 0.21754 Suppose I estimate models for the 2 races in a combined model like this: fm1 - lmer( y ~ -1 + Race / (x) + (-1 + Race | PLACE), data=dat, family=binomial) This gives fixed effects estimates that are pretty easy for nonstatisticians to understand. One can look and see the effect of a variable x on people of different races. But the random effect is a bit hard to understand. Since the Race variable is dichotomous, My aim was to see if the variance of the random effect is different for the 2 racial categories. Here are the estimates: Random effects: Groups Name Variance Std.Dev. Corr PLACE RACE_ALLWhite 0.0095429 0.097688 RACE_ALLNonwhite 0.1286597 0.358692 1.000 I can't quite grasp what the correlation means. I BELIEVE the variance values indicate that the experiences of whites are homogeneous across cities, because the variance is negligible for them, while the experiences of Nonwhites are much more city-dependent. What does it mean when the correlation is 1.0? The correlation takes on that value when there are no city-level variables in this model, so I GUESS that it means that all city-level variation is attributed to the random effect. What do you think? If i put in some city level predictors, then the estimates of the variance components change--they essentially disappear to the minimum values--and the correlation is not 1.0 anymore. Random effects: Groups Name Variance Std.Dev. Corr PLACE RACEWhite5e-102.2361e-05 RACENonwhite 5e-102.2361e-05 0.001 This indicates that, after adding in the city level variables, the unaccounted for city-level variation is very small. Correct? Now, back to the idea that there is always an implicit individual level random effect in a logistic regression. Is it meaningful to ask is that individual level random effect different for people of different races? If so, How can I estimate that? If e_i is the implicit random error, can I ask for another random effect for Nonwhites only, say u_iN, in a model like so: z_i = a + b*x_i + e_i + u_iN Suppose the unique respondent number is ID and we create a new variable NonwhiteID = 0 for Nonwhites = ID for Nonwhites Here's my idea about how to check to see if the individual level variance component for Nonwhites is different from the baseline of Whites by fitting this: fm1 - lmer( y ~ -1 + Race / (x) + (-1 + Race | PLACE) + (1 | NonwhiteID), data=dat, family=binomial) Here, again, I leave out the city-level variables. Random effects: Groups Name Variance Std.Dev. Corr NonwhiteID (Intercept) 5.e-10 2.2361e-05 PLACE RACEWhite 1.0575e-02 1.0283e-01 RACENonwhite1.2880e-01
Re: [R] Normal and Poisson tail area expectations in R
Perfect, Chuck. I got a closed-form solution after some algebraic labor,
but your solution is simple and elegant.
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
-Original Message-
From: Charles C. Berry [mailto:[EMAIL PROTECTED]
Sent: Thursday, June 14, 2007 1:36 PM
To: Ravi Varadhan
Cc: 'kavindra malik'; r-help@stat.math.ethz.ch
Subject: RE: [R] Normal and Poisson tail area expectations in R
Ravi,
This looks simple to me.
km_G - function(lambda,k)
lambda*ppois(k-1,lambda,lower=FALSE) -
k*ppois(k,lambda,lower=FALSE)
Am I confused here?
Chuck
On Wed, 13 Jun 2007, Ravi Varadhan wrote:
More interesting is the Poisson convolution. I don't know if there is an
analytic solution to this. I looked at Jolley's Summation of Series and
Abramowitz and Stegun, but no help there. It seems that discrete FFT
technique should work. Does anyone know the answer?
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of kavindra malik
Sent: Wednesday, June 13, 2007 5:45 PM
To: Charles C. Berry
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] Normal and Poisson tail area expectations in R
Thank you very much. This solves the problem I was trying to solve. I am
new
to R and am learning. A great lesson in the power of R...
Charles C. Berry [EMAIL PROTECTED] wrote: On Wed, 13 Jun 2007,
kavindra malik wrote:
I am interested in R functions for the following integrals / sums
(expressed best I can in text) -
Normal: G_u(k) = Integration_{Lower limit=k}^{Upper limit=infinity} [(u
-k) f(u) d(u)], where where u is N(0,1), and f(u) is the density function.
Poisson: G(lambda,k) = Sum_{Lower limit=k}^{Upper limit=infinity} [(x-k)
p(x, lambda)] where P(x,lambda) is the Poisson prob function with
parameter
lambda.
The Normal expression is very commonly used in inventory management to
determine safety stocks (and its tabular values can be found in some
texts) - and I am also looking for Poisson and/or Gamma as that'd fit
the situation better.
I am wondering if there are standard functions in R that might allow me
to
get these values, instead of needing to do the numerical integration, etc.
myself.
Not that I know of, but it is not difficult to do the integration:
k - 1.1 # for example
integrate(function(x) (x-k)*dnorm(x),lower=k,upper=Inf)
0.06861951 with absolute error 5.5e-07
see
?integrate
?qnorm
?qpois
?qgamma
Thank you very much.
-
Sucker-punch spam with award-winning protection.
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Charles C. Berry(858) 534-2098
Dept of Family/Preventive
Medicine
E mailto:[EMAIL PROTECTED] UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
-
[[alternative HTML version deleted]]
__
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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.
Charles C. Berry(858) 534-2098
Dept of Family/Preventive
Medicine
E mailto:[EMAIL PROTECTED] UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented,
[R] how to fit y=m*x
Hi There, I have a set of data (xi,yi).I want to fit them with the equation y=mx. note: in the above equation, there is no intercept. I don't know how to use common software such as R , matlab, sas, or spss to do this kind of regression. Does anyone know how to do this? I know it is easy to use least square method to do this by programming. But I want to find if there exists some common software which can do this. Thank you very much. Van __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to fit y=m*x
Hi, try : ln(y~x) From: [EMAIL PROTECTED] Reply-To: [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch Subject: [R] how to fit y=m*x Date: Thu, 14 Jun 2007 11:25:54 -0700 Hi There, I have a set of data (xi,yi).I want to fit them with the equation y=mx. note: in the above equation, there is no intercept. I don't know how to use common software such as R , matlab, sas, or spss to do this kind of regression. Does anyone know how to do this? I know it is easy to use least square method to do this by programming. But I want to find if there exists some common software which can do this. Thank you very much. Van __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. _ Découvrez le Blog heroic Fantaisy d'Eragon! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to fit y=m*x
Probably lm(y ~ x - 1) will be better. y~x doesn't remove the intercept, and ln() is a typo (I hope!) Andrew On Thu, Jun 14, 2007 at 06:33:02PM +, Ndoye Souleymane wrote: Hi, try : ln(y~x) From: [EMAIL PROTECTED] Reply-To: [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch Subject: [R] how to fit y=m*x Date: Thu, 14 Jun 2007 11:25:54 -0700 Hi There, I have a set of data (xi,yi).I want to fit them with the equation y=mx. note: in the above equation, there is no intercept. I don't know how to use common software such as R , matlab, sas, or spss to do this kind of regression. Does anyone know how to do this? I know it is easy to use least square method to do this by programming. But I want to find if there exists some common software which can do this. Thank you very much. Van __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. _ D?couvrez le Blog heroic Fantaisy d'Eragon! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Andrew Robinson Department of Mathematics and StatisticsTel: +61-3-8344-9763 University of Melbourne, VIC 3010 Australia Fax: +61-3-8344-4599 http://www.ms.unimelb.edu.au/~andrewpr http://blogs.mbs.edu/fishing-in-the-bay/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Annotating trellis graphics
On 6/13/07, Alan S Barnett [EMAIL PROTECTED] wrote:
I'm using xyplot to generate a trellis plot with each panel containing a
scatterplot and a best fit line. Is it possible to write the slope of
the best fit line in each panel?
Sure. The only question is, where (inside the panel) do you want it written?
Here are a couple of possibilities:
## writes the slope at a location that happens to be empty in both
## panels in this example
xyplot(len ~ dose | supp, ToothGrowth,
panel = function(x, y, ...) {
panel.xyplot(x, y, ...)
fm - lm(y ~ x)
panel.abline(reg = fm)
slope - round(coef(fm)[2], 3)
panel.text(1.5, 5, lab = slope)
})
## needs the user to click on a suitable position for each panel
library(grid)
xyplot(len ~ dose | supp, ToothGrowth,
panel = function(x, y, ...) {
panel.xyplot(x, y, ...)
fm - lm(y ~ x)
panel.abline(reg = fm)
slope - round(coef(fm)[2], 3)
message(Click on desired location)
panel.text(grid.locator(native), lab = slope)
})
-Deepayan
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] how to fit y=m*x
summary(lm(y ~ x - 1)) Use google (R linear regression without intercept) Read the posting guide. There. On 6/14/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Hi There, I have a set of data (xi,yi).I want to fit them with the equation y=mx. note: in the above equation, there is no intercept. I don't know how to use common software such as R , matlab, sas, or spss to do this kind of regression. Does anyone know how to do this? I know it is easy to use least square method to do this by programming. But I want to find if there exists some common software which can do this. Thank you very much. Van __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Christophe Pallier (http://www.pallier.org) [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Normal and Poisson tail area expectations in R
Inspired by Chuck's elegant solution to the Poisson tail area problem, here
is a simple solution to the normal tail area expectation that does not use
integrate().
Gu.k - function(k) {1/sqrt(2*pi) * exp(-k*k/2) - k * pnorm(k, lower=FALSE)}
k - 1:10
Gu.k(k)
[1] 8.331547e-02 8.490703e-03 3.821543e-04 7.145258e-06 5.346166e-08
1.563570e-10 1.760326e-13 7.550262e-17 1.224779e-20 7.474560e-25
sapply(k, function(k)integrate(function(x)
(x-k)*dnorm(x),lower=k,upper=Inf)$val)
[1] 8.331547e-02 8.490702e-03 3.821543e-04 7.145259e-06 5.346163e-08
1.563570e-10 1.760326e-13 7.550262e-17 1.224779e-20 7.474560e-25
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Ravi Varadhan
Sent: Thursday, June 14, 2007 2:08 PM
To: 'Charles C. Berry'
Cc: 'kavindra malik'; r-help@stat.math.ethz.ch
Subject: Re: [R] Normal and Poisson tail area expectations in R
Perfect, Chuck. I got a closed-form solution after some algebraic labor,
but your solution is simple and elegant.
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
-Original Message-
From: Charles C. Berry [mailto:[EMAIL PROTECTED]
Sent: Thursday, June 14, 2007 1:36 PM
To: Ravi Varadhan
Cc: 'kavindra malik'; r-help@stat.math.ethz.ch
Subject: RE: [R] Normal and Poisson tail area expectations in R
Ravi,
This looks simple to me.
km_G - function(lambda,k)
lambda*ppois(k-1,lambda,lower=FALSE) -
k*ppois(k,lambda,lower=FALSE)
Am I confused here?
Chuck
On Wed, 13 Jun 2007, Ravi Varadhan wrote:
More interesting is the Poisson convolution. I don't know if there is an
analytic solution to this. I looked at Jolley's Summation of Series and
Abramowitz and Stegun, but no help there. It seems that discrete FFT
technique should work. Does anyone know the answer?
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of kavindra malik
Sent: Wednesday, June 13, 2007 5:45 PM
To: Charles C. Berry
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] Normal and Poisson tail area expectations in R
Thank you very much. This solves the problem I was trying to solve. I am
new
to R and am learning. A great lesson in the power of R...
Charles C. Berry [EMAIL PROTECTED] wrote: On Wed, 13 Jun 2007,
kavindra malik wrote:
I am interested in R functions for the following integrals / sums
(expressed best I can in text) -
Normal: G_u(k) = Integration_{Lower limit=k}^{Upper limit=infinity} [(u
-k) f(u) d(u)], where where u is N(0,1), and f(u) is the density function.
Poisson: G(lambda,k) = Sum_{Lower limit=k}^{Upper limit=infinity} [(x-k)
p(x, lambda)] where P(x,lambda) is the Poisson prob function with
parameter
lambda.
The Normal expression is very commonly used in inventory management to
determine safety stocks (and its tabular values can be found in some
texts) - and I am also looking for Poisson and/or Gamma as that'd fit
the situation better.
I am wondering if there are standard functions in R that might allow me
to
get these values, instead of needing to do the numerical integration, etc.
myself.
Not that I know of, but it is not difficult to do the integration:
k - 1.1 # for example
integrate(function(x) (x-k)*dnorm(x),lower=k,upper=Inf)
0.06861951 with absolute error 5.5e-07
see
?integrate
?qnorm
?qpois
?qgamma
Thank you very much.
-
Sucker-punch spam with award-winning protection.
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[R] question about formula for lm
Dear all; Is there any way to make this to work?: .x-rnorm(50,10,3) .y-.x+rnorm(50,0,1) X-data.frame(.x,.y) colnames(X)-c(Xvar,Yvar) Ytext-Yvar lm(Ytext~Xvar,data=X) # doesn't run lm(Yvar~Xvar,data=X) # does run The main idea is to use Ytext as input in a function, so you just type Yvar and the model should fit Also, I need to avoid the expression X$Yvar~X$Xvar Thanks for any idea PM __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Course: 2-day Short R/S-Plus at JSM - Salt Lake City July - August 2007
Greetings! XLSolutions Will schedule a series of 2-day R/S-plus courses during JSM in Salt Lake City. Please email us your interest and dates that work best for you from July 26th - August 3rd. www.xlsolutions-corp.com/courselist.htm Payment due AFTER the class Email us for group discounts. Email Sue Turner: [EMAIL PROTECTED] Phone: 206-686-1578 Visit us: www.xlsolutions-corp.com/courselist.htm Please let us know if you and your colleagues are interested in these classes to take advantage of group discount. Register now to secure your seat! Cheers, Elvis Miller, PhD Manager Training. XLSolutions Corporation 206 686 1578 www.xlsolutions-corp.com __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] question about formula for lm
Why not using: lm(X[[Ytext]]~Xvar,data=X) ThPe Pedro Mardones wrote: Dear all; Is there any way to make this to work?: .x-rnorm(50,10,3) .y-.x+rnorm(50,0,1) X-data.frame(.x,.y) colnames(X)-c(Xvar,Yvar) Ytext-Yvar lm(Ytext~Xvar,data=X) # doesn't run lm(Yvar~Xvar,data=X) # does run The main idea is to use Ytext as input in a function, so you just type Yvar and the model should fit Also, I need to avoid the expression X$Yvar~X$Xvar Thanks for any idea PM __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
