[R] R: package "plotrix"

I got plotrix running after updating R. My problem is now solved. Thank you. Maura -Messaggio originale- Da: Jim Lemon [mailto:j...@bitwrit.com.au] Inviato: lun 19/07/2010 10.58 A: mau...@alice.it Cc: r-h...@stat.math.ethz.ch Oggetto: Re: package "plotrix" On 07/19/2010 01:59 AM, mau...@

[R] R: package "plotrix"

-Messaggio originale- Da: Uwe Ligges [mailto:lig...@statistik.tu-dortmund.de] Inviato: dom 18/07/2010 18.58 A: mau...@alice.it Cc: j...@bitwrit.com.au; r-h...@stat.math.ethz.ch Oggetto: Re: [R] package "plotrix" On 18.07.2010 17:59, mau...@alice.it wrote: > I installed package plotrix

[R] package "plotrix"

I installed package plotrix because reading its vignette it looks like it can help me solve a "legend" problem. The package instaleed correctly on my Mac OS/X 10.5.8 But I cannot reproduce the examples centered on function "lgendg". > library(plotrix) > plot(0.5,0.5,xlim=c(0,1),ylim=c(0,1),type="n

[R] removing a non empty directory

I'd like to remove automatically a directory that may be non empty. I tried: > file.remove(NewDir, recursive=TRUE) [1] FALSE Warning message: In file.remove(NewDir, recursive = TRUE) : cannot remove file 'Prostate_Validated_mirWalk', reason 'Directory not empty' Is there another command to remov

[R] R: selecting and excluding files through a pattern

Actually this pattern will select the files whose name contains "csv". Whereas I'd like to exscude them. Maura -Messaggio originale- Da: Jorge Ivan Velez [mailto:jorgeivanve...@gmail.com] Inviato: gio 10/06/2010 17.30 A: mau...@alice.it Cc: r-h...@stat.math.ethz.ch Oggetto: Re: [R] select

[R] selecting and excluding files through a pattern

I have the following files list: > list.files() [1] "Prostate-Cancer_cvs_Dir" [2] "Prostate_Cancer-miRNAs&Genes.Pathway.xml" [3] "Prostate_Cancer_Pathways-miRNAs-GeneTargets-Dir" [4] "Prostate_Cancer_Pathways-miRNAs-GeneTargets-Dir.zip" [5] "Prostate

[R] how can I control the x-axis tick labels

I am trying to generate a plot whose x-axis values are the following: data_out[,1] [1] 1979 1958 1937 1916 1895 1874 1853 1832 1811 1790 1769 1748 1727 1706 1685 1664 1643 1622 1601 1580 1559 [22] 1538 1517 1496 1475 1454 1433 1412 1391 1370 1349 1328 1307 1286 1265 1244 1223 1202 1181 1160

[R] after updating biomaRt cannot connect any more

I recently updated R 2.10.1 Patched (2010-02-20 r51163) This morning I reinstalled biomaRt using biocLite. Now I can no more connect to biomaRt and even the following instruction is hanging for a while until the same error message pops up. > listMarts() Error in value[[3L]](cond) : Request to

[R] R: why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?

-Messaggio originale- Da: Steve Lianoglou [mailto:mailinglist.honey...@gmail.com] Inviato: ven 28/05/2010 17.06 A: mau...@alice.it Cc: r-h...@stat.math.ethz.ch Oggetto: Re: [R] why biomaRt cannot extract 3UTR sequences for 1941 ENSGx ? Hi, Two things: 1. You mistakenly posted this

[R] why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?

I executed the following lines several times from a script as well as pasting them in an R shell. Systematically biomaRt is failing. The problem is to extract the 3UTR sequences corresponding to a vector containing 1941 Ensembl Transcript numbers (some are duplicated ... is this s problem ?) Ple

[R] PROBLEM SOLVED: how to extract the 1st field from a vector of strings

-Messaggio originale- Da: mau...@alice.it Inviato: gio 27/05/2010 16.37 A: r-h...@stat.math.ethz.ch Oggetto: how to extract the 1st field from a vector of strings I have the following vector of strings (shown only the first 3 elements) > desc[1:3] [1] "hsa-let-7a MIMAT062 Homo sapi

[R] how to extract the 1st field from a vector of strings

I have the following vector of strings (shown only the first 3 elements) > desc[1:3] [1] "hsa-let-7a MIMAT062 Homo sapiens let-7a" [2] "hsa-let-7a* MIMAT0004481 Homo sapiens let-7a*" [3] "hsa-let-7a-2* MIMAT0010195 Homo sapiens let-7a-2*" > is.vector(desc) [1] TRUE > A <- unlist(strs

[R] how to avoid a subset of a matrix to become a column vector

I am assigning subset of a matrix A [n,3] where n>1 to a temporary matrix TMP I do not know how many rows of A will be assigned to TMP because this is established by a run-time test. I expect TMP to be a matrix [m,3], m >=1 But when 1 row only is transferred from A to TMP then TMP becomes [3,1]

[R] R: R: website address for the pseuso-XLS files

Through clicking on the xls file oocalc (OpenOffice spreadsheet module) is automatically launched. But in my case it cannot load it correctly regardless of my choices (separator, etc..). Maybe I should switch to another Linux distribution. Thank you very much. Maura -Messaggio originale-

[R] R: website address for the pseuso-XLS files

Thank you. May I know the version of your OO and the operating system it runs on ? I use Linux/SuSE 11.1 running OO 3.0.0.9-1.9 Maura -Messaggio originale- Da: ted.hard...@manchester.ac.uk [mailto:ted.hard...@manchester.ac.uk] Inviato: mar 25/05/2010 15.22 A: r-h...@stat.math.ethz.ch Cc:

[R] website address for the pseuso-XLS files

http://gigamail.rossoalice.alice.it/messages/readMessageFrameset.aspx?DeliveryID=ba40cf18-29db-4404-a3ce-af26f760ecf9 Please, paste the website address above shown in your web browser address field. Make sure the whole string is pasted with no space or any other character. Telecom couldn't generat

[R] Follow-up: how can I read a non-standard XLS file

I am uploading 2 XLS-similar files to server www.alice.it. I expect many people in this mailing list won't understand the instructions for grabbing the files because of the different language (sorry I do not have control on that. Telecom has). But it's really very simple. The message you receive w

[R] how can I read a non-standard XLS file

I have attached a file downloaded from database mirWalk. Apparently it is in XLS format (this is the extension of the downloaded file). However, I cannot open it with OpenOffife spreadsheet program and Excel itself cannot separate the columns as it does when a true XLS file is loaded. I tried to

[R] looking for Variable selections models, techniques, methods

We still have a long way to go with the data we were given by some drug discovery scientists. The problem is to select the few variables (Collective Variables), from a set of variables sampled during a Molecular Dynamics simulation, which exhibit a consistent and coherent relationship with the

[R] errors returned upon trying to update JGR

I have upgraded R and am currently running the following version: R version 2.10.1 Patched (2010-02-20 r51163) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 The characteristics of my system are the following: OS: Linux 2.6.27.29-0.1-default x86_64 Current user

[R] how to remove one row at a time from a matrix keeping its nrow consistent

After some headache with debugging my script, I finally isolated the problem taht I am going to illustrate in the following example. I expected matrix nrow to decrease consistently till 1. Instead, when the matrix is left with one row only, its nrow jumps to 2 because the matrix gets transposed.

[R] WMTSA "wavCWTPeaks" : Error in if (time.start < times.range[1]) time.start <- times.range[1]

I have attached the signal that causes the error message in this email subject. Only columns 1 and 3 have to be considered. It is the work trajectory of a molecule migrating between two equilibrium conformations. The curve has 2 peaks, as shown in its plot. But I keep missing the 2nd one. Here is

[R] How to update JGR

I recently updated R on Linus/SuSE 11.1 I complained because no on-line help was available from JGR after R update. I was told to update JGR as well. How can I do that ? I installed JGR on SuSE three times in the past with different R versions.Every time it's been a nightmare. I am afraid to have

[R] R: Generative Topographic Map

I am running GTM on the same datda space points but changing the number of latent space points, the number of basis functions and parameter sigma. I found a combination of such parameters that works fine. On the other hand on page 7 of the paper "The Generative Topographic Mapping" by Swensen, Bi

[R] R: Generative Topographic Map

Thank you. I figured that out myself last night. I always forget that read.table does not actually read data into a matrix. GTM MatLab toolbox comes with a nice guide to use the package which may as well become an R vignette. Anyway, I got the singular matrix warnings myself and do not know whe

[R] Generative Topographic Map

I tried to use R version of package I noticed the original MatLab Pckage is much better documented. I had a look at the R demo code "gtm_demo" and found that variable Y is used in advanced of being created: I wrote my own few lines as follows: inDir <- "C:/Documents and Settings/Monville/Alani

[R] Is there any R package that can find the maxima of a 1-D time series

Is there any R package that can help me with digging out the maxima of a 1-D trajectory ? I have 975 1-D curves. They are only known as time series. That is a set of points ordered with respect to time. Some curves exhibit one only peak. Others have two peaks of different height. We wish to f

[R] R: R help unavailable

Actually the problem exists only if I use JGR. If I launch R from a terminal window then the text on-line help works. It used to work with JGR too but with R version 2.9.0. Now, JGR shows the new R version is running but the on-line help is no more available from JGR. Perhaps JGR implementors wil

[R] R help unavailable

I have recently replaced R-2.9.0 with R-2.10.1 Patched. Apparently the installation completed successfully but right now I realized that the on-line help does not work any more. When I type "?" a message pops up warning that "Help will not be available. Path not found" ... regardless of the R-co

[R] Is package "dr" appropriate for reducing the dimensionality of molecules conformational space ?

I anticipate lacking of prior experience with dimensionality reduction problems. Some scientists concerned with drug discovery performed several steered Molecular Dynamics simulations of the alanine-dipeptide molecule dragged by a radial force from an equilibrium conformation to another differen

[R] how to pass external parameters to an R script

How, if possible, can I run an R script, from command line, passing external parameters just like I can run a C main program passing parameters: # Cprog p1 p2 p3 Cprog can access its arguments (p1,p2,p3) through the built-in structures "argv" and "argc". Since R is built on C language I would

[R] R-patched-2.10.1-50.1.x86_64 installlation error

here is the message I get upon trying to upgrade R from the provided RPM package for SuSE 11.1 YaST2 conflicts list - generated 2010-02-15 14:00:50 nothing provides libreadline.so.6()(64bit) needed by R-patched-2.10.1-50.1.x86_64 [ ] do not install R-patched-2.10.1-50.1.x86_64

[R] (no subject)

here is the message I get upon trying to upgrade R from the provided RPM package for SuSE 11.1 (http://cran.r-project.org): YaST2 conflicts list - generated 2010-02-15 14:00:50 nothing provides libreadline.so.6()(64bit) needed by R-patched-2.10.1-50.1.x86_64 [ ] do not install R-

[R] installation of package 'e1071' had non-zero exit status

I tried twice to install package "e1071"as it provides the Hamming distance. The installation failed twice. I am running R version 2.9.0 (2009-04-17). Any suggestion is welcome. Thank you, Maura tutti i telefonini TIM! [[alternative HTML version deleted]]

[R] R: Dimensional reduction package

Thank you. Sorry. My question is rather ambiguous. Imeant to aske for Dimensionality Reduction methods and/or Intrinsic Dimensionality Estimation methods that can deal with non-linear data. That is, data that do not lie on a hyper-plane. ISOMAP is one of such methods. LLE, AutoEncoder, GTM Kerne

[R] Dimensional reduction package

Is there any R package which implements non-linear dimensionality reduction (LLE, ISOMAP, GTM, and so on) and/or intrinsic dimensionality estimation ? Thank you, Maura tutti i telefonini TIM! [[alternative HTML version deleted]] __ R-help@r

[R] finding files whose name does NOT contain a given character

Unluckily I dela with miRNA files whose name may contain the character "*". Because of the special meaning of "*" I have to remove it. I found out how to make list.files() extract only those file names which contain a "*" Namely: # list.files(pattern="\\*") Now I have to process all files whose

[R] Updating R on Linux

I know my question has been asked many times. Please, forgive me for asking it once more. It's time to update R version. I run R on Windows, Linux, and Mac OS/X. I think I remember on Windows R comes with the un-installer. So I uninstall it first and then I install the latest version. On Mac OS

[R] R: can R scripts detect signals sent by the task scheduler ?

I have just updated R version to 2.10 for Windows. I cannot find package "fork" which seems to include the exception handling functions. The list that pops up when I select Install Package does not contain any fork package (even spelt with capital letters). Where am I supposed to get it from ?

[R] can R scripts detect signals sent by the task scheduler ?

In general, is it possible to run R scripts through cron jobs ? Is it possible to make the script detect the system interrupt, save its current status and then exit so that next time it is rescheduled it can pick up from where it left ? Examples, if any, are more then welcome. Thank you in adv

[R] MatLab SimBiology

Is there any R package that implements the same capability of MatLab toolbox called SimBiology ? We are expecially interested in protein-protein interactions and network analysis. As far as I know SimBiology implements a system of ODEs reflecting the kinetic chemical reactions. We would be more

[R] NULL elements in lists ... a nightmare

I can define a list containing NULL elements: > myList <- list("aaa",NULL,TRUE) > names(myList) <- c("first","second","third") > myList $first [1] "aaa" $second NULL $third [1] TRUE > length(myList) [1] 3 However, if I assign NULL to any of the list element then such element is deleted from the

[R] R: How can I avoid a for-loop through sapply or lapply ?

Thank you very much. It works fine. Maura -Messaggio originale- Da: Steve Lianoglou [mailto:mailinglist.honey...@gmail.com] Inviato: mar 29/09/2009 18.08 A: mau...@alice.it Cc: r-h...@stat.math.ethz.ch Oggetto: Re: [R] How can I avoid a for-loop through sapply or lapply ? Hi, On Sep 29,

[R] How can I avoid a for-loop through sapply or lapply ?

Through converting a miRNAs file from FASTA to character format I get a vector which looks like the following: > nml [1] "hsa-let-7a MIMAT062 Homo sapiens let-7a" [2] "hsa-let-7b MIMAT063 Homo sapiens let-7b" [3] "hsa-let-7c MIMAT064 Homo sapiens let-7c"

[R] Textplot question

I have a long list of flags with relative values to print out. If I draw it all on a panel of a (2x2) plot it gets chopped at the bottom. I wonder whether it is possible to plot it on two columns. Something like: Flag1 Value1Flag4 Value4 Flag2 Vauel2Flag5 Value5 Flag3 Value3

[R] R: upgraging R from 2.9.0 to 2.9.1

Great ! Then I can wait a couple more days. Anyway, I do not need or want more than one R version at a time. So my question is: How can I avoid having coexisting R versions when I install a new one ? Thank you, Maura -Messaggio originale- Da: Robert Baer [mailto:rb...@atsu.edu] Inviato:

[R] upgraging R from 2.9.0 to 2.9.1

I am still running 2.9.0 and came across a package that was built with 2.9.1. I got a warning upon loading the package. I tried to launch a function from such a package. It seems to hang up. I can't believe it takes forever. I am resolved to upgrade my R version to the newest one. But on a Window

[R] Help with identify() points on a PAM clusplot

I created a clusplot from PAM results. It represents how signals have been classified. Signals are identified by a numerical label. My trial distance matrix is made up of 10 rows, one for eacjh signal. I assigned the signals iidentifiers as rownames of the distance matrix. rwn [1] "1104" "1332"

[R] help with functions "spec" and "specprop"

I deal with mono-channel breathing signals sampled at 30[Hz] which are non-linear and non-stationary. My goal is to classify the signals according to common breathing patterns Trend remotion is necessary for cluster analysis but quite challenging. In fact, quasi-periodic patterns that span a numb

[R] R: how to get R interpreter to remember constant values without using any memory location

Thank you for all your suggestiona. I tried to write a self-contained example which turned oiut to confuse people's miind. I realized also the formulation of my question was unclear. Sorry for that. What I had in mind was something similar to Fortran Parameter declaration. I spent some time dea

[R] how to get R interpreter to remember constant values without using any memory location

Maybe I expect too much from a non compiled language. Anyway, I wonder whether it is possible in R to set constant values without using any memory location that would take useless space bacause such values are not going to be changed along the program. It's just a way to assign a mnemnic name to

[R] R: how import Excel data into R?

I recently downloaded an XLS file from a web site into a data.frame. You may want to try out the following: > ?install.packages(gdata) > library(gdata) > ?read.xls Maura -Messaggio originale- Da: r-help-boun...@r-project.org per conto di Inchallah Yarab Inviato: mer 05/08/2009 17.56 A: r

[R] How to catch an error using try

Sometimes the following function call causes a database exception: > gene.seq <- getSequence (id=gene.map[,"ensembl_transcript_id"], > type="ensembl_transcript_id", + seqType="3utr", mart=hmart) I understand the above function must be called by try to capture the ev

[R] R: how to avoid a script from hanging up

Thank you very much. The instructions you suggested allow the script itself to decide whether to exit spontaneously. What I am still missing is how to prevent the script from restarting from scratch. I'll try to explain my problem a little bit better. Please, assume I have 3 huge data.frames cal

[R] how to avoid a script from hanging up

I am submitting this problem to the R forum , rather than the Bioconductor forum, because its nature is closer to programming style than any Bioinformatic contents. I have implemented an R script to extracts many strings through querying 3 Bioinformatic databases in the same loop cycle. Ideal

[R] How to stop an R script when running JGR on a Linux/SuSE system

When I need to stop a running R script on Windows or Mac I just use the key which kills the current script and returns the control to R interpreter. But when I run R from JGR the is useless as well as the other available keyboard keys. Just recently not even clicking on the STOP-symbol (a big

[R] Looking for example of usage of function unz

I would greatly appreciate some example of correct usage of function unz. I have to download and uncompress the following web compressef file: ftp://ftp.sanger.ac.uk/pub/mirbase/targets/v5/arch.v5.txt.homo_sapiens.zip I tried the following command that does not work: Targets.rec <- readLines(zz

[R] R: R: Is there a way to extract some fields data fromHTML pages through any R function ?

It works if the web file adress is of the type: "http://";. It does not work if the web file adress is of the type: "'ftp://";. > outFile <- > read.xls("ftp://ftp.sanger.ac.uk/pub/mirbase/sequences/CURRENT/miRNA.xls";) Error in xls2csv(xls, sheet, verbose = verbose, ..., perl = perl) : Unable

[R] EOF revisited

I learnt from this forum to test for EOF reached with fiunction readLines as follows: con <- file("MyFle.txt","r") repeat { line <- readLines(con,n=1) if (length(line) == 0) break } It works fine if I read one line at a time. Since now I have a huge file so that it would take forever

[R] How to prpare the input data to writeFASTA ? Examples of CharacterToFASTArecords ...

I realize function write FASTA expects a list with two items, respectively, description and sequence. However, just passing a list won't work (please, see code at the bottom of this message) I saw there is the helper function CharacterToFASTArecords(x) that presumably generates the right input

[R] how to use writeFASTA in modality "append"

It looks like Biostrings function "writeFASTA" overwrites the output file at each run. It seems it does not support the "append" parameter. I have to generate one big file gathering a miRNA identifier and relative sequence followd by a variable number of dara records pertaining such a miRNA

[R] How can I test for End-Of-FIle

I have a long text file with uneven record length and variable structure. Therefore I have to read it line-by-line. I found out I can open a connection to the file and read in one line at a time. Something like: con <- file("MyFle.txt","r") while (End-Of-File) { line <- readLines(con,n=1)

[R] R: R: Is there a way to extract some fields data from HTML pages through any R function ?

It helps. But it is overly sophisticated. I have already downloaded and used the Excel file containing the validated stuff. Since there are R commands to download gzip as well as FASTA files, I wonder whether it is possible to automatically download the Excel file from http://mirecords.umn.edu

[R] R: Is there a way to extract some fields data from HTML pages through any R function ?

I tried to apply the scheme you suggested to open the web page on "http://mirecords.umn.edu/miRecords/index.php"; and got the followiing: > result <- postForm("http://mirecords.umn.edu/miRecords/index.php";, + searchType="miRNA", species="Homo sapiens", + searchBox="hsa-let-7a", submitButton="Se

[R] R: Is there a way to extract some fields data from HTML pages through any R function ?

Thank you so much. I emailed the people who are in charge of maintaining miRecords and related info. I asked them for an available data transfer protocol like ftp or similar to avoid manually downloading haindreds of sequences from their web site. I got no feedback at all. Thanks again, Maura

[R] Is there a way to extract some fields data from HTML pages through any R function ?

I deal with a huge amount of Biology data stored in different databases. The databases belongig to Bioconductor organization can be accessed through Bioconductor packages. Unluckily some useful data is stored in databases like, for instance, miRDB, miRecords, etc ... which offer just an interacti

[R] is there a way to extract fata from web pages through some R function ?

I deal with a huge amount of Biology data stored in different databases. The databases belongig to Bioconductor organization can be accessed through Bioconductor packages. Unluckily some useful data is stored in databases like, for instance, miRDB, miRecords, etc ... which offer just an interacti

[R] how to call Perl from R

I read some archived posts about calling R from Perl scripts. There seems to be an R package creating the necessaary interface. I'd like to do the opposite. That is to call Perl from an R script. I wonder whether this is possible at all ??? What about Bioperl which is a Perl variation built to d

[R] R: Cannot install pakages from Bioconductor besides the default installation

tallPkgGroups' > 3: In safeSource() : Redefining 'biocinstallRepos' >> > biocLite("biomaRt") > Running biocinstall version 2.4.11 with R version 2.9.0 > Your version of R requires version 2.4 of Bioconductor. > Warning in install.packages(pkgs = pkgs, repos

[R] question about package biomaRt

Can biomaRt connect to data base "http://mirecords.umn.edu"; or a branch of it ... for instance the validated miRNAs list ..? Thank you very much. Maura tutti i telefonini TIM! [[alternative HTML version deleted]] __ R-help@r-project.org m

[R] Cannot install pakages from Bioconductor besides the default installation

> > biocLite("biomaRt") Running biocinstall version 2.4.11 with R version 2.9.0 Your version of R requires version 2.4 of Bioconductor. Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : argument 'lib' is missing: using '/ho

[R] help with installation of local gzip-ped packages

I was suggested to install two tar-red and gzip-ped packages that are not part of CRAN or BioConductors yet. I read the R manual about Administration and could only find a good description of how to install packages not canonically included in CRAN repository, on UNIX systems. I work on Linu

[R] R: JGR installation errors

install "rJava" in advance of JGR. > > Thank you very much, > Maura > > > As root: > > linux-326k:/home/mauede # sudo R CMD javareconf > Java interpreter : /usr/bin/java > Java version : 1.6.0_0 > Java home path : /usr/lib64/jvm/java-1.6.0-openjdk-1

[R] JGR installation errors

same error if I try to install "rJava" in advance of JGR. Thank you very much, Maura As root: linux-326k:/home/mauede # sudo R CMD javareconf Java interpreter : /usr/bin/java Java version : 1.6.0_0 Java home path : /usr/lib64/jvm/java-1.6.0-openjdk-1.6.0/jre Java compiler: /u

[R] is there any R function to read xls (Excel) format files ?

Sorry for this trivial question. I have just installed R on SuSE/Linux and cannot cope with the character terminal. I am going to install JGR that will make my life easier at searching for existing R functions/packages. In the meantime (higher-priority things to do) I would appreciate your answer

[R] shall I uninstall an old R installation in advance of installing a new one ?

I have resumed developing R code on SuSE/Linux version 11.1 I installed the latest 64-bit R version available for my platform. Accidentally I figured out I still had an old R installation that, surprisingly, was not wiped out by the new SuSE installation from scratch. I suspect the new and old R

[R] R: R and miRecords

Thank you so much. Sorry for my basic questions that must read very silly for Biologists. As a physicist I was supposed to help Biology research with physics facets (free energy minimization, Molecular Dynamics, and so on). Unluckily, the student in charge of providing the test data (miRNA seque

[R] R and miRecords

I wonder whether R provides an interface to access miRecords data. Particularly, I am looking for extracting humans miRNA and target genes sequences. All such information is stored in there in a set of structured web site pages (http://mirecords.umn.edu/miRecords) I would greatly appreciate any

[R] help with package "simsalabim"

I have attached a text file representing the centralized amplitude of a signal, sampled at 30Hz, whose length N = 6922 My goal is to remove the trend. I am using package "simsalabim". I ran command decompSSA with L = length(Amps)/5 The reason is that I have SSA/MTM toolkit running in Mac/OS.

[R] searchpaths

May I use "searchpaths()" with arguments partially matching file names that are found in different directories ? My question is whether this is th R function equivalent of Linux "find" or Windows "search". Both O.S. calls are given a starting point so that they search all diectories from then d

[R] ACF roots

I have a number of signals whose ACF may or may not cross the zero line. Whether roots exist or not is a piece of useful information for me. Likewise, if any root exists, I'd like to know its lag value. Unluckily R function ACF does not seem to provide such information. I wonder whether someone c

[R] R: R: Harmonic Analysis

Actually I do use DWT for features extraction which is aimed at clustering signals bearing statistically comparable patterns. Trend can easily fool any clustering function. This is why detrending is the number 1 step in the whole procedure. Sparing the quasi-harmonic components that bear most of

[R] R: Harmonic Analysis

Well, the time series I am dealing with are non-linear and not-stationary. Maura -Messaggio originale- Da: r-help-boun...@r-project.org per conto di stephen sefick Inviato: mer 27/05/2009 14.58 A: r-h...@stat.math.ethz.ch Oggetto: Re: [R] Harmonic Analysis why will a fourier transform

[R] Harmonic Analysis

I am looking for a package to perform harmonic analysis with the goal of estimating the period of the dominant high frequency component in some mono-channel signals. I guess there are presumably a number of CRAN packages allowing for such analysis. However, my search with keywords was not succe

[R] how to implement a circular buffer with R

Some wavelet analysis experts have implemented periodic boundary conditions for signals. I need to implement a circular buffer. Something like: "12345abcdefgh12345abcdefgh" so that at each step the riightmost element is moved to the leftmost index and everything else is properly shifted: "h1

[R] stationarity tests

How can I make sure the residual signal, after subtracting the trend extracted through some technique, is actually trend-free ? I would greatly appreciate any suggestion about some Stationarity tests. I'd like to make sure I have got the difference between ACF and PACF right. In the following

[R] Spearman rho

I read that Spearman rho can be used to detect the presence of trend in a time series. However, I cannot figure out how to use such a test to thsi purpose. First of all which one of the available functions and how to pass my mono-channel time series which contains both positive and negative v

[R] R: corrupted smoothing kernel ?

I have just installed R2.9.0 on my Windows XP system. I have followed the same installation procedure I have been using for over a year. That is installation from the "exe" file. "kernel" belongs to package "stats"which is (I think) installed by default. I loaded it but did not use the command:

[R] corrupted smoothing kernel ?

I am trying to use the "kernel" function. To understand how it works I tried out some of the examples. None of them works as shown in the following: > kernel("daniell", 50) # Error in kernel("daniell", 50) : unused argument(s) (50) > kernel("daniell", 10) # Error in kernel("daniell", 10) :

[R] Gaussian local detrending and smoothing within a moving time window

Is there an R function implementing a Gaussian local detrending and smoothing within a moving time window ? I used ksmooth over the entire time series. Plotting the data before and after this operation shows that the signal is actuslly smoother but the tend is still there. I wonder whether ksmoo

[R] wrong if-else syntax

What is wrong in the following nested if-else statements: if (Condition_1) { # begin IF_1 statement_1 statement_2 statement_3 if (Condition_2) { # begin IF_2 a<- a +1 } # end IF_

[R] what happens if a function removes an external (global) variable ?

My program consists of a number of functions and a main script. It loops through many time series analyzing one at a time. I have declared a number of arrays and scalar variables in the main script namespace (using C++ terminology) because those data structures ar shared by many functions. let

[R] eager to learn how to use "sapply", "lapply", ...

After a year my R programming style is still very "C like". I am still writing a lot of "for loops" and finding it difficult to recognize where, in place of loops, I could just do the same with one line of code, using "sapply", "lapply", or the like. On-line examples for such high level function d

[R] R: constrained optimization

Thank you. Unluckily what makes the problem only apparenttly simple (for me) is that we have not differentiable functions and the parameter space is not continuous ... which reduces dramatically the number of choices. I would be grateful to chat with anyone who has tackled a similar problem. Ma

[R] constrained optimization

Is there any R package addressing problems of constrained optimization ? I have the following "apparently" simple problem: Given a set V with fixed cardinality:nv Given a set S whose cardinality is a parameter:nHat Let the cardinality of the intersection S.and.V be:

[R] R: R: R: how to split and handle a big R program into multiple files

Submitting to CRAN is one of my goals. What we are implementing is not done yet either in R or MatLab. There exists some Fortran applications of the algorithms we are implementing for general use. it'll still take me some time before I get there. Maura -Messaggio originale- Da: Duncan

[R] R: R: how to split and handle a big R program into multiple files

I read the on-line documentation. What I am still missing is how I run my program after encapsulating it in a package. I will have to load the package ... just guessing Thank you maura -Messaggio originale- Da: baptiste auguie [mailto:ba...@exeter.ac.uk] Inviato: gio 23/04/2009 12.17 A:

[R] R: how to split and handle a big R program into multiple files

It looks like I can store each function in a different file and have "main file" containing the "include-like" directiives and the main instructions. Something like: source("Program_Global_Constants.R") source("Program_Global_Variables.R") source("Program_Fun1.R") source("Program_Fun2.R") source

[R] R: how to split and handle a big R program into multiple files

Is that an R command ? I browswd for the on-line hlp about such a command but could not find it. Thank you. maura -Messaggio originale- Da: baptiste auguie [mailto:ba...@exeter.ac.uk] Inviato: gio 23/04/2009 11.48 A: mau...@alice.it Cc: r-help Help Oggetto: Re: [R] how to split and handl

[R] how to split and handle a big R program into multiple files

I am working on a program totally written in R which is now getting bigger and bigger so that editling the only file that contains all the functions is becoming more and more unmanageable. I wonder whether it is possible to spread the R code, making up the same program, in a number of smaller fi

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