gmane.comp.lang.r.general

Re: Spatstat - K2 index

Rolf Turner — 2008-12-02T01:52:46

On 2/12/2008, at 4:30 AM, Gough Lauren wrote: In the first instance questions about a contributed package should be directed to the maintainer(s) of that package. It is not clear to me what your question is. Can't get ***what*** function to run? The file E5374-example.R sources ``Funktionen/K2.R'' to provide the function K2, which is called upon later in this script. Have you obtained the file K2.R? If not, that is your first problem. cheers, Rolf Turner ###################################################################### Attention:\ This e-mail message is privileged and confid...{{dropped:9}} ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Re: optimization problem

Hans W. Borchers — 2008-12-02T01:21:58

Why not use one of the global optimizers in R, for instance 'DEoptim', and then apply optim() to find the last six decimals? I am relatively sure that the Differential Evolution operator has a better chance to come near a global optimum than a loop over optim(), though 'DEoptim' may be a bit slow (only for quite large numbers of parameters). Regards, Hans Werner Mike Prager wrote:

Re: [BioC] BioC 2.3 standard installation

Hervé Pagès — 2008-12-02T01:06:10

[back to the lists] So it seems that r-base-dev forgets to depend on libatlas-base-dev You can fix this by installing libatlas-base-dev manually: apt-get install libatlas-base-dev This should solve the compilation/linking problem with KernSmooth, preprocessCore and any other package that needs to be linked against the BLAS/ATLAS/LAPACK libraries on Ubuntu 8.10 (Intrepid Ibex). Note that this problem only affects people that get their R-2.8 from r-base + r-base-dev Cheers, H. Tiandao Li wrote:

Re: Variables inside a for

David Winsemius — 2008-12-02T00:51:14

?as.formula copied from the help file: ## Create a formula for a model with a large number of variables: xnam <- paste("x", 1:25, sep="") (fmla <- as.formula(paste("y ~ ", paste(xnam, collapse= "+"))))

Variables inside a for

Raphael Saldanha — 2008-12-02T00:45:45

Hi! I had a database with some variables in sequence. Let me say: TX01, TX02, TX03 and TX04. But I need to run some regressions changing the variables... so: variable <- paste("TX0", 1:4, sep="") for(i in 1:4){ test[i] <- lm(variable[i] ~ INCOME, data=database) } But doesn't work... lm tries to find a variable inside database named variable[i] ... Suggestions? King regards! Raphael Saldanha Brasil [[alternative HTML version deleted]] ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Re: Failure to subset in R v 2.8.0

Peter Dalgaard — 2008-12-02T00:15:30

... Hmm. Does any of these make us any wiser? mode(c$month) any(c$month==11) table(c$month) dput(unique(c$month))

linear functional relationships with heteroscedastic &non-Gaussian errors - any packages around?

Jarle Brinchmann — 2008-12-01T23:34:53

Hi, I have a situation where I have a set of pairs of X & Y variables for each of which I have a (fairly) well-defined PDF. The PDF(x_i) 's and PDF(y_i)'s are unfortunately often rather non-Gaussian although most of the time not multi--modal. For these data (estimates of gas content in galaxies), I need to quantify a linear functional relationship and I am trying to do this as carefully as I can. At the moment I am carrying out a Monte Carlo estimation, sampling from each PDF(x_i) and PDF(y_i) and using a orthogonal linear fit for each realisation but that is not very satisfactory as it leads to different linear relationships depending on whether I do the orhtogonal fit on x or y (as the errors on X & Y are quite different using the covariance matrix isn't all that useful either) Does anybody know of code in R to do this kind of fitting in a Bayesian framework? My concern isn't so much on getting _the_ best slope estimate but rather to have a good estimate of the uncertainty on the slope. Cheers, Jarle. ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Comparing output from linear regression to outputfromquasipoisson to determine the model that fits best.

John Sorkin — 2008-12-01T23:00:05

R 2.7 Windows XP I have two model that have been run using exactly the same data, both fit using glm(). One model is a linear regression (gaussian(link = "identity")) the other a quasipoisson(link = "log"). I have log likelihoods from each model. Is there any way I can determine which model is a better fit to the data? anova() does not appear to work as the models have the same residual degrees of freedom: fit1<-glm(PHYSFUNC~HIV,data=KA) summary(fit1) fitQP<-glm(PHYSFUNC~HIV,data=KA,family=quasipoisson) summary(fitQP) anova(fit1,fitOP) Program OUTPUT: Call: glm(formula = PHYSFUNC ~ HIV, data = KA) Deviance Residuals: Min 1Q Median 3Q Max -4.197 -4.192 -2.192 2.808 19.808 Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) 4.19670 0.08508 49.33 <2e-16 *** HIV -0.00487 0.12071 -0.04 0.968 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for gaussian family taken to be 22.78134) Null deviance: 142429 on 6253 degrees of freedom Residual deviance: 142429 on 6252 degrees of freedom (213 observations deleted due to missingness) AIC: 37302 Number of Fisher Scoring iterations: 2 Call: glm(formula = PHYSFUNC ~ HIV, family = quasipoisson, data = KA) Deviance Residuals: Min 1Q Median 3Q Max -2.897 -2.895 -1.193 1.250 6.644 Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) 1.434297 0.020280 70.72 <2e-16 *** HIV -0.001161 0.028780 -0.04 0.968 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for quasipoisson family taken to be 5.432011) Null deviance: 35439 on 6253 degrees of freedom Residual deviance: 35439 on 6252 degrees of freedom (213 observations deleted due to missingness) AIC: NA Number of Fisher Scoring iterations: 5 Analysis of Deviance Table Model 1: PHYSFUNC ~ HIV Model 2: PHYSFUNC ~ HIV Resid. Df Resid. Dev Df Deviance 1 6252 142429 2 6252 35439 0 106989 Thanks, John John David Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics University of Maryland School of Medicine Division of Gerontology Baltimore VA Medical Center 10 North Greene Street GRECC (BT/18/GR) Baltimore, MD 21201-1524 (Phone) 410-605-7119 (Fax) 410-605-7913 (Please call phone number above prior to faxing) Confidentiality Statement: This email message, including any attachments, is for th...{{dropped:6}} ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Re: [BioC] BioC 2.3 standard installation

Tiandao Li — 2008-12-01T22:57:21

DONE! Packages in library '/usr/local/lib/R/site-library': affyio Tools for parsing Affymetrix data files annaffy Annotation tools for Affymetrix biological metadata annotate Annotation for microarrays AnnotationDbi Annotation Database Interface Biobase Biobase: Base functions for Bioconductor DBI R Database Interface DynDoc Dynamic document tools genefilter genefilter: methods for filtering genes from microarray experiments geneplotter Grapics related functions for Bioconductor GO.db A set of annotation maps describing the entire Gene Ontology hgu95av2.db Affymetrix Human Genome U95 Set annotation data (chip hgu95av2) KEGG.db A set of annotation maps for KEGG limma Linear Models for Microarray Data marray Exploratory analysis for two-color spotted microarray data multtest Resampling-based multiple hypothesis testing RColorBrewer ColorBrewer palettes ROC utilities for ROC, with uarray focus RSQLite SQLite interface for R XML Tools for parsing and generating XML within R and S-Plus. xtable Export tables to LaTeX or HTML Packages in library '/usr/lib/R/library': base The R Base Package boot Bootstrap R (S-Plus) Functions (Canty) class Functions for Classification cluster Cluster Analysis Extended Rousseeuw et al. codetools Code Analysis Tools for R datasets The R Datasets Package foreign Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, dBase, ... graphics The R Graphics Package grDevices The R Graphics Devices and Support for Colours and Fonts grid The Grid Graphics Package KernSmooth Functions for kernel smoothing for Wand & Jones (1995) lattice Lattice Graphics MASS Main Package of Venables and Ripley's MASS methods Formal Methods and Classes mgcv GAMs with GCV smoothness estimation and GAMMs by REML/PQL nlme Linear and Nonlinear Mixed Effects Models nnet Feed-forward Neural Networks and Multinomial Log-Linear Models rpart Recursive Partitioning spatial Functions for Kriging and Point Pattern Analysis splines Regression Spline Functions and Classes stats The R Stats Package stats4 Statistical Functions using S4 Classes survival Survival analysis, including penalised likelihood. tcltk Tcl/Tk Interface tools Tools for Package Development utils The R Utils Package (END) [[alternative HTML version deleted]] ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Re: Failure to subset in R v 2.8.0

Rolf Turner — 2008-12-01T22:53:32

I just tried: set.seed(42) c <- data.frame(month=sample(1:12,50,TRUE),blah=sample(letters[1:4], 50,TRUE)) c[c$month==11,] and got month blah 1 11 b 21 11 a 28 11 b 30 11 a 39 11 a 47 11 b All appears to be in harmony. So there would appear to be something funny about your data frame ``c'', rather than there being anything wrong with ``[''. Is c$month a factor, perhaps? If so, what are its levels? Also have a look at str(c). BTW ``c'' is a lousy name for an object, since it is the name of the built-in function which effects concatenation. cheers, Rolf Turner On 2/12/2008, at 11:32 AM, Alan Cohen wrote: ###################################################################### Attention:\ This e-mail message is privileged and confid...{{dropped:9}} ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Re: chron and R 2.8

Gabor Grothendieck — 2008-12-01T22:50:10

I've had an offline conversion with Stephen about this and it seems that in R 2.8.0 order is much slower when applied to chron objects than previously. The fix for zoo users is to enter this line (which is already in the development version of zoo) before using any chron objects from zoo in your session: ORDER.chron <- ORDER.dates <- ORDER.times <- function(x, ...) order(as.numeric(x), ...) On Mon, Dec 1, 2008 at 1:12 PM, stephen sefick gmail.com> wrote: ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Re: [BioC] BioC 2.3 standard installation

Hervé Pagès — 2008-12-01T22:42:56

Background: some CRAN or Bioconductor packages contain native code that needs to be compiled and then linked against a system library. Some of those libraries are not part of a standard Ubuntu installation and need to be installed explicitly (sudo apt-get install -dev). In the case of preprocessCore, the output below suggests that it needs to be linked against the BLAS and LAPACK libraries. Not sure but I think those are part of a default R installation unless R has been configured with --with-blas and --with-lapack which might be your case. Not sure what's going on. Just a couple of suggestions: - Make sure you have Ubuntu pkg r-base-dev - Try to install KernSmooth (recommended pkg) from source: > install.packages('KernSmooth') This will replace the one you got when you installed Ubuntu pkg r-cran-kernsmooth KernSmooth also needs to be linked against BLAS so if this fails then it means something is wrong with your R installation (in that case R-help might be a better place to ask for help). H. Tiandao Li wrote:

Re: controlling the number of times a script is repeated in a loop

Carl Witthoft — 2008-12-01T22:42:35

quote: On Sun, Nov 30, 2008 at 12:21 PM, Salas, Andria Kay wrote: > I am running a large for loop and at the end of each iteration a matrix is produced. The program changes the columns in the matrix, and each time a column is added the name of that column is "y". All original columns have no column name. Due to the nature of the program, all original columns will eventually be replaced with new columns each with the column name "y". It is at this point that I want the program to stop running the for loop (right now I just have it running for 20 iterations resulting in a matrix with a mix of old and new columns). I was thinking maybe I could do something with an if else statement and the command colnames. For example: > > If(colnames all are "y") (stop) else (run the program again) Have a look at ?"while" : while(!(colnames all are "y")) { run the program again } Hadley endquote I may be misunderstanding you, but if you know the number of columns in the matrix, and on every iteration, one of them is changed, why not just set the loop up as R>for (i in 1:ncol(your_matrix)) ? Carl ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Re: Failure to subset in R v 2.8.0

stephen sefick — 2008-12-01T22:37:49

Does it not work in the official release of R 2.8.0? On Mon, Dec 1, 2008 at 5:32 PM, Alan Cohen smh.toronto.on.ca> wrote:

Failure to subset in R v 2.8.0

Alan Cohen — 2008-12-01T22:32:14

Hello, I've been using a pre-release version of R v 2.8.0 for Windows for the last couple months. I think that there have been consistent problems with subsetting data sets, but I had usually been able to find work-arounds or was unable to confirm this as a bug. I think now I have, and would love advice on what to do if I've made some error. The data set in question ("c") has 500,000 observations and 44 variables. The problematic variable, "month," takes integer values 1:12, and all are present in the data set: [1] 11 10 9 8 12 1 7 4 6 2 5 3 However, I can't select observations of c for certain values of month: [1] STATE DISTRICT TALUK VILLAGE TYPE SERIALNO INTDATE QH101P [9] QH114 QH115A1 QH115B1 QH115C1 QH115A2 QH115B2 QH115C2 QH115A3 [17] QH115B3 QH115C3 QH115A4 QH115B4 QH115C4 QH115A5 QH115B5 QH115C5 [25] QH116 QH117A1 QH117B1 QH117C1 QH117A2 QH117B2 QH117C2 QH117A3 [33] QH117B3 QH117C3 QH117A4 QH117B4 QH117C4 QH117A5 QH117B5 QH117C5 [41] phase year month stdistid.rch <0 rows> (or 0-length row.names) I get the same result for c[c[,43]==11,], and [1] 0 This is true for most values of month (1,2,4,5,7,8,10,11), but the multiples of 3 work, apparently correctly. Other variables do not have this problem (the columns shift in the email, but these three observations have month=11): STATE DISTRICT TALUK VILLAGE TYPE SERIALNO INTDATE QH101P QH114 QH115A1 QH115B1 QH115C1 QH115A2 QH115B2 QH115C2 QH115A3 QH115B3 87556 11 2 1 1 1 5 1187 6 0 0 0 0 0 0 0 0 0 87557 11 2 1 1 1 10 1187 3 0 0 0 0 0 0 0 0 0 87558 11 2 1 1 1 14 1187 5 0 0 0 0 0 0 0 0 0 QH115C3 QH115A4 QH115B4 QH115C4 QH115A5 QH115B5 QH115C5 QH116 QH117A1 QH117B1 QH117C1 QH117A2 QH117B2 QH117C2 QH117A3 QH117B3 QH117C3 87556 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 87557 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 87558 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 QH117A4 QH117B4 QH117C4 QH117A5 QH117B5 QH117C5 phase year month stdistid.rch 87556 0 0 0 0 0 0 1 1998 11 1102 87557 0 0 0 0 0 0 1 1998 11 1102 87558 0 0 0 0 0 0 1 1998 11 1102 The data set is called directly from a csv file, where all variables should be stored in the same way, and using as.numeric(as.character(c$month)) does not help. Nor does restarting R, restarting the computer, or trying the operation on smaller subsets of c. I'd appreciate any help you an provide. Sincerely, Alan Cohen ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Adding a time difference to a datetime stamp

Brigid Mooney — 2008-12-01T21:24:16

I am trying to figure out a way to add a certain number of hours to a date/time stamp. Specifically, I have a string of date/time stamps that all have the time at midnight. I would like to be able to keep the date the same, but add a certain number of hours to create a new timestamp that is a few hours later. Below is the procedure I have tried so far with no luck: startDate <- "2008-11-01" endDate <- "2008-11-05" OutDates <- seq(as.Date(startDate), as.Date(endDate), by="day") "2008-11-01" "2008-11-02" "2008-11-03" "2008-11-04" "2008-11-05" FourOclock <- as.difftime("16:00:00") Time difference of 16 hours Afternoons <- OutDates + FourOclock "2008-11-17" "2008-11-18" "2008-11-19" "2008-11-20" "2008-11-21" Gives the wrong answer, adding 16 days instead of 16 hours, and throws the following warning: Warning message: Incompatible methods ("+.Date", "Ops.difftime") for "+" I am stumped on this one and would appreciate any/all recommendations. Thanks! [[alternative HTML version deleted]] ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Re: [BioC] BioC 2.3 standard installation

Tiandao Li — 2008-12-01T20:53:19

I always followed http://cran.r-project.org/bin/linux/ubuntu/ to install R on Ubuntu 8.1. I had no errors before! Warning in install.packages("XML") : argument 'lib' is missing: using '/usr/local/lib/R/site-library' --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done trying URL 'http://cran.fhcrc.org/src/contrib/XML_1.98-1.tar.gz' Content type 'application/x-gzip' length 648274 bytes (633 Kb) opened URL ================================================== downloaded 633 Kb * Installing *source* package 'XML' ... checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -E checking for sed... /bin/sed checking for xml2-config... no Cannot find xml2-config ERROR: configuration failed for package 'XML' ** Removing '/usr/local/lib/R/site-library/XML' The downloaded packages are in /tmp/RtmpqCLrkQ/downloaded_packages Warning message: In install.packages("XML") : installation of package 'XML' had non-zero exit status On Mon, Dec 1, 2008 at 1:42 PM, HervÃ© PagÃ¨s fhcrc.org> wrote: [[alternative HTML version deleted]] ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Re: odfWeave and XML... on a Mac

Max Kuhn — 2008-12-01T20:51:13

In case anyone has a similar issue, this problem was related to how the results were being sent to the file. The offending code chunk used: <>= x<- 5 x < at > which writes out the text "5" without any XML around it. When OO opens the document up, it ignores this text (instead of crashing) and shows nothing. This works fine: <>= x<- 5 odfCat(x) < at > ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Re: align two lattice plots with grid

baptiste auguie — 2008-12-01T20:38:08

Many thanks, this tool from latticeExtra does exactly what I was trying to achieve! Best wishes, Baptiste On 1 Dec 2008, at 20:06, Deepayan Sarkar wrote: ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Re: align two lattice plots with grid

Deepayan Sarkar — 2008-12-01T20:06:35

The most transparent approach is to manipulate your data into a suitable format; here's a crude first attempt: xyplot(c(y2, y) ~ c(x, x) | gl(2, 100), groups = rep(c("1", "2"), c(150, 50)), scales = list(y = "free"), layout = c(1, 2), strip = FALSE) In general, the latticeExtra package has some tools to combine arbitrary trellis objects (thanks to Felix Andrews): library(latticeExtra) update(c(p2, p1, x.same = TRUE), layout = c(1, 2), ylab = list(c("a", "BIG LABEL"), y = c(1/6, 2/3)), par.settings = list(layout.heights = list(panel = c(1, 2)))) -Deepayan ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Re: How to refer to a list member by variable

hadley wickham — 2008-12-01T19:16:39

On Mon, Dec 1, 2008 at 12:53 PM, Reitsma, Rene - COB bus.oregonstate.edu> wrote: foo[[goo]] which you'll find in ?"$" under the heading "Recursive (list-like) objects" Hadley