search for: pleydell

I am experiencing strange results using dmvnorm. I define a scaled distance matrix from the coordinates bellow and then calculate a covariance matrix using a spherical correlation function. Then with certain combinations of range and sill parameters dmvnorm is returning values greater than 1. Surely the results of dmvnorm should be in the interval 0:1 (or do I just nead a holiday?). In addition

...ped' Possible actions: 1: abort (with core dump) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection: 1 I am running Ubuntu jaunty on a laptop. Any ideas as to what I might need to configure next? thanks David -- David Pleydell UMR BGPI CIRAD TA A-54/K Campus International de Baillarguet 34398 MONTPELLIER CEDEX 5 FRANCE Tel: +33 4 99 62 48 65 - Secr?tariat : +33 4 99 62 48 21 Fax : +33 4 99 62 48 22 http://umr-bgpi.cirad.fr/trombinoscope/pleydell_d.htm https://sites.google.com/site/drjpleydell/

...d over many different *.c files. So my question... is there a way to obtain a more verbose output that could point me to the lines of code that generate the message? Without this information debugging is rendered unnecessarily hard, time consuming and frustrating. many thanks David -- David Pleydell, INRA, UMR-1351 CMAEE, Domaine Duclos, Prise D'eau, 97122 Petit Bourg, Guadeloupe dpleydell at antilles.inra.fr pleydell at cirad.fr Tel +33 5 90 25 54 42 Fax +33 5 90 94 03 96

...re are 345 data points. The improvement shown by the AIC by adding a trend component to the model seems quite small given the number of data points, is there a test to see if the improvement to the model fit is significant? Thanks David ************************************************ David Pleydell D 31 Peel Building Telford Institute of Environmental Systems School of Environment and Life Sciences University of Salford M5 4WT phone: +44 161 2952094 fax: +44 161 295 5015

I am trying to do a classic R -d valgrind --vanilla < mypkg-Ex.R as described in http://cs.swan.ac.uk/~csoliver/ok-sat-library/internet_html/doc/doc/R/2.9.1/doc/manual/R-exts.html#Using-valgrind The problem is valgrind crashes imediately. I am using Ubuntu 10.04 LST (actually Biolinux) on a 64bit Dell Precision laptop with 4 core-i5 Intel processors. I have R-2-15-0 installed from source

Hi I am struggling to fit a non-linear trend using the likfit function in geoR. Specifically I want a sigmoidal function, something like SSfpl in the nls package to fit the trend. But it seems trend.spatial in geoR only works with lm or glm type models. Any ideas how I can specify the model to calculate the kriging parameters using REML, including the parameters of a sigmoidal trend function

Hi I have R 1.6.2 and use WinEdt as a text editor. I have just upgraded to R 1.8.0 but can't set up the SWinRegistry program. Using the recommended "Install packages from local zip files" menu option I get > install.packages("C:/R/SWinRegistry_0.3-2_binary.zip", .libPaths()[1], CRAN = NULL) Error in file(file, "r") : unable to open connection In addition:

Full_Name: David Pleydell Version: 2.2.1 OS: Debian Etch Submission from: (NULL) (193.55.70.206) There appears to be a conflict between the chol functions from the Matrix and the SparseM packages. chol() can only be applied to a matrix of class dspMatrix if SparseM is not in the path. with gratitude David > library(...

...the required .h files and in Makevars they have "PKG_CFLAGS = -I./gsl". I have copied this approach, but wonder if using the standard "R CMD build myPackage" "R CMD check myPackage" needs modifying in some way? All hints or ideas welcome. Thanks David -- David Pleydell UMR BGPI CIRAD TA A-54/K Campus International de Baillarguet 34398 MONTPELLIER CEDEX 5 FRANCE Tel: +33 4 99 62 48 65 - Secr?tariat : +33 4 99 62 48 21 Fax : +33 4 99 62 48 22 http://umr-bgpi.cirad.fr/trombinoscope/pleydell_d.htm https://sites.google.com/site/drjpleydell/

Hi, I have a trouble trying to use \href in a rd doc. See example below: \references{ \href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2702787/}{Vaniscotte A., Pleydell D., Raoul F., Quere J.P., Coeurdassier M., Delattre P., Li T., Qian W., Takahashi K., Weidmann J.C., Qiu J., Giraudoux P. 2009 Modelling and spatial discrimination of small mammal assemblages: an example from western Sichuan (China). Ecological Modelling, 220: 1218-1231.} } The Rcmd check giv...

Lets say I have two source files file1.c and file2.c The latter just contains sub-routines to be used by the first. i.e. in file1.c I have the line #include "file2.c" Let's say "R CMD SHLIB file1.c" runs perfectly and I want to include the code in a package, "R CMD build" also runs fine but R CMD check" gives * checking whether package

...presenting the results of data analyses. Journal of Wildlife Management, 65, 373-378; Burnham, K.P. and Anderson, D.R. (2002) Model Selection and Multimodel Inference: a Practical Information-Theoretic Approach, 2nd edn., Springer-Verlag, New York. 353 pp } \author{ Patrick Giraudoux and David Pleydell: pgiraudo at univ-fcomte.fr, dpleydel at univ-fcomte.fr } \seealso{ \code{\link{AIC}},\code{\link{logLik}} } \examples{ library(MASS) anorex.1 <- lm(Postwt ~ Prewt*Treat, data = anorexia) selMod(anorex.1) anorex.2 <- glm(Postwt ~ Prewt*Treat, family=gaussian,data = anorexia) selMod(ano...

...# Approach 1: loop on k1 output1 = matrix(0,nrow=n,ncol=k2) pt1 = proc.time(for (i in 1:k1) output1 = output1 + m1[,i]*m2) ## Approach 2: loop on k2 output2 = matrix(0,nrow=n,ncol=k2) pt2 = proc.time(for (i in 1:k2) output2[,i] = rowSums( m1*m2[,i] )) ## Same result sum(output1-output2) -- David Pleydell Laboratoire de Biologie Environnementale USC INRA-EA 3184 Universit? de Franche-Comt? Place Leclerc F 25030 Besan?on France (0033) 0381665763 dpleydel at univ-fcomte.fr

"R Installation and Administration", section 2.5 "Sub-architectures" describes calling specific builds of R using the call "R --arch=name". I am trying to build and install three versions of R-2.9.1, each configured with a different valgrind-instrumentation level ("Writing R Extensions", section 4.3.2 "Using valgrind"). My goal is to be able to

Hi, please help!! I've been trying to fit variogram models using the REML method in the gstat package. Every time the Windows GUI crashes. For example library(gstat) data(meuse) x <- variogram(zinc ~ 1, ~x + y, meuse) v <- vgm(140000, "Sph", 800, nug = 10000) plot(x, model = fit.variogram(x, model = v, fit.method=5)) Other fit methods are non problematic (eg. fit.method=7

We are trying to use the corCompSymm function in nlme The example from the help pages for the corAR1 function gives the following > corAR1(0.2, form = ~ 1 | Mare) Correlation structure of class corAR1 representing Phi 0.2 We are expecting a somewhat similar correlation specification with the help page example for corCompSymm, but just get an error instead > corCompSymm(0.5, form = ~ 1 |

"R Installation and Administration", section 2.5 "Sub-architectures" describes calling specific builds of R using the call "R --arch=name". I am trying to build and install three versions of R-2.9.1, each configured with a different valgrind-instrumentation level ("Writing R Extensions", section 4.3.2 "Using valgrind"). My goal is to be able to

I understand global variables can be a bad idea, but even so I would like to understand what is going on here... ### DESCRIPTION OF PROGRAM ### ...I have a strange bug on a global variable in some C code which I am compiling using $ MAKEFLAGS="CFLAGS=-g -O0" R CMD SHLIB myProgram.c the global variable in question is the log likelihood. In an old version of the program I initialized