r-sig-geo-request at r-project.org wrote:
Send R-sig-Geo mailing list submissions to r-sig-geo at r-project.org To subscribe or unsubscribe via the World Wide Web, visit
https://stat.ethz.ch/mailman/listinfo/r-sig-geo or, via email, send a message with subject or body 'help' to r-sig-geo-request at r-project.org You can reach the person managing the list at r-sig-geo-owner at r-project.org When replying, please edit your Subject line so it is more specific than "Re: Contents of R-sig-Geo digest..." Today's Topics: 1. Soil/Agricultural modeller position at ISRIC, Wageningen (Tomislav Hengl) 2. Geographically weighted model workshop in April 2013 at the NCG Ireland (Paul Harris) 3. Least cost path (hughsturrock) 4. Re: Least cost path (Jacob van Etten) 5. Re: Least cost path (hughsturrock) 6. Re: Writing a rasterBrick into a single NetCDF file (Robert J. Hijmans) 7. Re: warning: size of values file does not match the number of cell (Robert J. Hijmans) 8. Re: calculate CRPS on rasters (Robert J. Hijmans) 9. Re: Faster way of calculating the mean of multiple ascii files? (Robert J. Hijmans) 10. Determining changes in events counts along paths (Aren Cambre) 11. Re: Adehabitat crashed R on MacOS 2.15.2 (Els Ducheyne) 12. Re: calculate CRPS on rasters (Lorenzo Alfieri) ---------------------------------------------------------------------- Message: 1 Date: Wed, 28 Nov 2012 10:53:02 +0100 From: Tomislav Hengl <hengl at spatial-analyst.net> To: R-sig-Geo at r-project.org Subject: [R-sig-Geo] Soil/Agricultural modeller position at ISRIC, Wageningen Message-ID: <50B5DEFE.8080000 at spatial-analyst.net> Content-Type: text/plain; charset=UTF-8; format=flowed For more info see: http://www.academictransfer.com/employer/WUR/vacancy/16419/lang/en/ Job description A dedicated soil scientist, agricultural studies or physical geographer (MSc or PhD) who will support the aim of ISRIC to allow efficient exchange of soil data between soil scientists and the users community of global development issues and by adding the 4th dimension (time) to our soil information. Strong conceptual abilities are required to scientifically link these issues, especially the use of GIS and remote sensing information in combination with spatial and dynamic modelling. The candidate should have therefore experience in data management in combination with quantitative modelling of soil-water-plant processes, including soil formation processes, land-use change scenarios on degradation and modelling of carbon and water dynamics. Willingness to work in an international environment. Command of French or Spanish is an asset as well as flexibility and sensitivity to interact with multiple cultures. Requirements - Soil scientist or physical geographer (MSc or PhD) - Experience in spatial database management, GIS and remote sensing - Experience in dynamic modelling of soil- and landscape-related processes - Experience in teaching or willingness to learn - Experience in practical field research is an asset - Good interpersonal, communication and writing skills. Major duties: - Develop soil-related modelling approaches to link thematic issues for efficient soil data exchange - Develop methods to link remote sensing data, GIS and soil-water-crop modelling by adding the 4th dimension to soil data - Understand methodologies for quantitative assessment of global thematic issues, including land and soil degradation, land productivity, availability and dynamics of soil water and carbon - Support the development of user friendly toolkits for modelling. Conditions of employment Scale 10 with maximum salary of 3755.,- (Euro?s gross per month). Social benefits including holiday and ?end of year? allowances. Contract duration: 2 years, with annual renewal based on performance and possibility for extension Maximum working hours per week: 38 Contract type: Temporary, 2 jaar Organisation Wageningen UR (University & Research centre) ISRIC ? World Soil Information is an ICSU accredited World Data Centre and has a leading role in international projects aimed at developing a new soil map of the world. Awareness on the importance of soils in global developments has increased in the policy arena and society and it is now widely realized that soils play a key role in food production, climate change, maintenance of biodiversity, production of energy crops and the management of soil water. ISRIC is developing web-based systems to realize its mission and objectives. For more information see www.isric.org Wageningen University & Research centre Delivering a substantial contribution to the quality of life. That's our focus ? each and every day. Within our domain, healthy food and living environment, we search for answers to issues affecting society ? such as sustainable food production, climate change and alternative energy. Of course, we don?t do this alone. Every day, 6,500 people work on ?the quality of life?, turning ideas into reality, on a global scale. Could you be one of these people? We give you the space you need. For further information about working at Wageningen UR, take a look at www.wageningenur.nl/en/Jobs.htm. -- T. Hengl http://www.wewur.wur.nl/popups/vcard.aspx?id=HENGL001 ------------------------------ Message: 2 Date: Wed, 28 Nov 2012 11:33:28 +0000 (GMT) From: Paul Harris <Paul.Harris at nuim.ie> To: R-sig-Geo at r-project.org Subject: [R-sig-Geo] Geographically weighted model workshop in April 2013 at the NCG Ireland Message-ID: <93f7ca483aef40ba.50b5f688 at nuim.ie> Content-Type: text/plain Dear list We are pleased to announce a three-day workshop on Geographically Weighted Modelling in R being run at the National Centre for Geocomputation, National University of Ireland Maynooth on 24-26 April 2013. For details see http://ncg.nuim.ie/redir.php?action=events/20130424 Instructors for the course are: Martin Charlton, Chris Brunsdon (Liverpool University), Binbin Lu, Isabella Gollini and Paul Harris. For queries and to register for the course - please contact Paul Harris - paul.harris at nuim.ie - before 31 March 2013. Places are on a 'first come first serve' basis. cheers Paul Paul Harris, National Centre for Geocomputation, National University of Ireland, Maynooth, Co Kildare. Tel: 00353- 0 1-7086204 Fax: 00353- 0 1-7086456 [[alternative HTML version deleted]] ------------------------------ Message: 3 Date: Wed, 28 Nov 2012 07:20:34 -0800 (PST) From: hughsturrock <hughsturrock at hotmail.com> To: r-sig-geo at r-project.org Subject: [R-sig-Geo] Least cost path Message-ID: <1354116034680-7581785.post at n2.nabble.com> Content-Type: text/plain; charset=us-ascii Hi all, I am trying to model travel times to from any given point to its nearest hospital (in rural Africa). I've been looking at doing this in ArcGIS and R and it looks like if I can create a 'cost' raster, there are plenty of functions like shortestPath in R {gdistance} and Cost Path in Arc that can work this out. This is fine for factors like landcover, where the cost can be assumed to be identical irrespective of which direction you are moving through that pixel, but I'm having difficulty working out how I would asign slope (from an elevation model) a cost given that the cost of a slope depends on the direction of travel. Does anyone know of a way to model the least costly path over an elevation raster which would account for the direction of travel? That way I could look at both travel to and from the hospital.. Thanks! Hugh -- View this message in context: http://r-sig-geo.2731867.n2.nabble.com/Least-cost-path-tp7581785.html Sent from the R-sig-geo mailing list archive at Nabble.com. ------------------------------ Message: 4 Date: Wed, 28 Nov 2012 16:19:45 +0000 (GMT) From: Jacob van Etten <jacobvanetten at yahoo.com> To: hughsturrock <hughsturrock at hotmail.com>, "r-sig-geo at r-project.org" <r-sig-geo at r-project.org> Subject: Re: [R-sig-Geo] Least cost path Message-ID: <1354119585.30845.YahooMailNeo at web29701.mail.ird.yahoo.com> Content-Type: text/plain Dear Hugh, Take a look at the gdistance vignette, example 1. Best, Jacob. ________________________________ From: hughsturrock <hughsturrock at hotmail.com> To: r-sig-geo at r-project.org Sent: Wednesday, 28 November 2012, 10:20 Subject: [R-sig-Geo] Least cost path Hi all, I am trying to model travel times to from any given point to its nearest hospital (in rural Africa). I've been looking at doing this in ArcGIS and R and it looks like if I can create a 'cost' raster, there are plenty of functions like shortestPath in R {gdistance} and Cost Path in Arc that can work this out. This is fine for factors like landcover, where the cost can be assumed to be identical irrespective of which direction you are moving through that pixel, but I'm having difficulty working out how I would asign slope (from an elevation model) a cost given that the cost of a slope depends on the direction of travel. Does anyone know of a way to model the least costly path over an elevation raster which would account for the direction of travel? That way I could look at both travel to and from the hospital.. Thanks! Hugh -- View this message in context: http://r-sig-geo.2731867.n2.nabble.com/Least-cost-path-tp7581785.html Sent from the R-sig-geo mailing list archive at Nabble.com. _______________________________________________ R-sig-Geo mailing list R-sig-Geo at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo [[alternative HTML version deleted]] ------------------------------ Message: 5 Date: Wed, 28 Nov 2012 09:40:47 -0800 (PST) From: hughsturrock <hughsturrock at hotmail.com> To: r-sig-geo at r-project.org Subject: Re: [R-sig-Geo] Least cost path Message-ID: <1354124447953-7581788.post at n2.nabble.com> Content-Type: text/plain; charset=us-ascii Great, thanks everyone. Very helpful! -- View this message in context: http://r-sig-geo.2731867.n2.nabble.com/Least-cost-path-tp7581785p7581788.html Sent from the R-sig-geo mailing list archive at Nabble.com. ------------------------------ Message: 6 Date: Wed, 28 Nov 2012 11:18:30 -0800 From: "Robert J. Hijmans" <r.hijmans at gmail.com> To: Mark Payne <markpayneatwork at gmail.com> Cc: r-sig-geo at r-project.org Subject: Re: [R-sig-Geo] Writing a rasterBrick into a single NetCDF file Message-ID: <CANtt_hztDjBUJX1736Bk3KUb_Cnj6O_6Cm=H=co+ySFBAKyj-Q at mail.gmail.com> Content-Type: text/plain Mark, That is a good suggestion that I will implement. Thanks, Robert On Tue, Nov 27, 2012 at 3:56 AM, Mark Payne <markpayneatwork at gmail.com>wrote: Hi, I have a rasterStack with several layers. I would like to write this into a single NetCDF file, where each layer is stored as a variable. Is there anyway that this can be done? At the moment (raster 2.0-31), the layers are written as a third dimension, rather than than as separate variables. I can see situations where people might want to do both, so maybe an options switch to writeRaster could be a good solution? Cheers, Mark _______________________________________________ R-sig-Geo mailing list R-sig-Geo at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo [[alternative HTML version deleted]] ------------------------------ Message: 7 Date: Wed, 28 Nov 2012 11:22:50 -0800 From: "Robert J. Hijmans" <r.hijmans at gmail.com> To: Mark Payne <markpayneatwork at gmail.com> Cc: r-sig-geo at r-project.org Subject: Re: [R-sig-Geo] warning: size of values file does not match the number of cell Message-ID: <CANtt_hzrZdNyzf-QAR06wBE5XYGu8CaJw4pMpu3Lai6WmPXXiA at mail.gmail.com> Content-Type: text/plain Mark, It means that aggregate create a temporary file (because it is a large dataset) that is not correct. Given then number of cells and the datatype, the file should have a certain size, which apparently it has not. A common cause of this is a full disk (temp folder) which you can perhaps fix with removeTmpFiles. It could be because of a bug in aggregate. It could be a false alarm. Can yo send me the print of "min.bath" and of "file.info (filename(min.bath))$size" Robert On Tue, Nov 27, 2012 at 3:37 AM, Mark Payne <markpayneatwork at gmail.com>wrote: Hi, I have a large raster file (netcdf) that I am trying to process ie bathr class : RasterLayer dimensions : 10800, 21600, 233280000 (nrow, ncol, ncell) resolution : 0.01666667, 0.01666667 (x, y) extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax) coord. ref. : NA data source : /work/up/common/bathymetry/ETOPO1/ETOPO1_Ice_c_gmt4.nc names : z values : -10803, 8333 (min, max) zvar : z Processing this with aggregate() gives the following warning: min.bath <- aggregate(bathr,fact=out.agg,fun=min,expand=FALSE) Warning message: In .rasterFromRasterFile(grdfile, band = band, objecttype) : size of values file does not match the number of cells (given the data type) What does this warning mean? I've seen previously on the list that there was a bug associated with this warning - the message has only appeared for me since upgrading from about raster 2.0-12 (can't remember the exact version, unfortunately) to 2.0-31. Best wishes, Mark _______________________________________________ R-sig-Geo mailing list R-sig-Geo at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo [[alternative HTML version deleted]] ------------------------------ Message: 8 Date: Wed, 28 Nov 2012 11:25:36 -0800 From: "Robert J. Hijmans" <r.hijmans at gmail.com> To: Lorenzo Alfieri <alfios17 at hotmail.com> Cc: R-sig-geo_Forum <r-sig-geo at r-project.org> Subject: Re: [R-sig-Geo] calculate CRPS on rasters Message-ID: <CANtt_hzGYYEk38TgYws+npfLwAg2Z6VG1fv0GW9YHjQiCvhbVw at mail.gmail.com> Content-Type: text/plain Lorenzo, Given that solution, I think you can also express this (in a memory-safe fashion) like this : CRPS <- overlay(obs, pred, fun=function(x,y) crps(x, y)$crps) Robert On Tue, Nov 27, 2012 at 3:11 AM, Lorenzo Alfieri <alfios17 at hotmail.com>wrote: Etienne, thank you for the tip Now it runs trough, by using CRPS <- raster(ncol=10, nrow=10) CRPS[] <- crps(obs[],pred[])$crps Lorenzo Date: Mon, 26 Nov 2012 21:37:13 -0500 Subject: Re: [R-sig-Geo] calculate CRPS on rasters From: etiennebr at gmail.com To: alfios17 at hotmail.com CC: r-sig-geo at r-project.org Lorenzo, I don't know about your specific function, but you can access matrix using the []'s. So maybe something like : CRPS <- raster(ncol=10, nrow=10) CRPS[] <- crps(obs[],pred[]) Etienne 2012/11/26 Lorenzo Alfieri <alfios17 at hotmail.com> CRPS <- raster(ncol=10, nrow=10) for (i in 1:length(obs)){ CRPS[i] <- crps(obs[i],pred[i])$CRPS [[alternative HTML version deleted]] _______________________________________________ R-sig-Geo mailing list R-sig-Geo at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo [[alternative HTML version deleted]] ------------------------------ Message: 9 Date: Wed, 28 Nov 2012 11:32:59 -0800 From: "Robert J. Hijmans" <r.hijmans at gmail.com> To: Swen Meyer <s.meyer at lmu.de> Cc: r-sig-geo at r-project.org Subject: Re: [R-sig-Geo] Faster way of calculating the mean of multiple ascii files? Message-ID: <CANtt_hw24Bg984zPe9jsEXQ_sy9Ch56RR=yXi2f+k-4SFvMOsA at mail.gmail.com> Content-Type: text/plain Swen, You do not provide much info (e.g. system.time() ) so I do not know where the bottleneck is. It could be in the call to "stack" which you can speed up with "quick=TRUE" (if you are sure that the rasters all line up). It could also be that the bottleneck is reading the data from file. Using ASCII is not a good idea (slow) in this type of application. If you have enough RAM, you might try reading all files in one step, instead of blocks: X_01 <- stack(Files[which(substring(**Files,(nchar(Files)-9),nchar(** Files)-6)==i)]) X_01 <- readAll(X_01) # this will fail if you have insufficient RAM X_01_sum <- mean((X_01)) Robert On Mon, Nov 26, 2012 at 7:51 AM, Swen Meyer <s.meyer at lmu.de> wrote: Dear All, I?m trying to process a couple of ascii grids (daily grids): size of one grid (344kb). the header of the ascii grids look like this: ncols 288 nrows 199 xllcorner 506255 yllcorner 4.35899e+006 cellsize 30 I have daily grids over 30 years and I like to find a fast way of calculating the monthly means for every month of those 30 years: the file structure is like this: grid1: "sb05_dem30m_20410101.024" grid2: "sb05_dem30m_20410102.024" grid3: "sb05_dem30m_20410103.024" ... gridn: "sb05_dem30m_YYYYMMdd.024" ... last grid: "sb05_dem30m_20701231.024" At the moment I?using R Vers. 2.15.1 on a Intel PC i5 CPU 760@ 2.80GHz 2.80GHz with 4GB RAM Windows7, and the raster package and this is my script: library(raster) setwd("G:\\hydro_modelling\\**Sardinia\\Wasim\\**RioCostara30m\\KNMI_REF\\ **output30m\\RUN2\\UNSATZON\\") Path="G:\\hydro_modelling\\**Sardinia\\Wasim\\**RioCostara30m\\KNMI_REF\\* *output30m\\RUN2\\SOILMOIST\\" x="sb05_dem30m_" #list files of folder with string x Files=list.files(pattern=x) # select files to process Files=Files[which((substring(**Files,nchar(Files)-3,nchar(** Files)))==".024")] for( i in unique(substring(Files,(nchar(**Files)-9),nchar(Files)-6))){ print(i) #stack files X_01 <- stack(Files[which(substring(**Files,(nchar(Files)-9),nchar(** Files)-6)==i)]) #mean the grid with raster package X_01_sum <- mean((X_01)) #Write monthly mean asci grid writeRaster(X_01_sum, filename=paste(Path,"** SoilMoisture_RM_Mean_",i,sep="**"), "ascii") } The script works, but it takes more than 30 min until the grids are precessed. Does anyone know of a faster way of meaning (summing) those grids and exporting them as a asci again? Best regards and thank you in advance, Swen -- ------------------------------**------------------------------**-- Dipl. - Geogr. Swen Meyer Department of Geography Physical Geography and Environmental Modeling Ludwig-Maximilian University of Munich Luisenstrasse 37 80333 Munich/Germany fon: +49 (0)89 2180-6665 fax: +49 (0)89 2180-6675 email: s.meyer at lmu.de web: www.geographie.uni-muenchen.de ______________________________**_________________ R-sig-Geo mailing list R-sig-Geo at r-project.org https://stat.ethz.ch/mailman/**listinfo/r-sig-geo<https://stat.ethz.ch/mailman/listinfo/r-sig-geo> [[alternative HTML version deleted]] ------------------------------ Message: 10 Date: Wed, 28 Nov 2012 20:15:29 -0600 From: Aren Cambre <aren at arencambre.com> To: r-sig-geo at r-project.org Subject: [R-sig-Geo] Determining changes in events counts along paths Message-ID: <CAA1mBrqvciDPhQ6j6i7eo6TYFmyf5Xr8em39AMX+3m3T48yX-g at mail.gmail.com> Content-Type: text/plain I have a road network and a set of events that occurs on the road network. I want to spot areas where there are significant changes in the amount of these events over time. I have proposed dividing the map into a grid and comparing event counts in each square between successive time periods. For example, I could use a grid with 1000 meter x 1000 meter squares and do a month-by-month comparison. This might be "good enough", but it still has two weaknesses: 1. A significant change in events could be diluted if the "center of mass" of these events' locations or times lies near a grid boundary or near the time division. 2. The grid size has to be a compromise between being large enough to catch clusters of events yet small enough to not include too many unrelated roadways. I think a better approach would be one that traverses paths and is able to organically spot these areas of changes over time. Another might be to overlay an offset grid and offset time over the original data to overcome the problem I identified in #1, although the end effect may not be much different than smaller grid and time slices. Any thoughts on this? Aren [[alternative HTML version deleted]] ------------------------------ Message: 11 Date: Thu, 29 Nov 2012 09:19:59 +0100 From: Els Ducheyne <educheyne at avia-gis.be> To: Mathieu Basille <basille at ase-research.org> Cc: Els Ducheyne <educheyne at avia-gis.be>, r-sig-geo at r-project.org Subject: Re: [R-sig-Geo] Adehabitat crashed R on MacOS 2.15.2 Message-ID: <729C9E16-0F5A-4C23-9D22-A59BF2241D26 at avia-gis.be> Content-Type: text/plain; charset=windows-1252 Dear Mathieu and Massimo Yes, that did the trick, installation of the framework solved the issue both on command line as in R GUI Thanks for the help. Could this be added to the documentation of the packages (the same issue occurs with adehabitatHS) Best and thanks again Els On 27 Nov 2012, at 17:25, Mathieu Basille <basille at ase-research.org> wrote: Dear Els, I can't really help on the Mac OS issue with tcl/tk since I'm using Linux. However, as the command line warning tells you, you'd better use 'adehabitatHS' [1] now, instead of the old 'adehabitat', which is no longer developed (bug fixes are added, but no new methods). I don't think it will solve your problem, though, but I really recommend to upgrade. Besides, you might want to have a look at the MADIFA instead of the ENFA. See [2] for further details. Best, Mathieu Basille. [1] http://cran.r-project.org/web/packages/adehabitatHS/index.html [2] Calenge, C.; Darmon, G.; Basille, M.; Loison, A. & Jullien, J.-M. (2008) The factorial decomposition of the Mahalanobis distances in habitat selection studies. Ecology, 89: 555-566 doi 10.1890/06-1750.1 Le 27/11/2012 10:57, Els Ducheyne a ?crit : Dear Massimo yes it works from command line, I do get a warning about the tcl tk though, so indeed this must be the source of the problem (see below) The good news is that at least I can carry out the code via the terminal if necessary (even it is not with the R Gui) Still hoping for a fix though Els R version 2.15.2 (2012-10-26) -- "Trick or Treat" Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: i386-apple-darwin9.8.0/i386 (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. [Previously saved workspace restored] library(adehabitat) Loading required package: ade4 Attaching package: ?ade4? The following object(s) are masked from ?package:base?: within Loading required package: tkrplot Loading required package: tcltk Loading Tcl/Tk interface ... done Loading required package: shapefiles Loading required package: foreign Attaching package: ?shapefiles? The following object(s) are masked from ?package:foreign?: read.dbf, write.dbf Be careful: it is now recommended to use the newpackages adehabitatMA, adehabitatLT, adehabitatHR, and adehabitatHS. These 4 packages are intended to become the future of adehabitat. The "classical" version of adehabitat will still be maintained for some time, but no new method will be added to the package. Warning message: In fun(libname, pkgname) : Can't find a usable tk.tcl in the following directories: /System/Library/Frameworks/Tcl.framework/Versions/8.5/Resources/Scripts/tk8.5 /System/Library/Frameworks/Tcl.framework/Versions/8.5/Resources/Scripts/tk8.5/Resources/Scripts /System/Library/Frameworks/Tcl.framework/Versions/8.5/Resources/tk8.5 /System/Library/Frameworks/Tcl.framework/Versions/8.5/Resources/tk8.5/Resources/Scripts ./lib/tk8.5 ./lib/tk8.5/Resources/Scripts ~/Library/Tcl/tk8.5 ~/Library/Tcl/tk8.5/Resources/Scripts /Library/Tcl/tk8.5 /Library/Tcl/tk8.5/Resources/Scripts /System/Library/Tcl/tk8.5 /System/Library/Tcl/tk8.5/Resources/Scripts /System/Library/Tcl/8.5/tk8.5 /System/Library/Tcl/8.5/tk8.5/Resources/Scripts ~/Library/Frameworks/tk8.5 ~/Library/Frameworks/tk8.5/Resources/Scripts /Library/Frameworks/tk8.5 /Library/Frameworks/tk8.5/Resources/Scripts /System/Library/Frameworks/tk8.5 /System/Library/Frameworks/tk8.5/Resources/Scripts ./library This probably means that tk wasn't installed properly. sessionInfo() R version 2.15.2 (2012-10-26) Platform: i386-apple-darwin9.8.0/i386 (32-bit) locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] tcltk stats graphics grDevices utils datasets methods [8] base other attached packages: [1] adehabitat_1.8.11 shapefiles_0.6 foreign_0.8-51 tkrplot_0.0-23 [5] ade4_1.4-17 On 27 Nov 2012, at 16:42, rpi <distem at rpi.edu> wrote: Els, i tried to run adehabitat form inside the Gui.app (64 bit) using R (installed from Homebrew ) .. and i got the same problem you had i tried to rebuild the gui.app using Xcode but no lucky .. same crash. trying to run R from the command line ? it is able to load adehabitat. seems to me a GUI.app problem .. can you check if your adehabitat code runs fine starting R from command line ? thanks, Massimo. Il giorno 27/nov/2012, alle ore 09:34, Els Ducheyne <educheyne at avia-gis.be> ha scritto: Dear Massimo I've just tried and it is still the same problem. Should I put it somewhere for R to find this? Best Els On 27 Nov 2012, at 15:03, epi <massimodisasha at gmail.com> wrote: did you tried to install XQuartz ? http://xquartz.macosforge.org/landing/ --Massimo. Il giorno 27/nov/2012, alle ore 09:00, Els Ducheyne <educheyne at avia-gis.be> ha scritto: Dear list I am trying to run ENFA for presence only records. I have installed adehabitat v1.18.11 on R2.15.2 on MacOS 10.8.2. I Whilst the library is successfully installed and loaded, it crashed R when I am trying to run other commands after loading the library. Did anyone experience this before? Is it the Tcl/Tk that causes the problem, could I load the package without the Tcl/Tk? I have tested under windows too with same version of adehabitat and R and there it works fine. Unfortunately, I will use the package for teaching and some students use MacOS so therefore I would like to find a solution. sessionInfo() R version 2.15.2 (2012-10-26) Platform: i386-apple-darwin9.8.0/i386 (32 bit) locale [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: stats graphics grDevices utils datasets methods base library(adehabitat) Loading required package: ade4 Attaching package: 'ade4' The following objects are masked from 'package:base' within loading required package:tkrplot loading required package: tcltk Loading Tcl/Tk interface sessionInfo() After the second sessionInfo() R does not respond, nor with any other command. The only option is Force quit and reboot. Thanks for any help Els _______________________________________________ R-sig-Geo mailing list R-sig-Geo at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo _______________________________________________ R-sig-Geo mailing list R-sig-Geo at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo _______________________________________________ R-sig-Geo mailing list R-sig-Geo at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo -- ~$ whoami Mathieu Basille, PhD ~$ locate --details University of Florida \\ Fort Lauderdale Research and Education Center (+1) 954-577-6314 http://ase-research.org/basille ~$ fortune ? Le tout est de tout dire, et je manque de mots Et je manque de temps, et je manque d'audace. ? -- Paul ?luard ------------------------------ Message: 12 Date: Thu, 29 Nov 2012 10:15:24 +0100 From: Lorenzo Alfieri <alfios17 at hotmail.com> To: <r.hijmans at gmail.com> Cc: R-sig-geo_Forum <r-sig-geo at r-project.org> Subject: Re: [R-sig-Geo] calculate CRPS on rasters Message-ID: <DUB107-W649F6E7FC94975EE3E9E28D75C0 at phx.gbl> Content-Type: text/plain; charset="iso-8859-1" Hi Robert, I was hoping to use the overlay function too, but it seems it doesn't work in this case. See the result: CRPS? <- overlay(obs, pred, fun=function(x,y) crps(x,y)$crps) Error in function (x, fun, filename = "", recycle = TRUE, ...)? : ? cannot use this formula, probably because it is not vectorized Lorenzo Date: Wed, 28 Nov 2012 11:25:36 -0800 Subject: Re: [R-sig-Geo] calculate CRPS on rasters From: r.hijmans at gmail.com To: alfios17 at hotmail.com CC: etiennebr at gmail.com; r-sig-geo at r-project.org Lorenzo, Given that solution, I think you can also express this?(in a memory-safe fashion)?like this : CRPS??<- overlay(obs, pred, fun=function(x,y) crps(x, y)$crps) Robert On Tue, Nov 27, 2012 at 3:11 AM, Lorenzo Alfieri <alfios17 at hotmail.com> wrote: Etienne, thank you for the tip Now it runs trough, by using CRPS <- raster(ncol=10, nrow=10) CRPS[] <- crps(obs[],pred[])$crps Lorenzo Date: Mon, 26 Nov 2012 21:37:13 -0500 Subject: Re: [R-sig-Geo] calculate CRPS on rasters From: etiennebr at gmail.com To: alfios17 at hotmail.com CC: r-sig-geo at r-project.org Lorenzo, I don't know about your specific function, but you can access matrix using the []'s. So maybe something like : CRPS <- raster(ncol=10, nrow=10) CRPS[] <- crps(obs[],pred[]) Etienne 2012/11/26 Lorenzo Alfieri <alfios17 at hotmail.com> CRPS <- raster(ncol=10, nrow=10) for (i in 1:length(obs)){ ? CRPS[i] <- crps(obs[i],pred[i])$CRPS ? ? ? ? [[alternative HTML version deleted]] _______________________________________________ R-sig-Geo mailing list R-sig-Geo at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo ------------------------------ _______________________________________________ R-sig-Geo mailing list R-sig-Geo at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo End of R-sig-Geo Digest, Vol 111, Issue 27 ******************************************