[R] netCDF to raster and spatial projection

I've recently started using R for spatial data. I'd be really grateful if you could could help me with this. Thanks! Sorry I don't provide a reproducible example. Please ask me if you have any questions about the data. I've extracted data from a multidimensional netCDF file. This file had

Re: [R] Pie charts using plotGooglemaps

Hi Boris, Your code works wonderful but still I need pies plotting over map of a country. For now I get axis where coordinates are shown and it works great. Regards On Wed, Apr 16, 2014 at 12:09 AM, Boris Steipe boris.ste...@utoronto.cawrote: Here you go: install.packages(plotrix)

Re: [R] I can't programe routine comp()

Hi see in line. From: Endy BlackEndy [mailto:pert...@gmail.com] Sent: Tuesday, April 15, 2014 5:38 PM To: PIKAL Petr Subject: Re: [R] I can't programe routine comp() Dear Pert, thank you for your advise. Unfortunately it does not work as you can see from the commands below.

Re: [R] netCDF to raster and spatial projection

Hi Beatriz Try to skip this step # Reprojecting into CH1903_LV03 # First, change the coordinate reference system (crs) proj4string(rasterDF1) - +init=epsg:21781 And just do this # Second, reproject the raster rasterDF1.CH - spTransform(rasterDF1,

Re: [R] netCDF to raster and spatial projection

Hi Frede, Thanks so much for your reply! I've tried what you said but I get the following error: Error in spTransform(rasterDF1, crs(+init=epsg:21781)) : load package rgdal for spTransform methods I've checked search() and rgdal is before sp. search() [1] .GlobalEnvpackage:chron

[R] R regular expression and locales

Hi everybody, I am developing some functions that use regular expressions and grepl, to check whether certain strings match a given pattern or not. In the regular expression I use some shortcuts such as [:alnum:]. Reading the documentation for regular expression there is one sentence that is not

Re: [R] Save multiple plots as pdf or jpeg

David you mentioned that one can deliver jpegs embedded in other formats like pdf. Do you know which programs can allow me to do that or how I can go on about it? Or does it involve some kind of loop whereby, it saves the plots as jpeg and then collates them into pdf. So it’s a multi-page

Re: [R] Fw: Save multiple plots as pdf or jpeg

Hello Uwe Can you explain what you mean by try to plot the sensity only with few hundreds of segemnts Do you mean that I should take some kind of sample and do it? And if so what's the best number for the sample and how do i ensure that its not biased? From: Uwe Ligges

Re: [R] Meta-analysis of prevalence at the country level with mgcv/gamm4

Hi Michael, Thank you for your input. Actually the idea of using the model to estimate a number of sick people by age group came later in the project, and I missed the issue with the ecological nature of the analysis. Initially, I intended to use the model to predict a single prevalence for each

Re: [R] Pie charts using plotGooglemaps

On 04/16/2014 04:43 AM, DrunkenPhD wrote: Sorry Jim not for my beginner level :((( So if my data are like this : xyCityVillage 19.943731440.7086377120425 20.221417141.492433611 20.095589139.948136444 20.950663640.64473471015 how do I plot for every point(x,y) a pie chart with

[R] Writing a function in a corrrect way

Hi all , I am about to make a package using gWidgets and RGTK, so for that I had put all my codes into a empty function to access it afterward by the function name using liketrade() . Here is the below code example :--- trade-function()

Re: [R] netCDF to raster and spatial projection

Well no need to have your data. Usually one can find some suitable data in the help for the functions under question. So here is a reproducible example from ?meuse.grid. data(meuse.grid) coordinates(meuse.grid) - ~x+y proj4string(meuse.grid) - CRS(+init=epsg:28992) # see ?meuse for this crs

Re: [R] Pie charts using plotGooglemaps

On 04/16/2014 07:59 PM, DrunkenPhD wrote: Ok this seems to work perfect, Dont want to be boring but what if plotting in real map smth like: hdf - get_map(location = c(20.166065, 41.270679), zoom = 8, maptype = 'roadmap') ggmap(hdf, extent = 'device') I'm not sure that this will work, as ggmap

Re: [R] Pie charts using plotGooglemaps

See inline On 04/16/2014 08:13 PM, DrunkenPhD wrote: No nothing : I tried : hdf - get_map(location = c(20.166065, 41.270679), zoom = 8, maptype = 'roadmap') sampledf-read.table(text=x y City Village 19.9437314 40.7086377 120 425 20.2214171 41.4924336 1 1 20.0955891 39.9481364 4 4

Re: [R] netCDF to raster and spatial projection

Hi Bea Well the first hit lead me to rasterProject{raster}. Will this suit you? rasterMG.proj - projectRaster(rasterMG, crs=CRS(+init=epsg:21781)) print(rasterMG.proj) class : RasterLayer dimensions : 116, 91, 10556 (nrow, ncol, ncell) resolution : 40.1, 40.1 (x, y) extent :

Re: [R] Pie charts using plotGooglemaps

On 04/16/2014 08:29 PM, Endri Raco wrote: I see function *segmentGoogleMaps* from package *plotGoogleMaps* does exactly what I need with data from dataset *meuse*. When I ran code: coordinates(sampledf)-~x+y # convert to SPDF proj4string(sampledf) - CRS('+init=epsg:28992')# adding Coordinate

Re: [R] Trend test for hazard ratios

On 04/15/2014 10:51 PM, David Winsemius wrote: On Apr 15, 2014, at 6:32 AM, Therneau, Terry M., Ph.D. wrote: You can do statistical tests within a single model, for whether portions of it fit or do not fit. But one cannot take three separate fits and compare them. The program needs context

Re: [R] The explanation of ns() with df =2

Dear Xing, My point wasn't that you should add 1 df for a constant to each cubic but that you need not subtract 1 for continuity. I'm sorry that I didn't make that clear. When you use the natural spline in a regression, there's a constant in the model as a separate term with 1 df, which in

Re: [R] netCDF to raster and spatial projection

Hi Frede, Thanks so much! It seems to work perfectly, exactly what I wanted to do! :) All the best, Bea On 16.04.2014 12:25, Frede Aakmann Tøgersen wrote: Hi Bea Well the first hit lead me to rasterProject{raster}. Will this suit you? rasterMG.proj - projectRaster(rasterMG,

Re: [R] Testing correlation of equation in a SUR model fitted by systemfit

Dear Paul On 15 April 2014 19:23, Paul Smith phh...@gmail.com wrote: How to test whether the correlation in the matrix of correlation of a two-equations SUR model fitted by package systemfit are significant? You can use a likelihood-ratio test to compare the SUR model with the corresponding

Re: [R] Pie charts using plotGooglemaps

I see function * segmentGoogleMaps* from package *plotGoogleMaps* does exactly what I need with data from dataset *meuse*. When I ran code: coordinates(sampledf)-~x+y # convert to SPDF proj4string(sampledf) - CRS('+init=epsg:28992')# adding Coordinate Referent Sys. # Create web map of Point data

Re: [R] Pie charts using plotGooglemaps

Ok this seems to work perfect, Dont want to be boring but what if plotting in real map smth like: hdf - get_map(location = c(20.166065, 41.270679), zoom = 8, maptype = 'roadmap') ggmap(hdf, extent = 'device') Regards On Wednesday, April 16, 2014 11:51:43 AM UTC+2, Jim Lemon wrote: On

Re: [R] Pie charts using plotGooglemaps

No nothing : I tried : hdf - get_map(location = c(20.166065, 41.270679), zoom = 8, maptype = 'roadmap') sampledf-read.table(text=x y City Village 19.9437314 40.7086377 120 425 20.2214171 41.4924336 1 1 20.0955891 39.9481364 4 4 20.9506636 40.6447347 10 15,header=TRUE) # make the

[R] Lazy loading of CSV file

Hi, in a package I am developing some functions need to use some external data. I have these data as a set of .csv files that I have placed in the inst/extdata folder. At the moment I have a file db-internal.r where I load all the internal databases that could be used by the functions in my

[R] multiple plots on same sheet in R

Dear useRs, I drew 12 separate raster maps. I want to combine them in such a way the they appear on the same sheet in R, which will later on be saved. Each row should contain three raster maps, so in total we should have 4 rows with each row containing 3 rasters. I know that mfrow() can do it

Re: [R] multiple plots on same sheet in R

Hi, Did you have a look at the rasterVis package? Regards, Pascal On Wed, Apr 16, 2014 at 9:33 PM, eliza botto eliza_bo...@hotmail.com wrote: Dear useRs, I drew 12 separate raster maps. I want to combine them in such a way the they appear on the same sheet in R, which will later on be

Re: [R] Lazy loading of CSV file

The standard way to put data into a package is to convert it to RDA as described in the Writing R Extensions document. This is faster and more compact than CSV. --- Jeff NewmillerThe .

Re: [R] Lazy loading of CSV file

Hi Jeff, thanks for your reply. I read about it in the documentation and I plan to build the functions to download the csv and convert to rda in the future. At the moment, however, I am looking for a quick and dirty solution to lazy load the files I already have. (I know I could convert them

Re: [R] indexing names for looping across computations done on pairs of matrices

A.K. Wonderful - thank you. The last set of code using sapply(), seq_along(), and get() worked like a charm and was what I was missing. Brian Brian S. Cade, PhD U. S. Geological Survey Fort Collins Science Center 2150 Centre Ave., Bldg. C Fort Collins, CO 80526-8818 email: ca...@usgs.gov

[R] interpreting weight in meta-analysis of proportion

Dear all, I use R 3.0 for Windows. I performed a meta-analysis of the prevalence (single proportion) reported in 14 different studyes using the command: res-metaprop(case,n,sm=PFT, comb.fixed=FALSE, comb.random=TRUE, studlab- paste(Study)) print(res) A referee ask a brief explanation

Re: [R] Lazy loading of CSV file

I just found out that the function delayedAssign is what I was looking for. 2014-04-16 16:51 GMT+02:00 Luca Cerone luca.cer...@gmail.com: Hi Jeff, thanks for your reply. I read about it in the documentation and I plan to build the functions to download the csv and convert to rda in the

Re: [R] multiple plots on same sheet in R

see: ?par Does running par(mfrow=c(4,3)) do the job? On Wed, Apr 16, 2014 at 7:33 AM, eliza botto eliza_bo...@hotmail.com wrote: Dear useRs, I drew 12 separate raster maps. I want to combine them in such a way the they appear on the same sheet in R, which will later on be saved. Each

[R] paper on cross-validation pitfalls

Dear All, We have recently published an article on cross-validation pitfalls http://www.jcheminf.com/content/6/1/10/ In the article, amongst other things, we discuss nested cross-validation and variable selection with cross-validation which I am sure is of interest to statistical modelling

Re: [R] Mean not working in function

Hi, Try: set.seed(48) dat1 - data.frame(matrix(sample(c(NA, 1:20), 4 * 20, replace = TRUE), ncol = 4), fac1 = sample(LETTERS, 20, replace = TRUE)) mysummary - function(dataf) { indx - sapply(dataf, is.numeric) for (name in names(dataf)[indx]) { cat(Variable name: , name, : Mean=, mean(dataf[,

[R] Extracting Width and Length of Each Shape in EPS File

Respected Fellows, I need little bit guidance regarding, how Can I Extract/Calculate/Measure width and length of each every shape in .eps file. EPS file is being generated from Adobe Illustrator. I have used grImport Library in R language to import eps file in R environment, but I couldn't

[R] Problems installing packages

Hello, I am woking on ubuntu 13.10 (saucy) And my version() function return: version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major 3 minor 1.0 year 2014 month 04 day 10 svn rev 65387 language R version.string R version 3.1.0 (2014-04-10)

[R] plot legend in filled.contour plot with infinite limits

Dear R-users, http://r.789695.n4.nabble.com/file/n4688905/example.jpg I would like to manipulate the legend bar of a filled.contour plot in the same way as it is done in the attached example I found on the web. So, in particular, I would like to limit my z-range and then have triangles at the

[R] Values cells

Hi folks, I’m using the raster package. I need to get the min and max values between the cells of a raster, something like this: [min, max]. How? --- Este email está limpo de vírus e malwares porque a proteção do avast! Antivírus está ativa. [[alternative HTML version deleted]]

Re: [R] Values cells

Well, if you are using the print method on a raster object what do you get then? Try this: library(raster) Loading required package: sp logo - raster(system.file(external/rlogo.grd, package=raster)) print(logo) class : RasterLayer band: 1 (of 3 bands) dimensions :

[R] Using pre-defined IRT parameters in ltm package

Hi all, I want to estimate scores using IRT when the model parameters are known. I'd like to define my parameters a priori using the ltm package, but haven't found much information on the manual. I appreciate any help on this. Thanks, Luana [[alternative HTML version deleted]]

[R] help incorporating data subset lengths in function with ddply

Dear R Community, I am having some trouble with a task that I hope you might be able to help with. I have a dataset that includes the time and corresponding stream discharge from numerous storms (example of structure with simplified data below). I would like to produce a field that details the

Re: [R] help incorporating data subset lengths in function with ddply

Hi Do you seek something like this: mydat - read.table(text= storm,Q_time,Q, duration s1,2008-08-07 21:15:00,0.000,1 s1,2008-08-07 21:16:00,3.020,2 s1,2008-08-07 21:17:00,6.041,3 s1,2008-08-07 21:18:00,9.061,4 s1,2008-08-07 21:19:00,12.082,5 s1,2008-08-07 21:20:00,15.102,6 s1,2008-08-07

Re: [R] Regarding snp data

On Apr 15, 2014, at 4:15 PM, Manan Amin wrote: Hello, I have a data file of 108mb with snps data of 0,1,2. I am new in the program and have to do this project. My first step is to get the p value using chisq.test function. I have tried running the function however since I am new

Re: [R] help incorporating data subset lengths in function with ddply

Hi Frede - Thank you for responding. Not quite what I am after. Notice that I included two data sets in my post, the first is the raw data whereas the second (the desired df) is similar but has a column of sequential numbers in another column at the end - that column of sequential numbers for each

[R] Help in analysis of similarity in Iramuteq

I am conducting the analysis of similarity and when I request the 3D graph the following error appears: erreur R None1 none none Can anyone help me? Thank you. Ana Karla S Soares -- Ana Karla Silva Soares Doutoranda em Psicologia Social - UFPB Mestre em Psicologia Social - UFPB Graduada em

Re: [R] Trend test for hazard ratios

On Apr 16, 2014, at 4:07 AM, Göran Broström wrote: On 04/15/2014 10:51 PM, David Winsemius wrote: On Apr 15, 2014, at 6:32 AM, Therneau, Terry M., Ph.D. wrote: You can do statistical tests within a single model, for whether portions of it fit or do not fit. But one cannot take three

Re: [R] problem on package survey , function svyglm,

On Tue, Apr 15, 2014 at 7:07 AM, Milan Bouchet-Valat nalimi...@club.frwrote: Le lundi 14 avril 2014 à 13:59 -0400, Hanze Zhang a écrit : Hi, I want to do logistic regression based on a complex sample design. I used package survey, but when I ran svyglm, an error message came out:

Re: [R] Problems installing packages

On 16.04.2014 14:59, Anton FRANCOIS wrote: Hello, I am woking on ubuntu 13.10 (saucy) And my version() function return: version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major 3 minor 1.0 year 2014 month 04 day 10 svn rev 65387

Re: [R] Values cells

I'm pretty sure this is described and not hard to find in the raster package documentation, which you can download from the CRAN package page. In addition, r-sig-geo is generally the best place to ask question related to R's 'geo' packages (which includes raster). -Don -- Don MacQueen Lawrence

Re: [R] Fw: Save multiple plots as pdf or jpeg

On 16.04.2014 11:00, Pavneet Arora wrote: Hello Uwe Can you explain what you mean by try to plot the sensity only with few hundreds of segemnts Do you mean that I should take some kind of sample and do it? And if so what's the best number for the sample and how do i ensure that its not

Re: [R] Extracting Width and Length of Each Shape in EPS File

Have you read the vignettes that accompany that package? You should also read the Posting Guide for this mailing list, as HTML email is not in general a good idea on this list. --- Jeff NewmillerThe

[R] [R-pkgs] Updates to Hmisc, rms, and greport packages

The Hmisc package has had a number of updates/fixes: Changes in version 3.14-4 (2014-04-13) * rcspline.eval: stop new logic for ignoring outer values when there are many ties when there are also many ties on interior values. Added new logic to use interior unique values of x when the

Re: [R] Extracting Width and Length of Each Shape in EPS File

Hi Here is a demonstration that might give you some ideas ... library(grImport) PostScriptTrace(flower.ps, flower.xml) flower - readPicture(flower.xml) grid.newpage() grid.picture(flower) # Extract each path, then look at the 'summary' for the path for (i in 1:flower@summary@numPaths) { bb

[R] xyplot y scale label help

Hi R usres, I would like to specify y label units in xyplot. I tried the yaxp, but it does not work. Following are my codes; trellis.device(col=F) xyplot(GY~N|S,data = Ahmed, layout=c(5,1,1), xlab=expression(paste(N rate (kg , ha^-1,))), ylab=expression(paste(Biomass yield (Mg ,ha^-1,))),

Re: [R] help incorporating data subset lengths in function with ddply

Note that ddply is a heavyweight solution, and as your data gets larger you may find that using it for little things like this hits performance. Also, df is a base function that you might actually want to use someday, and you also introduce confusion in the mind of someone reading your code if

Re: [R] help incorporating data subset lengths in function with ddply

Note that the solution you asked for is not robust in the presence of missing data, though Frede's suggestion or something like it would be. --- Jeff NewmillerThe . . Go Live...

[R] ggplot2: using coord_trans for logit - probability

I'm trying to see if how I can use coord_trans() with ggplot2 to transform the Y axis of a plot on the logit scale to the probability scale, as opposed to recalculating everything manually and constructing a new plot. Here is a simple example of the 'base' plot I'd like to transform:

Re: [R] ggplot2: using coord_trans for logit - probability

I think all you have to do is add type=response to your call for the predictions. Does this work for you # get fitted values on the logit scale pred - data.frame(Arthritis, predict(arth.logistic, se.fit=TRUE,type=response)) library(ggplot2) library(scales) # plot on logit

Re: [R] problem on package survey , function svyglm,

Thank you, guys. I merged strata and fitted my model. On Wed, Apr 16, 2014 at 5:33 PM, Thomas Lumley tlum...@uw.edu wrote: On Tue, Apr 15, 2014 at 7:07 AM, Milan Bouchet-Valat nalimi...@club.frwrote: Le lundi 14 avril 2014 à 13:59 -0400, Hanze Zhang a écrit : Hi, I want to do

Re: [R] ggplot2: using coord_trans for logit - probability

Sorry I jumped the gun. That does not provide you with the same plot as gg2 that you are aiming for. -T On Wed, Apr 16, 2014 at 7:37 PM, Tim Marcella timmarce...@gmail.com wrote: I think all you have to do is add type=response to your call for the predictions. Does this work for you #

[R] Labeling/identifying observations in plot after MclustDR from Mclust

Hi, I’m trying to figure out how to label points in a contour plot produced from the output of MclustDR, the dimension reduction function in the Mclust package. The original data frame has row names RRcoarse govtDeficitres_gdp GrossFixedCapForm_UN fuelExports AUS_76

Re: [R] : Quantile and rowMean from multiple files in a folder

Hi, Use this code after `lst2`. lapply(seq_along(lst2), function(i) { lstN - lapply(lst2[[i]], function(x) { datN - as.data.frame(matrix(NA, nrow = 101, ncol = length(names1), dimnames = list(NULL, names1))) x1 - x[, -1] qt - numcolwise(function(y)

Re: [R] The explanation of ns() with df =2

Dear John, Thanks for your patience, got your idea Best, Xing On Wed, Apr 16, 2014 at 4:11 AM, John Fox j...@mcmaster.ca wrote: Dear Xing, My point wasn't that you should add 1 df for a constant to each cubic but that you need not subtract 1 for continuity. I'm sorry that I didn't make

Re: [R] : Quantile and rowMean from multiple files in a folder

Hi AK, Thanks very much. Atem. On Wednesday, April 16, 2014 9:32 PM, arun smartpink...@yahoo.com wrote: Hi, Use this code after `lst2`. lapply(seq_along(lst2), function(i) {     lstN - lapply(lst2[[i]], function(x) {         datN - as.data.frame(matrix(NA, nrow = 101, ncol = length(names1),