Re: [R-es] R-foro: Re: Bases de datos R
Estimada Veronica, El comando R ls() deberia darte todos los objetos que tienes en el espacio de trabajo. Si quieres borrar un objeto en particular, por ejemplo el llamado datos, solo debes escribir R rm(datos) donde rm() es la funcion remove. Para mas ayuda consulta ?rm Ahora, si quieres borrar TODOS los objetos de la sesion de R sin reiniciar R, debes escribir R rm(list = ls()) Espero sea un poco mas claro. Saludos cordiales, Jorge.- 2015-04-08 15:58 GMT+10:00 pepeceb pepe...@yahoo.es: Hola Ver�nicasi le das la orden ls() te aparecer�n todos los objetos que has creadoLuego para eliminar el que quieras, basta con rm (objeto a eliminar) De todas formas, si vuelves a cargar una base de datos con el mismo nombre, elimina a la anterior y ya puedes trabajar con la nueva. De: Veronica Escorcia veronic...@hotmail.com Para: jose cebrian pepe...@yahoo.es Enviado: Mi�rcoles 8 de abril de 2015 4:30 Asunto: R-foro: Re: Bases de datos R R-foro � Foros � Foro de debate � Bases de datos R | | Re: Bases de datos Rde Veronica Escorcia - mi�rcoles, 8 de abril de 2015, 03:56 | | | Hola Manuel.Ya te expliqu� lo que m�s pude, no s� qu� m�s decirte :/ Me podr�as indicar por favor c�mo borrar todo para iniciar un nuevo proyecto? Es con Rcmdr, s�lo necesito saber c�mo eliminar las bases de datos que ya tengo cargadas y as� inicio de nuevo todo el proceso. Muchas gracias. Mostrar mensaje anterior | ResponderVer el mensaje en su contexto | Darse de baja de este foro Dar de baja de todos los foros [[alternative HTML version deleted]] ___ R-help-es mailing list R-help-es@r-project.org https://stat.ethz.ch/mailman/listinfo/r-help-es [[alternative HTML version deleted]] ___ R-help-es mailing list R-help-es@r-project.org https://stat.ethz.ch/mailman/listinfo/r-help-es
Re: [R] survreg FUNCTION
On 08 Apr 2015, at 10:14 , CHIRIBOGA Xavier xavier.chirib...@unine.ch wrote: Dear members, I am trying a survival analysis , I got: Error: could not find function survreg I already load the packages: survival the function: splines Load or install? I suspect you actually did the latter. What can I do? If installed and not loaded, load it with library(survival). -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
[R] survreg FUNCTION
Dear members, I am trying a survival analysis , I got: Error: could not find function survreg I already load the packages: survival the function: splines What can I do? Thanks for you help, Xavier __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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: [R] C compilation error (unknown type R_xlen_t) when installing Rmpi package
Support for long vectors (and hence R_xlen_t) was introduced in R 3.0.0. Your version is far outdated. If you wait a teeny but longer (after April 16) to update, you'll get R 3.2.0. Henrik On Apr 8, 2015 08:00, Sebastian L sl-resea...@outlook.com wrote: Hi, I am trying to use the parallel computing cluster of our university. To that end, I would like to install the Rmpi package on the cluster. The R version currently installed on the cluster is R version 2.15.2 (2012-10-26) -- Trick or Treat Platform: x86_64-redhat-linux-gnu (64-bit) I am trying to install the Rmpi package from the tar.gz source file, but encounter the following problem during the compilation process: What I run within R is install.packages(/home/myusername/Rpackages/Rmpi_0.6-5.tar.gz, repos = NULL, type = source, lib = /home/myusername/Rpackages/, configure.args=c(--with-Rmpi-libpath=/usr/mpi/gcc/openmpi-1.6.3/lib64/,--with-Rmpi-type=OPENMPI, --with-Rmpi-include=/usr/mpi/gcc/openmpi-1.6.3/include/)) and I get the following output with an error message: * installing *source* package ‘Rmpi’ ... ** Paket ‘Rmpi’ erfolgreich entpackt und MD5 Summen überprüft checking for openpty in -lutil... no checking for main in -lpthread... no configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DPACKAGE_NAME=\\ -DPACKAGE_TARNAME=\\ -DPACKAGE_VERSION=\\ -DPACKAGE_STRING=\\ -DPACKAGE_BUGREPORT=\\ -DPACKAGE_URL=\\ -I/usr/mpi/gcc/openmpi-1.6.3/include/ -DMPI2 -DOPENMPI -I/usr/local/include-fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c Rmpi.c -o Rmpi.o Rmpi.c: In Funktion »mpi_bcast«: Rmpi.c:605:2: Fehler: unbekannter Typname: »R_xlen_t« make: *** [Rmpi.o] Fehler 1 ERROR: compilation failed for package ‘Rmpi’ I can not quite figure out what happens here, and what unknown type name R_xlen_t possibly refers to. Thanks in advance __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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: [R] C compilation error (unknown type R_xlen_t) when installing Rmpi package
On 08/04/2015 16:00, Sebastian L wrote: Hi, I am trying to use the parallel computing cluster of our university. To that end, I would like to install the Rmpi package on the cluster. The R version currently installed on the cluster is This was a matter for the R-devel list as it involves compiled code: see the posting guide. R version 2.15.2 (2012-10-26) -- Trick or Treat Platform: x86_64-redhat-linux-gnu (64-bit) I am trying to install the Rmpi package from the tar.gz source file, but encounter the following problem during the compilation process: What I run within R is install.packages(/home/myusername/Rpackages/Rmpi_0.6-5.tar.gz, repos = NULL, type = source, lib = /home/myusername/Rpackages/, configure.args=c(--with-Rmpi-libpath=/usr/mpi/gcc/openmpi-1.6.3/lib64/,--with-Rmpi-type=OPENMPI, --with-Rmpi-include=/usr/mpi/gcc/openmpi-1.6.3/include/)) and I get the following output with an error message: * installing *source* package ‘Rmpi’ ... ** Paket ‘Rmpi’ erfolgreich entpackt und MD5 Summen überprüft checking for openpty in -lutil... no checking for main in -lpthread... no configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DPACKAGE_NAME=\\ -DPACKAGE_TARNAME=\\ -DPACKAGE_VERSION=\\ -DPACKAGE_STRING=\\ -DPACKAGE_BUGREPORT=\\ -DPACKAGE_URL=\\ -I/usr/mpi/gcc/openmpi-1.6.3/include/ -DMPI2 -DOPENMPI -I/usr/local/include-fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c Rmpi.c -o Rmpi.o Rmpi.c: In Funktion »mpi_bcast«: Rmpi.c:605:2: Fehler: unbekannter Typname: »R_xlen_t« make: *** [Rmpi.o] Fehler 1 ERROR: compilation failed for package ‘Rmpi’ I can not quite figure out what happens here, and what unknown type name R_xlen_t possibly refers to. It is a C type introduced in R 3.0.0. Find in the CRAN archives a version of Rmpi as old as your version of R (or at least earlier than 3.0.0) and install that. Note to the maintainer (Cc:ed) -- you need to correct the R version dependence. -- Brian D. Ripley, rip...@stats.ox.ac.uk Emeritus Professor of Applied Statistics, University of Oxford 1 South Parks Road, Oxford OX1 3TG, UK __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
[R] Coxme penalized log-likelihood mismatch
Hi, I need to extract the penalized log-likehood term from coxme objects but I find the values stored whitin the object different than the penalized term given in the summary output of coxme function. Both the Null and the Integrated values are identical but the penalized is always off. Any thoughts on why and how i can extract the right value to compute the AIC myself? (I know an AIC value is given in the output but I need to compute it myself inside a loop) Many thanks, Alexandre Lafontaine __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
[R] C compilation error (unknown type R_xlen_t) when installing Rmpi package
Hi, I am trying to use the parallel computing cluster of our university. To that end, I would like to install the Rmpi package on the cluster. The R version currently installed on the cluster is R version 2.15.2 (2012-10-26) -- Trick or Treat Platform: x86_64-redhat-linux-gnu (64-bit) I am trying to install the Rmpi package from the tar.gz source file, but encounter the following problem during the compilation process: What I run within R is install.packages(/home/myusername/Rpackages/Rmpi_0.6-5.tar.gz, repos = NULL, type = source, lib = /home/myusername/Rpackages/, configure.args=c(--with-Rmpi-libpath=/usr/mpi/gcc/openmpi-1.6.3/lib64/,--with-Rmpi-type=OPENMPI, --with-Rmpi-include=/usr/mpi/gcc/openmpi-1.6.3/include/)) and I get the following output with an error message: * installing *source* package ‘Rmpi’ ... ** Paket ‘Rmpi’ erfolgreich entpackt und MD5 Summen überprüft checking for openpty in -lutil... no checking for main in -lpthread... no configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DPACKAGE_NAME=\\ -DPACKAGE_TARNAME=\\ -DPACKAGE_VERSION=\\ -DPACKAGE_STRING=\\ -DPACKAGE_BUGREPORT=\\ -DPACKAGE_URL=\\ -I/usr/mpi/gcc/openmpi-1.6.3/include/ -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c Rmpi.c -o Rmpi.o Rmpi.c: In Funktion »mpi_bcast«: Rmpi.c:605:2: Fehler: unbekannter Typname: »R_xlen_t« make: *** [Rmpi.o] Fehler 1 ERROR: compilation failed for package ‘Rmpi’ I can not quite figure out what happens here, and what unknown type name R_xlen_t possibly refers to. Thanks in advance __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
[R] script works in Rstudio but not with Rscript
Greetings. I am new to R, but have quite a bit of experience programming with other languages (e.g., Perl, Java, Python, shell scripting). I'm now working on a project where I need to use R. A colleague wrote a number of small scripts that work fine in Rstudio, but a couple of them don't work when run using Rscript (which we're planning on doing). The behavior is basically the same on a few different machines (two of them are Linux, one I think is a Mac). To run the scripts using Rscript, we put one of the following lines at the top of the script: #!/usr/bin/Rscript #!/usr/bin/env Rscript or called the script using Rscript: Rscript scriptname In all cases, the behavior is the same. Here's one of the scripts: #!/usr/bin/env Rscript library(apcluster) options(stringsAsFactors = FALSE) args - commandArgs(TRUE) num - args[1] numClusters - num mydata - read.csv(input_data.csv) xData - mydata[, 1] yData - mydata[, 2] fit - apclusterK(negDistMat(r=2), mydata, K = numClusters) #Leave the rest commented for now #output - data.frame(xData, yData, c(as.data.frame(fit[1]), as.data.frame(fit[2]), as.data.frame(fit[3]))) #write.csv - write.table(output, file = output_AP.csv, sep = ,, row.names = FALSE, col.names = FALSE) Here's a call to the script: $ ./affinity_propagation.R 3 Attaching The following object is masked package:: heatmap Trying p = -15.41969 Number of clusters: 17 Error in tmpk - K : non-numeric argument to binary operator Calls: apclusterK ... apclusterK - .local - apclusterK - apclusterK - .local Execution halted The line with the expression tmpk - K is from the code for the apclusterK() function (from the apcluster library). The definition/value of tmpk is set using a call to the function length(). I mention this because the failure we're getting with the other script also seems to involve an expression with call to length(). Here's the error from calling that script: $ ./spectral_clustering.R 3 Loading required package: methods Error in length(tmpsig) * nc : non-numeric argument to binary operator Calls: specc - specc - .local - matrix Execution halted The script is calling the specc() function in the kernlab library. Any ideas what's going on here, why it's not working and what we can do to get it to work? Is there something that needs to be set or run in .Renviron or .Rprofile, say? Thanks. Milt Epstein Programmer in Computational Genomics Institute for Genomic Biology (IGB) University of Illinois at Urbana-Champaign (UIUC) mepst...@illinois.edu __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
[R] FW: r-sig-genetics is alive!
Dear all, a small heads up for R-sig-genetics, a mailing list devoted to population genetics in R. See below, and sorry about the double-posting. All the best Thibaut -- From: Jombart, Thibaut Sent: 08 April 2015 17:21 To: r-sig-genet...@r-project.org Subject: r-sig-genetics is alive! Dear all, after a rather quiet existence for the last few years, it may be good to send this reminder: r-sig-genetics is alive! Many awesome people have subscribed lately, and I am looking forward to seeing exciting discussions here. Posting guidelines have been freshly updated: https://stat.ethz.ch/mailman/listinfo/r-sig-genetics Coming soon: exciting news regarding future releases of a bunch of population genetics packages. All the best Thibaut == Dr Thibaut Jombart MRC Centre for Outbreak Analysis and Modelling Department of Infectious Disease Epidemiology Imperial College - School of Public Health Norfolk Place, London W2 1PG, UK Tel. : 0044 (0)20 7594 3658 http://sites.google.com/site/thibautjombart/ http://sites.google.com/site/therepiproject/ http://adegenet.r-forge.r-project.org/ Twitter: @thibautjombart __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
[R] How to calculate vif of each term of model in R?
I am beginner in R doing modelling in R, I loaded excel sheet in R, i have
chosen x elements and y elements then fitted model for linear and second order
regression. Now I have both models. I am bit confused how to calculate vif for
each term in model like
e.g model1-lm(y1~x1+x2+.x9) when I am using rms package then it's giving
me like
vif(model1)
x1 x2 x3 x4 x5 x6 x7
6.679692 1.520271 1.667125 3.618439 4.931810 2.073879 13.870630
x8 x9
220.969628 214.034135
now i want to compare each term with std vif as vif=10 and which will satisfy
this condition i want to delete that term and update model1. i have done
something like this
fun = function(model1) {
for(i in 1:length(model1)){
v=vif(model1)
ss=any(v[i]=10)
if(ss==1){update(model1,.~.,-v[i])}
else{print(no update)}
i-i+1
}
return(model1)
}
fun(model1)
but giving error as
Error in if (ss == 1) { : missing value where TRUE/FALSE needed.
please tell me how do i solve this problem.
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and provide commented, minimal, self-contained, reproducible code.
Re: [R-es] Temas para word markdown
Fernando, este enlace quizás te sirva https://vimeo.com/110804387 Hace ya muchos meses hice algo de esa manera, creando el template en Word, espero siga siendo válido. Daniel Merino El 8 de abril de 2015, 8:44, Fernando Macedo ferm...@gmail.com escribió: Buenas, estaba siguiendo el hilo de Informes Periódicos en R de Jesus Herranz y me surgió una duda. Actualmente estoy tratando de usar markdown para todo así cualquier cosa que haga me queda presentable para informar o presentar en algún lugar. En general estoy usando html y o pdf principalmente porque cuando trato de compilar en word la verdad que queda bastante feíto. Alguién sabe, o puede indicarme un enlace que indique, como agregar y cambiar los temas para word? Saludos DMTV Fernando Macedo Ayudante del área Mejoramiento Genético Facultad de Veterinaria - UdelarR - Uruguay Tel: 26284291 Cel.: 098596947 ferm...@gmail.com Alcanzó la sabiduría quien supo morir tan seguro como nació. Séneca El 08/04/15 a las 05:06, Jesus Herranz escribió: Finalmente era un tema de versión de RStudio como algunos compañeros habían indicado. Muchas gracias a todos. De: Carlos Ortega [mailto:c...@qualityexcellence.es] Enviado el: martes, 07 de abril de 2015 16:30 Para: Jesus Herranz CC: Jorge I Velez; R-help-es Asunto: Re: [R-es] Informes periódicos con R Hola Jesús, Mira los ejemplos, videos y hasta un libro de referencia en la propia página del creador del paquete: http://yihui.name/knitr/ Saludos, Carlos Ortega www.qualityexcellence.es El 7 de abril de 2015, 15:36, Jesus Herranz jesus.herr...@imdea.org escribió: Hola Jorge Perdona que sea tan pesado, pero no encuentro el fichero docx. Tampoco me manejo muy bien con RStudio. He insertado lo que me has dicho; pero solo tengo en la pantalla la opción “Knit HTML” y siempre me genera un HTML. He instalado “pander” pero no obtengo el docx Gracias Jesús De: Jorge I Velez [mailto:jorgeivanve...@gmail.com] Enviado el: martes, 07 de abril de 2015 13:54 Para: Jesus Herranz CC: R-help-es Asunto: Re: [R-es] Informes periódicos con R Hola Jesus, La idea es que tengas un documento markdown en RStudio y que el encabezado sea similar a --- title: Aquí va tu título author: Aquí quien escribió el documento date: Y la fecha... output: word_document --- Despues de los segundos --- escribes el texto que necesitas siguiendo la sintaxis clasica de markdown. Una vez compilado el documento desde RStudio (tambien puede hacerse directamente desde R con la funcion source) se generara el documento .docx que contiene toda la informacion que necesitas. Espero sea un poco mas claro. Saludos, Jorge.- 2015-04-07 21:50 GMT+10:00 Jesus Herranz jesus.herr...@imdea.org: Hola, Jorge Lo he mirado y parece que es una opción bastante buena, pero no logro saber cómo se salva en Word, solo lo logro en html Muchas gracias Jesús De: Jorge I Velez [mailto:jorgeivanve...@gmail.com] Enviado el: martes, 07 de abril de 2015 11:40 Para: Jesus Herranz CC: R-help-es Asunto: Re: [R-es] Informes periódicos con R Hola Jesus, Una forma es RStudio + Markdown. Hay infinidad de tutoriales en internet, pero la referencia basica es http://rmarkdown.rstudio.com/ Puedes organizar las salidas para que sean en Word, PDF o HTML. La escongencia depende de lo que quieras hacer posteriormente con el informe generado. Espero sea de utiilidad. Saludos cordiales, Jorge.- 2015-04-07 19:37 GMT+10:00 Jesus Herranz jesus.herr...@imdea.org: Hola Necesito elaborar un informe que se ejecutará mensualmente, ya que los datos en los que se basa irán cambiando. El informe estará en Word, y contiene texto fijo, tablas, gráficos y resultados obtenidos con R. El informe será ejecutado después por una persona que no sabe nada de R, al que le suministraré los scripts de R, pero debería ser bastante trasparente para él. ¿Qué paquetes me aconsejáis? y ¿alguna web con un tutorial? Prefiero algo sencillo, ya que no tengo mucho tiempo para dedicar a esto Gracias Jesús [[alternative HTML version deleted]] ___ R-help-es mailing list R-help-es@r-project.org https://stat.ethz.ch/mailman/listinfo/r-help-es [[alternative HTML version deleted]] ___ R-help-es mailing list R-help-es@r-project.org https://stat.ethz.ch/mailman/listinfo/r-help-es ___ R-help-es mailing list R-help-es@r-project.org https://stat.ethz.ch/mailman/listinfo/r-help-es -- Daniel [[alternative HTML version deleted]]
Re: [R] your suggestions in MRMs
Kristi, The row names are utterly arbitrary. Each row is a separate site, and sitelocation is a location variable (both intended to conceal the absolute location, which is confidential since it's on private property). It is NOT the Euclidean distance, nor is a row representing a pair of sites. If you look at the full example, dist() is used to calculate the Euclidean distance as part of the MRM code. Sarah On Wed, Apr 8, 2015 at 1:49 PM, Kristi Glover kristi.glo...@hotmail.com wrote: Hi R Users, I was trying to perfom multiple regression on resemblance matrices (MRMs). This technique in avaiable in ecodist package and looked at the example data to know how I need to organize my data set. I think the data is distance matrix but I was wondering the rows name. For example, there are (these are the subset of the data of graze) sitelocation forestpct 1.1.200112.187743 63.88 1.2.200112.186077 71.33 2.1.200112.406362 72.45 2.2.200112.416265 77.13 3.1.1998 8.409213 18.35 if we look at the first row, 1.1.2001: sitelocation (column) is 12.187.. which is the euclidean distance between two points (XY cordinates). But I was confused at the row name where 1.1.2001 which is to me is site1 and site1 of 2001. Isn't it supposed to be 0 if both are the same site. I think I misunderstood it. Any one can help me about what it is? I put the example for your reference install.packages(ecodist) library(ecodist) data(graze) graze[1:5,1:2] Thanks for your help KG -- Sarah Goslee http://www.functionaldiversity.org __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
[R] data-mining with multiple filters applied to multiple columns
Using this representative dataset of a much larger dataset:
dat - read.table(textConnection(ISEG IRCH div gw
1 1 265 229
1 2 260 298
1 3 234 196
54 1 432 485
54 39 467 485
54 40 468 468
54 41 460 381
54 42 489 502
1 1 265 317
1 2 276 225
1 3 217 164
54 1 430 489
54 39 456 495
54 40 507 607
54 41 483 424
54 42 457 404
1 1 265 278
1 2 287 370
1 3 224 274
54 1 412 585
54 39 473 532
54 40 502 595
54 41 497 441
54 42 447 467
1 1 230 258
1 2 251 152
1 3 199 179
54 1 412 415
54 39 439 538
54 40 474 486
54 41 477 484
54 42 413 346
1 1 230 171
1 2 262 171
1 3 217 263
54 1 432 485
54 39 455 482
54 40 493 419
54 41 489 536
54 42 431 504
1 1 1002 1090
1 2 1222 1178
1 3 1198 1177
54 1 1432 1485
54 39 1876 1975
54 40 1565 1646
54 41 1455 1451
54 42 1427 1524
1 1 1002 968
1 2 1246 1306
1 3 1153 1158
54 1 1532 1585
54 39 1790 1889
54 40 1490 1461
54 41 1518 1536
54 42 1486 1585
1 1 1002 1081
1 2 1229 1262
1 3 1142 1241
54 1 1632 1659
54 39 1797 1730
54 40 1517 1466
54 41 1527 1589
54 42 1514 1612),header=TRUE)
dat$seq - ifelse(dat$ISEG==1 dat$IRCH==1, 1, 0)
tmp - diff(dat[dat$seq==1,]$div)!=0
dat$idx - 0
dat[dat$seq==1,][c(TRUE,tmp),]$idx - 1
dat$ts - cumsum(dat$idx)
dat$iter - ave(dat$seq, dat$ts,FUN=cumsum)
dat$ct - seq(1:length(dat[,1]))
dat[1,]
# ISEG IRCH div gw seq idx ts iter ct
# 11 265 229 1 1 11 1
I'm attempting to carry out 2 data mining tasks:
1) for each time step ('ts') and each ISEG within those time steps, I want
to difference the max and min 'div' values and store the result. I got
close with this command, but the results were repeated:
with(subset(dat,ts==1 IRCH==1),
ave(div,ISEG,FUN=function(x){max(x)-min(x)}))
# 0 20 0 20 0 20
There are a few shortcomings with this line of script that I'm hoping could
be improved upon: (1) I hard-coded ts==1, ideally, the R script would
iterate over all 'ts', (2) I really only need the results printed once (0
20), and (3) it would be nice to store the results in something like this
(the results shown next are from a brute-force hand-calculation on the dat
data.frame):
ISEG IRCH ts div_diff
11 10
541 1 20
11 20
541 2 20
11 30
541 3 200
2) The second data-mining attempt is a bit more convoluted and to
demonstrate what I'd like to get, here it is in parts. First:
aggregate(gw ~ ISEG + iter, subset(dat,ts==1), sum)
ISEG iter gw
111 723
2 541 2321
312 706
4 542 2419
513 922
6 543 2620
Once again, ts==1 is hard-coded, but this would ideally loop through all
unique 'ts' in the dataset. Next, with this result, I'd like to difference
the maximum and minimum 'gw' values associated with each ISEG. I tried:
with(aggregate(gw ~ ISEG + iter, subset(dat,ts==1), sum), ave(gw, ISEG,
function(x){max(x)-min(x)}))
#Error in unique.default(x, nmax = nmax) :
# unique() applies only to vectors
but didn't know what to do with the error. for the result above, the
answer I'm seeking is:
ISEG diff
1 216
54 289
For ts==1, the value of 216 results from 922 - 706 [max(gw) - min(gw) for
ISEG==1] and the value of 289 results from 2620 - 2321 [max(gw) - min(gw)
for ISEG==54]. So, the culmination of what I'm after would be the result
from data-mining effort 1 + data-mining effort 2:
ISEG IRCH ts div_diff gw_diff
11 10 216
541 1 20 289
11 20 16
541 2 20 157
11 30 152
541 3 200 25
[[alternative HTML version deleted]]
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Re: [R] your suggestions in MRMs
Hi Sarah, Thanks for the reply. I again looked at the example, but I did not find the way to calculate the location variable. All example in the document (ecodist) has the Euclidean distance. did not find the example to conceal the absolute location. There are some example: page 21 and 22 : iris.md - distance(iris[,1:4], mahal): it is calculated distance matrix using four variables (I understood this one) page 26: space.d - distance(space, eucl), here space is XY coordinate, so on I am just wondering how I can conceal my absolute location (XY) and make my data compatible to your data set so that I can use your functions. I am sorry for bothering you, Sarah. example of my data set: column names (site, XY coordinates, temp, years) site1, 25.01;34.78 (XY cordicnate), 35degree celcius; year2001 site1, 25.01;34.78 (XY cordicnate), 33degree celcius; year2002 site2, 25.05; 35.56 (XY coordinate); 37degree celcius; year2001 site2, 25.05; 35.56 (XY coordinate); 32degree celcius; year2002 Thanks === Date: Wed, 8 Apr 2015 14:23:27 -0400 Subject: Re: [R] your suggestions in MRMs From: sarah.gos...@gmail.com To: kristi.glo...@hotmail.com CC: r-help@r-project.org Kristi, The row names are utterly arbitrary. Each row is a separate site, and sitelocation is a location variable (both intended to conceal the absolute location, which is confidential since it's on private property). It is NOT the Euclidean distance, nor is a row representing a pair of sites. If you look at the full example, dist() is used to calculate the Euclidean distance as part of the MRM code. Sarah On Wed, Apr 8, 2015 at 1:49 PM, Kristi Glover kristi.glo...@hotmail.com wrote: Hi R Users, I was trying to perfom multiple regression on resemblance matrices (MRMs). This technique in avaiable in ecodist package and looked at the example data to know how I need to organize my data set. I think the data is distance matrix but I was wondering the rows name. For example, there are (these are the subset of the data of graze) sitelocation forestpct 1.1.200112.187743 63.88 1.2.200112.186077 71.33 2.1.200112.406362 72.45 2.2.200112.416265 77.13 3.1.1998 8.409213 18.35 if we look at the first row, 1.1.2001: sitelocation (column) is 12.187.. which is the euclidean distance between two points (XY cordinates). But I was confused at the row name where 1.1.2001 which is to me is site1 and site1 of 2001. Isn't it supposed to be 0 if both are the same site. I think I misunderstood it. Any one can help me about what it is? I put the example for your reference install.packages(ecodist) library(ecodist) data(graze) graze[1:5,1:2] Thanks for your help KG -- Sarah Goslee http://www.functionaldiversity.org [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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: [R] your suggestions in MRMs
Kristi, You're completely missing the point, I think. Instead of providing X,Y coordinates in the sample dataset graze within the ecodist package, I provided one location, X if you'd like, called sitelocation. If you look at the example in ?MRM, data(graze) LOAR10.mrm - MRM(dist(LOAR10) ~ dist(sitelocation) + dist(forestpct), data=graze, nperm=100) This is a toy example,with only one species, geographic distance, and another potential explanatory variable. dist(LOAR10) - species distance; you'd use whatever set of species you're studying dist(sitelocation) - geographic distance, you'd use your x and y coordinates as in dist(xy.matrix) dist(forestpct) - you'd use whatever variable or variables are appropriate for your study I concealed the location of these sites BEFORE I made the data public, which is why there's one location variable instead of x,y coordinates. Each row of graze is a single site, with some information associated. You don't need to conceal your location for your own analysis. You just need to use the appropriate data within the dist() command to calculate the distances, and with the appropriate distance metrics if Euclidean isn't appropriate for your data. Reading the papers cited in ?MRM might help you understand the logic a bit better. Sarah On Wed, Apr 8, 2015 at 3:01 PM, Kristi Glover kristi.glo...@hotmail.com wrote: Hi Sarah, Thanks for the reply. I again looked at the example, but I did not find the way to calculate the location variable. All example in the document (ecodist) has the Euclidean distance. did not find the example to conceal the absolute location. There are some example: page 21 and 22 : iris.md - distance(iris[,1:4], mahal): it is calculated distance matrix using four variables (I understood this one) page 26: space.d - distance(space, eucl), here space is XY coordinate, so on I am just wondering how I can conceal my absolute location (XY) and make my data compatible to your data set so that I can use your functions. I am sorry for bothering you, Sarah. example of my data set: column names (site, XY coordinates, temp, years) site1, 25.01;34.78 (XY cordicnate), 35degree celcius; year2001 site1, 25.01;34.78 (XY cordicnate), 33degree celcius; year2002 site2, 25.05; 35.56 (XY coordinate); 37degree celcius; year2001 site2, 25.05; 35.56 (XY coordinate); 32degree celcius; year2002 Thanks === Date: Wed, 8 Apr 2015 14:23:27 -0400 Subject: Re: [R] your suggestions in MRMs From: sarah.gos...@gmail.com To: kristi.glo...@hotmail.com CC: r-help@r-project.org Kristi, The row names are utterly arbitrary. Each row is a separate site, and sitelocation is a location variable (both intended to conceal the absolute location, which is confidential since it's on private property). It is NOT the Euclidean distance, nor is a row representing a pair of sites. If you look at the full example, dist() is used to calculate the Euclidean distance as part of the MRM code. Sarah On Wed, Apr 8, 2015 at 1:49 PM, Kristi Glover kristi.glo...@hotmail.com wrote: Hi R Users, I was trying to perfom multiple regression on resemblance matrices (MRMs). This technique in avaiable in ecodist package and looked at the example data to know how I need to organize my data set. I think the data is distance matrix but I was wondering the rows name. For example, there are (these are the subset of the data of graze) sitelocation forestpct 1.1.2001 12.187743 63.88 1.2.2001 12.186077 71.33 2.1.2001 12.406362 72.45 2.2.2001 12.416265 77.13 3.1.1998 8.409213 18.35 if we look at the first row, 1.1.2001: sitelocation (column) is 12.187.. which is the euclidean distance between two points (XY cordinates). But I was confused at the row name where 1.1.2001 which is to me is site1 and site1 of 2001. Isn't it supposed to be 0 if both are the same site. I think I misunderstood it. Any one can help me about what it is? I put the example for your reference install.packages(ecodist) library(ecodist) data(graze) graze[1:5,1:2] Thanks for your help KG -- Sarah Goslee http://www.functionaldiversity.org -- Sarah Goslee http://www.stringpage.com http://www.sarahgoslee.com http://www.functionaldiversity.org __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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: [R] script works in Rstudio but not with Rscript
Does it work with R -f script? If so, then it's because Rscript does not attaching methods package by default, but R does. Try loading methods at the top of your script. My $.02 Henrik On Apr 8, 2015 07:41, Milt Epstein mepst...@illinois.edu wrote: Greetings. I am new to R, but have quite a bit of experience programming with other languages (e.g., Perl, Java, Python, shell scripting). I'm now working on a project where I need to use R. A colleague wrote a number of small scripts that work fine in Rstudio, but a couple of them don't work when run using Rscript (which we're planning on doing). The behavior is basically the same on a few different machines (two of them are Linux, one I think is a Mac). To run the scripts using Rscript, we put one of the following lines at the top of the script: #!/usr/bin/Rscript #!/usr/bin/env Rscript or called the script using Rscript: Rscript scriptname In all cases, the behavior is the same. Here's one of the scripts: #!/usr/bin/env Rscript library(apcluster) options(stringsAsFactors = FALSE) args - commandArgs(TRUE) num - args[1] numClusters - num mydata - read.csv(input_data.csv) xData - mydata[, 1] yData - mydata[, 2] fit - apclusterK(negDistMat(r=2), mydata, K = numClusters) #Leave the rest commented for now #output - data.frame(xData, yData, c(as.data.frame(fit[1]), as.data.frame(fit[2]), as.data.frame(fit[3]))) #write.csv - write.table(output, file = output_AP.csv, sep = ,, row.names = FALSE, col.names = FALSE) Here's a call to the script: $ ./affinity_propagation.R 3 Attaching The following object is masked package:: heatmap Trying p = -15.41969 Number of clusters: 17 Error in tmpk - K : non-numeric argument to binary operator Calls: apclusterK ... apclusterK - .local - apclusterK - apclusterK - .local Execution halted The line with the expression tmpk - K is from the code for the apclusterK() function (from the apcluster library). The definition/value of tmpk is set using a call to the function length(). I mention this because the failure we're getting with the other script also seems to involve an expression with call to length(). Here's the error from calling that script: $ ./spectral_clustering.R 3 Loading required package: methods Error in length(tmpsig) * nc : non-numeric argument to binary operator Calls: specc - specc - .local - matrix Execution halted The script is calling the specc() function in the kernlab library. Any ideas what's going on here, why it's not working and what we can do to get it to work? Is there something that needs to be set or run in .Renviron or .Rprofile, say? Thanks. Milt Epstein Programmer in Computational Genomics Institute for Genomic Biology (IGB) University of Illinois at Urbana-Champaign (UIUC) mepst...@illinois.edu __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
[R] your suggestions in MRMs
Hi R Users, I was trying to perfom multiple regression on resemblance matrices (MRMs). This technique in avaiable in ecodist package and looked at the example data to know how I need to organize my data set. I think the data is distance matrix but I was wondering the rows name. For example, there are (these are the subset of the data of graze) sitelocation forestpct 1.1.200112.187743 63.88 1.2.200112.186077 71.33 2.1.200112.406362 72.45 2.2.200112.416265 77.13 3.1.1998 8.409213 18.35 if we look at the first row, 1.1.2001: sitelocation (column) is 12.187.. which is the euclidean distance between two points (XY cordinates). But I was confused at the row name where 1.1.2001 which is to me is site1 and site1 of 2001. Isn't it supposed to be 0 if both are the same site. I think I misunderstood it. Any one can help me about what it is? I put the example for your reference install.packages(ecodist) library(ecodist) data(graze) graze[1:5,1:2] Thanks for your help KG [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
[R] extracting slot coords from a Polygons class object
Hi, I am struggling to extract the polygon vertices from a list of an object class Polygons, specifically the slot coords. I have a point, and i draw a buffer around with gBuffer, i am extracting the polygon form the SpatialPolygons class and i end up with a list of 1 one object Polygons class that seems to have slots, but if i try to extract them i get an error. So here it goes after i load the respective libraries: sp, maptools, rgdal, rgeos pt1 - data.frame(x=217680.2, y = 3817555) coordinates(pt1) - c(x, y) crs = +proj=utm +zone=11 +datum=NAD83 +units=m +no_defs +ellps=GRS80 +towgs84=0,0,0 proj4string(pt1) - CRS(crs) pt1.cpoly - gBuffer(pt1, width = 100, byid = TRUE) pt1.cpoly class : SpatialPolygons features: 1 extent : 217580.2, 217780.2, 3817455, 3817655 (xmin, xmax, ymin, ymax) coord. ref. : +proj=utm +zone=11 +datum=NAD83 +units=m +no_defs +ellps=GRS80 +towgs84=0,0,0 pt1.poly - pt1.cpoly@polygons pt1.poly [[1]] An object of class Polygons Slot Polygons: [[1]] An object of class Polygon Slot labpt: [1] 217680.2 3817554.7 Slot area: [1] 30901.7 Slot hole: [1] FALSE Slot ringDir: [1] 1 Slot coords: x y [1,] 217780.2 3817555 [2,] 217775.3 3817524 [3,] 217761.1 3817496 [4,] 217739.0 3817474 Etc. ….. pt1.crd - pt1.poly[[1]]@coords Error: no slot of name coords for this object of class Polygons So my question is: How do i access the coords slot i clearly see when i print pt1.poly on the screen? Thanks for any help, Monica __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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: [R] script works in Rstudio but not with Rscript
On Wed, Apr 8, 2015 at 11:20 AM, Milt Epstein mepst...@illinois.edu wrote: OK, this suggestion brings up some interesting results. No solution, however. But it's interesting ... and maybe some helpful leads. The basic/short answer to your question is no, it doesn't work with R -f script. The longer answer: Note that the script is currently set up to be called with a command line argument, ./affinity_propagation.R 3. So first I tried R -f affinity_propagation.R 3. That failed, but because it wasn't using the 3 as an argument. So I modified the code to hard-code the value 3 in there and not read the command line argument using commandArgs(TRUE). Then I ran the script using ./affinity_propagation.R -- and it worked! R -f affinity_propagation.R also worked. Then I noticed the --args command line option for R, and I ran R -f affinity_propagation.R --args 3 on the original script, and it failed, the same error as I described below. Also, when you say Try loading methods, do you mean just a line like the following?: library(methods) I tried that as well, and it didn't help, same error. Yes, that's what I meant. My suggestion was just a guess given that it is not that uncommon to see cases where a script works with 'R' but not with 'Rscript'. From your answers/tests, it's seems clear that your problem now has to do with parsing arguments. /Henrik So, given all that, any new ideas? Is the call to commandArgs() screwing something up? Can that be fixed somehow? Is there another library/function I could/should use to read command line arguments? Hmmm, playing around with things some more, it looks like if I do: num - as.integer(args[1]) rather than: num - args[1] things work. So maybe this is an issue with types, scalar vs. array, number vs. string? Milt Epstein Programmer in Computational Genomics Institute for Genomic Biology (IGB) University of Illinois at Urbana-Champaign (UIUC) mepst...@illinois.edu On Wed, 8 Apr 2015, Henrik Bengtsson wrote: Does it work with R -f script? If so, then it's because Rscript does not attaching methods package by default, but R does. Try loading methods at the top of your script. My $.02 Henrik On Apr 8, 2015 07:41, Milt Epstein mepst...@illinois.edu wrote: Greetings. I am new to R, but have quite a bit of experience programming with other languages (e.g., Perl, Java, Python, shell scripting). I'm now working on a project where I need to use R. A colleague wrote a number of small scripts that work fine in Rstudio, but a couple of them don't work when run using Rscript (which we're planning on doing). The behavior is basically the same on a few different machines (two of them are Linux, one I think is a Mac). To run the scripts using Rscript, we put one of the following lines at the top of the script: #!/usr/bin/Rscript #!/usr/bin/env Rscript or called the script using Rscript: Rscript scriptname In all cases, the behavior is the same. Here's one of the scripts: #!/usr/bin/env Rscript library(apcluster) options(stringsAsFactors = FALSE) args - commandArgs(TRUE) num - args[1] numClusters - num mydata - read.csv(input_data.csv) xData - mydata[, 1] yData - mydata[, 2] fit - apclusterK(negDistMat(r=2), mydata, K = numClusters) #Leave the rest commented for now #output - data.frame(xData, yData, c(as.data.frame(fit[1]), as.data.frame(fit[2]), as.data.frame(fit[3]))) #write.csv - write.table(output, file = output_AP.csv, sep = ,, row.names = FALSE, col.names = FALSE) Here's a call to the script: $ ./affinity_propagation.R 3 Attaching The following object is masked package:: heatmap Trying p = -15.41969 Number of clusters: 17 Error in tmpk - K : non-numeric argument to binary operator Calls: apclusterK ... apclusterK - .local - apclusterK - apclusterK - .local Execution halted The line with the expression tmpk - K is from the code for the apclusterK() function (from the apcluster library). The definition/value of tmpk is set using a call to the function length(). I mention this because the failure we're getting with the other script also seems to involve an expression with call to length(). Here's the error from calling that script: $ ./spectral_clustering.R 3 Loading required package: methods Error in length(tmpsig) * nc : non-numeric argument to binary operator Calls: specc - specc - .local - matrix Execution halted The script is calling the specc() function in the kernlab library. Any ideas what's going on here, why it's not working and what we can do to get it to work? Is there something that needs to be set or run in .Renviron or .Rprofile, say? Thanks. Milt Epstein Programmer in Computational Genomics Institute for Genomic Biology (IGB) University of Illinois at Urbana-Champaign (UIUC) mepst...@illinois.edu
Re: [R] extracting slot coords from a Polygons class object
You didn't parse the output you pasted in correctly: pt1.cpoly@polygons[[1]]@Polygons[[1]]@coords or coordinates(pt1.cpoly@polygons[[1]]@Polygons[[1]]) class(pt1.cpoly) [1] SpatialPolygons attr(,package) [1] sp So see ?SpatialPolygons-class for details. Sarah On Wed, Apr 8, 2015 at 5:07 PM, Monica Pisica pisican...@hotmail.com wrote: Hi, I am struggling to extract the polygon vertices from a list of an object class Polygons, specifically the slot coords. I have a point, and i draw a buffer around with gBuffer, i am extracting the polygon form the SpatialPolygons class and i end up with a list of 1 one object Polygons class that seems to have slots, but if i try to extract them i get an error. So here it goes after i load the respective libraries: sp, maptools, rgdal, rgeos pt1 - data.frame(x=217680.2, y = 3817555) coordinates(pt1) - c(x, y) crs = +proj=utm +zone=11 +datum=NAD83 +units=m +no_defs +ellps=GRS80 +towgs84=0,0,0 proj4string(pt1) - CRS(crs) pt1.cpoly - gBuffer(pt1, width = 100, byid = TRUE) pt1.cpoly class : SpatialPolygons features: 1 extent : 217580.2, 217780.2, 3817455, 3817655 (xmin, xmax, ymin, ymax) coord. ref. : +proj=utm +zone=11 +datum=NAD83 +units=m +no_defs +ellps=GRS80 +towgs84=0,0,0 pt1.poly - pt1.cpoly@polygons pt1.poly [[1]] An object of class Polygons Slot Polygons: [[1]] An object of class Polygon Slot labpt: [1] 217680.2 3817554.7 Slot area: [1] 30901.7 Slot hole: [1] FALSE Slot ringDir: [1] 1 Slot coords: x y [1,] 217780.2 3817555 [2,] 217775.3 3817524 [3,] 217761.1 3817496 [4,] 217739.0 3817474 Etc. ….. pt1.crd - pt1.poly[[1]]@coords Error: no slot of name coords for this object of class Polygons So my question is: How do i access the coords slot i clearly see when i print pt1.poly on the screen? Thanks for any help, Monica __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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. -- Sarah Goslee http://www.functionaldiversity.org __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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: [R] extracting slot coords from a Polygons class object
It would be better to ask this question on r-sig-geo. More people there
are more familiar with the structure of Spatial{*} classes.
-Don
--
Don MacQueen
Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925-423-1062
On 4/8/15, 2:07 PM, Monica Pisica pisican...@hotmail.com wrote:
Hi,
I am struggling to extract the polygon vertices from a list of an object
class Polygons, specifically the slot coords.
I have a point, and i draw a buffer around with gBuffer, i am
extracting the polygon form the SpatialPolygons class and i end up with
a list of 1 one object Polygons class that seems to have slots, but if i
try to extract them i get an error.
So here it goes after i load the respective libraries: sp, maptools,
rgdal, rgeos
pt1 - data.frame(x=217680.2, y = 3817555)
coordinates(pt1) - c(x, y)
crs = +proj=utm +zone=11 +datum=NAD83 +units=m +no_defs +ellps=GRS80
+towgs84=0,0,0
proj4string(pt1) - CRS(crs)
pt1.cpoly - gBuffer(pt1, width = 100, byid = TRUE)
pt1.cpoly
class : SpatialPolygons
features: 1
extent : 217580.2, 217780.2, 3817455, 3817655 (xmin, xmax, ymin,
ymax)
coord. ref. : +proj=utm +zone=11 +datum=NAD83 +units=m +no_defs
+ellps=GRS80 +towgs84=0,0,0
pt1.poly - pt1.cpoly@polygons
pt1.poly
[[1]]
An object of class Polygons
Slot Polygons:
[[1]]
An object of class Polygon
Slot labpt:
[1] 217680.2 3817554.7
Slot area:
[1] 30901.7
Slot hole:
[1] FALSE
Slot ringDir:
[1] 1
Slot coords:
x y
[1,] 217780.2 3817555
[2,] 217775.3 3817524
[3,] 217761.1 3817496
[4,] 217739.0 3817474
Etc. Š..
pt1.crd - pt1.poly[[1]]@coords
Error: no slot of name coords for this object of class Polygons
So my question is: How do i access the coords slot i clearly see when i
print pt1.poly on the screen?
Thanks for any help,
Monica
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] script works in Rstudio but not with Rscript
OK, this suggestion brings up some interesting results. No solution, however. But it's interesting ... and maybe some helpful leads. The basic/short answer to your question is no, it doesn't work with R -f script. The longer answer: Note that the script is currently set up to be called with a command line argument, ./affinity_propagation.R 3. So first I tried R -f affinity_propagation.R 3. That failed, but because it wasn't using the 3 as an argument. So I modified the code to hard-code the value 3 in there and not read the command line argument using commandArgs(TRUE). Then I ran the script using ./affinity_propagation.R -- and it worked! R -f affinity_propagation.R also worked. Then I noticed the --args command line option for R, and I ran R -f affinity_propagation.R --args 3 on the original script, and it failed, the same error as I described below. Also, when you say Try loading methods, do you mean just a line like the following?: library(methods) I tried that as well, and it didn't help, same error. So, given all that, any new ideas? Is the call to commandArgs() screwing something up? Can that be fixed somehow? Is there another library/function I could/should use to read command line arguments? Hmmm, playing around with things some more, it looks like if I do: num - as.integer(args[1]) rather than: num - args[1] things work. So maybe this is an issue with types, scalar vs. array, number vs. string? Milt Epstein Programmer in Computational Genomics Institute for Genomic Biology (IGB) University of Illinois at Urbana-Champaign (UIUC) mepst...@illinois.edu On Wed, 8 Apr 2015, Henrik Bengtsson wrote: Does it work with R -f script? If so, then it's because Rscript does not attaching methods package by default, but R does. Try loading methods at the top of your script. My $.02 Henrik On Apr 8, 2015 07:41, Milt Epstein mepst...@illinois.edu wrote: Greetings. I am new to R, but have quite a bit of experience programming with other languages (e.g., Perl, Java, Python, shell scripting). I'm now working on a project where I need to use R. A colleague wrote a number of small scripts that work fine in Rstudio, but a couple of them don't work when run using Rscript (which we're planning on doing). The behavior is basically the same on a few different machines (two of them are Linux, one I think is a Mac). To run the scripts using Rscript, we put one of the following lines at the top of the script: #!/usr/bin/Rscript #!/usr/bin/env Rscript or called the script using Rscript: Rscript scriptname In all cases, the behavior is the same. Here's one of the scripts: #!/usr/bin/env Rscript library(apcluster) options(stringsAsFactors = FALSE) args - commandArgs(TRUE) num - args[1] numClusters - num mydata - read.csv(input_data.csv) xData - mydata[, 1] yData - mydata[, 2] fit - apclusterK(negDistMat(r=2), mydata, K = numClusters) #Leave the rest commented for now #output - data.frame(xData, yData, c(as.data.frame(fit[1]), as.data.frame(fit[2]), as.data.frame(fit[3]))) #write.csv - write.table(output, file = output_AP.csv, sep = ,, row.names = FALSE, col.names = FALSE) Here's a call to the script: $ ./affinity_propagation.R 3 Attaching The following object is masked package:: heatmap Trying p = -15.41969 Number of clusters: 17 Error in tmpk - K : non-numeric argument to binary operator Calls: apclusterK ... apclusterK - .local - apclusterK - apclusterK - .local Execution halted The line with the expression tmpk - K is from the code for the apclusterK() function (from the apcluster library). The definition/value of tmpk is set using a call to the function length(). I mention this because the failure we're getting with the other script also seems to involve an expression with call to length(). Here's the error from calling that script: $ ./spectral_clustering.R 3 Loading required package: methods Error in length(tmpsig) * nc : non-numeric argument to binary operator Calls: specc - specc - .local - matrix Execution halted The script is calling the specc() function in the kernlab library. Any ideas what's going on here, why it's not working and what we can do to get it to work? Is there something that needs to be set or run in .Renviron or .Rprofile, say? Thanks. Milt Epstein Programmer in Computational Genomics Institute for Genomic Biology (IGB) University of Illinois at Urbana-Champaign (UIUC) mepst...@illinois.edu __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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. __ R-help@r-project.org mailing
Re: [R] script works in Rstudio but not with Rscript
args - commandArgs(TRUE) num - args[1] and then you get a complaint about something not being numeric. commandArgs() returns a character vector so try num - as.numeric(args[1]) and you may as well preface it with stopifnot(length(args)0) Bill Dunlap TIBCO Software wdunlap tibco.com On Wed, Apr 8, 2015 at 11:20 AM, Milt Epstein mepst...@illinois.edu wrote: OK, this suggestion brings up some interesting results. No solution, however. But it's interesting ... and maybe some helpful leads. The basic/short answer to your question is no, it doesn't work with R -f script. The longer answer: Note that the script is currently set up to be called with a command line argument, ./affinity_propagation.R 3. So first I tried R -f affinity_propagation.R 3. That failed, but because it wasn't using the 3 as an argument. So I modified the code to hard-code the value 3 in there and not read the command line argument using commandArgs(TRUE). Then I ran the script using ./affinity_propagation.R -- and it worked! R -f affinity_propagation.R also worked. Then I noticed the --args command line option for R, and I ran R -f affinity_propagation.R --args 3 on the original script, and it failed, the same error as I described below. Also, when you say Try loading methods, do you mean just a line like the following?: library(methods) I tried that as well, and it didn't help, same error. So, given all that, any new ideas? Is the call to commandArgs() screwing something up? Can that be fixed somehow? Is there another library/function I could/should use to read command line arguments? Hmmm, playing around with things some more, it looks like if I do: num - as.integer(args[1]) rather than: num - args[1] things work. So maybe this is an issue with types, scalar vs. array, number vs. string? Milt Epstein Programmer in Computational Genomics Institute for Genomic Biology (IGB) University of Illinois at Urbana-Champaign (UIUC) mepst...@illinois.edu On Wed, 8 Apr 2015, Henrik Bengtsson wrote: Does it work with R -f script? If so, then it's because Rscript does not attaching methods package by default, but R does. Try loading methods at the top of your script. My $.02 Henrik On Apr 8, 2015 07:41, Milt Epstein mepst...@illinois.edu wrote: Greetings. I am new to R, but have quite a bit of experience programming with other languages (e.g., Perl, Java, Python, shell scripting). I'm now working on a project where I need to use R. A colleague wrote a number of small scripts that work fine in Rstudio, but a couple of them don't work when run using Rscript (which we're planning on doing). The behavior is basically the same on a few different machines (two of them are Linux, one I think is a Mac). To run the scripts using Rscript, we put one of the following lines at the top of the script: #!/usr/bin/Rscript #!/usr/bin/env Rscript or called the script using Rscript: Rscript scriptname In all cases, the behavior is the same. Here's one of the scripts: #!/usr/bin/env Rscript library(apcluster) options(stringsAsFactors = FALSE) args - commandArgs(TRUE) num - args[1] numClusters - num mydata - read.csv(input_data.csv) xData - mydata[, 1] yData - mydata[, 2] fit - apclusterK(negDistMat(r=2), mydata, K = numClusters) #Leave the rest commented for now #output - data.frame(xData, yData, c(as.data.frame(fit[1]), as.data.frame(fit[2]), as.data.frame(fit[3]))) #write.csv - write.table(output, file = output_AP.csv, sep = ,, row.names = FALSE, col.names = FALSE) Here's a call to the script: $ ./affinity_propagation.R 3 Attaching The following object is masked package:: heatmap Trying p = -15.41969 Number of clusters: 17 Error in tmpk - K : non-numeric argument to binary operator Calls: apclusterK ... apclusterK - .local - apclusterK - apclusterK - .local Execution halted The line with the expression tmpk - K is from the code for the apclusterK() function (from the apcluster library). The definition/value of tmpk is set using a call to the function length(). I mention this because the failure we're getting with the other script also seems to involve an expression with call to length(). Here's the error from calling that script: $ ./spectral_clustering.R 3 Loading required package: methods Error in length(tmpsig) * nc : non-numeric argument to binary operator Calls: specc - specc - .local - matrix Execution halted The script is calling the specc() function in the kernlab library. Any ideas what's going on here, why it's not working and what we can do to get it to work? Is there something that needs to be set or run in .Renviron or .Rprofile, say? Thanks. Milt Epstein Programmer in Computational Genomics Institute for
