[R] How to obtain the unique communities when plotting VENNs?

Hey there guys. I am having a question about Venn diagrams. A colleague wrote a script based on the VennDiagram package a while ago, that I was able to adapt for my data. I wanted a Venn for the soil bacterial communities derived from forests of 4 different tree species. It worked fine for me, how

[R] R: help with metasens

Many thanks for your suggestion. I will try a new database search and the hc metaphor function. Mario PS: what is diagonal bacn? -Messaggio originale- Da: Michael Dewey [mailto:li...@dewey.myzen.co.uk] Inviato: mercoledì 12 agosto 2015 18.19 A: petre...@unina.it; r-help@r-project.org O

Re: [R] Doing PDF OCR with R

On 13/08/2015 1:29 AM, Jeff Newmiller wrote: > This code is using R like a command shell... there really is not much chance > that R is the problem, and this is not a "tesseract" support forum, so this > seems quite off-topic. I would have guessed the same, but the error message looks like an R

[R] R: help with metasens

Obviously metafor and not metaphor. Sorry Mario [[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

[R] Finding top 25% observations in Dplyr

Hi All, I am working on a dataset baseball where i am grouping based on one var income in descending order. Now i need to find the top 25% of the observations from the income group for which i used top_n (0.25) but it is not finding the desired. Can you please suggest. Baseball%>% group_by(in

[R] Crosstabulation with a frequency variable

Hi all, I've had a few years experience with R, which is why this is so frustrating, my problem seems so simple but I can't find a solution. I have a data frame in the following form: data.frame(var1=c(0,0,1,1),var2=c(0,1,0,1),freq=c(11,12,13,14)) How do I create a crosstab with frequencies?

[R] Basic editing of XML file

Dear RUser,I’m tryingto operate some very slight editing to the values of an XML file. I looked abit everywhere and it appears that dealing with XML files is not that easy… besidemy XML files might be a bit weirdly structured. Anyway, let me give you an exampleof it : Root(xmlfile)     

Re: [R] Finding top 25% observations in Dplyr

I don't know how to do it in plyr but xx <- seq(1:300) nn <- trunc( length(xx)/4) yy <- xx[nn, ] should come close. Have a look at ?ceiling or ?floor as an alternative to trunc() John Kane Kingston ON Canada > -Original Message- > From: shivibha...@ymail.com > Sent: Thu, 13 Aug

Re: [R] Crosstabulation with a frequency variable

Hi, There are lots of ways to do it in base R, but a long time ago I got frustrated and wrote a crosstab function that did exactly what I wanted: library(ecodist) mydata <- data.frame(var1=c(0,0,1,1),var2=c(0,1,0,1),freq=c(11,12,13,14)) crosstab(var1, var2, freq, data=mydata) 0 1 0 11 12 1 1

Re: [R] Basic editing of XML file

Hi, Your email client is set to send in HTML format which has mangled your message. Please set your client to send plain text to R-help. You could use the XML package to modify the attributes of a given node. > library(XML) # make an reproducible example > z <- newXMLNode("BLABLA", + attr

Re: [R] How to obtain the unique communities when plotting VENNs?

Hi Krissey, I don't have an answer for you but here are some hints on how to ask questions on R-help. http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example and http://adv-r.had.co.nz/Reproducibility.html In particular we probably need your actual code and some sa

Re: [R] Crosstabulation with a frequency variable

Hi, As Sarah noted, there are a variety of ways in R to accomplish this, such as: DF <- data.frame(var1 = c(0, 0, 1, 1), var2 = c(0, 1, 0, 1), freq = c(11, 12, 13, 14)) > xtabs(freq ~ var1 + var2, data = DF) var2 var1 0 1 0 11 12 1 13 14 See ?xtabs Regards, Marc Schwartz > On

Re: [R] Crosstabulation with a frequency variable

Well, just using base R, ... > with(mydata,tapply(freq,list(var1,var2),I)) 0 1 0 11 12 1 13 14 Cheers, Bert Bert Gunter "Data is not information. Information is not knowledge. And knowledge is certainly not wisdom." -- Clifford Stoll On Thu, Aug 13, 2015 at 6:39 AM, Sarah Goslee wro

Re: [R] R: help with metasens

diagonal bacn is a typo, sorry for that. My brain meant to type diagonal band, ie going in this case from north west to south east but my fingers failed completely. On 13/08/2015 10:25, Mario Petretta wrote: Many thanks for your suggestion. I will try a new database search and the hc metaphor

[R] georeferencing image from scratch

I want to change a MSS landsat image which has bad georeferencing. I have a grid of points with correct georeferences and want to use them to reproject the image to a correct reference system. Is there some way to this with raster or other packages? in idrisi I used to resample the image using a

[R] lme4 package installation

Hello I've downloaded the tar.gz file of the package "lme4" and when I use the coomand: install.packages("lme4_1.1-8.tar.gz", repos = NULL, type = "source") appears an error that suspends the installation: In file included from external.cpp:8:0: predModule.h:12:23: fatal error: RcppEigen.h:

[R] georeferencing image from scratch

Hi all I want to change a MSS landsat image which has bad georeferencing. I have a grid of points with correct georeferences and want to use them to reproject the image to a correct reference system. Is there some way to this with raster or other packages? in idrisi I used to resample the im

Re: [R] lme4 package installation

Have you trying installing it directly from CRAN? install.packages("lme4") Do you have all dependencies installed? install.packages() from CRAN will take care of that. You repos = NULL you have to install all dependencies manually. ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Re

Re: [R] How to obtain the unique communities when plotting VENNs?

Thanks a lot John - I will set up a new post and hopefully do better :) -- View this message in context: http://r.789695.n4.nabble.com/How-to-obtain-the-unique-communities-when-plotting-VENNs-tp4711056p4711081.html Sent from the R help mailing list archive at Nabble.com. __

Re: [R] Crosstabulation with a frequency variable

> On 13 Aug 2015, at 16:24 , Bert Gunter wrote: > > Well, just using base R, ... > >> with(mydata,tapply(freq,list(var1,var2),I)) > 0 1 > 0 11 12 > 1 13 14 If you insist on avoiding the stats package... However, I'd use sum() rather than I() to get an xtabs() workalike. -pd > > > Cheer

Re: [R] Crosstabulation with a frequency variable

Yes and yes. To be clear, 1. sum() is better. 2. xtabs is better (I just forgot about it and didn't bother to search). Maybe the best answer is in fact, ??crosstabulation which would have brought up xtabs(). So the moral is (to the OP), learn how to search before posting. Cheers, Bert Bert Gu

[R] Error: Gradient function might be wrong - check it! OPTMX

Hello, I am trying to estimate a non-linear GMM in R using Optimx. However, when I do the start test to compare my analytical gradient with the numerical gradient, I get the following error message Error: Gradient function might be wrong - check it! Below are the print out of my analytical and

Re: [R] add an idx column to the matrix

Hi dear all, Yes, your solution all are correct! it was my mistake and I found it. Thanks On Thu, Aug 13, 2015 at 1:07 AM, PIKAL Petr wrote: > Hi > > > > the error is not caused by missing 2 > > > > > set.seed(333) > > > x<-sample(0:1, 12, rep=T) > > > dim(x)<-c(3,4) > > > x[2,2]<-NA > > > cbi

Re: [R] Error: Gradient function might be wrong - check it! OPTMX

There are tolerances in the checks, and sometimes scaling of the problem leads to false positives on the checks. Try control = list(starttest=FALSE, etc.) to suppress the test. JN On 15-08-13 01:20 PM, Olu Ola via R-help wrote: > Hello, > I am trying to estimate a non-linear GMM in R using Optim

Re: [R] String Matching

I haven't tested this, but what about: df <- data.frame(mtch=c(matchString, string1, string2)) grep(searchString, df$mtch, ignore.case=FALSE) Depending on what your next step is, you might prefer grepl. Sometimes using fixed=TRUE in grep() helps. -Don -- Don MacQueen Lawrence Livermore Na

[R] stringr package question

Hi, I'm running R 3.2.1 and im having an unexpected problem... when I run the follwing code it returns an error library(stringr) str_extract("+proj=utm +zone=19 +datum=WGS84 +units=m +no_defs +ellps=WGS84 +towgs84=0,0,0", "+proj=[a-zA-Z0-9]*") But I can't find whats wrong with my code. Thanks

Re: [R] stringr package question

Hi, The + is a special character in regular expressions. If you want to match a literal + you need to escape it: str_extract("+proj=utm +zone=19 +datum=WGS84 +units=m +no_defs +ellps=WGS84 +towgs84=0,0,0", "\\+proj=[a-zA-Z0-9]*") Sarah On Thu, Aug 13, 2015 at 2:55 PM, Mauricio Romero wrote: >

Re: [R] stringr package question

thanks that makes sense... in the previous version of R it worked for some reason. On Thu, Aug 13, 2015 at 4:33 PM, Sarah Goslee wrote: > Hi, > > The + is a special character in regular expressions. If you want to > match a literal + you need to escape it: > > str_extract("+proj=utm +zone=19

Re: [R] stringr package question

"+" is a special character in regular expressions that requires a preceding pattern to apply to. See ?base::regex. You need to escape the special with a backslash to remove the special behavior, and escape the backslash so the R parser will be happy. str_extract("+proj=utm +zone=19 +datum=WGS84

Re: [R] stringr package question

Seems more likely to be related to changes in the options stringr uses when it invokes the regex code? See the different response coming from base R when told to use a different regex engine: grep( "+proj", "syz+project" ) [1] 1 grep( "+proj", "syz+project", perl=TRUE ) Error in grep("+proj

[R] Need help with Multi-line forestplots in R

Hello, I am working on ecological data covering a meta-analysis on invasive species traits. I am not very skilled in R and would love if someone could assist me in my production of multi-line forest plots. The data I have is: random effects mixed model and i

Re: [R] lme4 package installation

Hi all I have problem in installation lme4 and have tried over the past 2 days. It failed to install from the various countries. > install.packages("lme4") Warning: unable to access index for repository http://cran.stat.nus.edu.sg/src/contrib Warning: unable to access index for repository http://

[R] having error of downloading multiple files from password protected ftp in R

Hi all, I'm trying to download a bunch of files from a credential needed ftp address using R.* Below is my code:* == library(RCurl) url <- "ftp://xxx.com"; userpwd <- "user:pwd" filenames <- getURL(url, userpwd = userpwd, ftp.use.epsv = FALSE,dirlistonly = TRUE) fn <- unlis

[R] Multi-line forestplots, how to in R

Hello, I am working on ecological data covering a meta-analysis on invasive species traits. I am not very skilled in R and would love if someone could assist me in my production of multi-line forest plots. The data I have is: random effects mixed model and is further divided into subsets, I

[R] Parallel Processing

Helllo All, Need some help understanding parallel processing.  I set-up DoParallel and worked perfectly.  I tried to set-up using parallel package following the book Parallel R but I get the following error: Error in checkForRemoteErrors(val) :    4 nodes produced errors; first error: 'what' mu

Re: [R] lme4 package installation

On 13.08.2015 22:52, Teck Kiang Tan wrote: Hi all I have problem in installation lme4 and have tried over the past 2 days. It failed to install from the various countries. install.packages("lme4") Warning: unable to access index for repository http://cran.stat.nus.edu.sg/src/contrib This