Re: [R] table of contents link style in R's PDF docs

2013-09-27 Thread Ben Harrison
On 27/09/13 00:33, Duncan Murdoch wrote: On 25/09/2013 11:38 PM, Ben Harrison wrote: Hello, It's been the way it is for about 14 years, and I don't recall anyone else complaining, so I'd conclude it must have been set that way with you in mind. Ah-hah, I knew it! I *am* special. More

Re: [R] Read shortcuts of MS Excel files through R

2013-09-27 Thread Mark Lamias
Assuming you are trying to read the contents of the Excel files and not the shortcut itself, try something link this: #C:\users\mark\desktop\A1.xlsx.lnk is a shortcut I created on my desktop to an xlsx document in another directory #The windows type command, along with find gets the path to the

[R] Locating inefficient code

2013-09-27 Thread mohan . radhakrishnan
Hi, I have been using R for a few months and I have this working code. Don't seen any problem but this takes a long time. So if I have about 3 rows it takes a few minutes. If I have 10 it does not seem to complete. Original Data: Proto Recv-Q Send-Q Local-Address

Re: [R] Space between x-axis ticks

2013-09-27 Thread mohan . radhakrishnan
I attached a graph and it is not allowed. So the data is here. Var1 Freq 1 10.1.17.10 205 2 10.1.17.15 216 3 10.1.17.17 79 4 10.1.17.23 76 5 10.1.17.24 209 6 10.1.17.5 244 7 10.1.17.6 178 8 10.1.17.7 165 9 10.1.17.8 146 10

Re: [R] Space between x-axis ticks

2013-09-27 Thread Jim Lemon
On 09/27/2013 05:15 PM, mohan.radhakrish...@polarisft.com wrote: ... I am trying to clearly show the values in the x-axis in the attached graph. The tick marks are too close and the labels are blurred. ... Hi Mohan, If the tick marks are too close together, you can increase the

Re: [R] Space between x-axis ticks

2013-09-27 Thread mohan . radhakrishnan
Hi Jim 1. I use a bigger font using 'cex' but that worsens because tick marks are close 2. A wider png is also insufficient. The first tick is slightly away from the origin. I should be able to move it closer and then stagger the ticks. What is the 'staxlab'

Re: [R] Locating inefficient code

2013-09-27 Thread jim holtman
Is this what you want? Please use dput when providing data. Should be faster using regular expressions: x - read.table(text = Proto Recv-Q Send-Q Local-Address Foreign-Address State + tcp00172.20.100.2:60255 172.20.100.3:8209

Re: [R] Space between x-axis ticks

2013-09-27 Thread Jim Lemon
On 09/27/2013 06:13 PM, mohan.radhakrish...@polarisft.com wrote: Hi Jim 1. I use a bigger font using 'cex' but that worsens because tick marks are close 2. A wider png is also insufficient. The first tick is slightly away from the origin. I should be able to move it closer and then stagger the

Re: [R] min(NA,bla) != min(bla, NA)

2013-09-27 Thread Magnus Thor Torfason
Thanks for putting together such a quick fix! Unfortunately the policy for the system that I'm working on doesn't allow unreleased versions, so I'll have to work around this for a little bit longer. But I'll ask my sysadmins to install 3.0.3 as soon as it gets released. Best, Magnus On

[R] Compare species presence and absence between sites

2013-09-27 Thread Elaine Kuo
Dear List, I want to compare the presence and absence of bird species based on the sites in a matrix. The matrix has 5 rows for Island A, B, C, D, and E. It has 100 columns for bird species D001-D100. In each cell of the matrix, the presence-absence of bird species will be recorded as 1 or

Re: [R] min(NA,bla) != min(bla, NA)

2013-09-27 Thread Duncan Murdoch
On 13-09-27 6:00 AM, Magnus Thor Torfason wrote: Thanks for putting together such a quick fix! Unfortunately the policy for the system that I'm working on doesn't allow unreleased versions, so I'll have to work around this for a little bit longer. But I'll ask my sysadmins to install 3.0.3 as

Re: [R] Space between x-axis ticks

2013-09-27 Thread mohan . radhakrishnan
Hi Jim, Yes. The attached graph has less values. When there are more the values are too close even though after the beginning and ending tick there is enough space to evenly distribute the ticks. Is there a parameter to specifcy the space between the ticks. I used 'space' in boxplots.

Re: [R] Compare species presence and absence between sites

2013-09-27 Thread Rui Barradas
Hello, Something like this? different - function(x, y) x == 1 y == 0 set.seed(7054) mat - matrix(sample(0:1, 500, TRUE), nrow = 5) rownames(mat) - LETTERS[1:5] colnames(mat) - sprintf(D%03d, 1:100) different(mat[B,], mat[E,]) Hope this helps, Rui Barradas Em 27-09-2013 11:48, Elaine

Re: [R] R not ploting lines in the correct order

2013-09-27 Thread Shane Carey
Hi Sarah, thanks for your reply. Im not sure how to use dput? If I create an object of my data, does that mean you can read it in from your side or something? Here is my code: X Data Date 5.61 24/09/2012 09:13 5.80 16/10/2012 11:17 6.01 24/10/2012 21:43 5.65 11/09/2012 18:34 5.27

Re: [R] Space between x-axis ticks

2013-09-27 Thread Jim Lemon
On 09/27/2013 09:22 PM, mohan.radhakrish...@polarisft.com wrote: Hi Jim, Yes. The attached graph has less values. When there are more the values are too close even though after the beginning and ending tick there is enough space to evenly distribute the ticks. Is there a parameter to specifcy

Re: [R] Locating inefficient code

2013-09-27 Thread arun
Hi, Please use ?dput() dat1- structure(list(Proto = c(tcp, tcp, tcp, tcp, tcp, tcp ), `Recv-Q` = c(0L, 0L, 0L, 0L, 0L, 0L), `Send-Q` = c(0L, 0L, 0L, 0L, 0L, 0L), `Local-Address` = c(172.20.100.2:60255, 172.20.100.2:60247, :::172.20.100.2:80, :::172.20.100.2:80, :::172.20.100.2:80,

Re: [R] Compare species presence and absence between sites

2013-09-27 Thread arun
Just to add: If you wanted the difference of every combination of rows: set.seed(248)  mat1- matrix(sample(0:1,5*100,replace=TRUE),ncol=100,dimnames=list(LETTERS[1:5],paste0(D,sprintf(%03d,1:100))) )  dat-expand.grid(LETTERS[1:5],LETTERS[1:5],stringsAsFactors=FALSE)

Re: [R] R not ploting lines in the correct order

2013-09-27 Thread PIKAL Petr
Hm It seems to me that you want to plot some values from two objects X and Y. you shall at least show us output of str(X) and str(Y) but posting result of dput(X) and dput(Y) gives us an opportunity to test what objects you have and what you actually do with them. Just a guess. You think

Re: [R] R not ploting lines in the correct order

2013-09-27 Thread Sarah Goslee
If you use dput() correctly, those of us following along via email can create an exact duplicate of your R object. All you need to do is: dput(X) and paste the resulting output into email. You see, if I look at your object as you pasted it in, I can't tell if your Date column is a date format, or

Re: [R] Best and Worst values

2013-09-27 Thread arun
Ira, obj_name- load(arun.RData) Pred1- get(obj_name[1]) Actual1- get(obj_name[2]) dat2-

Re: [R] R not ploting lines in the correct order

2013-09-27 Thread Shane Carey
Ah ok, Here we go: structure(list(DATE = structure(c(1348477980, 1350386220, 1351114980, 1347388440, 1345650300, 1344558600, 1344955920, 1348489140, 1351169100, 1352297220, 1350471060, 1352303640, 1351797660, 1351772580, 1349213100, 1354275600, 1351257660, 1345728480, 1355914440, 1344552300,

Re: [R] Some issues with operations

2013-09-27 Thread arun
HI Vivek, I think there is only one row in the whole dataset which fulfills the condition.  If you need the dimension intact, use 'drop=FALSE'  which(rowSums(mat10)==ncol(mat1)) #CXCL14  # 2349  #Simplied some codes: dat1-

Re: [R] R not ploting lines in the correct order

2013-09-27 Thread PIKAL Petr
OK -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Shane Carey Sent: Friday, September 27, 2013 4:06 PM To: Sarah Goslee Cc: r-help@r-project.org Subject: Re: [R] R not ploting lines in the correct order Ah ok, Here we

Re: [R] R not ploting lines in the correct order

2013-09-27 Thread Shane Carey
Your a starbar, exactly what Im looking for. Thanks a mill!! On Fri, Sep 27, 2013 at 3:26 PM, PIKAL Petr petr.pi...@precheza.cz wrote: OK -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Shane Carey Sent: Friday,

Re: [R] R not ploting lines in the correct order

2013-09-27 Thread arun
Hi, Not sure if this helps, but you can try ?xts library(xts) X- structure( xt1- xts(X[,2],order.by=X[,1]) plot(xt1,type=o) A.K. - Original Message - From: Shane Carey careys...@gmail.com To: Sarah Goslee sarah.gos...@gmail.com Cc: r-help@r-project.org r-help@r-project.org Sent:

Re: [R] Calculating euclidean distance in R

2013-09-27 Thread Upton, Stephen (Steve) (CIV)
?read.csv to read your data in, then ?dist to calculate distances. steve -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Debasish Sahu Sent: Friday, September 27, 2013 12:26 AM To: r-help@r-project.org Subject: [R] Calculating

[R] exchange of axis labels in qqnorm function

2013-09-27 Thread Cleber N.Borges
Hello all, Are there a reason for this behaviour in qqnorm function? (the exchange of axis labels ) x - rnorm(1000) par( mfcol=c(1,2) ) qqnorm(x, xlab='X Axis', ylab='Y Axis', datax=FALSE ) #Default qqnorm(x, xlab='X Axis', ylab='Y Axis', datax=TRUE ) Thanks for any explanation.

[R] An Apply function question about changing type of variable

2013-09-27 Thread Vincent Guyader
Hi everyone, plese can you look at this few lines : data(iris) res-apply(iris,MARGIN=2,is) res[1,] the result is : Sepal.Length Sepal.Width Petal.Length Petal.Width Species character character character character character How can I conserve the type off each colum? apply seems to

Re: [R] snow::makeCluster on Windows hangs

2013-09-27 Thread Jeffrey Flint
Prof Ripley: Thank you for the help. - I used the manual option because it was suggested in some postings because it shows the parameters being used. The behavior was the same with and without the manual option (I needed to use ESC to get out). - Would there be some limitation in my

Re: [R] An Apply function question about changing type of variable

2013-09-27 Thread Ben Tupper
Hi, On Sep 27, 2013, at 11:27 AM, Vincent Guyader wrote: Hi everyone, plese can you look at this few lines : data(iris) res-apply(iris,MARGIN=2,is) res[1,] the result is : Sepal.Length Sepal.Width Petal.Length Petal.Width Species character character character character

[R] Logical indexing not working

2013-09-27 Thread Mariki Zietsman
I have a data frame frugivore.abundance.S1 where some columns are factors and others are numbers.For example these are my independent variables and density is my dependent variable. census-c(1:70)sites-c(1:5)birds-c(1:45) I want to select the data where sites is 1 and birds are 1,23,24 or 29 So

Re: [R] Logical indexing not working

2013-09-27 Thread William Dunlap
where ... birds are 1,23,24 or 29 ... birds==c(1,23,24,29) Use is.element(birds, c(1,23,24,29)) or (birds %in% c(1,23,24,29)) if you prefer typing percent signs. Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org

Re: [R] Logical indexing not working

2013-09-27 Thread Rui Barradas
Hello, Please don't post in HTML, it messes up the code and data. And please use ?dput to post your data: dput(fa1) # post the output of this. As for your problem, maybe if you try ?%in% fa1[sites==1 birds %in% c(1,23,24,29),] Hope this helps, Rui Barradas Em 27-09-2013 19:20, Mariki

Re: [R] Logical indexing not working

2013-09-27 Thread Sarah Goslee
Your post demonstrates why we ask people to NOT post in HTML. Attempting to decode it, I think the problem might be birds==c(1,23,24,29) Look at this: birds - c(2, 4, 1, 23, 8, 24) birds - data.frame(birds) birds[birds[,1] == c(1,23,24,29),] And compare birds[birds[,1] %in% c(1,23,24,29),]

[R] Error: C stack usage is too close to the limit when using list.files()

2013-09-27 Thread Jonathan Greenberg
R-helpers: I'm running a file search on my entire drive (Mac OS X) using: files_found - list.files(dir=/,pattern=somepattern,recursive=TRUE,full.names=TRUE) where somepattern is a search pattern (which I have confirmed via a unix find / -name somepattern only returns ~ 3 results). I keep

Re: [R] table of contents link style in R's PDF docs

2013-09-27 Thread Duncan Murdoch
On 26/09/2013 10:33 AM, Duncan Murdoch wrote: On 25/09/2013 11:38 PM, Ben Harrison wrote: Hello, I am mildly annoyed each time I use a PDF doc of an R package that the table of contents hyperlinks are *only* on the page numbers. To activate a hyperlink, one must carefully scan sideways from

[R] Plot lines whose angle and length depict vector quantities

2013-09-27 Thread Conor Ryan
I am trying to plot points on a map for each ship locations (lat/long), where each point is a line whose angle (degrees) denotes ships heading and whose line length denotes it's speed. Unfortunately arrows(); p.arrows (sfsmisc) and ms.arrows (TeachingDemos) require start and end coordinates but I

Re: [R] Error: C stack usage is too close to the limit when using list.files()

2013-09-27 Thread Ben Bolker
Jonathan Greenberg jgrn at illinois.edu writes: R-helpers: I'm running a file search on my entire drive (Mac OS X) using: files_found - list.files(dir=/,pattern=somepattern,recursive=TRUE,full.names=TRUE) where somepattern is a search pattern (which I have confirmed via a unix find /

Re: [R] Error: C stack usage is too close to the limit when using list.files()

2013-09-27 Thread Jonathan Greenberg
Ben: I'd like to avoid using that (previous version of my code solved it in that way) -- I would like cross-platform compatibility and I am pretty sure, along with Windows, vanilla Macs don't come with find either unless XCode has been installed. Is the list.files() code itself recursive when

Re: [R] Plot lines whose angle and length depict vector quantities

2013-09-27 Thread Sarah Goslee
It's a straightforward trigonometry problem, isn't it? On Fri, Sep 27, 2013 at 2:56 PM, Conor Ryan miol...@gmail.com wrote: I am trying to plot points on a map for each ship locations (lat/long), where each point is a line whose angle (degrees) denotes ships heading and whose line length

Re: [R] Error: C stack usage is too close to the limit when using list.files()

2013-09-27 Thread William Dunlap
Do you have some symbolic links that make loops in your file system? list.files() has problems with such loops and find does not. E.g., on a Linux box: % cd /tmp % mkdir dir dir/subdir % cd dir/subdir % ln -s ../../dir linkToUpperDir % cd /tmp % R --quiet list.files(dir, recursive=TRUE,

Re: [R] Error: C stack usage is too close to the limit when using list.files()

2013-09-27 Thread Berend Hasselman
On 27-09-2013, at 21:50, Jonathan Greenberg j...@illinois.edu wrote: Ben: I'd like to avoid using that (previous version of my code solved it in that way) -- I would like cross-platform compatibility and I am pretty sure, along with Windows, vanilla Macs don't come with find either unless

Re: [R] Plot lines whose angle and length depict vector quantities

2013-09-27 Thread Bert Gunter
On Fri, Sep 27, 2013 at 12:44 PM, Sarah Goslee sarah.gos...@gmail.com wrote: It's a straightforward trigonometry problem, isn't it? Indeed! ( (r,theta) to (x,y) coordinates ) . So I wonder if this is a homework problem. If so, the OP should note that we try not to do homework here. Cheers,

Re: [R] Error: C stack usage is too close to the limit when using list.files()

2013-09-27 Thread William Dunlap
Toss a couple of extra files in there and you will see the output grow exponentially. % touch dir/IMPORTANT_1 dir/subdir/IMPORTANT_2 and in R those two new files cause 82 more strings to appear in list.file's output: nchar(list.files(dir, recursive=TRUE)) [1] 11 18 33 40 55 62 77 84

[R] Help with nested and non-nested factors

2013-09-27 Thread Ana Arjona
Hi, I am trying to fit a multilevel model with lmer but have some doubts about the code: [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting

[R] Memory distribution using foreach

2013-09-27 Thread pakoun
Dear R users, I am struggling with memory issues and try to understand a few things. I am using an LSF cluster with PGI compiler and parallel mpi2 computing (whatever does that means..) and i submit a job like: bsub -R rusage[mem=3] -q queue -n 24 R CMD BATCH arguments.. myjob.r ..log

Re: [R] exchange of axis labels in qqnorm function

2013-09-27 Thread Rui Barradas
Hello, That's documented behavior. From the help page for ?qqnorm: datax: logical. Should data values be on the x-axis? (Try it without renaming the axis and it makes more sense.) Hope this helps, Rui Barradas Em 27-09-2013 15:38, Cleber N.Borges escreveu: Hello all, Are there a reason

Re: [R] Plot lines whose angle and length depict vector quantities

2013-09-27 Thread Greg Snow
The ms.arrows along with my.symbols in the TeachingDemos package does not require start and end points, it takes a single point along with the angle and length (and the length can be a single constant to have all the arrows the same length, or a variable to have different lengths). You can also

Re: [R] Memory distribution using foreach

2013-09-27 Thread Simon Zehnder
First of all LSF is a batch scheduling software. It usually expects an .lsf script. Usually the compilers on a cluster are interchangeable via the 'module switch unload module load module' and MPI-2 is the message passing interface standard. This is also rather an topic for the high-performance

Re: [R] Compare species presence and absence between sites

2013-09-27 Thread Elaine Kuo
Thanks Rui and Arun. Both worked well. One more question, what shall I add for Rui's code if only the comparison of TRUE (no FALSE) to be shown in the result? Elaine code different - function(x, y) x == 1 y == 0 set.seed(7054) mat - matrix(sample(0:1, 500, TRUE), nrow = 5) rownames(mat) -

Re: [R] An Apply function question about changing type of variable

2013-09-27 Thread R. Michael Weylandt michael.weyla...@gmail.com
On Sep 27, 2013, at 11:27, Vincent Guyader vincent.guya...@allstat.fr wrote: Hi everyone, plese can you look at this few lines : data(iris) res-apply(iris,MARGIN=2,is) res[1,] the result is : Sepal.Length Sepal.Width Petal.Length Petal.Width Species character character

Re: [R] Compare species presence and absence between sites

2013-09-27 Thread Rui Barradas
Hello, Maybe something like the following. res - different(mat[B,], mat[E,]) res[res] Rui Barradas Em 27-09-2013 23:11, Elaine Kuo escreveu: Thanks Rui and Arun. Both worked well. One more question, what shall I add for Rui's code if only the comparison of TRUE (no FALSE) to be shown in

Re: [R] Compare species presence and absence between sites

2013-09-27 Thread arun
Elaine, Try: set.seed(248)  mat1- matrix(sample(0:1,5*100,replace=TRUE),ncol=100,dimnames=list( c(Hokkaido,Honshu,Shikoku,Kyushu,Amami) ,paste0(D,sprintf(%03d,1:100))) ) ##to change  dat- expand.grid(rownames(mat1),rownames(mat1),stringsAsFactors=FALSE) dat1- dat[!paste0(dat[,1],dat[,2])%in%

[R] netCDF to raster and projection to UTM: output NA

2013-09-27 Thread gabriela bucini
Dear R colleagues, I'm facing a problem with the projection of a netCDF file. My original netCDF file is in lat/lon coordinates and I want to project it in UTM. I use the raster package with the functionraster to open the file and then projectRaster to change projection (I want to maintain a

Re: [R] Memory distribution using foreach

2013-09-27 Thread pakoun
Thank you Simon for your quick response. Now I understand a lot of things, and how to use them. Well they should offer some lessons my department how to work with the cluster but unfortunately they didnt and I am trying to find alone everything. Thanks again for the great advise Best wishes Panos

Re: [R] Plot lines whose angle and length depict vector quantities

2013-09-27 Thread Jim Lemon
On 09/28/2013 04:56 AM, Conor Ryan wrote: I am trying to plot points on a map for each ship locations (lat/long), where each point is a line whose angle (degrees) denotes ships heading and whose line length denotes it's speed. Unfortunately arrows(); p.arrows (sfsmisc) and ms.arrows

[R] makeCluster help needed

2013-09-27 Thread Jeffrey Flint
This is in regards to the SNOW library. I'm using Windows. The problem is that makeSOCKcluster hangs in R as well as the DOS command line. Below I've shown that it completes the Rscript until it reaches the line slaveLoop(master) , at which point it hangs. = In R:

[R] How to make LN(x) transformation in R?

2013-09-27 Thread Xiao Fang
Dear R colleagues, I am a newbie to R. I can not figure out how to compute Ln(x) value in R. My question may be so easy for you but I will really appreciate if you can help me. Thanks so much for your time! Kathy [[alternative HTML version deleted]]

Re: [R] How to make LN(x) transformation in R?

2013-09-27 Thread Berend Hasselman
On 28-09-2013, at 02:21, Xiao Fang xiaofang1...@gmail.com wrote: Dear R colleagues, I am a newbie to R. I can not figure out how to compute Ln(x) value in R. My question may be so easy for you but I will really appreciate if you can help me. Thanks so much for your time! Assuming you