Re: [R] outer() or some other function for regression prediction with 2 IVs

2012-07-10 Thread peter dalgaard
On Jul 10, 2012, at 05:35 , Joseph Clark wrote: Thanks. I was able to get what I wanted by doing this: predxn - function(s,d) { coef(m3)[1] + coef(m3)[2]*s + coef(m3)[3]*s^2 + coef(m3)[4]*d + coef(m3)[5]*d^2 } But it's not very elegant... You didn't take Michael's hint:

[R] [R-pkgs] package JM -- version 1.0-0

2012-07-10 Thread Dimitris Rizopoulos
Dear R-users, I'd like to announce the release of version 1.0-0 of package JM (already available from CRAN) for the joint modeling of longitudinal and time-to-event data using shared parameter models. These models are applicable in mainly two settings. First, when focus is in the survival

Re: [R] Read vector as multi-dimensional data in R by row

2012-07-10 Thread arun
Hi, Try this: b1-aperm(array(a,dim=c(5,2,2)),perm=c(2,1,3)) b1 , , 1 [,1] [,2] [,3] [,4] [,5] [1,]    1    2    3    4    5 [2,]    6    7    8    9   10 , , 2 [,1] [,2] [,3] [,4] [,5] [1,]   11   12   13   14   15 [2,]   16   17   18   19   20 A.K. - Original Message -

Re: [R] Skipping lines and incomplete rows

2012-07-10 Thread vioravis
Thanks a lot Rui and Arun. The methods work fine with the data I gave but when I tried the two methods with the following semi-colon separated data using sep = ;. Only the first 3 columnns are read properly rest of the columns are either empty or NAs.

Re: [R] How to add marker in Stacked bar plot?

2012-07-10 Thread Manish Gupta
Thanks it works fine. But can i control its width? Regards -- View this message in context: http://r.789695.n4.nabble.com/How-to-add-marker-in-Stacked-bar-plot-tp4635946p4635954.html Sent from the R help mailing list archive at Nabble.com. __

Re: [R] How to add marker in Stacked bar plot?

2012-07-10 Thread Manish Gupta
I found arrow is too thin. I have one arrow image. I want to put it there. How can i import external image and merge with stacked bar plot. Regards -- View this message in context: http://r.789695.n4.nabble.com/How-to-add-marker-in-Stacked-bar-plot-tp4635946p4635955.html Sent from the R help

[R] How to use external image with R plot?

2012-07-10 Thread Manish Gupta
Hi, I am wokring on stacked bar plot and i need to add one arrow dynamically. http://r.789695.n4.nabble.com/file/n4635959/arrow_glossy_right_red.jpg http://r.789695.n4.nabble.com/file/n4635959/Screenshot.10.png Final image: http://r.789695.n4.nabble.com/file/n4635959/Screenshot.1.png

Re: [R] Package 'MASS' (polr): Error in svd(X) : infinite or missing values in 'x'

2012-07-10 Thread Jessica Streicher
Hi Jeremy, newData-data.frame(JVeg5=factor(Jdata[,JVeg5]),scale(Jdata[,c(Elevation,Lat_Y_pos,Coast_dist,Stream_dist)])) Global - polr(JVeg5 ~ Elevation + Lat_Y_pos + Coast_dist + Stream_dist, data=newData, na.action = na.omit, Hess = TRUE) summary(Global) Does this still do

Re: [R] outer() or some other function for regression prediction with 2 IVs

2012-07-10 Thread Joseph Clark
I saw the hint but didn't know how to implement it, I learn more every day. Thanks for spelling it out! I knew there had to be a function like predict! // joseph w. clark , phd candidate \\ usc marshall school of business Subject: Re: [R]

Re: [R] Skipping lines and incomplete rows

2012-07-10 Thread Rui Barradas
Hello, My approach was slightly different, to use readLines to take care of the header and read.table for the data. This works with the new dataset you've posted, but we must use the option comment.char = . Try the following. head - readLines(test.txt, n=4)[4] dat - read.table(test.txt,

Re: [R] Extracting arithmetic mean for specific values from multiple .txt-files

2012-07-10 Thread vimmster
Dear Mr. Holtman, but I cannot leave out the value and cannot change the values to 1200.995 manually (for each test subject with a reaction time 1000 ms), because the first your lead to incomplete data and the latter would be too time-consuming. Dear Rui, here I have three files, which have

Re: [R] Skipping lines and incomplete rows

2012-07-10 Thread Rui Barradas
Or maybe it's better to coerce Temp and Press to numeric, if they are variables temperature and presssure. dat$Time - as.Date(dat$Time, format=%m/%d/%Y) dat$Temp - as.numeric(dat$Temp) dat$Press - as.numeric(dat$Press) This makes those '#N/A' values NA. Rui Barradas Em 10-07-2012 09:34, Rui

Re: [R] boxplot with cut

2012-07-10 Thread Rui Barradas
Hello, Maybe this iss what you're looking for. GD is your data.frame. multi.boxplot - function(x, by, ...){ x - as.data.frame(x) sp - split(x, by) len - length(sp) - 1 n - ncol(x) n1 - n + 1 boxplot(x[[ 1 ]] ~ by, at = 0:len*n1 + 1,

[R] how can I show the xlab and ylab information while using layout

2012-07-10 Thread Jie Tang
hi R-users: I want to draw three plot into one figure by layout and the script has been shown below. But I find R does not show the xlab and ylab information completely as shown the figure attached. How can I midify the script.? thank you . xxlab-paste(cpmd, (,ro,%),sep= )

Re: [R] how can I show the xlab and ylab information while using layout

2012-07-10 Thread Sarah Goslee
The margins you specified aren't large enough to hold the information you're trying to put in them, so you need to make them larger. Sarah On Tuesday, July 10, 2012, Jie Tang wrote: hi R-users: I want to draw three plot into one figure by layout and the script has been shown below. But

Re: [R] Extracting arithmetic mean for specific values from multiple .txt-files

2012-07-10 Thread Rui Barradas
Hello, Ok, I think that there were two problems. One, gsub substitutes all (g - global) occurrences of the search pattern, so both periods were removed. The other, it would allways consider column 8 as character, but when there are no values with two periods it's read in with class numeric.

Re: [R] How to use external image with R plot?

2012-07-10 Thread Michael Sumner
There are many ways to do this, here is one using an example from ?barplot library(jpeg) x - readJPEG(arrow_glossy_right_red.jpg) barplot(VADeaths, border = dark blue) rasterImage(x, 0, 60, 1, 80) You'll have to change those numbers to suit your plot, par('usr) gives a quick idea of the extents.

Re: [R] is it possible to insert a figure into into another new figure by r script

2012-07-10 Thread Thomas Adams
Jie, I think the R contributed package, grImport, by Paul Murrell does what you want. See this: http://www.jstatsoft.org/v30/i04/paper/ Tom On Mon, Jul 9, 2012 at 11:14 PM, Mikhail Titov m...@gmx.us wrote: Jie Tang totang...@gmail.com writes: hi R-users Now I have a figure in emf or

[R] image.plot transparent?

2012-07-10 Thread Chris82
Hi R users, I have a maybe strange problem. Normaly I do image.plot() with x,y coordinates and add=T and if I have some NA values in my data matrix z, the color will be transparent of these pixels. But now I have a disorted coordinate system and x,y are a matrix. It works also fine, but now NA

Re: [R] How to add marker in Stacked bar plot?

2012-07-10 Thread Jorge I Velez
Yes, you can. See the lwd argument under ?arrows. --JIV On Tue, Jul 10, 2012 at 2:16 AM, Manish Gupta mandecent.gu...@gmail.comwrote: Thanks it works fine. But can i control its width? Regards -- View this message in context:

Re: [R] Predicted values for zero-inflated Poisson

2012-07-10 Thread Laura Lee
Alain- Thanks again for the response. I guess my question is more related to R, which I'm learning as I go along. Could you provide guidance as to how I would code this in R? Thanks, Laura From: Alain Zuur [via R] [mailto:ml-node+s789695n4635920...@n4.nabble.com] Sent: Monday, July 09, 2012

Re: [R] how can I show the xlab and ylab information while using layout

2012-07-10 Thread Sarah Goslee
The mar argument to par(). Please do read ?par and perhaps the posting guide. Sarah On Tuesday, July 10, 2012, Jie Tang wrote: which parameter ? 2012/7/10 Sarah Goslee sarah.gos...@gmail.com javascript:_e({}, 'cvml', 'sarah.gos...@gmail.com'); The margins you specified aren't large enough

Re: [R] image.plot transparent?

2012-07-10 Thread Sarah Goslee
This may be device and OS dependent, so please provide the information requested in the posting guide, at a minimum the output of sessionInfo(). A small reproducible example is also necessary. Sarah On Tuesday, July 10, 2012, Chris82 wrote: Hi R users, I have a maybe strange problem.

[R] RGB components of plot() colours

2012-07-10 Thread Ted Harding
A quick question: Is there anywhere a listing of the RGB components of the named colours listed by colors()? For example, where would I find the RGB for orange1 or salmon? When I look at an EPS file from R where I have used these colours, it seems that for: salmon: 0.9804 0.5020 0.4471 rgb

Re: [R] number of decimal places in a number?

2012-07-10 Thread Martin Ivanov
Dear R users, Thank You very much for Your responsiveness. I think the suggestion of arun's modification of Josh's code works best and it is what I am going to implement. Cite Ellison: Surely the issue is not the particular numeric resolution of the numbers but the idea that the bounding box

[R] define stuff to be only usable in the same file

2012-07-10 Thread Jessica Streicher
Hello R-Help! I've looked around and have not found: A simple(short) way to hide functions and variables from the global environment. What i want is for a few of them to only be accessable from the scriptfile they're in. I probably could do fun things with environments , but that seems quite

[R] fill 0-row data.frame with 1 line of NAs

2012-07-10 Thread Liviu Andronic
Dear all Is there a simpler method to achieve the following: When I obtain an empty data.frame after subsetting, I need for it to contain one line of NAs. Here's a dummy example: (.xb - iris[ iris$Species=='zz', ]) [1] Sepal.Length Sepal.Width Petal.Length Petal.Width Species 0 rows (or

Re: [R] RGB components of plot() colours

2012-07-10 Thread Duncan Murdoch
On 12-07-10 9:05 AM, (Ted Harding) wrote: A quick question: Is there anywhere a listing of the RGB components of the named colours listed by colors()? For example, where would I find the RGB for orange1 or salmon? When I look at an EPS file from R where I have used these colours, it seems

Re: [R] define stuff to be only usable in the same file

2012-07-10 Thread Duncan Murdoch
On 12-07-10 9:13 AM, Jessica Streicher wrote: Hello R-Help! I've looked around and have not found: A simple(short) way to hide functions and variables from the global environment. What i want is for a few of them to only be accessable from the scriptfile they're in. I probably could do fun

Re: [R] RGB components of plot() colours

2012-07-10 Thread Sarah Goslee
R uses the sandard X11 colors, I believe, and if you're using linux there's a rgb.txt file on your computer that contains them. It's also available here http://cvsweb.xfree86.org/cvsweb/*checkout*/xc/programs/rgb/rgb.txt?rev=1.1 and a less-authoritative but prettier version:

Re: [R] Predicted values for zero-inflated Poisson

2012-07-10 Thread Achim Zeileis
On Tue, 10 Jul 2012, Laura Lee wrote: Alain- Thanks again for the response. I guess my question is more related to R, which I'm learning as I go along. Could you provide guidance as to how I would code this in R? That depends on what exactly you want to predict. As Alain said: The

Re: [R] fill 0-row data.frame with 1 line of NAs

2012-07-10 Thread Rui Barradas
Hello, If you write a function, it becomes less convoluted... empty - function(x){ if(NROW(x) == 0){ y - rep(NA, NCOL(x)) names(y) - names(x) y }else x } (.xb - iris[ iris$Species=='zz', ]) empty(.xb) Hope this helps, Rui

Re: [R] Plotting rpart trees with long list of class members

2012-07-10 Thread Jean V Adams
Thanks. Very helpful. You can use the information from the splits in the first tree, to define a new grouping variable, which will simplify the plot: suvar - sort(unique(test_set$list_var)) test_set$var_grp - as.factor(testtree$csplit[match(test_set$list_var, suvar)]) testtree2 - rpart (

Re: [R] image.plot transparent?

2012-07-10 Thread Prof Brian Ripley
On 10/07/2012 13:41, Sarah Goslee wrote: This may be device and OS dependent, so please provide the information requested in the posting guide, at a minimum the output of sessionInfo(). A small reproducible example is also necessary. I think not. My guess is it is part of a package which we

[R] customize packages' help index ( 00index.html file )

2012-07-10 Thread Damien Georges
Hi all, I'm writing my packages helps files and I'm not really satisfied by the visual results. I'm would like to make subsections in a package function help index file. I would like for example to put all S4 object documentation link together, then all the getters function.. and so on..

[R] identify.hclust() doesn't cut tree at the vertical position of the mouse pointer

2012-07-10 Thread WATSON Mick
Dear All According to the identify.hclust documentation the function cuts the tree at the vertical position of the pointer and highlights the cluster containing the horizontal position of the pointer. When I carry out this, the tree isn't cut where I click - in fact, there seems to be a limit

[R] Use of Sappy and Tappy for Mathematical Calculation

2012-07-10 Thread Rantony
Hi, i have a matrix like this, ABCXYZ... . - -- 1220 ... . 2435 ... . 3040 ... . Here, i need to get Sum of each

[R] fitting power growth

2012-07-10 Thread Thomas Hoffmann
Dear all I am using the x and y vectors as defined below and want do to a power law regression: y = a x^b using lm(log(y)~log(x)) gives reasonable values (b=1.23) but is not very popular due to biases of back-transformation from log to non-log values. Using

[R] Mac OS X R uninstallation question

2012-07-10 Thread Alastair
Hi, I've been using R for a number of years and have always installed the newest version when released. However I've just noticed that old versions of R are taking up quite a lot of disk space. lap-alastair:/ alastair$ du -h -d 1 /Library/Frameworks/R.framework/Versions/ 266M

Re: [R] Questions about doing analysis based on time

2012-07-10 Thread APOCooter
Thanks to everyone for their help so far. It's been greatly appreciated. I have a new, but similar problem: I have data that I have broken down by hour (median/mean for each hour). I would like to break it down further, by each half hour (0:00-0:29, 0:30-0:59, 1:00-1:29, 1:30-1:59, etc). I

[R] Count of elements in coulmns of a matrix

2012-07-10 Thread Rantony
Could you please tell me what is the function or method to get count of elements in all the columns in a matrix ? for eg :- ABC XYZPQR -- - -- 234 4 5 54 3 2 Result will be like

[R] gdata: Problem reading excel document containing non-US characters

2012-07-10 Thread Rolf Marvin Bøe Lindgren
I am using the gdata package to read in an Excel document. read.xls chokes on a “foreign” character. Here's the original code: require(gdata) dendro - read.xls(/tmp/avitot.xlsv3WiXg,fileEncoding=Latin1) Now, the fileEncoding=Latin1 ought to work, because if i copy the code for read.xls,

Re: [R] Count of elements in coulmns of a matrix

2012-07-10 Thread Sarah Goslee
It depends: what's in those empty space? Some combination of apply() and something else, depending on what your matrix *actually* looks like, and here dput() would be vastly preferable to copy and paste of something that didn't even come from an R session. The something else might involve

Re: [R] define stuff to be only usable in the same file

2012-07-10 Thread Jessica Streicher
On 10.07.2012, at 15:24, Duncan Murdoch wrote: On 12-07-10 9:13 AM, Jessica Streicher wrote: Hello R-Help! I've looked around and have not found: A simple(short) way to hide functions and variables from the global environment. What i want is for a few of them to only be accessable from

Re: [R] Mac OS X R uninstallation question

2012-07-10 Thread Prof Brian Ripley
Please ask Mac-specific questions on R-sig-mac. In particular, it is a little odd that these are not getting deleted when you install a new version. But *if all your packages are up to date* you do not need earlier versions of R.framework, so run update.packages(checkBuilt=TRUE) first.

Re: [R] fill 0-row data.frame with 1 line of NAs

2012-07-10 Thread Peter Ehlers
On 2012-07-10 06:57, Rui Barradas wrote: Hello, If you write a function, it becomes less convoluted... empty - function(x){ if(NROW(x) == 0){ y - rep(NA, NCOL(x)) names(y) - names(x) y }else x } (.xb - iris[ iris$Species=='zz',

Re: [R] define stuff to be only usable in the same file

2012-07-10 Thread Jessica Streicher
On 10.07.2012, at 16:45, Jessica Streicher wrote: On 10.07.2012, at 15:24, Duncan Murdoch wrote: On 12-07-10 9:13 AM, Jessica Streicher wrote: Hello R-Help! I've looked around and have not found: A simple(short) way to hide functions and variables from the global environment. What

Re: [R] fill 0-row data.frame with 1 line of NAs

2012-07-10 Thread Brian Diggs
On 7/10/2012 7:53 AM, Peter Ehlers wrote: On 2012-07-10 06:57, Rui Barradas wrote: Hello, If you write a function, it becomes less convoluted... empty - function(x){ if(NROW(x) == 0){ y - rep(NA, NCOL(x)) names(y) - names(x) y }else x } (.xb - iris[

[R] Help with vectors and rollapply

2012-07-10 Thread Raghuraman Ramachandran
Hello I have a vector a =(-2,0,0,0,1,0,0,3,0,0,-4) I want to replace all zeros into previous non-zero state. So for instance the above vector should be converted into: a= (-2,-2,-2,-2,1,1,1,3,3,3,-4) I tried many things and finally concluded that probably(?) rollapply may be the best way? I

Re: [R] multiple comparisons with generalised least squares

2012-07-10 Thread Ariel
racmar wrote I have also been searching various forums and books to see if there are any methods I could use and have only found people, such as yourself, asking the same question. I was looking into this recently, as well, and found that the problem has to do with building the

Re: [R] Count of elements in coulmns of a matrix

2012-07-10 Thread arun
Hi, Try this: list1-list(ABC=c(2,5),XYZ=c(3,4,4,2),PQR=c(4,5,3)) lapply(list1,function(x) length(x)) $ABC [1] 2 $XYZ [1] 4 $PQR [1] 3  list2-lapply(list1,function(x) length(x))  dat2-data.frame(list2)  dat2   ABC XYZ PQR 1   2   4   3 A.K. - Original Message - From: Rantony

[R] RGL 3D curvilinear shapes

2012-07-10 Thread PatGauthier
Dear useRs, I'm trying to simply fill in the area under a curve using RGL. Here' the set up: x - c(0.75,75.75,150.75,225.75,300.75,375.75,450.75,525.75,600.75,675.75, 0.5,50.5,100.5,150.5,200.5,250.5,300.5,350.5,400.5,450.5,

Re: [R] Help with vectors and rollapply

2012-07-10 Thread William Dunlap
It looks like you already have the zoo package loaded so you can use its na.locf(), which replaces NA's with the last non-NA value. Convert the 0s to NAs with replace() and feed the result into na.locf(): a - c(-2,0,0,0,1,0,0,3,0,0,-4) aOut - c(-2,-2,-2,-2,1,1,1,3,3,3,-4)

Re: [R] Predicted values for zero-inflated Poisson

2012-07-10 Thread Laura Lee
I want to predict the number of turtles for different levels of effort and combinations of covariates. So, for my dataset from which I built the model, would I compare sum(predict(ZIP,type=response)) to the observed bycatch to compare numbers? In order to predict for the new data (called effort),

Re: [R] Use of Sappy and Tappy for Mathematical Calculation

2012-07-10 Thread Nordlund, Dan (DSHS/RDA)
-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Rantony Sent: Tuesday, July 10, 2012 3:17 AM To: r-help@r-project.org Subject: [R] Use of Sappy and Tappy for Mathematical Calculation Hi, i have a matrix like this, ABC

Re: [R] Questions about doing analysis based on time

2012-07-10 Thread Rui Barradas
Hello, You can use cut.POSIXt from package base. cut(dat$SunDate, breaks=30 mins) Hope this helps, Rui Barradas Em 10-07-2012 13:43, APOCooter escreveu: Thanks to everyone for their help so far. It's been greatly appreciated. I have a new, but similar problem: I have data that I have

Re: [R] Extracting arithmetic mean for specific values from multiple .txt-files

2012-07-10 Thread vimmster
Dear Rui, thank you very much. Your solution works perfectly. One last question: I need to write a function, with ONE value (here: a ratio) for the correct reactions divided per trials or trialCount, respectively, FOR EACH test subject. / means divided by in the following. I need the ratio

[R] calculating the difference between days?

2012-07-10 Thread C W
Hi List, I have one column of beginning dates and one column of ending dates, I want to find their difference. And I want to ignore the trailing zeros, basically everything after the first colon mark. Begin_date End_date 01JAN2000:00:00:00:000

Re: [R] R to winbugs interface

2012-07-10 Thread Uwe Ligges
On 09.07.2012 19:27, PRAGYA SUR wrote: Yes that was the problem. Thank you very much. Can anyone tell me the meaning of The following object(s) are masked _by_ '.GlobalEnv': beta It means you have two instances of beta, one in your workspace ('.GlobalEnv') and one that is probably in

Re: [R] Predicted values for zero-inflated Poisson

2012-07-10 Thread Highland Statistics Ltd
*Laura Lee* laura.lee at ncdenr.gov mailto:r-help%40r-project.org?Subject=Re%3A%20%5BR%5D%20Predicted%20values%20for%20zero-inflated%20PoissonIn-Reply-To=%3C1341937636301-4636016.post%40n4.nabble.com%3E /Tue Jul 10 18:27:16 CEST 2012/

Re: [R] Extracting arithmetic mean for specific values from multiple .txt-files

2012-07-10 Thread Rui Barradas
Hello, I'm glad it help. As for this second question, you should explain yourself better. 1. What is a test subject, which column records its id? vpNum? 2. You say divided per trials or trialCount. Does this mean per trial number (example: divide by 1, by 2, by 3, etc, by 149) or per number

Re: [R] fill 0-row data.frame with 1 line of NAs

2012-07-10 Thread Peter Ehlers
On 2012-07-10 08:50, Brian Diggs wrote: On 7/10/2012 7:53 AM, Peter Ehlers wrote: On 2012-07-10 06:57, Rui Barradas wrote: Hello, If you write a function, it becomes less convoluted... empty - function(x){ if(NROW(x) == 0){ y - rep(NA, NCOL(x)) names(y) - names(x)

Re: [R] fill 0-row data.frame with 1 line of NAs

2012-07-10 Thread Rui Barradas
Hello, Em 10-07-2012 18:59, Peter Ehlers escreveu: On 2012-07-10 08:50, Brian Diggs wrote: On 7/10/2012 7:53 AM, Peter Ehlers wrote: On 2012-07-10 06:57, Rui Barradas wrote: Hello, If you write a function, it becomes less convoluted... empty - function(x){ if(NROW(x) == 0){

Re: [R] Predicted values for zero-inflated Poisson

2012-07-10 Thread Laura Lee
Alain- Thanks again for your reply. Yes, the offset for effort is only in the count part of the model. Sorry I wasn't clear about why I was using 'sum'...my effort data set contains records of trips with the effort given for each trip. I thought using sum would get me the total number of

Re: [R] Specify model with polynomial interaction terms up to degree n

2012-07-10 Thread YTP
Yep, that code is verbatim what I typed in, using version 2.14 ... seems weird. -- View this message in context: http://r.789695.n4.nabble.com/Specify-model-with-polynomial-interaction-terms-up-to-degree-n-tp4635130p4636031.html Sent from the R help mailing list archive at Nabble.com.

Re: [R] Use of Sappy and Tappy for Mathematical Calculation

2012-07-10 Thread arun
Hi,  dat1-data.frame(ABC=c(12,24,30),XYZ=c(20,35,40))  dat2-as.matrix(dat1)  #mean  dat2mean-apply(dat2,2,mean)  dat2mean   #   ABC  XYZ #22.0 31.7 dat2sum-apply(dat2,2,sum)  dat2median-apply(dat2,2,median)  dat2max-apply(dat2,2,max) dat2min-apply(dat2,2,min)  

[R] HELP me please with import of csv to R

2012-07-10 Thread F86
Hey, I am having problems with importing a csv file to R. I could read the file by typing: read.csv(file=/Users/kama/Desktop/skatter.csv, header=TRUE, sep=;) However, i can not analyze the skatter - for ex, when i type: skatter = read.csv(skatter.csv) i get this message: Error in

[R] problem for installing rgdal

2012-07-10 Thread stanislas rebaudet
Hello, I run [R] 2.14 on Mac OS 10.6 and I've been desperately trying to install rpy2 in order to compute spatial statistics on QGIS 1.7.3. rpy2 is dependent upon the rgdal [R]package that I've been unable to install in spite of up to date versions of GDAL and PROJ. More precisely, [R] console

[R] R code help to change table format

2012-07-10 Thread peziza
I am trying to input an OTU table into EstimateS, however, the format of the OTU table has to be changed to fit the format EstimateS will accept. In R, I would like to change the format of the OTU table (from excel). Here is what I need to do, take Example 1 and create Example 2. The problem is

Re: [R] Skipping lines and incomplete rows

2012-07-10 Thread arun
Hello Ravi, I was not aware that your dataset have special character # before NA.  If it was just plain NA, it would have worked.  So, It's not because of sep= ;. See below: #Without # dat1-read.table(text=  Remove this line  Remove this line  Remove this line  Time;Actual Speed;Actual

Re: [R] calculating the difference between days?

2012-07-10 Thread arun
Hi, Try this: dat3-read.table(text= Begin_date  End_date 01JAN2000:00:00:00:000  02FEB2002:00:00:00:000 24MAR2012:00:00:00:000  18MAY2012:00:00:00:000 01OCT2003:00:00:00:000  02FEB2004:00:00:00:000 01JAN2000:00:00:00:000  02FEB2000:00:00:00:000

[R] Times Series Data using GLS

2012-07-10 Thread MRB305
I am trying to use regression to determine the interaction between a couple of variables while correcting for autocorrelation. Thus far, I have created the code: model - gls(yvar~xvar1*xvar2, correlation = corARMA (p=2), method = ML, data = data) I'm having a difficult time understanding the

[R] Changing x-axis values displayed on histogram

2012-07-10 Thread jlwoodard
Is it possible to change the x-axis values in a histogram to reflect binned values? Here are my data: histexample-c(6,7,7,8,8,8,9,9,9,9,9,10,10,10,10,10,10,10,11,11,11,11,11,11,12,12,12,12,13,13,13,14,14,14,15,16) hist(histexample) Now, I'll bin pairs of adjacent values together (e.g., 5-6,

[R] Need HELP: how find and use a csv file?

2012-07-10 Thread Faradj Koliev
Hey, I am having some problems with importing a csv file into R and then saving it for analyzing. I got a csv file ( skater.csv) which i could read by typing: read.csv(file=/Users/kama/Desktop/skatter.csv, header=TRUE, sep=;) However, when i enter:skatter.csv-read.csv(skatter.csv,

Re: [R] Package 'MASS' (polr): Error in svd(X) : infinite or missing values in 'x'

2012-07-10 Thread Rune Haubo
Hi Jeremy, I think Jessica is right that probably you could make polr converge and produce a Hessian if the data are better scaled, but there might also be other things not allowing you to get the Hessian/vcov. Could be insightful if you showed us the result of str(Jdata) Also, I am thinking

Re: [R] HELP me please with import of csv to R

2012-07-10 Thread Sarah Goslee
Hi, On Tue, Jul 10, 2012 at 12:48 PM, F86 farad...@gmail.com wrote: Hey, I am having problems with importing a csv file to R. I could read the file by typing: read.csv(file=/Users/kama/Desktop/skatter.csv, header=TRUE, sep=;) So that command does work? However, i can not analyze the

[R] Understanding cenros Error

2012-07-10 Thread Rich Shepard
Before reading water chemistry into a data frame I removed all missing data. Yet when I try to run cenros() to summarize a specific chemical I get an error that I do not understand: with( subset(chem, param=='Ag'), cenros(quant,ceneq1) ) Error in lm.fit(x, y, offset = offset, singular.ok =

Re: [R] calculating the difference between days?

2012-07-10 Thread C W
When the days and time are identical, difftime() gives difference in secs. I still want difference in days. Say, below my last row is identical dat3-read.table(text= Begin_date End_date 01JAN2000:00:00:00:000 02FEB2002:00:00:00:000 24MAR2012:00:00:00:000

Re: [R] Need HELP: how find and use a csv file?

2012-07-10 Thread Sarah Goslee
You don't actually have to post more than once. Really. skatter - read.table(file.choose(), header=TRUE, sep=;) or skatter - read.table(/Users/kama/Desktop/skatter.csv, header=TRUE, sep=;) or whatever the actual path to the file is. As a new user of R, you should read the Introduction to R

Re: [R] Need HELP: how find and use a csv file?

2012-07-10 Thread Rich Shepard
On Tue, 10 Jul 2012, Faradj Koliev wrote: I got a csv file ( skater.csv) which i could read by typing: read.csv(file=/Users/kama/Desktop/skatter.csv, header=TRUE, sep=;) Try: skatter - read.csv('/Users/kama/Desktop/skatter.csv', header = T, sep = ';') Rich

Re: [R] calculating the difference between days?

2012-07-10 Thread C W
Actually, when specifying unit=days inside difftime() will do. -M On Tue, Jul 10, 2012 at 3:55 PM, C W tmrs...@gmail.com wrote: When the days and time are identical, difftime() gives difference in secs. I still want difference in days. Say, below my last row is identical

Re: [R] Changing x-axis values displayed on histogram

2012-07-10 Thread Sarah Goslee
Hi, Thanks for providing a small reproducible example. You can disable the default axis and make your own custom version: hist(histexample,breaks=bins, xaxt=n) axis(1, at=seq(5.5, 15.5, by=2), labels=c(5-6, 7-8, 9-10, 11-12, 13-14, 15-16)) Sarah On Tue, Jul 10, 2012 at 3:34 PM, jlwoodard

Re: [R] Specify model with polynomial interaction terms up to degree n

2012-07-10 Thread William Dunlap
a) Please supply some context in your mail message. Not everyone reads R-help via nabble. b) poly(raw=TRUE, x, degree=degree) was changed for 2.15.0 to allow it to output a non-full-rank matrix. See the NEWS file in 2.15.0 or after: # in R-2.15.1 n - news() n[grepl(poly, n$Text),]

Re: [R] Use of Sappy and Tappy for Mathematical Calculation

2012-07-10 Thread R. Michael Weylandt michael.weyla...@gmail.com
On Jul 10, 2012, at 11:30 AM, Nordlund, Dan (DSHS/RDA) nord...@dshs.wa.gov wrote: -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Rantony Sent: Tuesday, July 10, 2012 3:17 AM To: r-help@r-project.org Subject: [R] Use of

Re: [R] calculating the difference between days?

2012-07-10 Thread Jorge I Velez
What's wrong with manipulating the results arun got? dat3-read.table(text= Begin_date End_date 01JAN2000:00:00:00:000 02FEB2002:00:00:00:000 24MAR2012:00:00:00:000 18MAY2012:00:00:00:000 01OCT2003:00:00:00:000 02FEB2004:00:00:00:000 01JAN2000:00:00:00:000

Re: [R] Changing x-axis values displayed on histogram

2012-07-10 Thread jlwoodard
Perfect! Thanks so much, Sarah! -- View this message in context: http://r.789695.n4.nabble.com/Changing-x-axis-values-displayed-on-histogram-tp4636032p4636051.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org

Re: [R] R code help to change table format

2012-07-10 Thread Rui Barradas
Hello, You should say what is the package you are using, EstimateS returns hundreds of hits. [ package sos, findFn() ]. As for the question, try sp - 1:5 ab - c(3, 2, 2, 2, 4) rep(sp, ab) Hope this helps, Rui Barradas Em 10-07-2012 18:23, peziza escreveu: I am trying to input an OTU

Re: [R] Need HELP: how find and use a csv file?

2012-07-10 Thread R. Michael Weylandt michael.weyla...@gmail.com
On Jul 10, 2012, at 2:56 PM, Rich Shepard rshep...@appl-ecosys.com wrote: On Tue, 10 Jul 2012, Faradj Koliev wrote: I got a csv file ( skater.csv) which i could read by typing: read.csv(file=/Users/kama/Desktop/skatter.csv, header=TRUE, sep=;) Try: skatter -

Re: [R] Need HELP: how find and use a csv file?

2012-07-10 Thread mlell08
On 10.07.2012 20:11, Faradj Koliev wrote: However, when i enter:skatter.csv-read.csv(skatter.csv, header=TRUE) i get this message: Error in file(file, rt) : cannot open the connection In addition: Warning message: In file(file, rt) : I have tried with: skatter.csv-file.choose()

Re: [R] Mann-Whitney by group

2012-07-10 Thread Oxenstierna
This works very well--thanks so much. By way of extension: how would one extract elements from the result object? For example: thing=apply(Dtb[,3:10], 2, function(x) wilcox.test(x~Dtb$Group)) summary(thing)$p.value Does not provide a list of p-values as it would in a regression object.

[R] -1.1 - 0.1 + 1.2 is NOT null! Why?

2012-07-10 Thread ollestrat
Hello, I fear its a stupid question,..but here it is: If I do this simple calculation with the R console, I surprisingly do not get a zero. Why? -1.1-0.1+1.2 [1] -2.220446e-16 greetings, Ole -- View this message in context:

[R] Download large file from https url with progress meter

2012-07-10 Thread Gregory Jefferis
Dear useRs, I would like to download a large (15Mb) file from a github https url with a progress meter. My first attempt was: zip_url=https://github.com/jefferis/AnalysisSuite/zipball/master; zip_file=tempfile() download.file(zip_url,zip_file) Error in download.file(zip_url, zip_file) :

Re: [R] -1.1 - 0.1 + 1.2 is NOT null! Why?

2012-07-10 Thread Richard M. Heiberger
This is the behavior of the floating point number representation. Decimal fractions do not come out even in binary notation. Please see FAQ 7.31 On Tue, Jul 10, 2012 at 4:17 PM, ollestrat stratm...@gmx.de wrote: Hello, I fear its a stupid question,..but here it is: If I do this simple

Re: [R] -1.1 - 0.1 + 1.2 is NOT null! Why?

2012-07-10 Thread William Dunlap
It is for the same reason that if you must work with numbers stored with 2 significant decimal digits 1-(1/3+1/3+1/3) is 0.01 (== 10 ^ -2). Double precision numbers, supported by your computer hardware and used by R, are stored using 52 significant binary digits and 2^-52 is about -2.220446e-16.

Re: [R] -1.1 - 0.1 + 1.2 is NOT null! Why?

2012-07-10 Thread Rolf Turner
In addition to taking cognisance of Richard Heiberger's reply you should also learn to distinguish between the concept of null and zero. They are not at all the same thing. cheers, Rolf Turner On 11/07/12 08:17, ollestrat wrote: Hello, I fear its a stupid question,..but here

[R] Thanks! RE: boxplot with cut

2012-07-10 Thread Vining, Kelly
Thanks for your help, Rui! That works and will save me a lot of trouble. --Kelly -Original Message- From: Rui Barradas [mailto:ruipbarra...@sapo.pt] Sent: Tuesday, July 10, 2012 2:24 AM To: Vining, Kelly Cc: r-help@r-project.org Subject: Re: [R] boxplot with cut Hello, Maybe this iss

Re: [R] -1.1 - 0.1 + 1.2 is NOT null! Why?

2012-07-10 Thread Rolf Turner
But R-ish NULL is *NOT* equal to R-ish zero, and that's what counts here. cheers, Rolf Turner On 11/07/12 09:19, Erdal Karaca wrote: german Null == english zero :-) 2012/7/10 Rolf Turner rolf.tur...@xtra.co.nz mailto:rolf.tur...@xtra.co.nz In addition to taking

Re: [R] Mann-Whitney by group

2012-07-10 Thread R. Michael Weylandt michael.weyla...@gmail.com
Untested, I think you need to lapply() over thing with some sort of extractor: lapply(thing, function(x) x[['p.value']]) Michael On Jul 10, 2012, at 3:45 PM, Oxenstierna david.chert...@gmail.com wrote: This works very well--thanks so much. By way of extension: how would one extract

Re: [R] HELP me please with import of csv to R

2012-07-10 Thread peter dalgaard
On Jul 10, 2012, at 21:44 , Sarah Goslee wrote: But note that if sep=; then you don't have a csv file and should properly use read.table() instead. That's not actually true. In a substantial part of the world, csv files are semicolon separated. That's what read.csv2() is for. (Yes, it is

Re: [R] -1.1 - 0.1 + 1.2 is NOT null! Why?

2012-07-10 Thread massimodisasha
Il 7/10/12 4:17 PM, ollestrat ha scritto: Hello, I fear its a stupid question,..but here it is: If I do this simple calculation with the R console, I surprisingly do not get a zero. Why? -1.1-0.1+1.2 [1] -2.220446e-16 greetings, Ole -- View this message in context:

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