[R] Assessing the fit of a nonlinear model to a new dataset

Hi all, I am attempting to apply a nonlinear model developed using nls to a new dataset and assess the fit of that model. At the moment, I am using the fitted model from my fit dataset as the starting point for an nls fit for my test dataset (see below). I would like to be able to view the

Re: [R] Accessing examplars in apcluster (apcluster package)

Dear Sachin, If you need the exemplars for further processing, you can access them via the 'exemplars' slot of the resulting APResult object. See the following example: apres - apcluster(negDistMat(r=2), x, details=TRUE) apres APResult object Number of samples = 150 Number of

Re: [R] help with kriging interpolation

Hei, Non-parametric linear spatial interpolation algorithm Ordinary Kriging using geoR package library(geoR) # 1. Create a geodata object (wMatrix contains coords and data # ? as.geodata --- for more info my_geoData - as.geodata(wMatrix, coords.col=1:2, data.col=3); # 2. Create a

Re: [R] question about message

Please keep your posts on the mailing list... I don't do one-on-one consulting without a contract. Please carefully re-read my last email and follow its advice before posting again. You may yet have a problem that is on topic here, but until you can give us a reproducible example that runs or

Re: [R] custom startup/welcome message

On 04/05/13 03:43, Prof Brian Ripley wrote: On 04/04/2013 21:31, R. Michael Weylandt wrote: On Thu, Apr 4, 2013 at 9:49 AM, lejeczek pelj...@yahoo.co.uk wrote: yeap, I've done it, I was hoping for a complete customization, and even Rprofile.site adds only to what is being printed by default

[R] CV in SVM

Good morning. I am using package e1071 to develop a SVM model. My code is: x - subset(dataset, select = -Score) y - dataset$Score model - svm(x, y,cross=10) print(model) summary(model) As 10-CV produces 10 models, I need two things: 1) To have access to each model from 10-CV.

[R] line profiling

Hello, This is about the new line profiling feature in R 3.0.0. As I was testing it, I find the results somewhat disappointing so I'd like to get your opinion. I put some poorly written code in a test.R file, here are the contents: double - function(x) { out - c() for (i in x) { out -

Re: [R] Full Documentation of R analysis

Dear all, thanks for your help which solves the problem! However, I would like to remark that I find the R CMD BATCH command options inconsistent and incomplete, since the .RData path and file name is not (always) the same as the R script and there is no easy control over the

Re: [R] E-learning environment for R

Hi Matthieu, Thank you for pointing the Coursera cource. I didn't find a way to access the archives, video or exercises. I will keep the course in my mind, though. Pekka Hi Pekka There was last semester a online class on coursera.org, given by Roger Peng:

Re: [R] Full Documentation of R analysis

The root directory or script file name should be given only in one place (the R CMD BATCH command argument) and the other file names should be derived from it. Why? I can think of lots of instances where it would be very unwise to assume that data files would be in the same directory

[R] RStudio and R version 3.0

Windows 7 32 bit R 3.0 RStudio that previously worked with R versions prior to R3.0 Colleagues, I just downloaded R 3.0. When I try to launch RStudio (which was previously on my computer), I get a message, R Session has a fatal error. Any suggestions for getting RStudio up and running would

Re: [R] RStudio and R version 3.0

Dear John, According to the Rstudio website you need the latest version of Rstudio to work with R 3.0.0. I had the same problem yesterday (on WinXP). Installing the latest Rstudio solved it. Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for

[R] R on portable drives

Hi Team, Does anyone knows about using R through pen drive or any other portable drive. Best, Bhupendrasinh Sent via BlackBerry from T-Mobile __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting

Re: [R] R on portable drives

Hi You can simply copy intalled files to USB stick. Regards Petr -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Bhupendrasinh Thakre Sent: Friday, April 05, 2013 2:18 PM To: r-help@r-project.org Subject: [R] R on

Re: [R] Canadian politcal party colours in ggplot2

Thanks, works just fine now. I used to always set options(stringsAsFactors=FALSE) but found that since most people don't it was hard to run example code that I found on the net. Or else I'd forget what I'd done when posting a requruest for help to R-help. If I was doing a lot of intensive

Re: [R] R on portable drives

I have not done it in a couple of years but for some time I always carried a Windows version on R on a USB stick. If you are using Windows just install to the stick rather than your hard drive and you have a fully functioning R. John Kane Kingston ON Canada -Original Message-

Re: [R] categorized complete list of R commands?

On 13-04-05 12:46 AM, ivo welch wrote: hi michael: now give my code and your middle rewrites code to an R novice and ask them to guess what it does. ;-). my personal rule, for the most part, is to go with the clever idiomatic way when performance or space matter AND, and to go for the simple

Re: [R] summing vectors/matrices

Hi -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Nicolas L. Gutierrez Sent: Thursday, April 04, 2013 3:17 PM To: r-help@r-project.org Subject: [R] summing vectors/matrices Hi All, I have a large dataset I need to

Re: [R] R on portable drives

On 05/04/2013 13:20, PIKAL Petr wrote: Hi You can simply copy intalled files to USB stick. On only one OS, and none was stated. For Windows, see http://cran.r-project.org/bin/windows/base/rw-FAQ.html#Can-I-run-R-from-a-CD-or-USB-drive_003f . On all other OSes, the R script contains an

Re: [R] line profiling

On 13-04-05 6:39 AM, Florent D. wrote: Hello, This is about the new line profiling feature in R 3.0.0. As I was testing it, I find the results somewhat disappointing so I'd like to get your opinion. I put some poorly written code in a test.R file, here are the contents: double - function(x) {

Re: [R] scanning data in R

I did not see a reply to your question. I don't know if you can do it within scan but why not just read in the file and then drop the 21? dat - scan(stop.txt, sep = \t) dat1 - dat[dat!= 21] John Kane Kingston ON Canada -Original Message- From: jamilnase...@gmail.com Sent: Wed,

Re: [R] Canadian politcal party colours in ggplot2

I never thought of looking at the logo (headslap!). Thanks. Ista's link to the wiki provides #EA6D6A which seems pretty close. However, when I see #FF6600, it really looks correct though the difference seems minor, at least on the screen. Looks like Wiki may be slightly off so I'll

Re: [R] Assessing the fit of a nonlinear model to a new dataset

Rebecca, I'm not sure why you are interested in the t-statistics and p-values for the iterations, but you could perhaps save the nls() fit after 1, 2, 3, ... iterations using the argument nls.control(maxiter = n). Jean On Fri, Apr 5, 2013 at 12:06 AM, Rebecca Lester

Re: [R] Better way of writing R code

Katherine, To preserve the original order, you could create a new variable for the currency data frame (BEFORE the merges), then use this variable to reorder at the end. currency_df$orig.order - 1:dim(currency_df)[1] You can do another merge for the other currency, you just need to specify

Re: [R] line profiling

On 05/04/2013 6:39 AM, Florent D. wrote: Hello, This is about the new line profiling feature in R 3.0.0. As I was testing it, I find the results somewhat disappointing so I'd like to get your opinion. I put some poorly written code in a test.R file, here are the contents: double - function(x)

Re: [R] RStudio and R version 3.0

On Fri, 05 Apr 2013 08:00:16 -0400 John Sorkin jsor...@grecc.umaryland.edu wrote: Windows 7 32 bit R 3.0 RStudio that previously worked with R versions prior to R3.0 Colleagues, I just downloaded R 3.0. When I try to launch RStudio (which was previously on my computer), I get a message,

Re: [R] Assessing the fit of a nonlinear model to a new dataset

On 05/04/2013 14:26, Adams, Jean wrote: Rebecca, I'm not sure why you are interested in the t-statistics and p-values for the iterations, but you could perhaps save the nls() fit after 1, 2, 3, ... iterations using the argument nls.control(maxiter = n). But those statistics are only even

Re: [R] arrayInd and which

David, Thanks for your help and time. Your explanation was just what I needed. And to the rest of you good R folks I would still be interested to see a working example of arrayInd, what it's supposed to do and what it's used for. I have read the doc page a number of times and it's still not

[R] How to perform a grouped shapiro wilk test on dataframe

Hello, I was wandering if it is possible to perform on a dataframe called 'all' a shapiro wilk normality test for COUNTS by variable Group ACTIVITY? Could it be done using plyer? I saw an eg that applies to an array but not to a dataframe:

Re: [R] arrayInd and which

On Fri, Apr 5, 2013 at 2:08 PM, Keith S Weintraub kw1...@gmail.com wrote: And to the rest of you good R folks I would still be interested to see a working example of arrayInd, what it's supposed to do and what it's used for. A little utility function for dealing with the

[R] How to see values of hypsographic curve in R

Hi Experts, Could I ask one question ? I have plotted hypsographic curve for one watershed. I want to see the values of curve as I have to create elevation-volume curve from it. Could you please explain me how to see data that is used in curve ? Best Regards,..Anup

[R] Cross Validation with SVM

Good morning. I am using package e1071 to develop a SVM model. My code is: x - subset(dataset, select = -Score) y - dataset$Score model - svm(x, y,cross=10) print(model) summary(model) As 10-CV produces 10 models, I need two things: 1) To have access to each model from 10-CV.

Re: [R] windows to remote R(linux) via putty with X11 forwarding

to answer (partially) my own question seems like not possible without X windows onthat putty from windows box R help - how to make R plot under Linux http://r.789695.n4.nabble.com/how-to-make-R-plot-under-Linux-td1562060.html regards On 04/04/13 14:46, lejeczek wrote: hi everybody windows

[R] multi user environment concept of access/authorization levels

hi everybody the subject may seem a bit over the top but, I wonder if there is way in R to separate/segregate users into different access levels/categories simply, user A cannot perform certain tasks, cannot use certain libraries or their certainfunctions? possible now? in the futuremaybe?

[R] (no subject)

Hello, I am running error rate analysis. It is my results below. When I compare aov1 and aov2, X square = 4.05, p = 0.044, which indicates that adding the factor Congruity improved the fitting of model. However, the following Z value is less than 1 and p value for Z is 1, which means that

[R] list filter rules

hi moderators off R topic anything I post to the list gets held... makes me sad, why me? regards [[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] results of model comparisons and summary()

Hello, I am running error rate analysis. It is my results below. When I compare aov1 and aov2, X square = 4.05, p = 0.044, which indicates that adding the factor Congruity improved the fitting of model. However, the following Z value is less than 1 and p value for Z is 1, which means that

[R] white heteroskedasticity standard errors NLS

Hello Is there any function to calculate White's standard errors in R in an NLS regression. The sandwich and car package do it but they need an lm object to calculate the error's. Does anyone have idea how to do it for an NLS object ? Regards The woods are lovely, dark and deep But I have

[R] Internet connection

Tried several ways to connect to Internet. Perhaps R help could point me in the right direction to make this connection work. setInternet2(use = TRUE) download.file( +

Re: [R] Malmquist-Luenberger Productivity Index programmed in R?

Hi Jan. I hope you are OK. I'm stuck in the same problem. Did you find an answer for this question? Thanks in advance, Edgar -- View this message in context: http://r.789695.n4.nabble.com/Malmquist-Luenberger-Productivity-Index-programmed-in-R-tp4643842p4663436.html Sent from the R help

Re: [R] HELP FOR COMPUTING ENVIRONMENTAL EFFICIENCY INDEX/ LUENBERGER INDEX

Hi Wang. I hope you are OK. I'm stuck in the same problem. Did you find an answer for this question? Thanks in advance, Edgar -- View this message in context: http://r.789695.n4.nabble.com/HELP-FOR-COMPUTING-ENVIRONMENTAL-EFFICIENCY-INDEX-LUENBERGER-INDEX-tp4647883p4663437.html Sent from

[R] retrieveing value from KS test

Hi. how can i insert the value of p_value from KS.test into vector? Regards, Irit. -- View this message in context: http://r.789695.n4.nabble.com/retrieveing-value-from-KS-test-tp4663439.html Sent from the R help mailing list archive at Nabble.com.

Re: [R] Internet connection

On Fri, Apr 5, 2013 at 3:20 PM, Gary gwengst...@yahoo.com wrote: Tried several ways to connect to Internet. Perhaps R help could point me in the right direction to make this connection work. setInternet2(use = TRUE) download.file( +

[R] mixed formatting of integer and numeric (e. g., by summary.default())

Hello, eveRybody, I've been trying to find the origin for the following formatting-inconsistency: E. g., look at the number of digits in summary.defaults()'s output when NAs occur: in my example below the number of NA's is displayed as an integer, the rest as numeric (floating point

Re: [R] mixed formatting of integer and numeric (e. g., by summary.default())

On 05/04/2013 16:46, Gerrit Eichner wrote: Hello, eveRybody, I've been trying to find the origin for the following formatting-inconsistency: E. g., look at the number of digits in summary.defaults()'s output when NAs occur: in my example below the number of NA's is displayed as an integer, the

Re: [R] Better way of writing R code

Hi, You can preserve the order using join().  Though, in this case, merge would be easier. library(plyr) both- join(currency_df,rate_df,type=left) names(both)[14:15]- paste0(currency_,names(both)[14:15]) names(rate_df)[2]- other_currency both2-

Re: [R] white heteroskedasticity standard errors NLS

On Fri, 5 Apr 2013, Nilesh Gupta wrote: Hello Is there any function to calculate White's standard errors in R in an NLS regression. The sandwich and car package do it but they need an lm object to calculate the error's. The infrastructure in sandwich is object-oriented and _not_ limited to

Re: [R] Extract lines from file

HI, btw, could this program be modified such that it take direct input from my input.txt file???  Lines1-readLines(utpalmtbl.txt) Lines1 #[1] OG1: or10|1345 or10|387 or10|474 or11|1203 or11|182 or10|2158 or12|637 #[2] OG2: or10|1562 or10|1584 or10|1977 or11|2263 or11|43  #[3]

Re: [R] moderator has not updated email address: can not post to r-help

On 04.04.2013 08:35, Anupam Tyagi wrote: The list moderator has not updated email address from previous employer. i can not post to r-help. Is there a way around this? Unsubscribe and resubscribe? Uwe Ligges Anupam. [[alternative HTML version deleted]]

Re: [R] Extract lines from file

Hi Utpal, You can use the same script from my previous email.   Lines1- readLines(groups.txt) library(stringr) res-paste(gsub((.*\\:).*,\\1,Lines1),unlist(lapply(str_match_all(Lines1,or10\\|\\d+),paste,collapse= )),sep= ) write.table(res,res1.txt,row.names=FALSE,col.names=FALSE,quote=FALSE)  

[R] Composite Quantile Regression

Does anyone know of R functions for doing composite quantile regression (Hou and Yuan Ann Stat 36:1108, 2008)? The paper's authors do not talk about software in their paper or on their web sites. Thanks Frank - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this

Re: [R] Composite Quantile Regression

I have no idea, but I cannot help taking this chance to say how much I love Hastie and Tibshirani. There are two types of authors in the world: those who are chased by desperate readers for software packages, and those who chase the readers desperately with their packages (cf Hastie's recent

Re: [R] How to perform a grouped shapiro wilk test on dataframe

Hi, Try this: dat1- read.csv(sample.csv,sep=\t,stringsAsFactors=FALSE)  with(dat1,tapply(COUNTS,list(ACTIVITY),function(x) if (length(unique(x))==1) NA else shapiro.test(x))) #$activity1 #[1] NA #$activity2 #    Shapiro-Wilk normality test #data:  x #W = 0.4588, p-value = 8.025e-11 #

Re: [R] retrieveing value from KS test

Hello, First of all, it's ks.test, all lower case. You can do the following. x - rnorm(100) # Make up some data y - rnorm(100) ks - ks.test(x, y) ks$p.value # This is the value you want See ?ks.test, section Value for a complete list of the components of the object returned by ks.test.

Re: [R] model.frame: object is not a matrix [solved]

The problem was that my formula had 2 ~ in it. It also had a lot of duplicate terms, but by themselves they don't cause trouble. Ross On 4/4/2013 5:30 PM, Ross Boylan wrote: Over a decade ago there was a problem with model.frame when the variable names were long:

Re: [R] arrayInd and which

On Apr 5, 2013, at 8:07 AM, R. Michael Weylandt wrote: On Fri, Apr 5, 2013 at 2:08 PM, Keith S Weintraub kw1...@gmail.com wrote: And to the rest of you good R folks I would still be interested to see a working example of arrayInd, what it's supposed to do and what it's used for. A little

[R] transforming data prior to CCA

Hi everyone, I´m a student and relatively new to R so apologies in advance if this question seems stupid or obvious to you. I have collected a dataset with about 60 species of diatoms (count data from 19 different sample sites) and environmental variables for each site (salinity, pH, etc.). It´s

[R] convert annual data to quarterly frequency

Hi, I was wondering if there is a package I can use to convert my 22 annual observations to quarterly time series so that I will have 88 observations. Also, will there be any harm in doing so? will I loose any important data specific info? I want to run VARs in levels using TY method. Due to

[R] create a square buffer around a coordinate for a raster

Hello all, I'm working with two landsat scenes from 2011 and 1987 with different extents and want to run a cpa over a square with a side length of 10 km. I unfortunately only have the coordinates for the center point. I tried to use a buffer to create the extent but have no idea how to make a

[R] Text Encoding

Dear R-Help, I am using the RDF package/ R 2.14 with the RDF package to download data from a website, and then use R to manipulate it. Text on the website is UTF-8. The RDF package's rdf_load command is converting it into a different encoding, which converts non-ASCII characters to unicode

Re: [R] Assessing the fit of a nonlinear model to a new dataset

Given nls has a lot of C code (and is pretty complicated), I doubt you'll find much joy doing that. nlxb from my nlmrt package is all in R, but you'll need to do quite a bit of work at each stage. I don't form the J' J matrix, and do a Marquardt approximation by adding appropriate rows to the

[R] Fwd: transforming data prior to CCA

Dear Saskia, First of all, I think that your question would be better answered in other list of discussion like ordn...@colostate.edu. Secondly, CCA does not assume that your data are normal and homocedastic, the model assume an unimodal and simetric response of species , but is robust to

Re: [R] Fwd: transforming data prior to CCA

Thanks a lot, I will try it :) -- View this message in context: http://r.789695.n4.nabble.com/transforming-data-prior-to-CCA-tp4663454p4663479.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list

Re: [R] list filter rules

On Apr 5, 2013, at 5:31 AM, lejeczek wrote: hi moderators off R topic anything I post to the list gets held... makes me sad, why me? regards [[alternative HTML version deleted]] Perhaps the AI that runs the list thinks you should be using your caps-shift more often? (More

Re: [R] How to perform a grouped shapiro wilk test on dataframe

Hi, library(plyr) res-ddply(dat1,.(ACTIVITY), summarise, cbind(if(length(unique(COUNTS))==1) NA else shapiro.test(COUNTS)$p.value, if(length(unique(COUNTS))==1) NA else shapiro.test(COUNTS)$statistic)) res1- data.frame(ACTIVITY=res[,1],as.data.frame(res[,2]),stringsAsFactors=FALSE)

Re: [R] moderator has not updated email address: can not post to r-help

On Apr 3, 2013, at 11:35 PM, Anupam Tyagi wrote: The list moderator has not updated email address from previous employer. i can not post to r-help. Is there a way around this? Why would you assume this to be the moderators' responsibility? You have access to all of your subscription

Re: [R] Better way of writing R code

On Apr 4, 2013, at 6:48 AM, Gabor Grothendieck wrote: On Thu, Apr 4, 2013 at 9:32 AM, Adams, Jean jvad...@usgs.gov wrote: Katherine, You should cc the R-help on all correspondence. The more eyes that see your query, the quicker and probably the better the response will be. Send your

Re: [R] Superscript

I have not had the chance to implement this yet, but thanks to you both for your help. This r-help should be complimented on how helpful it is. Its really topnotch. Thanks On Thu, Apr 4, 2013 at 11:11 PM, Paul Johnson pauljoh...@gmail.com wrote: On Thu, Apr 4, 2013 at 4:39 AM, Shane Carey

Re: [R] categorized complete list of R commands?

On 04 Apr 2013, at 07:34 , ivo welch wrote: every time I read the R release notes for the next release, I see many functions that I had forgotten about and many functions that I never knew existed to begin with. (who knew there were bibtex facilities in R? obviously, everyone except me.)

[R] Undesired vertical lines in png file output using 'cairo-png'

Hello all, I'm writing a file to PNG on Windows 7 using 'cairo-png'. I've been using it without problem for a while, but abruptly I'm getting what look like unplotted areas. I'm using the cairo-png specifically because it sucessfully generates a transparent background, whereas 'windows' doesn't.

[R] Reversing data transformation

Hi everybody, I would be very grateful if you could give me your thoughts on the following issue. I need to perform Box-Cox (bcPower€) transformation on my data. To do this, I calculated lambda using the function '€powerTransform'€. powerTransform(data) However, I got an error

Re: [R] multi user environment concept of access/authorization levels

On 05.04.2013 14:15, lejeczek wrote: hi everybody the subject may seem a bit over the top but, I wonder if there is way in R to separate/segregate users into different access levels/categories simply, user A cannot perform certain tasks, cannot use certain libraries or their certainfunctions?

Re: [R] (no subject)

Ana, I cannot help you with how to include weights in your analysis. However, you can use formals(poLCA) or ?poLCA to see that weights is not one of the acceptable arguments. R ignores arguments not used by the called function because functions within the called function may use them. You can

[R] Creating quintiles on monthly basis

Hi, I am trying in R to indicate in which quintile a value of a variable is for every month of my data frame in this case based on volatility. For each month I want to know for each stock if it is in the most volatile quintile of if it is in one of the others. So far I have come up with the

[R] Cross posted Re: Creating quintiles on monthly basis

Also posted at StackOverflow but now has an example dataset there. Cedric: You are requested not to cross-post to Rhelp. There are many other requests in the Posting Guide as well including a request that you not post in HTML. -- David. On Apr 5, 2013, at 5:20 PM, Cedric Suykens wrote: Hi,

Re: [R] Iterative regression through a series

Thank you , Rui--it works very well now.  I'll have to check out the attributes and classes of the things you changed to understand what was going wrong before.  Integer versus numeric, perhaps.  I'll look into seq_len() as well.   Many, many thanks for your help.  It will make this and several