Re: [R] Error in a regression

2016-10-24 Thread Jim Lemon
Hi Andrea, Assuming that your model is something like: lm(y~x,data=mydata) See what: cor(mydata$y,mydata$x) returns. If it is very very close to 1 or -1, there lies your problem. If one or more of your predictor variables is an almost perfect predictor of the response, you don't have much room

Re: [R] rsync: failed to connect to cran.r-project.org (137.208.57.37): No route to host (113)

2016-10-24 Thread Bob Rudis
I ran traceroutes & BGP traces from Marseille & Paris routers to that CRAN IPv4 address (it's 10hrs after your mail, tho) and there's no network errors. You can use any CRAN mirror, though. You aren't limited to that one. On Mon, Oct 24, 2016 at 9:49 AM, Etienne Borocco wrote: > I still have the

Re: [R] Extract word from string based on pattern match

2016-10-24 Thread Ista Zahn
On Oct 24, 2016 6:05 PM, "Joe Ceradini" wrote: > > Excellent - thanks David! > Regex syntax never fails to scare the crap out of me :) > > David absolutely solved my problem (in record time, no less), so it > can be put to rest. However, if anyone knows how to accomplish the > same thing through n

Re: [R] Extract word from string based on pattern match

2016-10-24 Thread Joe Ceradini
Excellent - thanks David! Regex syntax never fails to scare the crap out of me :) David absolutely solved my problem (in record time, no less), so it can be put to rest. However, if anyone knows how to accomplish the same thing through non base packages, like stringr or stringi, I'd be interested

[R] Extract word from string based on pattern match

2016-10-24 Thread Joe Ceradini
R Helpers, I would like to extract the entire word beginning with "BT" (or "BT-") and not any thing else in the string. Or, I would like to extract from BT up until the next space. test <- data.frame(x = c("abc", "Sample BT-1501-2E stuff", "Bt-1599-3E stuff")) test So, from test$x I would like t

Re: [R] nlme

2016-10-24 Thread Jeff Newmiller
Wild guess: Santiago is putting a and b in his formula when they are the coefficients he wants to extract? If Mr S wants better answers he needs to read about reproducibility and avoid HTML format email. -- Sent from my phone. Please excuse my brevity. On October 24, 2016 2:58:42 PM CDT, Wil

Re: [R] function which returns number of occurrences of a pattern in string

2016-10-24 Thread Jan Kacaba
Bob and Max, I thank you. It helped me much. 2016-10-21 3:47 GMT+02:00 Bob Rudis : > `stringi::stri_count()` > > I know that the `stringr` pkg saves some typing (it wraps the > `stringi` pkg), but you should really just use the `stringi` package. > It has many more very useful functions with not

Re: [R] nlme

2016-10-24 Thread William Dunlap via R-help
> summary(nlme(Btronc~a+b*dbh**2*haut, data=cbind(dat,g="a"), fixed=a+b_1, > start=start, > > groups=~g, weights=varPower(form=~dbh))) Shouldn't 'fixed' be a formula? Perhaps a+b~1? Bill Dunlap TIBCO Software wdunlap tibco.com On Mon, Oct 24, 2016 at 9:03 AM, Santiago Bueno wrote: > Dear peo

Re: [R] nlme

2016-10-24 Thread Andrew Robinson
Without access to the data, or commented, minimal, self-contained, reproducible code, it's pretty hard to speculate. I suggest that you reframe your question so that we can see what you can see. Andrew On 25 October 2016 at 03:03, Santiago Bueno wrote: > Dear people: > > > I am getting the foll

[R] nlme

2016-10-24 Thread Santiago Bueno
Dear people: I am getting the following error when trying to run the piece of code below. Any insights?? Error in nlme.formula(Btronc ~ a + b * dbh^2 * haut, data = cbind(dat, : object 'a' not found library(nlme) start <- coef(lm(Btronc~I(dbh**2*haut),data=dat)) names(start) <- c("a",

Re: [R] Finding starting values for the parameters using nls() or nls2()

2016-10-24 Thread dave fournier
I've spent quite a bit of time trying to convince people on various lists that the solution to these kinds of problems lies in the stable parameterization of the model. I write the solutions in AD Model Builder because it is easy. But R people are generally stuck in R (or mired) so the message

[R] Krippendorff's alpha bootstrapping implementation

2016-10-24 Thread Klaus Krippendorff
I noticed the 2014 discussion of bootstrapping Krippendorff's alpha referring to Andrew Hayes website. Whoever is interested in this algorithm: One of Andrew Hayes' student discovered an oddity in the distribution obtained by this algorithm when data are very sparse. This has been corrected by a

Re: [R] Error in a regression

2016-10-24 Thread Bert Gunter
Probably not. This is a statistics issue, not an R issue. But you need to show us your code to make sure it's not a syntax error. Assuming it's not, you'll need to consult a local statistical expert for help. Bert [[alternative HTML version deleted]]

[R] Error in a regression

2016-10-24 Thread Andrea Marcela Huerfano Barbosa
Hi guys, When I try to do a linear regression into the console appears this warning message: >* attempting model selection on an essentially perfect fit is nonsense* Some one could tell me what does it mean and maybe a way to solve it. Thanks in advance, Andrea Marcela [[alternative HT

Re: [R] using nested ifelse when i want to process values from more than 3 columns of data frame

2016-10-24 Thread Mark Sharp
Indira, I think you are wanting to define a new column (target) with "all_true", "all_false", or "other" based on columns H1, H2, H3, and H8 all being equal to 1, all being equal to 0, and other wise respectively. If so, then you do not need apply() or ifelse(). I believe this does what you we

Re: [R] using nested ifelse when i want to process values from more than 3 columns of data frame

2016-10-24 Thread David L Carlson
You really need to provide more information. The error message without the command that generated it and the structure of the data sets you are using is a bare minimum. A reproducible example is often necessary to debug code such as this. You can simplify your code substantially with something

Re: [R] using nested ifelse when i want to process values from more than 3 columns of data frame

2016-10-24 Thread Indhira, Anusha
Got past the syntax error,now I got new error below Error in match.fun(FUN) : c("'ifelse((kmeans.data$HBV51OpenDmd & kmeans.data$HBV52OpenDmd & ' is not a function, character or symbol", "' kmeans.data$HBV53OpenDmd & kmeans.data$HBV8OpenDmd) == 1, ' is not a function, character or symbol", "'

[R] Error in DESeq Installation

2016-10-24 Thread Yogesh Gupta
Dear all when I run this cammand to install DESeq it show somw error: ## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R";) biocLite("DESeq") it shows this error: > source("https://bioconductor.org/biocLite.R";) Bioconductor version 3.4 (BiocInstalle

[R] using nested ifelse when i want to process values from more than 3 columns of data frame

2016-10-24 Thread Indhira, Anusha
Hi, I would like to process each row of data frame having 8 columns of which I am interested in 4 columns for my analysis.I tried using apply function but I get syntax error,although I checked for missing syntaxes ,couldn't figure out the mistake.Can you also suggest me more efficient way to p

Re: [R] rsync: failed to connect to cran.r-project.org (137.208.57.37): No route to host (113)

2016-10-24 Thread Etienne Borocco
I still have the same problem today. Has the issue been fixed in Vienna? Le 19/10/2016 à 22:46, Duncan Murdoch a écrit : > On 19/10/2016 11:36 AM, Etienne Borocco wrote: >> Hello, >> >> I folowed this tutorial here: >> http://singmann.org/installing-r-devel-on-linux/ >> >> I tried to install r-de

Re: [R] Lattice equivalent to ggplot function

2016-10-24 Thread Carlos Ortega
Hi, Yes, it is available in "latticeExtra" package in function "panel.smoother()". Thanks, Carlos Ortega www.qualityexcellence.es 2016-10-24 15:13 GMT+02:00 Sébastien Bihorel : > Hi, > > The ggplot2 includes the very convenient stat_summary function to summarize > y variable data and plot this

[R] Lattice equivalent to ggplot function

2016-10-24 Thread Sébastien Bihorel
Hi, The ggplot2 includes the very convenient stat_summary function to summarize y variable data and plot this summary statistic in a y vs x graph. I need to implement similar functionality in a lattice-based framework. Googling this topic using keywords like lattice, equivalent, stat_summary, did

[R] Limit the y-axis line with ggplot2 (not the axis itself, but the line used at the left of the graph)

2016-10-24 Thread Marc Girondot via R-help
Hello everybody, Using ggplot2 package, is there a way to force to stop the y-axis line at a specified point ? (not using ylim because I want that some text written using annotate() at the top of the graph is still shown). Bellow is a simple example to show what I would like do: Thanks a lot

Re: [R] Error In DESeq installation

2016-10-24 Thread Martin Morgan
On 10/23/2016 10:13 PM, Yogesh Gupta wrote: Dear All, I am getting error in DESeq installation in R. package ‘DESeq’ is not available (for R version 3.3.1) source("http://www.Bioconductor.org/biocLite.R";) Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help biocLite("BiocUpgr