Re: [R] Non linear regression - Von Bertalanffy Growth Function - singular gradient matrix at initial parameter estimates
Packages nlmrt or minpack.lm use a Marquardt method. minpack.lm won't proceed if the Jacobian singularity is at the starting point as far as I'm aware, but nlxb in nlmrt can sometimes get going. It has a policy that is aggressive in trying to improve the sum of squares, so will use more effort than nls when both work. JN On 15-08-18 12:08 PM, Xochitl CORMON wrote: Dear all, I am trying to estimate VBGF parameters K and Linf using non linear regression and nls(). First I used a classic approach where I estimate both parameters together as below with alkdyr being a subset per year of my age-length-key database and running in a loop. vbgf.par - nls(Lgtcm ~ Linf *(1 - exp(-K * (Age - tzero))), start = c(K= 0.07, Linf = 177.1), data=alkdyr) I obtain an estimation of both parameters that are strongly correlated. Indeed after plotting Linf ~ K and fitting a linear regression I obtain a function (Linf = a + b*K) with R2= 0.8 and a = 215, b = -763. In this context, to take into account explicitly correlation between parameters, I decided to fit a new non linear regression derivate from VBGF but where Linf is expressed depending on K (I am most interested in K). To do so, I tried this model: vbgf.par - nls(Lgtcm ~ (a + (b*k)) *(1 - exp(-k * (Age - tzero))), start = c(k= 0.07, a= 215, b=-763), data=alkdyr) Unfortunately at this point I cannot go further as I get the error message singular gradient matrix at initial parameter estimates. I tried to use alg= plinear (which I am not sure I understand properly yet). If I give a starting value for a and b only, I have an error message stating step factor below minFactor (even when minFactor is set to 1000). Any help will be more than welcome as this is quite urgent Best, Xochitl C. __ 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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Confussion matrix in tree clasiffication
Use predict.tree() with type=class on the object returned by tree(). Then use that to construct a cross tabulation against the original data. If you provide a reproducible example with data, I could be more specific. - David L Carlson Department of Anthropology Texas AM University College Station, TX 77840-4352 -Original Message- From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of jpara3 Sent: Wednesday, August 19, 2015 4:09 AM To: r-help@r-project.org Subject: [R] Confussion matrix in tree clasiffication Hi there! I want to create a confussion matrix after using the tree package to create a clasiffication tree, but I´m not sure of how to create this matrix. Can anyone please help me? Thanks Jesús - Guided Tours Basque Country Guided tours in the three capitals of the Basque Country: Bilbao, Vitoria-Gasteiz and San Sebastian, as well as in their provinces. Available languages. Travel planners for groups and design of tourist routes across the Basque Country. -- View this message in context: http://r.789695.n4.nabble.com/Confussion-matrix-in-tree-clasiffication-tp4711269.html Sent from the R help mailing list archive at Nabble.com. __ 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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ 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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] data format
This is the kind of problem the package tidyR has been designed for. On 19 Aug 2015, at 16:29, minikg min...@cmfri.org.in wrote: Hi, I have a dataset consisting of landmarks of each sample's coordinates as given below. landmark X Y X Y X Y P1 534 7 26 7 32 P2 46 45 48 42 44 48 P3 73 45 72 44 71 46 P4 92 43 90 43 89 42 please help me to change my data format to samplep1x1p1y1p2x2p2y2p3x3p3y3p4x4p4y4 1534 46 45 73 45 92 43 2726 48 42 72 44 90 43 3732 44 48 71 46 89 42 Thanks -- View this message in context: http://r.789695.n4.nabble.com/data-format-tp4711278.html Sent from the R help mailing list archive at Nabble.com. __ 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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. signature.asc Description: Message signed with OpenPGP using GPGMail __ 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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Running R in Server
Dear all, Thenks for replying to my query. *@Amaud: If I understand correctly what you want to do, you might be able to create a HTML report using RMarkdown and host that on the website. If you really need a web app, I suggest looking into Shiny. You can make a shiny app, host it for free on the cloud. You will have a lot to learn, but it will be time well spent. https://www.rstudio.com/ https://www.rstudio.com/* Obviously I have shiny as an option.But I was thinking PHP based GUI is a better fit for me as I have very limited resources in my team who can create a Shiny app and implement it with the all the functionalities of a PHP based GUI. *Have a look at deployR on Revolutioanalytic website. There is a free open-source solution for windows.* I'll check this. *@John: Statement: You have a Windows desktop and have used R on it, so you are familiar with R in a Windows environment.* *Statement: You are not Linux (Ubuntu) trained.* *Statement: You wrote an R script on Windows, which works, but you need to run it on Ubuntu.* *The above is my starting point. Now I have some questions.* *Can you connect to the Ubuntu server from your Windows desktop? If so, how? If not, I'm confused about how you could get anything to run on the Ubuntu server.* My developer has given me an username and password which I can use to connect the server using Putty. The GUI is being developed in Ubuntu server only using PHP and my the results of my RScript (figures and tables) will be the input of the GUI. Having said that, I have limited knowledge how to implement the R and run the script in server after loggin in to the server. *Where does this dataset reside? On you desktop? On a Windows shared folder? On the Ubuntu server? Other?* Right now, on my desktop. But soon the dataset will be residing on a server. *Who or what edits the dataset? That is, is it always yourself? Some one in your group? Some other human? Some automated process?* The input data of my Rscript again comes from another app and the database is also residing on the same server. The update of the dataset is being done by the app automatically. *Why can't you run the R script as you do now, then deploy the results to the Ubuntu server? Since I don't know the environment that the Ubuntu server runs in, I can't address how to deploy an updated file into it. I assume you have some sort of deployment software. It could be as easy as being able to ftp the results from your desktop to the proper places on the Ubuntu server.* I cannot run the R script as I do now because the Rscript will also be called for automatically so that the results of the Rscript go as an input to the end app. PFA the architecture picture. *@Loris: However, you'll probably have to make sure that all the packages you* *need are installed on the server.* This is where I need a help. Thanks and Regards, Swagato __ 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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error message from allEffects(model) / effect(model) ‘range’ not meaningful for factors
Hi, m - lm(y~x) # no problem allEffects(m)# also no problem model: y ~ x x effect x abc 3.322448 3.830997 4.969154 effect(x, m) # ditto x effect x abc 3.322448 3.830997 4.969154 Effect(x, m) # ditto x effect x abc 3.322448 3.830997 4.969154 Best, John --- John Fox, Professor McMaster University Hamilton, Ontario, Canada http://socserv.socsci.mcmaster.ca/jfox/ -Original Message- From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Robert Zimbardo Sent: Tuesday, August 18, 2015 8:50 PM To: r-help@r-project.org Subject: [R] Error message from allEffects(model) / effect(model) ‘range’ not meaningful for factors Hi I cannot figure out why the effects package throws me error messages with the following simple code: rm(list=ls(all=TRUE)); set.seed(1); library(effects) # set up data x - factor(rep(letters[1:3], each=100)) y - c(rnorm(100, 3, 3), rnorm(100, 4, 3), rnorm(100, 5, 3)) # fit linear model m - summary(lm(y~x)) # no problem # now the problem plot(allEffects(m)) # Error in Summary.factor(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, : # ‘range’ not meaningful for factors plot(effect(x, m)) # Error in Summary.factor(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, : # ‘range’ not meaningful for factors Any ideas? It's go to be something superobvious, but I don't get it. Thanks, RZ __ 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://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ 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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Output In R
At least provide a sample of the data and then the desired output. All we get from your email is that it does not show the desired result and we are at a lost to understand what that is. I know it was suggested that you write it out as a CSV file and then you can use EXCEL to page through the data. Jim Holtman Data Munger Guru What is the problem that you are trying to solve? Tell me what you want to do, not how you want to do it. On Wed, Aug 19, 2015 at 1:20 AM, Shivi82 shivibha...@ymail.com wrote: Hi Loris, I have already tried options(max.print=99) but does not show the desired result. As posted above it want to share the outcome with the business owner where there could be multiple entries. -- View this message in context: http://r.789695.n4.nabble.com/Output-In-R-tp4711227p4711264.html Sent from the R help mailing list archive at Nabble.com. __ 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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Rodbc retrieve data
Diaz, paste() and paste0() will work here. paste0() defaults to between character vector elements and paste() defaults to (single blank character) between character vector elements. See ?paste. I do not recall, but you may have to escape the symbol, but that is another topic. Try this. title (main = paste0(Mapa de los dblinks del entorno: , dbName),sub=Luis Diaz - Emergencies improvments) Mark P.S. Spelling correction - improvements R. Mark Sharp, Ph.D. Director of Primate Records Database Southwest National Primate Research Center Texas Biomedical Research Institute P.O. Box 760549 San Antonio, TX 78245-0549 Telephone: (210)258-9476 e-mail: msh...@txbiomed.org On Aug 19, 2015, at 7:11 AM, Diaz Garcia, Luis Carlos luis.d...@tecnocom.es wrote: Hi every one first I would like to introduce myself, as I'm new here. I'm Luis from Barcelona, I'm Oracle dba and I need to create some nice graphs. So, I was looking for a solution and I saw R... I think it's a good tool to make the task I need. So here is the task: I need to get all the dblink from one database and draw the result of the query. The dblink will have the origin database name, the destination, the name of the link the type too. So I look into the R doc and I saw the way to get the data from my database: library(RODBC) con - odbcConnect(DPL03, uid=myuser, pwd=mypass,believeNRows=FALSE ) dbName - sqlQuery(con, SELECT instance_name from v$instance,errors=FALSE) Now I have dbName with one value, the name of my instance, but I don't know how to insert this data into this: plot.new() title (main =Map of the dbLinks of the database,sub=Luis Diaz - Emergencies improvments) As you see, I create a screen to plot where I'll draw shapes and lines but the first issue is to insert here the name of my instance, but I can't. I try to concatenate like this: title (main =Mapa de los dblinks del entorno: + dbName ,sub=Luis Diaz - Emergencies improvments) But I have an error, and if I use print(dbName) the value is printed but outside of the plot.new() screen. Some one can help ? Thanks in advance ! Cheers __ 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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ 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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] match.arg: how to prevent users from not specifying a value
If you want to force the user to enter the 'type' argument,
move the vector of choices out of the argument list
and into the call to match.arg():
f1 - function(type, ...) {
match.arg(type, c(A, B, C))
}
f1()
#Error in match.arg(type, c(A, B, C)) :
# argument type is missing, with no default
f1(X)
#Error in match.arg(type, c(A, B, C)) :
# 'arg' should be one of “A”, “B”, “C”
f1(B)
#[1] B
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Tue, Aug 18, 2015 at 5:42 PM, Youyi Fong yf...@fhcrc.org wrote:
Hello, I have a function that looks like
f=function( type=c(dummy,A,B,C), ... ) {
type-match.arg(type)
if (type==dummy) stop(Please choose a type that is not dummy.)
...
}
I put a dummy in the list of choices as a mechanism to prevent users
from not specifying a value for type when calling the function. My
question is whether there is a better way to achieve it that does not
need dummy.
Thanks,
Youyi
__
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] match.arg: how to prevent users from not specifying a value
Hello, I have a function that looks like
f=function( type=c(dummy,A,B,C), ... ) {
type-match.arg(type)
if (type==dummy) stop(Please choose a type that is not dummy.)
...
}
I put a dummy in the list of choices as a mechanism to prevent users
from not specifying a value for type when calling the function. My
question is whether there is a better way to achieve it that does not
need dummy.
Thanks,
Youyi
__
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://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] equivalent of repeated measures anova using lmer
I am trying to run a linear mixed effects model similar to the 2*2*2 anova design. My DV is reaction time and fixed factors are time (pre vs. post:within-subject), condition (congruent vs. incongruent: within subject) and stimulation (vertex vs. DLPFC: between subject) My concerns are: a)I have very few participants: 7 in the vertex condition and 7 in the DLPFC condition. b)2 out of the 7 participants participated in both vertex and DLPFC condition. How do I compute a nested lmer model with reaction time as DV and time, condition and stimulation as factors? and how do i account for random intercepts and slopes with few number of participants? Thanks for all the help -- View this message in context: http://r.789695.n4.nabble.com/equivalent-of-repeated-measures-anova-using-lmer-tp4711265.html Sent from the R help mailing list archive at Nabble.com. [[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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Output In R
HI Boris, The reason i want to see or show 3 million rows in console is that i need to present it to a business user. So here my end objective is to present the final output to the business user. So lets say when i write a code: select(june,waybill:type,contains(sfxcode)) so here there could be multiple instances where sfx code could appear which will not accommodate in console. I tried using max print option and increased to (max.print=99) but still only shows few rows of data. What other option to i have. Thanks. -- View this message in context: http://r.789695.n4.nabble.com/Output-In-R-tp4711227p4711263.html Sent from the R help mailing list archive at Nabble.com. __ 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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Plot z=f(x,y) analytically
Hi, I've been led to believe that in R it is possible to produce a 3d analytical plot of a function. I've been pointed in the direction of plot3d(), so the command is something like plot3d(x^2+y^2,(x,-3,3),(y,-3,3)). And a smart person out there is going to tell me where this syntax comes from (or belongs to), there is also a R package called MapleSoft ( I believe) which is commercial, and there is always Mathematica. So is there a R function to plot z=f(x,y) without obtain or generating data. Cheers, Mike -- View this message in context: http://r.789695.n4.nabble.com/Plot-z-f-x-y-analytically-tp4711272.html Sent from the R help mailing list archive at Nabble.com. __ 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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] repeated measures anova equivalent using lmer
I am trying to run a linear mixed effects model similar to the 2*2*2 anova design. My DV is reaction time and fixed factors are time (pre vs. post:within-subject), condition (congruent vs. incongruent: within subject) and stimulation (vertex vs. DLPFC: between subject) My concerns are: a)I have very few participants: 7 in the vertex condition and 7 in the DLPFC condition. b)2 out of the 7 participants participated in both vertex and DLPFC condition. How do I compute a nested lmer model with reaction time as DV and time, condition and stimulation as factors? and how do i account for random intercepts and slopes with few number of participants? Thanks for all the help [[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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] data format
Hi, I have a dataset consisting of landmarks of each sample's coordinates as given below. landmarkX Y X Y X Y P1 534 7 26 7 32 P2 46 45 48 42 44 48 P3 73 45 72 44 71 46 P4 92 43 90 43 89 42 please help me to change my data format to sample p1x1p1y1p2x2p2y2p3x3p3y3p4x4p4y4 1 534 46 45 73 45 92 43 2 726 48 42 72 44 90 43 3 732 44 48 71 46 89 42 Thanks -- View this message in context: http://r.789695.n4.nabble.com/data-format-tp4711278.html Sent from the R help mailing list archive at Nabble.com. __ 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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Error message from allEffects(model) / effect(model) ‘range’ not meaningful for factors
Hi I cannot figure out why the effects package throws me error messages with the following simple code: rm(list=ls(all=TRUE)); set.seed(1); library(effects) # set up data x - factor(rep(letters[1:3], each=100)) y - c(rnorm(100, 3, 3), rnorm(100, 4, 3), rnorm(100, 5, 3)) # fit linear model m - summary(lm(y~x)) # no problem # now the problem plot(allEffects(m)) # Error in Summary.factor(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, : # ‘range’ not meaningful for factors plot(effect(x, m)) # Error in Summary.factor(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, : # ‘range’ not meaningful for factors Any ideas? It's go to be something superobvious, but I don't get it. Thanks, RZ __ 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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Output In R
Hi Loris, I have already tried options(max.print=99) but does not show the desired result. As posted above it want to share the outcome with the business owner where there could be multiple entries. -- View this message in context: http://r.789695.n4.nabble.com/Output-In-R-tp4711227p4711264.html Sent from the R help mailing list archive at Nabble.com. __ 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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Rodbc retrieve data
Hi every one first I would like to introduce myself, as I'm new here. I'm Luis from Barcelona, I'm Oracle dba and I need to create some nice graphs. So, I was looking for a solution and I saw R... I think it's a good tool to make the task I need. So here is the task: I need to get all the dblink from one database and draw the result of the query. The dblink will have the origin database name, the destination, the name of the link the type too. So I look into the R doc and I saw the way to get the data from my database: library(RODBC) con - odbcConnect(DPL03, uid=myuser, pwd=mypass,believeNRows=FALSE ) dbName - sqlQuery(con, SELECT instance_name from v$instance,errors=FALSE) Now I have dbName with one value, the name of my instance, but I don't know how to insert this data into this: plot.new() title (main =Map of the dbLinks of the database,sub=Luis Diaz - Emergencies improvments) As you see, I create a screen to plot where I'll draw shapes and lines but the first issue is to insert here the name of my instance, but I can't. I try to concatenate like this: title (main =Mapa de los dblinks del entorno: + dbName ,sub=Luis Diaz - Emergencies improvments) But I have an error, and if I use print(dbName) the value is printed but outside of the plot.new() screen. Some one can help ? Thanks in advance ! Cheers __ 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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error message from allEffects(model) / effect(model) ‘range’ not meaningful for factors
You rm is of class summary.lm Is that what allEffects is expecting? On 19/08/2015 01:49, Robert Zimbardo wrote: Hi I cannot figure out why the effects package throws me error messages with the following simple code: rm(list=ls(all=TRUE)); set.seed(1); library(effects) # set up data x - factor(rep(letters[1:3], each=100)) y - c(rnorm(100, 3, 3), rnorm(100, 4, 3), rnorm(100, 5, 3)) # fit linear model m - summary(lm(y~x)) # no problem # now the problem plot(allEffects(m)) # Error in Summary.factor(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, : # ‘range’ not meaningful for factors plot(effect(x, m)) # Error in Summary.factor(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, : # ‘range’ not meaningful for factors Any ideas? It's go to be something superobvious, but I don't get it. Thanks, RZ __ 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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Michael http://www.dewey.myzen.co.uk/home.html __ 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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] html posts tags remove home page
In html, How to remove posts from one category displaying on the home page by using tags. Thanks,Valentin [[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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] html posts tags remove home page
This is a mailing list on the topic of R. Your email does not appear to be related to that topic, so either look for a different mailing list/web forum where your question would be on topic, or provide a concrete example of your problem. If you do post here again, please use plain text format since the HTML formatting produced by default from your email program corrupts most examples. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On August 19, 2015 12:23:42 AM PDT, Valentin Cojocaru valentin.cojoc...@hotmail.com wrote: In html, How to remove posts from one category displaying on the home page by using tags. Thanks,Valentin [[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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ 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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] glm help
Dear All, I´m running a glm with poisson errors and have a doubt when ploting the predicted values. One of my variables has a positive slope in the summary output, but when I plot the predicted values on the original plot it draws a line with negative slope. I appreciate your comments on this and any other aspect of the analysis. Attached is the script and data in different formats just in case. Thanks in advanced, Joaquín. -- *Joaquín Aldabe* *Grupo Biodiversidad, Ambiente y Sociedad* Centro Universitario de la Región Este, Universidad de la República Ruta 15 (y Ruta 9), Km 28.500, Departamento de Rocha *Departamento de Conservación* Aves Uruguay BirdLife International Canelones 1164, Montevideo https://sites.google.com/site/joaquin.aldabe https://sites.google.com/site/perfilprofesionaljoaquinaldabe my4-read.table(file.choose(), header=T, dec=,) my4s-as.data.frame(scale(my4[,c(6,10,12,13,16)], center=T, scale=T)) my4S-cbind(BBSA=my4$BBSA, Field_name=my4$Field_name,Grassland_type=my4$Grassland_type, Flood=my4$Flood, Year=my4$Year,my4s) m2.glm=glm(BBSA~AMGP+Distance_to_lagoon+Grass_height, family=quasipoisson, data=my4S summary(m2.glm) #residuales par(mfrow=c(2,2)) plot(m2.glm)#pretty good #predict amgp=seq(-0.51, 5.44, length.out=100) grass=seq(-0.85,2.83, length.out=100) dist=seq(-1.59,1.53, length.out=100) newdata=data.frame(AMGP=amgp, Distance_to_lagoon=dist,Grass_height=grass) pred.m2.glm=exp(predict(m2.glm,newdata)) plot(BBSA~Grass_height, data=my4S) lines(newdata$Grass_height,pred.m2.glm) plot(BBSA~AMGP, data=my4S) lines(newdata$AMGP,pred.m2.glm)#why negative slope if summary output is positive plot(BBSA~Distance_to_lagoon, data=my4S) lines(newdata$Distance_to_lagoon, pred.m2.glm)__ 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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] data format
This looks like data for a morphometrics analysis so you should know about package geomorph. Data like yours is often stored as a three dimensional array so we switch to that format and then use the two.d.array() function in package geomorph: Assuming your dataset is called dat: arr - array(as.matrix(dat[, -1]), dim=c(4, 2, 3)) library(geomorph) mat - two.d.array(arr) colnames(mat) - paste0(p, rep(1:4, each=2), + rep(c(x, y), 4), rep(1:4, each=2)) mat p1x1 p1y1 p2x2 p2y2 p3x3 p3y3 p4x4 p4y4 [1,]5 34 46 45 73 45 92 43 [2,]7 26 48 42 72 44 90 43 [3,]7 32 44 48 71 46 89 42 dat2 - data.frame(sample=1:3, mat) dat2 sample p1x1 p1y1 p2x2 p2y2 p3x3 p3y3 p4x4 p4y4 1 15 34 46 45 73 45 92 43 2 27 26 48 42 72 44 90 43 3 37 32 44 48 71 46 89 42 - David L Carlson Department of Anthropology Texas AM University College Station, TX 77840-4352 -Original Message- From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of minikg Sent: Wednesday, August 19, 2015 9:29 AM To: r-help@r-project.org Subject: [R] data format Hi, I have a dataset consisting of landmarks of each sample's coordinates as given below. landmarkX Y X Y X Y P1 534 7 26 7 32 P2 46 45 48 42 44 48 P3 73 45 72 44 71 46 P4 92 43 90 43 89 42 please help me to change my data format to sample p1x1p1y1p2x2p2y2p3x3p3y3p4x4p4y4 1 534 46 45 73 45 92 43 2 726 48 42 72 44 90 43 3 732 44 48 71 46 89 42 Thanks -- View this message in context: http://r.789695.n4.nabble.com/data-format-tp4711278.html Sent from the R help mailing list archive at Nabble.com. __ 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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ 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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Plot z=f(x,y) analytically
You probably want function persp3d() in package rgl. You have to define the formula as a function and specify the limits correctly, but you were close: library(rgl) persp3d(function(x, y) x^2+y^2, xlim=c(-3, 3), ylim=c(-3, 3)) - David L Carlson Department of Anthropology Texas AM University College Station, TX 77840-4352 -Original Message- From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of chappo007 Sent: Wednesday, August 19, 2015 6:48 AM To: r-help@r-project.org Subject: [R] Plot z=f(x,y) analytically Hi, I've been led to believe that in R it is possible to produce a 3d analytical plot of a function. I've been pointed in the direction of plot3d(), so the command is something like plot3d(x^2+y^2,(x,-3,3),(y,-3,3)). And a smart person out there is going to tell me where this syntax comes from (or belongs to), there is also a R package called MapleSoft ( I believe) which is commercial, and there is always Mathematica. So is there a R function to plot z=f(x,y) without obtain or generating data. Cheers, Mike -- View this message in context: http://r.789695.n4.nabble.com/Plot-z-f-x-y-analytically-tp4711272.html Sent from the R help mailing list archive at Nabble.com. __ 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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ 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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Plot z=f(x,y) analytically
R has several options for projecting a 3 dimensional plot onto a 2 dimensional plane and plotting the result. Which is best depends on what you want. You mention a function plot3d but not which package it comes from. You are more likely to receive prompt and useful help when you do your part of the homework and tell us which package it is from (it is not in the default packages). In fact, with a name like that, there could easily be more than one package with a function of that name and if we tell you how to use the function from a different package than you are using then the help will probably be more confusing than helpful. In base R you can use functions like persp, image, and contour (after using a function like outer), the help pages have examples. If you load the lattice package then you can use wireframe, levelplot, or contourplot, again the help pages have examples. The TeachingDemos package has functions rotate.persp and rotate.wireframe that create an interactive interface to the corresponding plots. The help page for the plot3d function in the RGL package (one likely candidate for the function you mentioned) points to the plot3d.function function in the See Also section which has examples that you could plug your function into. On Wed, Aug 19, 2015 at 5:47 AM, chappo007 consult...@logiccorp.com wrote: Hi, I've been led to believe that in R it is possible to produce a 3d analytical plot of a function. I've been pointed in the direction of plot3d(), so the command is something like plot3d(x^2+y^2,(x,-3,3),(y,-3,3)). And a smart person out there is going to tell me where this syntax comes from (or belongs to), there is also a R package called MapleSoft ( I believe) which is commercial, and there is always Mathematica. So is there a R function to plot z=f(x,y) without obtain or generating data. Cheers, Mike -- View this message in context: http://r.789695.n4.nabble.com/Plot-z-f-x-y-analytically-tp4711272.html Sent from the R help mailing list archive at Nabble.com. __ 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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Gregory (Greg) L. Snow Ph.D. 538...@gmail.com __ 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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] match.arg: how to prevent users from not specifying a value
... and you could also use missing() (?missing for details) if you
wanted to give the user more verbose instructions, e.g.
f1 - function(type, ...) {
if(missing(type)){
cat(You must enter a 'type' argument that is one of etc\n)
return(invisible())
}
match.arg(type, c(A, B, C))
}
Bert Gunter
Data is not information. Information is not knowledge. And knowledge
is certainly not wisdom.
-- Clifford Stoll
On Wed, Aug 19, 2015 at 9:19 AM, William Dunlap wdun...@tibco.com wrote:
If you want to force the user to enter the 'type' argument,
move the vector of choices out of the argument list
and into the call to match.arg():
f1 - function(type, ...) {
match.arg(type, c(A, B, C))
}
f1()
#Error in match.arg(type, c(A, B, C)) :
# argument type is missing, with no default
f1(X)
#Error in match.arg(type, c(A, B, C)) :
# 'arg' should be one of “A”, “B”, “C”
f1(B)
#[1] B
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Tue, Aug 18, 2015 at 5:42 PM, Youyi Fong yf...@fhcrc.org wrote:
Hello, I have a function that looks like
f=function( type=c(dummy,A,B,C), ... ) {
type-match.arg(type)
if (type==dummy) stop(Please choose a type that is not dummy.)
...
}
I put a dummy in the list of choices as a mechanism to prevent users
from not specifying a value for type when calling the function. My
question is whether there is a better way to achieve it that does not
need dummy.
Thanks,
Youyi
__
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
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__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] match.arg: how to prevent users from not specifying a value
Great. missing is what I was looking for, and it seems to also work
with interfaces like
f=function( type=c(A,B,C), ... ) {
}
Thanks!
Youyi
On Wed, Aug 19, 2015 at 9:35 AM, Bert Gunter bgunter.4...@gmail.com wrote:
... and you could also use missing() (?missing for details) if you
wanted to give the user more verbose instructions, e.g.
f1 - function(type, ...) {
if(missing(type)){
cat(You must enter a 'type' argument that is one of etc\n)
return(invisible())
}
match.arg(type, c(A, B, C))
}
Bert Gunter
Data is not information. Information is not knowledge. And knowledge
is certainly not wisdom.
-- Clifford Stoll
On Wed, Aug 19, 2015 at 9:19 AM, William Dunlap wdun...@tibco.com wrote:
If you want to force the user to enter the 'type' argument,
move the vector of choices out of the argument list
and into the call to match.arg():
f1 - function(type, ...) {
match.arg(type, c(A, B, C))
}
f1()
#Error in match.arg(type, c(A, B, C)) :
# argument type is missing, with no default
f1(X)
#Error in match.arg(type, c(A, B, C)) :
# 'arg' should be one of “A”, “B”, “C”
f1(B)
#[1] B
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Tue, Aug 18, 2015 at 5:42 PM, Youyi Fong yf...@fhcrc.org wrote:
Hello, I have a function that looks like
f=function( type=c(dummy,A,B,C), ... ) {
type-match.arg(type)
if (type==dummy) stop(Please choose a type that is not dummy.)
...
}
I put a dummy in the list of choices as a mechanism to prevent users
from not specifying a value for type when calling the function. My
question is whether there is a better way to achieve it that does not
need dummy.
Thanks,
Youyi
__
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://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R-es] pregunta XLConnect
Hola José. Lo importante, para empezar es que la versión de R y la de Java sean iguales (de 32 o de 64 bits). Parece que tengas el Sistema Operativo y R en 64 bits y Java en 32bits. Es la primera comprobación que haría. Un Saludo, Miguel. De: R-help-es [r-help-es-boun...@r-project.org] en nombre de Dr. José A. Betancourt Bethencourt [josebetancourt@infomed.sld.cu] Enviado: miércoles, 19 de agosto de 2015 14:27 Para: r-help-es@r-project.org Asunto: [R-es] pregunta XLConnect Estimados El correo m�o jbetanco...@iscmc.cmw.sld.cu mailto:jbetanco...@iscmc.cmw.sld.cu que est� en la lista de r est� inhabilitado hasta el d�a primero, apreciar�a que me respondieran por este si es posible Estimados Al tratar de instalar el paquete XLConnect me informa lo que esta abajo �C�mo se puede superar esta deficiencia? library(XLConnect) Loading required package: XLConnectJars Error : .onLoad failed in loadNamespace() for 'rJava', details: call: fun(libname, pkgname) error: JAVA_HOME cannot be determined from the Registry Error: package �XLConnectJars� could not be loaded sessionInfo() R version 3.2.1 (2015-06-18) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 8 x64 (build 9200) locale: [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 [3] LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C [5] LC_TIME=Spanish_Spain.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_3.2.1 Saludos cordials Jos� -- Este mensaje le ha llegado mediante el servicio de correo electronico que ofrece Infomed para respaldar el cumplimiento de las misiones del Sistema Nacional de Salud. La persona que envia este correo asume el compromiso de usar el servicio a tales fines y cumplir con las regulaciones establecidas Infomed: http://www.sld.cu/ [[alternative HTML version deleted]] Nota: A información contida nesta mensaxe e os seus posibles documentos adxuntos é privada e confidencial e está dirixida únicamente ó seu destinatario/a. Se vostede non é o/a destinatario/a orixinal desta mensaxe, por favor elimínea. A distribución ou copia desta mensaxe non está autorizada. Nota: La información contenida en este mensaje y sus posibles documentos adjuntos es privada y confidencial y está dirigida únicamente a su destinatario/a. Si usted no es el/la destinatario/a original de este mensaje, por favor elimínelo. La distribución o copia de este mensaje no está autorizada. See more languages: http://www.sergas.es/aviso-confidencialidad ___ R-help-es mailing list R-help-es@r-project.org https://stat.ethz.ch/mailman/listinfo/r-help-es
Re: [R] Bayesian data analysis recommendations
If you need the link to the latest email address of a package maintainer just use the maintainer function: ?maintainer On Aug 15, 2015, at 10:59 AM, Jeff Slagle jeffrey.sla...@gmail.com wrote: I have a question about AtelieR out on stackoverflow.com. Perhaps you could forward the link to: Yvonnick Noel University of Brittany Department of Psychology Rennes, France Here is the link: AtelieR GTK GUI http://stackoverflow.com/q/32023277/5229811?sem=2 Thank you, Jeff [[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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ 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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Confussion matrix in tree clasiffication
Hi there! I want to create a confussion matrix after using the tree package to create a clasiffication tree, but I´m not sure of how to create this matrix. Can anyone please help me? Thanks Jesús - Guided Tours Basque Country Guided tours in the three capitals of the Basque Country: Bilbao, Vitoria-Gasteiz and San Sebastian, as well as in their provinces. Available languages. Travel planners for groups and design of tourist routes across the Basque Country. -- View this message in context: http://r.789695.n4.nabble.com/Confussion-matrix-in-tree-clasiffication-tp4711269.html Sent from the R help mailing list archive at Nabble.com. __ 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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Response Variable Coding
Very simple question that I want confirm. Let's say that I have a response variable. What are the appropriate ways that it can be coded for a logistic regression model? 1. It can be 0/1 and a factor 2. It can be 1/2 and a factor 3. It can be characters and a factor, where the second letter takes on the 1. (bad/good becomes 0/1). 4. ? 5. ? My question isare 1, 2, and 3 all correct, and are there other coding schemes that glm can take. Thanks! [[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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] [FORGED] Response Variable Coding
On 20/08/15 09:43, Abraham Mathew wrote: Very simple question that I want confirm. Let's say that I have a response variable. What are the appropriate ways that it can be coded for a logistic regression model? 1. It can be 0/1 and a factor 2. It can be 1/2 and a factor 3. It can be characters and a factor, where the second letter takes on the 1. (bad/good becomes 0/1). 4. ? 5. ? My question isare 1, 2, and 3 all correct, and are there other coding schemes that glm can take. When in doubt, RTFM! :-) From ?binomial: For the binomial and quasibinomial families the response can be specified in one of three ways: As a factor: ‘success’ is interpreted as the factor not having the first level (and hence usually of having the second level). As a numerical vector with values between 0 and 1, interpreted as the proportion of successful cases (with the total number of cases given by the weights). As a two-column integer matrix: the first column gives the number of successes and the second the number of failures. That pretty well says it all. One thing to note: If the response is a *numeric* vector of 0's and 1's it will produce the same result as it would if it were converted to a factor. (This is because the default weights are all 1.) HTH cheers, Rolf Turner -- Technical Editor ANZJS Department of Statistics University of Auckland Phone: +64-9-373-7599 ext. 88276 __ 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://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
