Dear friends, I have a doubt about how to use discriminant analysis. Could you possibly help me?
Briefly, here is my case. I have clustered 64 subtropical tree species using k-means non-hierarchical cluster analysis. The cluster analysis was based on 10 continuous traits measured for individuals of each species. The analysis yielded 5 groups that interestingly correspond to empirical expectations about forest ecology. I have some 20 more species for which I do not have all 10 variables but need to fit into the five groups classification. Based on the literature, I proceeded with a Discriminant Analysis, which selected three of the ten variables as most strongly related to the groups, and found regressions related to each group. There is a separate regression for each of the five groups. And here comes my difficulties: 1 - How will I assign a given new species to any single group if there is a separate equation for each group? Should I fit the species data in each group's equation and then chech which one resulted in a result nearer to that group number? This seems very awkward. 2 - The DA provides an untransformed equation with a constant but also a standardized version withoug the constant and with one less group (4 instead of 5). I suppose I should use the unstandardized version, shouldn't I? Thank you in advance for any help. Sincerely, Alexandre Dr. Alexandre F. Souza Professor Adjunto II Departamento de Botanica, Ecologia e Zoologia Universidade Federal do Rio Grande do Norte (UFRN) http://www.docente.ufrn.br/alexsouza Curriculo: lattes.cnpq.br/7844758818522706 ----- Mensagem original ----- De: r-sig-ecology-requ...@r-project.org Para: r-sig-ecology@r-project.org Enviadas: Fri, 21 Jun 2013 07:00:01 -0300 (BRT) Assunto: R-sig-ecology Digest, Vol 63, Issue 17 Send R-sig-ecology mailing list submissions to r-sig-ecology@r-project.org To subscribe or unsubscribe via the World Wide Web, visit https://stat.ethz.ch/mailman/listinfo/r-sig-ecology or, via email, send a message with subject or body 'help' to r-sig-ecology-requ...@r-project.org You can reach the person managing the list at r-sig-ecology-ow...@r-project.org When replying, please edit your Subject line so it is more specific than "Re: Contents of R-sig-ecology digest..." Today's Topics: 1. Re: Working with trajectories: ltraj. (Clement Calenge) 2. New book: Beginner's Guide to GLM and GLMM with R (Highland Statistics Ltd) 3. Re: ordipointlabel with shortened names (Gavin Simpson) ---------------------------------------------------------------------- Message: 1 Date: Thu, 20 Jun 2013 14:25:32 +0200 From: Clement Calenge <clement.cale...@oncfs.gouv.fr> To: Dylann Kersusan <kersusan.dyl...@gmail.com> Cc: "r-sig-ecology@r-project.org" <r-sig-ecology@r-project.org> Subject: Re: [R-sig-eco] Working with trajectories: ltraj. Message-ID: <51c2f4bc.80...@oncfs.gouv.fr> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed [snip] > I am trying to select only a part of the trajectory stored in this ltraj > class object, following an example from Calenge in the package > 'adehabitatLT': > > lim <- as.POSIXct(strptime(c("28/05/2010 02:00:40", "30/06/2010 02:00:41"), > "%d/%m/%Y %H:%M:%S")) > ltrj.bis <- gdltraj(ltrj.obj, min=lim[1], max=lim[2], type="POSIXct" ) > > but for some reasons it does not work properly. I got this error message > that I do not understand: > > Error in `[.default`(res, , names(res) %in% which, drop = FALSE) : > number of dimensions incorrect > > > Anyone has an idea about why it doesn't work? You have identified a bug in the function gdltraj. I have corrected this bug and uploaded a new version of the package to CRAN. It will be available soon. Meanwhile, you can use this function instead: gdltraj <- function (x, min, max, type = c("POSIXct", "sec", "min", "hour", "mday", "mon", "year", "wday", "yday")) { if (!inherits(x, "ltraj")) stop("x should be of class \"ltraj\"") if (!attr(x, "typeII")) stop("x should be of type II (time recorded)") type <- match.arg(type) if (type == "POSIXct") { x <- lapply(x, function(y) { infol <- attr(y, "infolocs") if (!is.null(infol)) infol <- infol[(y$date > min) & (y$date < max), , drop=FALSE] y <- y[(y$date > min) & (y$date < max), ] if (!is.null(infol)) attr(y, "infolocs") <- infol return(y) }) } else { x <- lapply(x, function(y) { da <- as.POSIXlt(y$date)[[type]] infol <- attr(y, "infolocs") if (!is.null(infol)) infol <- infol[(da >= min) & (da < max), ,drop=FALSE] y <- y[(da >= min) & (da < max), ] if (!is.null(infol)) attr(y, "infolocs") <- infol return(y) }) } if (all(sapply(x, nrow) == 0)) stop("No relocations within the specified interval") x[sapply(x, nrow) == 0] <- NULL class(x) <- c("ltraj", "list") attr(x, "typeII") <- TRUE attr(x, "regular") <- is.regular(x) x <- rec(x) return(x) } HTH Cl?ment Calenge -- Cl?ment CALENGE Cellule d'appui ? l'analyse de donn?es Direction des Etudes et de la Recherche Office national de la chasse et de la faune sauvage Saint Benoist - 78610 Auffargis tel. (33) 01.30.46.54.14 ------------------------------ Message: 2 Date: Thu, 20 Jun 2013 13:29:22 +0100 From: Highland Statistics Ltd <highs...@highstat.com> To: r-sig-ecology@r-project.org Subject: [R-sig-eco] New book: Beginner's Guide to GLM and GLMM with R Message-ID: <51c2f5a2.5060...@highstat.com> Content-Type: text/plain; charset=windows-1252; format=flowed Members of this mailing list may be interested in the following new book: Beginner's Guide to GLM and GLMM with R. - A frequentist and Bayesian perspective for ecologists - Zuur AF, Hilbe JM and Ieno EN This book is only available from: http://www.highstat.com/BGGLM.htm This book presents Generalized Linear Models (GLM) and Generalized Linear Mixed Models (GLMM) based on both frequency-based and Bayesian concepts. Using ecological data from real-world studies, the text introduces the reader to the basics of GLM and mixed effects models, with demonstrations of binomial, gamma, Poisson, negative binomial regression, and beta and beta-binomial GLMs and GLMMs. The book uses the functions glm, lmer, glmer, glmmADMB, and also JAGS from within R. JAGS results are compared with frequentist results. R code to construct, fit, interpret, and comparatively evaluate models is provided at every stage. Otherwise challenging procedures are presented in a clear and comprehensible manner with each step of the modelling process explained in detail, and all code is provided so that it can be reproduced by the reader. Readers of this book have free access to: Chapter 1 of Zero Inflated Models and Generalized Linear Mixed Models with R. (2012a) Zuur, Saveliev, Ieno. Chapter 1 of Beginner's Guide to Generalized Additive Models with R. (2012b) Zuur, AF. Keywords Introduction to GLM Poisson GLM and Negative binomial GLM for count data Binomial GLM for binary data Binomial GLM for proportional data Other distributions GLM applied to red squirrel data Bayesian approach ? running the Poisson GLM Running JAGS via R Applying a negative binomial GLM in JAGS GLM applied to presence-absence Polychaeta data Model selection using AIC, DIC and BIC in jags Introduction to mixed effects models GLMM applied on honeybee pollination data Poisson GLMM using glmer and JAGS Negative binomial GLMM using glmmADMD and JAGS GLMM with auto-regressive correlation GLMM for strictly positive data: biomass of rainforest trees gamma GLM using a frequentist approach Fitting a gamma GLM using JAGS Truncated Gaussian linear regression Tobit model in JAGS Tobit model with random effects in JAGS Binomial, beta-binomial, and beta GLMM applied to cheetah data Kind regards, Alain Zuur -- Dr. Alain F. Zuur First author of: 1. Analysing Ecological Data (2007). Zuur, AF, Ieno, EN and Smith, GM. Springer. 680 p. URL: www.springer.com/0-387-45967-7 2. Mixed effects models and extensions in ecology with R. (2009). Zuur, AF, Ieno, EN, Walker, N, Saveliev, AA, and Smith, GM. Springer. http://www.springer.com/life+sci/ecology/book/978-0-387-87457-9 3. A Beginner's Guide to R (2009). Zuur, AF, Ieno, EN, Meesters, EHWG. Springer http://www.springer.com/statistics/computational/book/978-0-387-93836-3 4. Zero Inflated Models and Generalized Linear Mixed Models with R. (2012) Zuur, Saveliev, Ieno. http://www.highstat.com/book4.htm Other books: http://www.highstat.com/books.htm Statistical consultancy, courses, data analysis and software Highland Statistics Ltd. 6 Laverock road UK - AB41 6FN Newburgh Tel: 0044 1358 788177 Email: highs...@highstat.com URL: www.highstat.com URL: www.brodgar.com ------------------------------ Message: 3 Date: Thu, 20 Jun 2013 08:08:17 -0600 From: Gavin Simpson <gavin.simp...@ucl.ac.uk> To: Kevin McCluney <kemcc...@ncsu.edu> Cc: r-sig-ecology@r-project.org Subject: Re: [R-sig-eco] ordipointlabel with shortened names Message-ID: <1371737297.2393.13.camel@chrysothemis> Content-Type: text/plain; charset="UTF-8" Resending as I had some mail trouble yesterday and don't see this one to have gone through. See in-line below... On Tue, 2013-06-18 at 12:58 -0700, Kevin McCluney wrote: > Hi, > > I've been trying to use ordipointlabel() to add taxa names to an nmds > (metaMDS) graph in VEGAN. I can add the full names from the database, but I > would like to use the shortened names I created using make.cepnames(). I've > tried: > > pl3v2 <- ordipointlabel(mds, dis="sp", add = TRUE, lab=shnam) I'm afraid this is not possible yet - the labels are hard coded from the species scores. Hence I suggest you do names(foo) <- make.cepnames(names(foo)) where foo is your data frame. Then refit the NMDS. I'll see about allowing the passing in of labels but it won't happen for a few weeks. HTH G > But I get the following error message: > > Error in text.default(lab, labels = labels, col = col, cex = cex, font = > font, : > graphical parameter "lab" has the wrong length > In addition: Warning message: > In text.default(lab, labels = labels, col = col, cex = cex, font = font, : > NAs introduced by coercion > > I've also tried "labels" instead of "lab" and I get: > > Error in text.default(lab, labels = labels, col = col, cex = cex, font = > font, : > formal argument "labels" matched by multiple actual arguments > > I guess this function doesn't yet work like orditorp? Can anyone think of a > workaround? > > I've tried orditkplot: > > orditkplot(pl3v2, dis = "sp") > > But I get this error: > > Error in structure(.External("dotTclObjv", objv, PACKAGE = "tcltk"), class = > "tclObj") : > [tcl] bad screen distance "-NaN". > > I've also tried using identify(), but I have a few taxa that are literally > right on top of each other and try as I might, I can't get all of the taxa > that are on top of each other to show up. > > Any help would be appreciated. Thanks! > > Kevin E. McCluney, PhD > Post-doctoral Research Scholar > Department of Entomology > North Carolina State University > > > > -- > View this message in context: > http://r-sig-ecology.471788.n2.nabble.com/ordipointlabel-with-shortened-names-tp7578224.html > Sent from the r-sig-ecology mailing list archive at Nabble.com. > > _______________________________________________ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > -- Gavin Simpson, PhD [t] +1 306 337 8863 Adjunct Professor, Department of Biology [f] +1 306 337 2410 Institute of Environmental Change & Society [e] gavin.simp...@uregina.ca 523 Research and Innovation Centre [tw] @ucfagls University of Regina Regina, SK S4S 0A2, Canada -- Gavin Simpson, PhD [t] +1 306 337 8863 Adjunct Professor, Department of Biology [f] +1 306 337 2410 Institute of Environmental Change & Society [e] gavin.simp...@uregina.ca 523 Research and Innovation Centre [tw] @ucfagls University of Regina Regina, SK S4S 0A2, Canada ------------------------------ _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology End of R-sig-ecology Digest, Vol 63, Issue 17 _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology