[R-sig-eco] Discriminant Analysis Crisis
Chris Howden
chris at trickysolutions.com.au
Mon Jun 24 03:09:20 CEST 2013
The lda function has a corresponding predict function which u can use
to classify new data. Try having a look at that and it's help
contents.
Chris Howden
Founding Partner
Tricky Solutions
Tricky Solutions 4 Tricky Problems
Evidence Based Strategic Development, IP Commercialisation and
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(mobile) 0410 689 945
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On 22/06/2013, at 11:19, Alexandre Fadigas de Souza
<alexsouza at cb.ufrn.br> wrote:
> 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-request at r-project.org
> Para: r-sig-ecology at 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 at r-project.org
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> When replying, please edit your Subject line so it is more specific
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>
>
> 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.calenge at oncfs.gouv.fr>
> To: Dylann Kersusan <kersusan.dylann at gmail.com>
> Cc: "r-sig-ecology at r-project.org" <r-sig-ecology at r-project.org>
> Subject: Re: [R-sig-eco] Working with trajectories: ltraj.
> Message-ID: <51C2F4BC.80900 at 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 <highstat at highstat.com>
> To: r-sig-ecology at r-project.org
> Subject: [R-sig-eco] New book: Beginner's Guide to GLM and GLMM with R
> Message-ID: <51C2F5A2.5060208 at 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: highstat at 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.simpson at ucl.ac.uk>
> To: Kevin McCluney <kemcclun at ncsu.edu>
> Cc: r-sig-ecology at r-project.org
> Subject: Re: [R-sig-eco] ordipointlabel with shortened names
> Message-ID: <1371737297.2393.13.camel at 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 at 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.simpson at 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.simpson at uregina.ca
> 523 Research and Innovation Centre [tw] @ucfagls
> University of Regina
> Regina, SK S4S 0A2, Canada
>
>
>
> ------------------------------
>
> _______________________________________________
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> R-sig-ecology at r-project.org
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>
>
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