search for: hellinger

Hi, while working with decision trees and unbalanced data, I came across the use of the Hellinger distance as an alternative to information gain [1,2], when dealing with skewed data. Does anybody know of R implementations of this approach to decision trees? Thanks, [1] http://www.cse.nd.edu/Reports/2008/TR-2008-06.pdf [2] http://csmr.ca.sandia.gov/~wpk/slides/wdmda-sem.pdf -- Rajarshi Guha N...

Hello, everybody, I hope somebody could help me with a dist() function. I have a data frame of size 2*4087 (col*row), where col corresponds to the treatment and rows are species, values are Hellinger distances, I should reconstruct a distance matrix with a dist() function. I know that "euclidean" method should be used. When I type: dist(dframe,"euclidean") it gives me a truncated table, where values are missing. I suppose that I have to define something for the values, but...

.../RDA/LU2_basin_RDA_1.csv", row.names = 1) comm <- read.csv("F:/Sher_sophi_new3/RDA/Final_true_OTUs_97_1.csv", row.names = 1) x1 = as.matrix(WQ_RDA) x2 = as.matrix(LU2_loc_RDA) x3 = as.matrix(LU2_bas_RDA) comm = as.matrix(t(comm)) RDA_Ger = varpart(comm, x1, x2, x3, transfo="hellinger", scale = FALSE, na.action = na.omit I get this error message: Error in as.vector(x, mode) : cannot coerce type 'closure' to vector of type 'any' Can anyone help me figure out what am I doing wrong? Thanks, Sophi -- Sophi Marmen Ph.D candidate Marine B...

...e * library(vegan) library(ggplot2) library(dplyr) rassspec<-read.csv("C:/Users/hp/Desktop/R_data/rassspec.csv", header=T, stringsAsFactors=T) rassevee<-read.csv("C:/Users/hp/Desktop/R_data/rassenv.csv", header=T, stringsAsFactors=T) sptrans <- decostand(rassspec, "hellinger") envtrans <- decostand(rassevee, "hellinger") vare.cca <- cca(sptrans, envtrans) Any kind of help will be appreciable Thanking you regards Shailendra Pal Research Scholar Plant Ecology Lab (Prof. S.C. Garkoti) School of Environmental Sciences JNU, New Delhi 110067 [[alt...

...not familiar with the vegan package, so I am just making a guess here. If 'na.action=na.omit' is part of the call to varpart, try removing it from the function call and moving it above as follows: options(na.action="na.omit") RDA_Ger <- varpart(comm, x1, x2, x3, transfo="hellinger", scale = FALSE) Maybe that will help. Regards, Eric On Sat, Sep 16, 2017 at 6:53 PM, Sophi Marmen <sofimarman at gmail.com> wrote: > I'm trying to perform a RDA analysis in the vegan package using the > "varpart" function. > > I have a matrix of community...

...tended matrix of geographical coordinates" -ie the matrix of geographical coordinates completed by adding all terms of a cubic trend surface regression- . This is the command I use (package vegan): >rda(Helling ~ x+y+x*y+x^2+y^2+x*y^2+y*x^2+x^3+y^3) where Helling is the matrix of Hellinger-transformed presence/absence data The result returned by R is exactly the same as the one given by: >anova(rda(Helling ~ x+y) Ie the quadratic and cubic terms are not taken into account I hope you can help me with that: "how can I perform a RDA on an extended matrix of geograph...

...a=meanAG, span=1, panel=function(x,y,span){ panel.grid(h=0, v=-1) panel.xyplot(x,y,cex=1.0,points="jitter") panel.loess(x,y, span) panel.axis(side="bottom",at=TRUE, labels=c(expression(Bray-Curtis^{1}),expression(Bray-Curtis^{2}),expression(Canberra),expression(Gower),expression(Hellinger),expression(Kulczynski))) }) http://www.nabble.com/file/p18964008/meanAG.csv meanAG.csv -- View this message in context: http://www.nabble.com/replacing-default-labels-in-lattice-tp18964008p18964008.html Sent from the R help mailing list archive at Nabble.com.

Hi I am looking for an implementation (or alternative to) Mallow's distance or the Earth Mover's distance to compare distributions or unnormalized distributions (signatures). Is there an implementation in R or can somebody recommend an alternative? Thanks Rainer -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of

...+in the form E(X) for the expectation of X where X is some distribution or +in the form E(X,f) for the expectation of f(X) where X is some distribution and f some function in X, * further functionals: var, sd, IQR, mad, median * truncated moments, * distances between distributions (Hellinger, Kolmogorov, total variation, "convex contamination") * lists of distributions, * conditional distributions in factorized form * conditional expectations in factorized form ----------------------------------------------------------------------------------------- ************ "distrDo...

...+in the form E(X) for the expectation of X where X is some distribution or +in the form E(X,f) for the expectation of f(X) where X is some distribution and f some function in X, * further functionals: var, sd, IQR, mad, median * truncated moments, * distances between distributions (Hellinger, Kolmogorov, total variation, "convex contamination") * lists of distributions, * conditional distributions in factorized form * conditional expectations in factorized form ----------------------------------------------------------------------------------------- ************ "distrDo...

...n the form E(X) for the expectation of X where X is some distribution or +in the form E(X,f) for the expectation of f(X) where X is some distribution and f some function in X, * further functionals: var, sd, IQR, mad, median, kurtosis, skewness * truncated moments * distances between distributions (Hellinger, Kolmogorov, total variation, "convex contamination") * conditional distributions in factorized form * conditional expectations in factorized form ----------------------------------------------------------------------------------------- ************ "distrDoc": "distrDoc&qu...

...n the form E(X) for the expectation of X where X is some distribution or +in the form E(X,f) for the expectation of f(X) where X is some distribution and f some function in X, * further functionals: var, sd, IQR, mad, median, kurtosis, skewness * truncated moments * distances between distributions (Hellinger, Kolmogorov, total variation, "convex contamination") * conditional distributions in factorized form * conditional expectations in factorized form ----------------------------------------------------------------------------------------- ************ "distrDoc": "distrDoc&qu...

Hello I am using Jari Oksanen's CCA routine from the Vegan package on some estuary data, following a technique applied in (Anderson, M.J. & Gribble, N.A., 1998, Partitioning the variation among spatial, temporal and environmental components in a multivariate data set, Australian Journal of Ecology 23, 158-167). Some steps in the process require that the dependent matrix be constrained by

I need to use the Bhattacharyya distance metric to determine population separation. Has anyone written a Bhattacharyya distance metric function in R? -- View this message in context: http://old.nabble.com/Bhattacharyya-distance-metric-tp26221259p26221259.html Sent from the R help mailing list archive at Nabble.com.

...+in the form E(X) for the expectation of X where X is some distribution or +in the form E(X,f) for the expectation of f(X) where X is some distribution and f some function in X, * further functionals: var, sd, IQR, mad, median * truncated moments, * distances between distributions (Hellinger, Kolmogorov, total variation, "convex contamination") * lists of distributions, * conditional distributions in factorized form * conditional expectations in factorized form ----------------------------------------------------------------------------------------- We look forward to receivi...

...+in the form E(X) for the expectation of X where X is some distribution or +in the form E(X,f) for the expectation of f(X) where X is some distribution and f some function in X, * further functionals: var, sd, IQR, mad, median * truncated moments, * distances between distributions (Hellinger, Kolmogorov, total variation, "convex contamination") * lists of distributions, * conditional distributions in factorized form * conditional expectations in factorized form ----------------------------------------------------------------------------------------- We look forward to receivi...

...extreme value distribution classes, *expectations +in the form E(X) for the expectation of X where X is some distribution or +in the form E(X,f) for the expectation of f(X) where X is some distribution and f some function in X, * truncated moments, * distances between distributions (Hellinger, Kolmogorov, total variation, "convex contamination") * lists of distributions, * conditional distributions in factorized form * conditional expectations in factorized form ----------------------------------------------------------------------------------------- Short Description of &quo...

...extreme value distribution classes, *expectations +in the form E(X) for the expectation of X where X is some distribution or +in the form E(X,f) for the expectation of f(X) where X is some distribution and f some function in X, * truncated moments, * distances between distributions (Hellinger, Kolmogorov, total variation, "convex contamination") * lists of distributions, * conditional distributions in factorized form * conditional expectations in factorized form ----------------------------------------------------------------------------------------- Short Description of &quo...

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CRAN (and crantastic) updates this week New packages ------------ * allan (1.0) Alan Lee http://crantastic.org/packages/allan Automates Large Linear Analysis Model Fitting * andrews (1.0) Jaroslav Myslivec http://crantastic.org/packages/andrews Andrews curves for visualization of multidimensional data * anesrake (0.3) Josh Pasek http://crantastic.org/packages/anesrake This