search for: dissimilarities

Displaying 20 results from an estimated 207 matches for "dissimilarities".

2004 Jun 29
PAM clustering: using my own dissimilarity matrix
...triangular) as input for pam() or / / > fanny() clustering algorithms. / / > The problem is that this algorithms can only accept a dissimilarity / / > matrix, normally generated by daisy(). / / > However, daisy only accept 'data matrix or dataframe. Dissimilarities / / > will be computed between the rows of x'. / / > Is there any way to say to that your data are already a similarity / / > matrix (triangular)? / / > In Kaufman and Rousseeuw's FORTRAN implementation (1990), they showed an / / > opt...
2013 Sep 06
Fwd: calculating dissimilarity index of islands (vegan and betapart)
Dear List, This is Elaine, a postgraduate studying in bird distributions in East Asia. I want to calculate Simpson dissimilarity index, based on a presence/absence matrix of bird species in islands in East Asia. (matrix row: 36 islands/matrix column: species ID) (R package vegan to make NMDS and R package betapart) In most papers using vegan for NMDS and betapart for
2013 Dec 08
Why daisy() in cluster library failed to exclude NA when computing dissimilarity
...;/ But why when I tried this code library(cluster) x <- c(1.115,NA,NA,0.971,NA) y <- c(NA,1.006,NA,NA,0.645) df <-,y)) daisy(df,metric="gower") It gave this message: Dissimilarities : x y NA Metric : mixed ; Types = I, I, I, I, I Number of objects : 2 Warning messages: 1: In min(x) : no non-missing arguments to min; returning Inf 2: In max(x) : no non-missing arguments to max; returning -Inf I welcome other alternative than gower. I expect the dissimilarity output give...
2003 Jan 07
Extracting means for given strata from dissimilarity object
Is there a way of extracting mean distance or dissimilarity for a given strata from a 'dist' or 'dissimilarity' object, e.g. extract mean distances for each species in Anderson's iris data? data(iris) iris.dist<-dist(iris[,1:4]) then what? Mikkel Grum, PhD Genetic Diversity Scientist International Plant Genetic Resources Institute (IPGRI) Sub-Saharan Africa Group ***
2004 Dec 08
similarity matrix conversion to dissimilarity
...elated and cannot be trimmed to the same length, I am at a loss for what to do. For a set with so many unrelated sequences of different lengths, the only thing I have been able to is an all-against-all BLAST to create the matrix, but this gives high scores for similarities, not high scores for dissimilarities. The only thought I had was to use the reciprocal of the BLAST score as some perverse measure of distance. I am not subscribed to the list, so can I ask for responses directly to my email address? Thank-you, Tom Isenbarger -- isen at thomas a isenbarger (608) 265-0850
2006 Sep 26
cauculating dissimilarities in R
Dear All, I?ve got a statistical question on calculating dissimilarities in R. I want to calculate the different types of dissimilarities on the ?flower? dataset found in the package ?cluster?. Flower is a data frame with 18 observations on 8 variables. Variable 1 and 2 are binary, variable 3 is asymmetric binary, variable 4 is nominal, variable 5 and 6 are ordered and...
2011 Jun 23
MST dissimilarity
Dear R-helpers, I need to quantify dissimilarity of two minimum spanning trees, specifically dissimilarity of their topologies. (They connect the same objects but they are calculated from different sets of variables.) Are you aware of any R-function doing this? Best regards Ondrej Mikula
2013 Mar 08
analytical strategy for MDS/ smacof /dissimilarity matrix
Dear all, My data includes almost three thousand people who rank ten categories into three variables. The simple example below is almost same except I have many missing values. x <- cbind( sample( LETTERS[1:10] , 3000 , replace = TRUE ) , sample( LETTERS[1:10] , 3000 , replace = TRUE ) , sample( LETTERS[1:10] , 3000 , replace = TRUE ) ) I try to figure
2016 Apr 12
Dissimilarity matrix and number clusters determination
Hi, I already have a dissimilarity matrix and I am submitting the results to the elbow.obj method to get an optimal number of clusters. Am I reading the below output correctly that I should have 17 clusters? code: top150 <- sampleset[1:150,] {cluster1 <- daisy(top150 , metric = c("gower") , stand = TRUE , type = list(symm
2010 Sep 21
partial dbRDA or CCA with two distance objects in Vegan.
I am trying to use the cca/rda/capscale functions in vegan to analyse genetic distance data ( provided as a dist object calculated using dist.genpop in package adegenet) with geographic distance partialled out ( provided as a distance object using dist function in veganthis method is attempting to follow the method used by Geffen et al 2004 as suggested by Legendre and . FORTIN
2005 Apr 20
results from sammon()
Dear all, I'm trying to get a two dimensional embedding of some data using different meythods, among which princomp(), cmds(), sammon() and isoMDS(). I have a problem with sammon() because the coordinates I get are all equal to NA. What does it mean? Why the method fails in finding the coordinates? Can I do anything to get some meaningful results? Thank you very much Domenico
2011 Mar 18
akima::interp "scales of x and y are too dissimilar"
Dear R users, I want to do a fitted.contour plot of selected columns of a dataframe M with M$AM and M$Irradiance as x and y axes respectively. The level of the contour shall be determined by M$PR. Some words on my data first. Dataframe M looks like: head(M$Irradiance) [1] 293 350 412 419 477 509 head(M$AM) [1] 2.407 2.161 1.964 1.805 1.673 1.563 head(M$PR) [1] 70.102 72.600 75.097 80.167
2006 Aug 03
questions on plotting dedrograms
Hi, i've two questions concerning the plot of a dendrogram. first, i use hclust for clustering and if i plot the dendrogram, then the maximal height is the maximal dissimilarity found in my data. but i want to have a arbitary maximal height. for example if the maximal dissimilarity in my data is 50 and i want a height of 100, the plot should be compressed by 1/2 and the line to the
2013 Jun 22
metaMDS Error, Nan similar or negative values
...0 0 74 0 169 When I tried to perform metaMDS, it was not working, with the error > ord1 <- metaMDS( X ="bray") Square root transformation Wisconsin double standardization Error in if (any(dist < -sqrt(.Machine$double.eps))) warning("some dissimilarities are negative -- is this intentional?") : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In distfun(comm, method = distance, ...) : you have empty rows: their dissimilarities may be meaningless in method “bray” 2: In distfun(comm, method = distance, ...) : missi...
2013 Jul 22
about mix type clust algorithm
Hi: I have tried to find the appropriate clust algorithm for mixed type of data. The suggested way I see is: 1. use daisy to get the dissimilarity matrix 2. use PAM/hclust by providing the dissimilarity matrix, to get the clusters but by following this, when the data set grows bigger say 10,000 rows of data, the dissimilarity matrix will be O(n^2), and out of memory will occur. I
2006 Jun 01
@model.errors.empty? => true; @model.valid? => false
Hi, So, how can the situation described in the subject come to be? In other words, what could be invalidating the model, yet not generating an error? thanks, jh ps. here''s the breakpoint session paste: irb(#<#<Class:0xb72eec00>:0xb72eeb10>):003:0> @project.errors.empty? => true irb(#<#<Class:0xb72eec00>:0xb72eeb10>):004:0> @project.valid? => false
2017 Aug 17
PAM Clustering
Sorry, I never use pam. In the help, you can see that pam require a dataframe OR a dissimilarity matrix. If diss=FALSE then "euclidean" was use.So, I interpret that a matrix of dissimilarity is generated automatically. Problems may be in your data. Indeed pam(ruspini, 4)$diss write a dissimilaty matrix while pam(MYdata,10)$diss wite NULL 2017-08-17 16:03 GMT+02:00 Sema Atasever
2017 Aug 17
PAM Clustering
Dear Germano, Thank you for your fast reply, In the above code, *MYData *is the actual data set. Do not we need to convert *MYData to *the dissimilarity matrix using *pam(as.dist(**MYData**), k = 10, diss = TRUE*)* code line?* *Regards.* On Thu, Aug 17, 2017 at 2:58 PM, Germano Rossi <germano.rossi at> wrote: > try this > > MYdata <-
2013 Apr 11
Ordination Plotting: Warning: Species scores not available
Hi, I am working with a species-by-trait .csv file (columns=traits, rows=species) and get the following warning message when trying to plot results of both metaMDS and pcoa:  "Warning message: In ordiplot(x, choices = choices, type = type, display = display,  :   Species scores not available" I am using a Gower's transformation in both procedures within the metaMDS or pcoa
2008 Sep 03
how to reduce stress value in isoMDS?
I apply isoMDS to my data, but the result turns out to be bad as the stress value stays around 31! Yeah, 31 ,not 3.1... I don't know if I ignore something before recall isoMDS. My code as follow: m <- read.table("e:/tsdata.txt",header=T,sep=",") article_number <- ts(m, start = 2004,end=2008, frequency = 1 ,names=colnames(m))