similar to: Indicator Species analysis; trouble with multipatt

Hi Ansely, As Jim points out we really need some sample data to go with the code. Have a look at ?dput which is the best way to supply sample data here or have a look at http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example and/or http://adv-r.had.co.nz/Reproducibility.html for some general suggestions on asking questions here---including discussions of using

Hi Ansley It looks good to me but I did not run the analysis as I am too lazy to install "indicspecies". The inclusion of the raw data is a great help. John Kane Kingston ON Canada -----Original Message----- From: daily.puja at gmail.com Sent: Tue, 19 Apr 2016 08:16:54 -0400 To: jrkrideau at inbox.com Subject: Re: [R] Indicator Species analysis; trouble with multipatt Thanks for the

R version 3.2.2. library(vegan) I was to look at community tables from my dendrograms and am trying out the vegemite command. This is the error I get: Error in vegemite(apst, apst.clusters) : Cowardly refusing to use longer than 1 char symbols: Use scale I thought the problem was that I was using the log transformed data, but I tried it on the raw (which is single digit numbers), and still

Hi all, I'm trying to connect to a share on an NT server from a Redhat Linux 7.2 server with the following command: smbmount //Fac-Staff/tansley$ /home/tomansley/law_share -o username=LAW\\tansley,password=realpassword The same command works from my linux workstation!!! Anybody got any clue as to what might be holding me up? I was thinking maybe my firewall but am not sure. Any help

Hi all, My server is connected to a UPS but whenever there is a power failure or spike it seems that once all the clients come back up they cannot connect. I have to restart the server each time. This is no hardship but I was just wondering if anybody had the same problem and if so and they fixed it, how? Thanks Tom Ansley

Hi! I am trying to analyse my data using amova (http://www.oga-lab.net/RGM2/func.php?rd_id=pegas:amova): My input to R is a DNA sequence file, format=fasta dna<- read.dna("XX.fasta", format="fasta") #left other options as default d<- dist.dna(dna, model="raw") g<- read.table("XXX.design") Load necessary libraries: library(pegas)

I've been attempting to understand the one-sample run test for randomness. I've found run.test{tseries} and run.test{lawstat}. Both use a large sample approximation for distribution of the total number of runs in a sample of n1 observations of one type and n2 observations of another type. I've been unable to find R code to generate the exact distribution and would like to see how

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Dear all, Dose anyone know whether there is a good R packege or program for Mantel's randomization test? Thanks in advance. ------------------------ Takashi Mizuno zoono at sci.osaka-cu.ac.jp Plant Ecology Lab. Osaka City University ------------------------ -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read

Hi, I'm interested in incorporating some interaction terms between my explanatory variables (distance matrices in this case) when I'm using the function MRM of the package ecodist. The function is doing a multiple regression on distance matrices. I can get the function to work perfectly on my explanatory matrices by adding a (+) sign as known. However, when I try to use the (*) sign or

Hi, I've got a dataset with 7 variables for 8 different species. I'd like to test the null hypothesis of no difference among species for these variables. MANOVA seems like the appropriate test, but since I'm unsure of how well the data fit the assumptions of equal variance/covariance and multivariate normality, I want to use a permutation test. I've been through CRAN looking at

Hi all, We've just had a power outage and the pc's can now no longer connect to the server. The server had power backup and did not go down which seems strange. Now when I try to connect the error message in smbd.log is smbd/connection.c:yield_connection(62) yield_connection: tdb_delete failed with error Record does not exist. and on the workstation it denies access citing security

I would like to perform partial mantel tests on only within group values, with "between group" values assigned to NA. This is possible in package ncf partial.mantel.test, however this sues a different permutation to that used in ecodist.ecodist will not accept data with NA values, returning a "matrix is not square error. is it possible to perform this test in ecodist? many thanks

Hi everyone, I'm looking to produce a side-by-side histogram of the number of trips taken by jays with a particular number of acorns after accounting for year (year "one" and year "two"). I know this involves indexing first then creating a histogram but I'm not sure how I'd do this. I want to explore the possibilities that jays are altering their strategies in

Dear R Group I have the following data for which I am trying to create subject wise lattice plot for a given attribute and product . though the lattice plot is generated, for some reasons that i dont understand in each plot the subject panels take a random order, I would rather want all the plots to display the subject order in the same order as how i have ordered this particular factor level.

Hi R Users, I created interaction plots in ggplot2 and was trying to add output of two way ANOVA models, especially only interaction ( example treatment*control F(XX, XX) = xxx, p = xxx) into figures, but i was not able to add. Would you mind to help on how I can add information into each figure? I have attached the example data and the code that I used for this. dat<-structure(list(Sites

Hi - I am interested in solving variance components for the data below with respect to the response variable, Expression within R. However, the covariates aren't independent and they also have a class (of which the total variance explained by covariates in that class I am most interested in). Very naively, I have tried to look at each individual covariates variance like this >

I'm creating a lattice barchart based off a pretty complicated data structure. The barchart comes out quite nice ( thanks to lattice ) but the problem is that the horizontal axis comes out all scrunched because the barchart doesn't know that the intervals of Var.1 are really "associated" with the conditioning variable Var.2. Therefore, all the intervals of Var.1 are put on

Both of the approx functions work correctly individually, but they are not being distinguished in the for loop by the if statments. Any help would be appreciated. for loop of interest is below x <- (structure(list(Site = structure(c(2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,

OK, so maybe last night was a little too much at one throw, so I have reduced the data to two stations- one that has precipitation and one that does not. This is going to be in the context of a larger data set. I would like to be able to issue a ggplot command and have cum sum just act on the facets (factors) to apply this. library(chron) library(ggplot2) DF <- structure(list(date_time =