search for: taxa

Hello all, I have a *.csv file that looks like this (actual file is orders of magnitude larger): Site taxa no.ind forest LMA 1 forest LCY 1 forest SCO 1 meadow LMA 2 meadow LCY 1 meadow PNT 3 I am interested in, bu...

taxa <- (structure(list(Date = structure(c(4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L), .Label = c("2006/04", "2006/05", "2006/07", "2006/10", "2006/12", "2007/02", "2007/04", "2007/06"...

...imes more than two spaces separating the entries, I obtain a result with columns full of NAs. Then I tried sub() to replace the all multi-spaces to get only one space that separates each entry but that didn't work either. Do you know a good way to convert this matrix? Thanks already, Kim taxa.vec "B03_MAH 0.2115 0.2087 0.2087 0.2147 0.2115 0.2176" taxa.vec "F02_SSBH 0.2162 0.2191 0.2133 0.2130 0.2220 0.2158" taxa.vec "G04_MAH 0.2083 0.2111 0.2055 0.2115 0.2140 0.2087" taxa.vec "A04_MAH 0.2097 0.2126 0.2069 0.2065 0....

Hello I apologise for the length of this entry but please bear with me. In short: I need a way of subsampling communities from all possible communities of n taxa taken 1:n at a time without having to calculate all possible combinations (because this gives me a memory error - using combn() or expand.grid() at least). Does anyone know of a function? Or can you help me edit the combn or expand.grid functions to generate subsamples? In long: I have been cr...

I've been comparing variables among objects (taxa) related by known trees, using phylogentically independent contrasts in the ape package, and want to move on to more complex models e.g. by using gls with appropriate correlation terms. My trees contain lots of (hard) polytomies and information about ancestors, which I've been including- creati...

...the initial stages of ordination etc of ecological data (vegetation or other species) that is usually stored in a database or flatfile in the list format above. It is similar to a cross tabulation like the function xtabs(), however its useful to be able to control whether a measured abundance for a taxa is included or a boolean (presence/absence) for the taxa in a given plot. Im new to such analyses in R, but before writing it myself hope or suspect that such a function or library is out there (although I dont see it after some quick searching in things like Vegan or BiodivesityR or labdsv). Th...

...creating compatible matrices. I can create matrices from my numerical data using the 'distance(x, method)' function from ecodist, but the row/column names are out put as numbers. While when i create a phyo-distance matrix using 'cophenetic(x)' from APE, the row/column names are the taxa names. Different data sets incorporate different taxa from the tree, which requires me to prune it for each data set, meaning I cannot just convert the taxa names to corresponding numbers in the data matrix (because the numbers will change for each data set). Anyways, my question is, is there an e...

...L, 8L, 12L, 7L, 6L, 11L, 5L, 10L, 4L, 3L, 2L, 1L, 9L), .Label = c("119", "148", "179", "185", "190", "198", "202", "215", "61", "BC", "HC", "SC"), class = "factor"), EPT.Taxa = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 1L, NA, 3L, 1L, 5L, 7L, 3L, 11L, 3L, 14L, 12L, 12L, 0L, 0L, 4L, 0L, 5L, 3L, 2L, 6L, 1L, 8L, 6L, 9L, 1L, 0L, 2L, 0L, 5L, 2L, 1L, 0L, 2L, 4L, 6L, 8L, NA,...

Hello, How can I create a symmetric contingency table from two categorical vectors having different length of levels? For example one vector has 98 levels TotalData1$Taxa.1 [1] "Aconoidasida" "Actinobacteria (class)" "Actinopterygii" "Alphaproteobacteria" [5] "Amoebozoa" "Amphibia" "Anthozoa" "Aquificae (cl...

I''m walking through an example in the "Head First Rails" book, but, instead doing the examples using Rails3.0.0.rc. But, I''m getting this error when browsing for example: http://localhost:3000/advs/1 undefined method `eq'' for nil:NilClass Provided that my advs_controller.rb is as follows: http://pastie.org/private/cd9zntg2ite57ept288kfa Any ideas why

Hi Derek, I was getting this too, with three tables, called taxa, databases and references I found I could add an irregular pluralisation for taxa: Inflector.inflections do |inflect| inflect.irregular ''taxon'', ''taxa'' end to the environment.rb, but no amount of modification there would a...

...lt;-mydata2$tfamily[mydata2$tspecies%in%com[[i]][[5]][[1]]] hgenus<-mydata2$tgenus[mydata2$tspecies%in%com[[i]][[5]][[1]]] hspecies<-mydata2$tspecies[mydata2$tspecies%in%com[[i]][[5]][[1]]] hier<-cbind(hspecies,hgenus,hfamily,horder,hclass) s<-nrow(hier) s<-ifelse(s>1000,s/10,s) taxa<-taxa2dist(hier[sample(s,replace=F),]) abd<-t(cbind(c(1:s),rep(1,s))) taxdiv<-taxondiveO(abd,taxa) if(class(result)=="try-error") result[[i]] <- NA else result[[i]] <-taxdiv #it doesnt work result[[i]]<-as.data.frame(result[[i]])[1,]},silent=T) taxind<-do.call(rbind...

...ationCode PCA1 1 DE582 -1.5592527 2 DE38 0.3530658 3 FR02116570 2.8057854 > > names (Fish89PCA) [1] "StationCode" "PCA1" > Fish89TiTAN <- titan(Fish89PCA, Fish89Abund, minsplt=5, + numprm=250, nboot=500, boot=TRUE, deviance=TRUE) [1] "Taxa frequency screen complete" [1] "Function definition complete" Error in is.data.frame(x) : subscript out of bounds This essror mesage is killing me. I checked the data tables and the internet, but nowhere any satisfying answer. Can anybody help me please? Thanks in advance!! --...

...example plot (taken from the rioja help file) made the function. Cheers, Brendan Wiltse library(vegan) ## decorana data(RLGH) library(rioja) ## Not run: # create appropriately sized graphics window windows(width=12, height=7) # quartz() on Mac, X11 on linux ## End(Not run) # remove less abundant taxa mx <- apply(RLGH$spec, 2, max) spec <- RLGH$spec[, mx > 3] depth <- RLGH$depth$Depth #basic stratigraphic plot strat.plot(spec, y.rev=TRUE) #scale for percentage data strat.plot(spec, y.rev=TRUE, scale.percent=TRUE) # plot by sample depth strat.plot(spec, yvar = depth, y.rev=TRUE, scale...

...n/R.bin Well, that isn't quite it because I tried it and it didn't work! Any advice greatly appreciated. Thanks in advance. Mike -- Michael B. Miller, Ph.D. Assistant Professor Division of Epidemiology and Community Health and Institute of Human Genetics University of Minnesota http://taxa.epi.umn.edu/~mbmiller/

Hello everyone I have problem with axis labels on graphs, I have my code as below: plot(0,0,xlim=c(1,ncol(PA)),ylim=c(1,nrow(PA)),main="Stratigraphic Range",xlab="Time Bins",ylab="Taxa",cex.axis=1.5,cex.lab=2,cex.main=2.5,mgp=c(5,1.5,0),xaxt="n") text(1:(length(strat_name)), y= 0, adj=1, srt=45,labels=strat_name,xpd=TRUE, cex=1) #adds text to x axis giving the strat names abline(v=(1:ncol(PA))+.5,col="grey",lty=3) cl <- rep(1,nrow(PA)) cl[DistM$...

Dear R Community, I am pleased to announce that a new version of the mefa R package is available at the CRAN. mefa is a package for multivariate data handling in ecology and biogeography. It provides object classes to represent the data coded by samples, taxa and segments (i.e., subpopulations, repeated measures). It supports easy processing of the data along with relational data tables for samples and taxa. An object of class mefa is a project specific compendium of the dataset and can be easily used in further analyses. Methods are provided for extrac...

Hi Sirs and Madams. My question is more statistical than related with the use of R software and I hope it will not seems so silly and elemental. I'm analyzing a set of data of some soil organism collected in diferent landscapes, soils taxa, and depths. The sample was performed thinking in a factorial structure with four factors: Specie, Landscape, Soil and Depth. Because not all the species appear in each sample there are so many zeros in the matrix data. Checking the normal distribution I'm not sure If I must check it in the...

...ld help me with the following. I want to do calculate this equation: Ps(t)= (?_(r=1)^N Xtr* 1/?drs)/(?_(r=1)^N 1/?drs) Ps(t) ? Probability that taxon t will occur at site s (300 sites s) N ? Number of sites = from 1 to 49 Xtr ? Value for taxon t at site r (I have this information in a table, 40 taxa (columns) t, 49 sites r) drs ? Distance from site r to site s (this information is on a table, s sites (columns)) I thought that R would be the software to use, but I am experiencing some difficulties Thanks to everyone, P.Branco -- View this message in context: http://www.nabble.com/Calculate...

Dear R Community, I am pleased to announce that a new version of the mefa R package is available at the CRAN. mefa is a package for multivariate data handling in ecology and biogeography. It provides object classes to represent the data coded by samples, taxa and segments (i.e., subpopulations, repeated measures). It supports easy processing of the data along with relational data tables for samples and taxa. An object of class mefa is a project specific compendium of the dataset and can be easily used in further analyses. Methods are provided for extrac...