similar to: Extract data

Dear List, I have a data frame called trait with roughly 800 species in, each species have 15 columns of information: Species 1 2 3 etc.. a t y h b f j u c r y u etc.. I then have another data frame called com with the composition of species in each region, there are 506 different communities: community species NA1102 a NA1102 c NA0402 b NA0402 c AT1302 a AT1302 b etc.. What

Dear List, I am familier with binary models, however i am now trying to get predictions from a ordinal model and have a question. I have a data set made up of 12 categorical predictors, the response variable is classed as 1,2,3,4,5,6, this relates to threat level of the species ( on the IUCN rating). Previously i have combined levels 1 and 2 to form = non threatened and then combined 3-6 to

Dear List, I am unsure if this is the correct list to post to, if it isn't I apologise. I am using SSH to access a Linux version of R on a remote computer as it offers more memory and processing power. The model will take 1-2 days to run, I am accessing R through Putty and when I close the connection and open R again, I am faced with a new session. As a Linux newbie, I was

I hope you can help with this one. I have two matricies: 1. A species abundance matrix: <http://r.789695.n4.nabble.com/file/n4643979/2species_matrix.jpg> 2. A species trait score matrix: <http://r.789695.n4.nabble.com/file/n4643979/2trait_matrix.jpg> The trait matrix lists trait scores for each species as listed in the species abundance matrix. I would like to create a script

Hi, First I should note I am relatively new to R so I would appreciate answers that take this into account. I am trying to perform an MDS ordination using the function ?metaMDS? of the ?vegan? package. I want to ordinate species according to a set of functional traits. ?Species? here refers to ?sites? in traditional vegetation analyses while ?traits? here correspond to ?species? in such

Dear R user, I have a question on using R to analyze data with repeated measurements. I have 2 species with several strains (12) per species, each of which has been measured twice with for a given trait. No particular covariance, just two measures. Now I want to analyze the data with an ANOVA (aov) considering these repeated measures to get the MSq and SSq for the species and strain level. I

Hi, I should preface this problem with a statement that although I am sure this is a really easy function to write, I have tried and failed to get my head around writing functions in R. I can use R where functions exist to do what I want done, but have found myself completely incapable of writing them myself. The problem is that I have a table with several rows of species and several columns of

I have a host-parasite association matrix in which parasite species are rows and host species columns and cells contain the frequency of interactions. Some parasites are associated with many hosts, and some hosts harbor several parasites, and I want to repeatedly select only one single representative host per "generalized" (multi-host) parasite to create a new matrix in which no hosts

Dear all, I would like to add mixed effects in a multinomial model and I am trying to use MCMCglmm for that. The main problem I face: my data set consits of a trapping data set, where the observation at eah trap (1 or 0 for each species) have been aggregated per traplines. Therefore we have a proportion of presence/absence for each species per trapline. ex: ID_line mesh habitat Apsy Mygl

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

Hi All, I am writing a simulation that examines the effects of species extinctions on ecological communties by sequentially removing individuals of a given species (sometimes using weighted probabilities) and replacing the lost individuals with species identities randomly sampled from the remaining individuals. Thus I use two dataframes. One contains all the individuals and their species

Hello, I am trying to help a colleague with an R problem (see below) to whit I can only generate a very inelegant solution. Any advice would be welcome. Thanks, Brian If you have two matrices, say a species by trait matrix (Matrix 1 below) and a plot by species matrix (Matrix 2 below), is there a straightforward way to prune one matrix so that the species list matches those in a

Dear List, i am trying to produce a 3d plot using wireframe using the code: wireframe(Residuals_FD ~ Elevation * Temperature, data = data2, scales = list(arrows = FALSE), drape = TRUE, colorkey = TRUE) As you can see when the code (using the data below) is run the plot area is set-up correctly but the actual surface is missing? Any help would be greatly appreciated. Chris #data Elevation

I am creating an application to run a fishing tournament (see http:// www.ruby-forum.com/topic/51209 for a little background) Now I am running into an issue trying to calculate a leader board. each participate can enter multiple fish but only the largest fish per a given species counts towards the overall score. My entries table looks like this:

The following command produces red axis line in a pairs plot: pairs(iris[1:4], main = "Anderson's Iris Data -- 3 species", pch = "+", col = c("red", "green3", "blue")[unclass(iris$Species)]) Trying to fool pairs in the following way produces the same plot as above: pairs(iris[1:4], main = "Anderson's Iris Data -- 3

Hello, I have tried to find this out some other way, but unsuccessful I have to try this list. I assume this should be quite simple. I have a dataset with 4 columns, "Sample_no", "Species", "Nitrogen", "Carbon" in csv format. In the species column I have many different species with varying number of obs per species Eg "Sample_no"

I have a data frame with two factors (sampling 'unit', 'species'). I want to calculate the number of unique 'species' per 'unit.' I can calculate the number of unique values for each variable separately, but can't get a count for each ?unit?. > data=read.csv("C:/Desktop/sr_sort_practice.csv") > attach(data) > data[1:10,] unit species 1

Greetings, I am new to R and am hoping to get some tips from experienced R-programmers. I have a dataset that I've read into R as a dataframe. There are 5 columns: Plot location,species name, a species number code (unique to each species name), abundance, and treatment. There are 272 plots in each treatment, but only the plots in which the species was recorded have an abundance value. For

Hopefully I will not be flamed for this on the list, but I am starting out with R and having some trouble with combining plots. I am playing with the famous iris dataset (checking out example dataset in R while reading through Introduction to datamining) What I would like to do is create three graphs (combined boxplots) besides each other for each of the three species (Setosa, Versicolour and

Can anyone point me in the right direction of figuring out what downweight() is doing? I am using vegan to perform CCA on diatom assemblage data. I have a lot of rare species, so I want to reduce the influence of rare species in my CCA. I have read that some authors reduce rare species by only including species with an abundance of at least 1% in at least one sample (other authors use 5% as a