search for: assemblages

Hi. For a spatial analysis (its visualization) I need to produce a map of conditions and traits. When I used SpatialPixelsDataFrame (sp package) my grid cells were regular and between each row was a small gap, which is not only messy but incorrect. So I generated the coords of each grid from the centroids in order to elongate the cells manually (or does anybody know another way to solve this?).

Hello List, My question is an elementary one. I have run a fuzzy kmeans cluster using FANNY to group freshwater fish assemblages. I then went in the field to validate that classification and have retrieved new assemblage data for a new suite of streams. Therefore I would like to use Predict to determine how well the original clustering fits the new data. However I have not figured out a straightforward way to get predict to...

Hi, I hope someone knows the answer to this or has a real good reference about it (I am using Legendre & Legendre, Numerical Ecology, 1998).... My data is a data.frame with locations as rows and vegetation assemblages / species as columns. I've done a PCA, a correspondance analysis (CA) using ca in ca package and a detrended correspondance analysis (DCA) using decorana from vegan package. As far as i understand what i've done .... the relationships between vegetation categories and locations should be si...

Dear all, I am trying to model variation of distribution of species assemblages according to environmental variables. For that I use a log linear multinomial regression. In order to select variables that mostly discriminate the assemblages, I tried to apply a hierarchical partitioning protocol to my data set. For that I have adapted the all.regs() for multinomial model. Th...

...ee example below: \references{ \href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2702787/}{Vaniscotte A., Pleydell D., Raoul F., Quere J.P., Coeurdassier M., Delattre P., Li T., Qian W., Takahashi K., Weidmann J.C., Qiu J., Giraudoux P. 2009 Modelling and spatial discrimination of small mammal assemblages: an example from western Sichuan (China). Ecological Modelling, 220: 1218-1231.} } The Rcmd check gives: * checking R code for possible problems ... OK * checking Rd files ... WARNING checkRd: (7) multignome.Rd:38: Tag \href not recognized I saw there is already a link on the issue http://bu...

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

I want to analyze the co-occurrence of some species. In some papers, the authors said that the index"the number of species combinations (COMBO)" is a good index. I try to calculate the index by R language. But I can not get the right value. I think that I do not understand the concept of the index because my english is not good. The concept: *The number of species combinations *This

System info: Mandrake 9.0 R Version 1.6.1 ESS 5.1.21 Emacs 21.2.1 ------------------- Colleagues I've been calling R-code embedded in my LaTex document using Sweave, but would like to make things more convenient. At present as I understand it you first process the R chunks of code using the Sweave function called from within R to process a "precursor file" e.g. foo.sw to get a

System info: Mandrake 9.0 R Version 1.6.1 ESS 5.1.21 Emacs 21.2.1 ------------------- Colleagues I've been calling R-code embedded in my LaTex document using Sweave, but would like to make things more convenient. At present as I understand it you first process the R chunks of code using the Sweave function called from within R to process a "precursor file" e.g. foo.sw to get a

Hello everyone, I am totally new to the R program. I have had a look at some pdf documents that I downloaded and that explain how to do many things in R; however, I still cannot figure out how to do what I want to do, which is to perform Discriminant Correspondence Analysis on a rectangular matrix of data that I have in an Excel file. I know R users frown upon Excel and recommend converting Excel

...y much. Jian Zhang # The following function calculates Fisher's alpha from counts of individuals and species. # Note that this program assumes that the true value of alpha lies within the range 0.001¨C10000 # (a likely assumption for local assemblages of organisms). # The function returns "-1" if there is a problem. calc.alpha=function(n.orig, s.orig) { a=numeric() len.n=length(n.orig) len.s=length(s.orig) if(len.n != len.s) { return(-1) } for(i in 1:len.n) { if(n.orig[i]<=0 | s.orig[i]<=0 | n.o...

Hi, I'm trying to find out what threshold of indicator value in labadsv should be used to accept a specie as an indicator one? So far I assumed that indval=0.5 is high enough to avoid any mistakes but it was based only in my intuition. I'd be greatful for any advise best regards Agnieszka

Hi Folks, Following up a bit on the GFS vs. EVMS thread from last month... Hi Folks, I''m about to migrate from a dedicated RH9 server (mostly email, list serving, web serving) to a couple of new machines that I''ll be deploying in a colocation arrangement - with a lot more control over configuration. My current box is pretty basic - using RAID-1 and nightly backups to

Dear list members, I have a data.frame so shaped: Sector Quadrants Plot Sic Time Species1 Species2 Species3 .. Species-n 1 1 1 1 5 0 0 1 . 0 2 1 1 1 12 1 1 1 . 0 3 1 1 1 34 0 1 0 . 0 4 1 1 1 23 1 1 0 . 0 5 2 1 1 22 1 1 1 . 1 6 2 1 1 10 1 1 1 . 1 7 2 1 1 2 1 0 0 . 0 8 2 1 1 2 0 0 1 . 0 9 3 1 1 12 0 0 0 . 1 . . . . . . . . . .

Dear members, I am performing multivariate analysis on marine benthic populations using R. At first glance I found ca and VEGANO packages to be the suitable for the task, but neither has incorporated Detrended Canonical Correspondence Analysis (DCCA), which is just the method I want to apply on my data. I've looked for alternative packages containing the method, but my suspicion is that

Emperors1000@aol.com wrote: > > Dear reader, > The emperorsclothes list does not seem to be working. Please forgive us if > you receive this post twice. - Jared Israel, www.tenc.net > ************************** > URL for this article: http://emperors-clothes.com/articles/rozoff/abyss.htm > > To join the Emperor's Clothes email list, go to >

I'm not sure how you are incorporating time period into your data structure. Typically we are looking at plots or assemblages as the rows and taxa as the columns. Time period adds a third dimension that could be added as blocks of rows. For example, depending on the resolution of your data, one approach would be to have up to 8 rows for each locality: Loc1.1000, Loc1.2000, . . . Loc1.8000. If a locality did not have certa...

--- Prof Brian D Ripley <ripley@stats.ox.ac.uk> wrote: >A matrix list? R lists are just vectors with elements of different types, >and R matrices are just vectors with a dimension attribute. When I saw the above I tried to create a matrix from a list but could not get it to work: my.lm <- lm( rnorm(10) ~ I(1:10) ) my.list <- list(1, 2, 3, 4, 5, 6, my.lm, my.lm, my.lm)

Hi, The department of economics at our university (Budapest) is planning a course on numerical methods in economics. They are trying to decide which software to use for that, and I would like to advocate R. The other alternative is Matlab. I have found comparisons in terms of computational time for matrix algebra, but I don't think that is relevant: the bottleneck for economists is usually