search for: assemblag

...XMIN, XMAX, YMIN, YMAX - corner points to a list of polygons (and keeping at least the ID as individuell reference). I really don?t get it, how can I read data of this format as a list of polygons? ?head"(ID, XMIN, XMAX, YMIN, YMAX, lat, lng, altc_mean) polys <- Polygons(list(Polygon(assemblage[,c("XMIN", "XMAX", "YMIN", "YMAX?)])), ID=assemblage$ID) SP <- SpatialPolygons(polys) SPDF <- SpatialPolygonsDataFrame(SP, data=data.frame(x= assemblage$lng, y= assemblage$lat, row.names=row.names(SP))) Already thanks for your help, Stefan...

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 t...

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...

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....

...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://...

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 rule, but this removes at least half my sp...

...I do not understand the concept of the index because my english is not good. The concept: *The number of species combinations *This index scans the columns of the presence-absence matrix and keeps track of the number of unique species combinations that are represented in different sites. For an assemblage of n species, there are 2n possible species combinations, including the combination of no species being present (Pielou and Pielou 1968). In most real matrices, the number of sites (= columns) is usually substantially less than 2n, which places an upper bound on the number of species combinations...

...,results=hide>>= average.trawl.spp.composition() @ %%%% insert figure generated from sweave code \begin{figure} \includegraphics[scale=0.6]{../figures/bycatch_by_weight} \caption{\label{catch by weight} Proportions of selected species (from Table \ref{ts length regressions}) in the fish assemblage using catch rate ($kg\ km{-1}$) as an approximation for fish density (neglecting variable capture efficiencies). Note: there were no oblique banded rattails in this dataset, although we have a \textit{<TS>-length} regression for them (see Table \ref{ts length regress...

...,results=hide>>= average.trawl.spp.composition() @ %%%% insert figure generated from sweave code \begin{figure} \includegraphics[scale=0.6]{../figures/bycatch_by_weight} \caption{\label{catch by weight} Proportions of selected species (from Table \ref{ts length regressions}) in the fish assemblage using catch rate ($kg\ km{-1}$) as an approximation for fish density (neglecting variable capture efficiencies). Note: there were no oblique banded rattails in this dataset, although we have a \textit{<TS>-length} regression for them (see Table \ref{ts length regress...

...ting whether the eigenvalues bar plot should be displayed nf if scannf FALSE, an integer indicating the number of kept axes Examples data(perthi02) plot(discrimin.coa(perthi02$tab, perthi02$cla, scan = FALSE)) For clarification, my data consists of measurements of morphological characters of an assemblage of biological specimens. I have already performed Principal Co-ordinates Analysis, Principal Compionents Analysis and Cluster Analysis in another program (PAST) in order to see if the data fall into distinct groupings that might represent different morphological species. I now want to test the gro...

...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...

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

...ches work with BSD). Am I correct that I can run BSD DomUs with the current release of Xen 3? Any thoughts/suggestions here? 5. Any suggestions regarding running databases on all of this (mostly to support my list manager, sympa)? 6. Any suggestions regarding management tools for this motley assemblage of stuff? 7. Am I going to take tremendous performance hits from all of this? 8. Am I crazy for considering all of this? (Maybe heresy on this list, but am I better off considering an all Linux/vserver, or all BSD/jails approach?) Thanks very much, in advance, for any suggestions. Miles Fid...

.... 0 1 1 2 1 4 0 1 1 . 0 2 1 2 1 4 0 0 0 . 0 3 1 2 1 9 0 0 0 . 0 .. .. . . . . 3504 876 219 8 12 0 1 0 . 1 where sector are nested within quadrants, quadrants within plot and plots within SIC. For each sector time spent to collect plant assemblage is available. What I'm trying to perform is an analysis of rarefaction of species richness considering area and time. I'm practical with the vegan package but here I need some different analyses. My first step should be the analysis of species rarefaction with area and my question is: how...

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

...: The funds and support to attack any country or > countries, even those not even remotely implicated in yesterday's attacks, > and the use of whatever weaponry, conventional and otherwise, he should > choose to employ. > > What in fact Mr. Bush will soon be armed with - by that assemblage of > professional politicians on the Hill who yesterday evening broke into a > spontaneous chorus of God Bless America, right out of the closing scene of > the revanchist Hollywood film, The Deer Hunter - is an unlimited, permanent > blank check to wage la guerre eternal - war without...

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 cer...

--- 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