search for: denslow

...es occurrences (0/1 values, columns). I want to count the number of new species that occur at a given time sample. For the matrix above the answer would be 1. Is there a simple way to figure out if the species has never occurred before and then sum them up? Thanks in advance, Micheal -- Michael Denslow I.W. Carpenter Jr. Herbarium [BOON] Department of Biology Appalachian State University Boone, North Carolina U.S.A. -- AND -- Communications Manager Southeast Regional Network of Expertise and Collections sernec.org 36.214177, -81.681480 +/- 3103 meters

Dear List, I'm trying to interpret the results of the Kruskal's Non-metric Multidimensional Scaling algorithm (isoMDS, MASS package). The 'goodness of fit' is reported as "The final stress achieved (in percent)". What does this mean exactly? I've tried to google for an answer but I've not come up with a definitive answer. Regards, Dieter -- Dieter Vanderelst

...tes.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.8.1 Michael Denslow Graduate Student I.W. Carpenter Jr. Herbarium [BOON] Department of Biology Appalachian State University Boone, North Carolina U.S.A. -- AND -- Communications Manager Southeast Regional Network of Expertise and Collections sernec.org

Dear R users, I am a new user (probably obvious by my question) and have really learned a lot from reading this list. Thank you all very much. My main struggles with R are with data manipulation. So here is my question... I have data that is organized as below, this is a short example. value count 11232 25 15885 24 22464 20 etc... the 'value' field is distances and the

Dear R-helpers, I am running metaMDS in the vegan package, which uses isoMDS in MASS, to perform Nonmetric Multidimentional Scaling (NMDS). I have seen some authors report a p-value for the NMDS ordination based on randomization of the dataset. As I understand it this is meant to compare the stress in your dataset to multiple runs of randomized data. I do not see a way to perform such a test in

...pp.asc) : object 'bat.asc' not found In addition: There were 12 warnings (use warnings() to see them) > > write.csv(overlap.matrix, paste(out.dir, "all_species.csv",sep='')) > " Date: Fri, 17 Feb 2012 12:18:55 +0100 From: Roger.Bivand at nhh.no To: michael.denslow at gmail.com CC: r-sig-geo at r-project.org; skopp at esri.com Subject: Re: [R-sig-Geo] R / ArcGIS On Fri, 17 Feb 2012, Michael Denslow wrote: > On Fri, Feb 17, 2012 at 2:15 AM, Edzer Pebesma > <edzer.pebesma at uni-muenster.de> wrote: >> Hi, >> >> I might succeed m...

Is there a R-package with a function that returns me the timezone, if I hand over longitude and latitude? I know online services like http://ws.geonames.org/timezone?lat=-38.01&lng=147 and http://www.earthtools.org/webservices.htm#timezone and wodner if this exists for R too. Thanks for helping, thomas

Dear R-helpers, I have a data frame that is similar to the one below. The row names are species and the E1, E2, E3 columns are presence/absence for a given site. I have an additional column 'origin' which has information about the species. E1 E2 E3 origin BASA 0 0 1 N BASO 0 0 1 N BRCO 0 0 1 U CAER 0 0 0 E CAGI 0 1 0 C CEFL 0 1 1 N I

Hi, I'm trying to use metaMDS with a dissimilarity matrix of angles, not Bray-Curtis, and I wanted to know if there is an in-built function to produce a plot of stress values against dimensions, that could be used to determine the 'true' dimension of the solution. The number of objects is only a lowly 8 so any solution higher than 2-dimensional is not likely to be interpretable,

Is there any R package which implements non-linear dimensionality reduction (LLE, ISOMAP, GTM, and so on) and/or intrinsic dimensionality estimation ? Thank you, Maura tutti i telefonini TIM! [[alternative HTML version deleted]]

Dear R users, I would like to draw map and import it in maptools/spatstat packages. The 'raw data' I have come from a web page (<map>...</map>) and are basically a list of coordinates of a polygon. I would like to know how to import them in R; I checked the maptools packages, but all the examples use existing .dbf files. I just have a (serie of) text file(s) looking like

Dr. Stevens, Hi, my name is Trey Scott, and I'm a grad student of Brian McCarthy's. He referred me to you because of your expertise in handling complex R problems. We were hoping you could help us solve a nagging problem that is prohibiting me from producing graphicl output. Here is a simple mock-up of the matrix I'm using a b c d e f 1i 1 4

Dear all, I tried: > iris > species.n <- as.numeric(Species) > plot(iris, col = species.n) > savePlot(filename="IrisTestPlot", type="png") and got the error message: Fehler in savePlot(filename = "IrisTestPlot", type = "png") : kann nur aus 'X11(type="*cairo")' Devices kopieren (sorry, I have a german version of R). I

Dear all, i have a programming problem that should be simple, though i am stuck with it. Please note that this is not a specific geonames problem, though i use it as an example - it´s just a basic problem with lapply. I use the geonames webservices with the R geonames packages which works almost smoothly. I have a vector of Zipcodes and i want to do a geonames lookup for all of them, which

Hi everyone, I am doing PCA with labdsv package. I was trying to create a biplot graphs in order to observe arrows related to my variables. However when I run the script for this graph, the console just keep saying: *Error in nrow(y) : element 1 is empty; the part of the args list of 'dim' being evaluated was: (x)* could please someone tell me what this means? what i am doing

Dear all, I'm running a set of nonparametric MDS analyses, using a wrapper for isoMDS, on a 800x800 distance matrix. I noticed that setting the parameter k to larger numbers seriously increases the calculation time. Actually, with k=10 it calculates already longer than for k=2 and k=5 together. It's now calculating for 6 hours, and counting... There is quite a difference between the

Hello R experts, I've used metaMDS to run NMDS on some fish abundance data, and am also working on correlating environmental data to the NMDS coordinates. I'm fairly new to metaMDS and NMDS in general, so I have what are probably some very basic questions. My fish abundance data consists of 66 sites for which up to 20 species of fish were identified and counted. I ran metaMDS on this data

Dear all, I've been using R on a Mac to process some data for export to ArcMap GIS (which only runs on Windows). ArcMap seems to require tab-delimited data (my data are in 3 columns), so I've been using the sep="\t" argument. However, this resulted in strange end-of-line characters when displayed on a PC. I looked in the write.table help file to find that eol="\r\n"

Hi R-fans, I would like put out a question to all R users on this list and hope it will create some feedback and discussion. 1) What are your 3 most useful R package? and 2) What R package do you still miss and why do you think it would make a useful addition? Pulling answers together for these questions will serve as a guide for new users and help people who just want to get a hint where to