similar to: Data manipulation question (opposite of table?)

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

Dear R help, Apologies for the less than informative subject line. I will do my best to describe my problem. Consider the following matrix: mdat <- matrix(c(1,0,1,1,1,0), nrow = 2, ncol=3, byrow=TRUE, dimnames = list(c("T1", "T2"), c("sp.1", "sp.2", "sp.3"))) mdat In my actual data I have time

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

Dear R help, This seems to be a commonly asked question and I am able to run examples that have been proposed, but I can't seems to get this to work with my own data. Reproducible code is below. Thank you in advance for any help you can provide. The main problem is that I can not get the confidence lines to plot correctly. The secondary problem is that predict is not able to find my object

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

Hello, We have a user that switched from Linux to Windows with his engineering software. Previously he was using NFS to access data and there were no performance complaints. Now, with Windows, the same procedures take minutes instead of seconds. I created some log files in Samba 4.10.16-25.el7_9 (recompiled with gpfs support and using the gpfs vfs module) with debuglevel 10 to see if

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 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

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

This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. ---559023410-851401618-1218751024=:15885 Content-Type: TEXT/PLAIN; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: QUOTED-PRINTABLE I didn't describe the problem clearly. It's about the number of distinct=20 values. So just

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

I just upgraded to 1.6.2.rc-1 after running betas 2 and 3 with no problems and while everything seems fine i get these message at startup and than all is well. Should I be worried or do i need to let the team know about this? Also, is not finding "/dev/dahdi/transcode" a problem I should be worried about? And lastly conf2ael always segfaults when I try to run it. it did run once

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, I have a string in a controller that represents a url for my website. For example the string might be /cont/act/id and I want to break this up using the routes defined in my config/routes.rb file so that I get a hash like {:controller => ''cont'', :act => ''act'', :id=>''id''} How can I access all of the information stored in