similar to: hold position of vertices constant in network {statnet}?

I'm having trouble with the ordisurf function in the vegan package. I have created an ordination plot (cmdscale) of 60 samples based on Bray-Curtis dissimilarities, and would like to overlay various soil edaphic characteristics as possible clues to the clustering I observe in my plot. However, I find that ordisurf creates a surface on the plot that is a perfect, even gradient - and

I am beginning to work with the 'ape' package in R, and have run into some trouble. I generated a UPGMA tree based on DNA sequence distance in Paup* and read it into R, where it became an object of class "phylo". However, I need it to be classified as a "dendrogram" for my purposes (to use it to order the layout of a heatmap). I get an error using as.hclust.phylo

Dear R users: There appears to be a conflict between the statnet package and the igraph package. With igraph loaded into memory, the network() function of statnet failed, returning the error to the effect that the matrix being converted was "not a graph object." Removing igraph from memory restored statnet to proper function. Apologies if this is redundant. I could not find this

Dear R community, I am still new to R, but I am attempting to use it for (hopefully) all my plotting needs. I have been using lattice and Hmisc for most plots so far successfully, but I need help creating a plot I desire for some new data I have. This data frame consists of the same type of measurement (Eh) for 27 different locations. I have 8000+ measurements for each location, and my

Dear R community, once again I request your generous help on an R issue I cannot seem to figure out. I am trying to do some analysis for multiple sites, in my example I am using only two, but the same will done on many sites. It's just ONE line, so I hope somebody can give a me a hand by email. Look at the loop to make the plot x ~ y. If the curve function is removed from the loop

I need to do a simple cumulative sum by group and add the result to the data. I found an earlier thread in the help files with a few suggestions. Somewhat, one of the suggestions does not work with "my data", and I don't really understand why ? The error am getting using the "my data" below is... Error in data.frame(..., check.names = FALSE) : arguments imply

Dear R colleagues: Am trying to fit a simple NL model to determine Economical Optimum Nitrogen Rates. The segmented (quadratic + plateau) model only works with some y's, in some cases I get a "singular gradient" error. I'll appreciate any ideas in how to solve the singular gradient error. Thanks, Jose # The following code works using yield2 in the nls model but not using

Hello all, I am an R novice and I have a simple question and hope somebody can help me out. I need to place several labels in a plot, this labels are some kind of text and also some objects (which come from some more complicated R calculations). In one of this labels I'd like to place a superscript, however I cannot find a way to place both the expression and the object in the same

I apologize for what is likely a stupid question - I HAVE looked through "Writing R Extensions" and HAVE gone through existing help requests, but have not yet found an answer. I'm sorry if I've missed something obvious. I am planning on building a package in the near future. I have a number of C programs that I have written to interface with R (compiled using the R SHLIB, run

Dear R community, I am using xYplot() from the Hmisc package. The package works great to plot means + CI. But I am having issues handling the scales. I am plotting "Soil Clay content" vs "Soil depth" by "land use". Usually in this type of graphs it is better to place the variable "soil depth" in the y-axis and it should be ordered downward by depth (0-5

I'm running R 2.15.1x64, though the same problem persists for 2.13.0x32 and 2.13.0x64. I am trying to run compiled C code using the .C convention. The code compiles without problems, dynamically loads within the R workspace with no problems, and even runs and gives correct results with no problems. However, R will randomly crash within a few minutes of successfully using the compiled

Folks, This is so simple is driving me crazy. It's not really an R question is more an Statistics question. I applied a chemical in 3 different events during a growing season. I took 3 samples in each event to estimate mean applied chemical. Thus, I can easily estimate means and st.err by event. I can then estimate the total chemical applied for the whole season by adding the 3 means

----- Forwarded message from Mark Lewis <mlewis@webnoize.com> ----- Delivery-Date: Tue Nov 21 10:15:55 2000 Date: Tue, 21 Nov 2000 10:07:15 -0800 From: Mark Lewis <mlewis@webnoize.com> Reply-To: mlewis@webnoize.com Organization: Webnoize News X-Mailer: Mozilla 4.75 [en] (Win98; U) To: monty@xiph.org Subject: liked your article at http://xiph.org/about.html here's an article about

We have a position available for an experienced R programmer to provide support for software development for statnet, a suite of R packages for Exponential Random Graph Modeling (http://statnet.org -- most content is on the wiki). The current statnet development team includes several PhD level statisticians, some faculty from other disciplines, and an independent software developer. Funding

Hello, I am using the plot.igraph function in the igraph package to plot a network. How do I keep vertices from overlapping? One option would be to pass an argument that restricts vertices to occupy the same coordinates given their size. A second option would be to increase the area of the plot (and multiply the distance between vertices with a constant) while keeping the size of vertices the

Dear all, I have a directed graph - an Igraph to be more precise - which has some vertices attributes (like dorm, year etc). Edges and the graph itself do not have any attributes. Based on the attributes of the vertices, I'd like to calculate correlation among the edges (e.g. how likely people of the same dorm are connected?) for the whole graph. Also, I'd like to calculate

We need to change the way vertices are generated for windows. We currently have a addWindowGeometry screen function that takes care of this. It can be wrapped by plugins and it can generate any vertices and texture coordinates it wants. I'd like to change it so that the region for which to generate vertices and texture coordinates will be specified elsewhere and it doesn't have to be

Hello I have a dataset of people spending time in places. But most people don't hang out in all the places. it looks like: > Input<-data.frame(people=c("Marc","Marc","Joe","Joe","Joe","Mary"), + place=c("school","home","home","sport","beach","school"), +

Greetings! I want to follow the evolution of a Nelder-Mead function minimisation (a function of 2 variables). Hence each simplex will have 3 vertices. Therefore I would like to have a function which can output the coordinates of the 3 vertices after each new simplex is generated. However, there seems to be no way (which I can detect) of extracting this information from optim() (the

When the shape of all vertices is set to "square" and the size of the vertices is also set, one get following error (commands attached): Error in l[[which.min(sapply(l, function(p) (p[1] - x0)^2 + (p[2] - y0)^2))]] : attempt to select less than one element Is there a way to solve this problem? Robbie ## Load the igraph package library(igraph) ## Create and plot a small graph