similar to: Characteristic Path length calculation

Hi, I have a erdos-renyi game with 6000 nodes and probability 0.003. g1 = erdos.renyi.game(6000, 0.003) How to create a Watts Strogatz game with the same probability. g1 = watts.strogatz.game(1, 6000, ?, ?) What should be the third and fourth parameter to this argument. -- View this message in context: http://r.789695.n4.nabble.com/Watts-Strogatz-game-tp3491922p3491922.html Sent from the R

Hello I am a relatively new user of R and am struggling to use the 'network' package. I have a correlation matrix (produced using 'cor'), and want to draw a network where each item showing correlation above a threshold (say 0.5) is joined by a green line, and each item showing correlation below a threshold (say -0.5) is joined by a red line. Does anyone have any hints of how to

I have a graph with edge and vertex weights, stored in two data frames: --8<---------------cut here---------------start------------->8--- vertices <- data.frame(vertex=c("a","b","c","d"),weight=c(1,2,1,3)) edges <-

I am using the code below to output some network measures: central_social <- data.frame(V(s641_social)$name, indegree_social, outdegree_social, incloseness_social, outcloseness_social, betweenness_social, eigen_social) and I get the following error: Error in Re(z) : non-numeric argument to function I know this has to do with V but I cannot figure out what is wrong. s641-social is a graph

Dear R developers, I am seeking advice on some $subject matter. My package will have an update soon, that is not backward compatible with the current version. It will likely break much of the existing code. Many (~50) packages depend on 'igraph' and they, too, will most probably break with the new version. My intended solution is, that I create a snapshot of the current package, under

Hi, I have a simple beginner's question on removing a list of objects. Say I have objects C243.Daily1, C243.Daily2...C243.Daily5 in my workspace. I'd like to remove these without using rm five times. So I write. > a <- list(paste("C243.Daily",sep="",1:5)) > rm(a) Obviously this wouldn't work, as it would only remove the object a. But is there any way

Could someone tell me the difference between igraph and igraph0? I searched the CRAN web site, but cannot find an explantion of the differences. Thanks, Alan [[alternative HTML version deleted]]

Hi, I am using 'igraph' to make some plots. The problem I got is that I don't know how to label the nodes with gene names. My sample code: ## suppose I have 100 gene (nodes) ## --------------------------------------------------------------------------- graph <- set.vertex.attribute(graph, "color", value=c(rep(c('green','red'),50))) graph <-

Dear All, in some functions of my package, I use the Matrix S4 class, as defined in the Matrix package. I don't want to depend on Matrix, however, because my package is perfectly fine without Matrix, most of the functionality does not need Matrix. Matrix is so included in the 'Suggests' line. I load Matrix via require(), from the functions that really need it. This mostly works

Dear list, Does anyone know how to fit the power law distribution? I have the empirical distribution and would like to check whether it fits power law (with the power estimated from the data). Any hints are appreciated Best regards Galina [[alternative HTML version deleted]]

Hi everyone, I am using the fastgreedy.community function to get the $merges matrix and the $modularity vector. This serves my purpose of testing modularity of my graph. But I am "greedy" to plot the heat map and dendrrogram based on the $merges dendogram matrix. I know that heatplot does the graphics part but I am not sure if the dendogram generated by the heatplot will match the one

Hi, Given a simple example, test <- matrix(c(0.1, 0.2, 0.1, 0.2, 0.1, 0.1, 0.3, 0.1, 0.1), 3, 3) How to generate row indexes for which their corresponding row values are less than or equal to 0.2 ? For this example, row 2 and 3 are the correct ones. Thanks [[alternative HTML version deleted]]

Hi, I'm working on some social networks and I managed to create the graphs with labels and edges weight, but I would also like to change the size of the vertices according to the age of the persons in the network and the shape according to the gender. Now for the age, I have people with ages between 20 and 78, and I would like to have 4 categories (sizes): 20-35, 36-50, 50-65, >65. I have

Hi to all, does anybody knows whether there is a package to plot those http://www.equine-science.de/temp/graph.jpg graphs. the thickness of the points and/or the lines should be represent the numbers of behaviours With kind regards Knut

Hi all, I want to find all the mappings of one graph in another graph, based on their vertex labels Is there any way to do this in igraph based on vertex labels. (as far as i know Igraph allows the subgraph isomorphism based only on vertex and edge colors) Eg: graph 1: x(1) x(2) x(2) y(3) y(4) x(1) z(5) x(2) graph 2: x(1) y(2) # the brackets contain the corresponding vertex ids i would like my

I am having trouble plotting one of my graphs (think graph theory graph with edges and vertices, not scatterplots or histograms). For some pairs of vertices, I want multiple edges to be visible in my graph. As an example of this, in my script below, I want two edges to be visible from vertex 1 and vertex 9 (among some others) yet when I plot it, only one edge is visible.

I am using 'igraph' package to make some graphs of 'gene-gene interaction'. I can get a data.frame which has three columns. gene1 gene2 pvalue AGT MLR 1.2e-04 MLR 11BHSD1 1.71e-05 IFG2 11BHSD2 2.2e-07 . . . . . . . . . AGTR1 NPPA

Using Igraph, I create shortest paths, then convert the matrix into three column vectors - "vertex1", "vertex2", "shortestpath" - as the code below shows. #code for generating shortest path matrix and creating a 3 columns from an igraph graph object "y" y_s<-shortest.paths(y, weights = NULL) y_s <- melt(y_s)[melt(upper.tri(y_s))$value,] #Step 2: this

Hello, I am exporting a graph in "gml" format from igraph 0.5.5. When I open the file in Cytoscape v.2.7 I can't map the color attribute that I assign to the graph when I export it from igraph. Could anyone help me in this? Thanks. -- Warm Regards, Sandeep Amberkar BioQuant,BQ26, Im Neuenheimer Feld 267, D-69120,Heidelberg Tel: +49-6221-5451354 [[alternative HTML version

Hi, So I've been figuring out how to use igraph in R and like it for it's speed and simplicity. Now I have a graph built from an edgelist where vectors have a $name attribute. I have another dataframe with attributes tied to a vector ID, which is the same as the $name attribute of vectors represented in the graph. How can I iterate over the graph by V(g)$name and do