search for: bipartit

...: http://igraph.sourceforge.net/news.html The igraph homepage: http://igraph.sf.net Since there was no announcement about igraph version 0.5.1 on R-pkgs, here is a list of the more important new things of both version 0.5.2 and 0.5.1. NEW FEATURES IN THE 0.5.2 VERSION - We have some support for bipartite (two-mode) graphs now. See ?graph.incidence, ?get.incidence for dealing with incidence matrices, ?graph.bipartite for a way to create bipartite graphs, ?bipartite.projection for creating one-mode projections. See ?is.bipartite for deciding whether a graph has a bipartite structure. - A n...

...: http://igraph.sourceforge.net/news.html The igraph homepage: http://igraph.sf.net Since there was no announcement about igraph version 0.5.1 on R-pkgs, here is a list of the more important new things of both version 0.5.2 and 0.5.1. NEW FEATURES IN THE 0.5.2 VERSION - We have some support for bipartite (two-mode) graphs now. See ?graph.incidence, ?get.incidence for dealing with incidence matrices, ?graph.bipartite for a way to create bipartite graphs, ?bipartite.projection for creating one-mode projections. See ?is.bipartite for deciding whether a graph has a bipartite structure. - A n...

Hi! I am trying to implement non-bipartite matching. I have around 500 sites which can be clustered by 10 regions. I am able to calculate pairwise Mahalanobis distances between sites (thanks to another post in the forum). However, I want to constrain my match to sites within the same region. Thus I want to replace elements of the distance...

...l quantities that depend on the parameters. My theoretical Model which has 2 free parameters a,b and one independant variable X, is of the type: f(X;a,b;M,N,P)=a*f1(X;M)+b*f2(X;M,N)+f3(X;M,N,P) where f1 and f2 are partial fractions and f3 is a complicated non-linear function of X and M, which is bipartite in the range of X on which I want to make my fit. M, N et P are constants with errors (physical quantities that enter into the equation of the model). I do not know R very well and my questions are: 1.Is there a R-package where it is possible to define arbitrary basis functions for a linear Mode...

hi all. perhaps someone can help me with subsetting here............ i'm trying to use the nested() function in the bipartite package. my problem is that i have a list of 10,000 matrices and i want the output to be a vector of the nested() function on each of the 10,000 matrices (so i can use these numbers in a statistical test). here is what i'm working with currently: #to store 10,000 matrices of null.distr() in...

...lude -DNDEBUG -I/usr/local/include -fpic -g -O2 -c bNNI.c -o bNNI.o gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c bionjs.c -o bionjs.o gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c bipartition.c -o bipartition.o gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c delta_plot.c -o delta_plot.o gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c dist_dna.c -o dist_dna.o gcc -std=gnu99 -I...

...AN called ?backbone?. The package can be found here: https://cran.r-project.org/web/packages/backbone/index.html The backbone package provides methods for extracting from a weighted graph a binary or signed backbone that retains only the significant edges. The user may input a weighted graph, or a bipartite graph from which a weighted graph is first constructed via projection. Backbone extraction methods include: the stochastic degree sequence model (Neal, Z. P. (2014). https://doi.org/10.1016/j.socnet.2014.06.001), hypergeometric model (Neal, Z. (2013). https://doi.org/10.1007/s13278-013-0107-y), t...

...AN called ?backbone?. The package can be found here: https://cran.r-project.org/web/packages/backbone/index.html The backbone package provides methods for extracting from a weighted graph a binary or signed backbone that retains only the significant edges. The user may input a weighted graph, or a bipartite graph from which a weighted graph is first constructed via projection. Backbone extraction methods include: the stochastic degree sequence model (Neal, Z. P. (2014). https://doi.org/10.1016/j.socnet.2014.06.001), hypergeometric model (Neal, Z. (2013). https://doi.org/10.1007/s13278-013-0107-y), t...

Dear R users, I used to be able to use the package bipartite to calculate network metrics using the function networklevel, but now (with the new version 1.14) I keep getting the error messages below. I don't understand why I am getting these error messages given that colSums is not < 2, and the network isn't that small. I get the same error messa...

...so DensityGrid.o DensityGrid_3d.o NetDataTypes.o NetRoutines.o adjlist.o amd_1.o amd_2.o amd_aat.o amd_control.o amd_defaults.o amd_dump.o amd_info.o amd_order.o amd_post_tree.o amd_postorder.o amd_preprocess.o amd_valid.o arpack.o array.o atlas.o attributes.o basic_query.o bfgs.o bigint.o bignum.o bipartite.o blas.o bliss.o bliss_eqrefhash.o bliss_graph.o bliss_heap.o bliss_orbit.o bliss_partition.o bliss_timer.o bliss_utils.o cattributes.o centrality.o cliques.o clustertool.o cocitation.o cohesive_blocks.o colamd.o community.o complex.o components.o conversion.o cores.o cs_add.o cs_amd.o cs_chol.o c...

Hi, Does anyone know of a package in R that has a function to convert network data (e.g. an adjacency matrix or ) from 2-mode to 1-mode? I am conducting social network analysis. I know that Pajek has this function under Net --> Transform --> 2-mode to 1-mode --> Rows. I have searched the documentation under packages 'sna', 'network', 'igraph', and

...graph has multiple edges. - Added a function to calculate a diversity score for the vertices, graph.diversity(). - Graph Laplacian calculation (graph.laplacian()) supports edge weights now. - Biconnected component calculation, biconnected.components() now returns the components themselves. - bipartite.projection() calculates multiplicity of edges. - Maximum cardinality search: maximum.cardinality.search() and chordality test: is.chordal() - Convex hull computation, convex.hull(). - Contract vertices, contract.vertices(). _______________________________________________ R-packages mailing list...

...graph has multiple edges. - Added a function to calculate a diversity score for the vertices, graph.diversity(). - Graph Laplacian calculation (graph.laplacian()) supports edge weights now. - Biconnected component calculation, biconnected.components() now returns the components themselves. - bipartite.projection() calculates multiplicity of edges. - Maximum cardinality search: maximum.cardinality.search() and chordality test: is.chordal() - Convex hull computation, convex.hull(). - Contract vertices, contract.vertices(). _______________________________________________ R-packages mailing list...

...f variance and with small samples. Regression types supported are gee, cox regression, and conditional logistic regression. * TreeRank (1.0-0) Nicolas Baskiotis http://crantastic.org/packages/TreeRank Implementation of the TreeRank methodology for building tree-based ranking rules for bipartite ranking through ROC curve optimization. * TreeSim (1.0) Tanja Stadler http://crantastic.org/packages/TreeSim The package simulates phylogenetic trees under a constant-rate birth-death process, conditioned on having a fixed number of final tips, or a fixed age, or a fixed age and number...

I'm trying to plot Venn diagrams with more than 3 sets (5 actually) in order to describe graphically the genetic variation between populations. I tried the limma library but realised it can only plot 3 sets. Is there any solution? Of course I could plot the chart manually but it'll take too long (have other datasets)..... One of my dataset is given below. THanks for any advice. j

Hi there, I would like to make a 'bumps chart' like the ones described e.g. here: http://junkcharts.typepad.com/junk_charts/bumps_chart/ Purpose: I'd like to plot the proportion of people in select countries living for less then one USD pr day in 1994 and 2004 respectively. I have already constructed a barplot - but I think a bumps chart would be better # The barplot and data

CRAN (and crantastic) updates this week New packages ------------ * Bergm (1.0) Alberto Caimo http://crantastic.org/packages/Bergm Functions implementing Bayesian estimation for exponential random graph models via exchange algorithm Updated packages ---------------- lmtest (0.9-26), logcondens (1.3.5), MTSKNN (0.0-4), pmml (1.2.21), r2lUniv (0.9.4), rattle (2.5.11), rgdal (0.6-23),

CRAN (and crantastic) updates this week New packages ------------ Updated packages ---------------- New reviews ----------- This email provided as a service for the R community by http://crantastic.org. Like it? Hate it? Please let us know: cranatic at gmail.com.

...1.0-1), ape (2.5-3), archetypes (2.0-1), arm (1.3-05), aroma.affymetrix (1.6.0), aroma.core (1.6.0), asbio (0.3-10), ascii (0.7), automap (1.0-7), bayesmix (0.7-1), bbmle (0.9.5.1), bcp (2.2.0), bear (2.5.3), bibtex (0.2-0), bifactorial (1.4.4), bigmemory (4.2.3), binGroup (1.0-5), biOps (0.2.1.1), bipartite (1.12), blighty (3.1-0), bnlearn (2.1.1), bootruin (1.0-156), brglm (0.5-5), cairoDevice (2.13), caret (4.43), catspec (0.95), cgh (1.0-7.1), cluster (1.13.1), clusterSim (0.38-1), cmprskContin (1.6), coarseDataTools (0.2), coin (1.0-12), copula (0.9-7), corrplot (0.30), cshapes (0.2-4), ctv (0.6-...