diff --git a/CHANGELOG b/CHANGELOG new file mode 100644 index 0000000..771a056 --- /dev/null +++ b/CHANGELOG @@ -0,0 +1 @@ +2012/07 changed to mclustBIC in vblpcmstart function for compatibility with mclust 4 diff --git a/DESCRIPTION b/DESCRIPTION index 339cc8d..aa121e5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: VBLPCM Type: Package Title: Variational Bayes Latent Position Cluster Model for networks. -Version: 2.0 -Date: 2012-02-08 +Version: 2.1 +Date: 2012-07-06 Author: Michael Salter-Townshend Maintainer: Michael Salter-Townshend Description: A package to fit and simulate latent position and cluster @@ -12,6 +12,6 @@ Depends: MASS, boot, mclust, network, ergm, sna SystemRequirements: Gnu Scientific Library version >= 1.12 License: GPL (>= 2) LazyLoad: yes -Packaged: 2012-02-15 15:40:36 UTC; ripley +Packaged: 2012-07-10 12:22:05 UTC; mst Repository: CRAN -Date/Publication: 2012-02-15 15:44:03 +Date/Publication: 2012-07-10 13:57:10 diff --git a/MD5 b/MD5 index 6cf90e8..8c3ca7f 100644 --- a/MD5 +++ b/MD5 @@ -1,4 +1,5 @@ -dfe1234ffc6159d8bc4cb879c2f68781 *DESCRIPTION +610758964d2dd667e7cfea9ffb249d34 *CHANGELOG +a26299c31e6add62ae56c67ac68f3596 *DESCRIPTION 6066c73622b7572e7b444b0f1070c9cb *NAMESPACE 0ad99e90eeb440d8ce2350ebb220d2aa *R/KL.R 39bb7b6e908f3d787f79b01ef2f4dfa3 *R/VBLPCM.R @@ -11,7 +12,7 @@ b2971e93430601290bc92758c8587c1f *R/gof.vblpcm.R 4f34bb8f64709bfd1f77f32e38d202c0 *R/predict.R 203861162888e86a84e9b20d62f2d8ba *R/print.vblpcm.R 32ef7505c44b2245b165b30aa1ebf816 *R/roc.R -2acb40309ab1d6f67d2c28bd86f73f7a *R/start.R +fffb5665e0d76820065b068cb9cc3acd *R/start.R 4f69c86b26fbc64b90e83eb39a6ac450 *R/summarise_groups.R 1c1489335fb6f8be56280af5240adaf6 *R/summary.vblpcm.R 647c54e4383eed4d7bf283ee020e968c *R/vb_bic.R @@ -23,7 +24,7 @@ b2971e93430601290bc92758c8587c1f *R/gof.vblpcm.R 1276843b63a1602933616b872ee9317f *data/simulated.network.rda 4ccabdb12a6c7592d26cceab34755ee0 *man/E_to_Y.Rd 62b220ff6a4b95449f21d7eabbbd5848 *man/VBLPCM-internal.Rd -4db2abb48ae00cc3dde11aab8104e820 *man/VBLPCM-package.Rd +dc8e2243fb722fa471c6f2b3c82a1fec *man/VBLPCM-package.Rd 1d21ac5b8c3d8909d4782465e94cec14 *man/Y_to_E.Rd b08842a305ad02114fee7ce021dbf4d5 *man/Y_to_M.Rd 722b273c922c4daaccf40eb94c0776a7 *man/Y_to_nonE.Rd @@ -35,7 +36,7 @@ e8cb13745bc8110e00fd70d8b67f98a7 *man/log_like_forces.Rd 65d65a84e27489040342eabeadb09d26 *man/plot.vblpcm.Rd 8e9b57714508a170b5d11ae4472b27a9 *man/predict.vblpcm.Rd ebf0dedf3bb3c17568c54f79d34b752d *man/print.vblpcm.Rd -ca7266e009f2abc53b8256e28e55d427 *man/sampson.Rd +6e2b9aa81742ce41f558357e3d0dc524 *man/sampson.Rd 1d1c511715c82a3261f3d548fdf31e49 *man/simulated.network.Rd e77ae23391ebacc4c3394ea97a7b9c4e *man/summary.vblpcm.Rd 9b07344bce55dd7bd95a1a3bbbe86081 *man/vblpcmBIC.Rd diff --git a/R/fruchterman_reingold.R b/R/fruchterman_reingold.R old mode 100755 new mode 100644 diff --git a/R/start.R b/R/start.R index 608207b..06fb1fd 100644 --- a/R/start.R +++ b/R/start.R @@ -145,8 +145,8 @@ vblpcmstart<-function(g.network, G=1, d=2, LSTEPS=5e3, model="plain", CLUST=0, } if (d>1) { - fitmc<-summary(EMclust(initial_V_z,G=G,modelNames="VII"),initial_V_z) - } else fitmc<-summary(EMclust(initial_V_z,G=G,modelNames="V"),initial_V_z) + fitmc<-summary(mclustBIC(initial_V_z,G=G,modelNames="VII"),initial_V_z) + } else fitmc<-summary(mclustBIC(initial_V_z,G=G,modelNames="V"),initial_V_z) if (is.null(fitmc$bic)) { print("Couldn't fit initial clustering using mclust") @@ -155,8 +155,8 @@ vblpcmstart<-function(g.network, G=1, d=2, LSTEPS=5e3, model="plain", CLUST=0, G=1 if (d>1) { - fitmc<-summary(EMclust(initial_V_z,G=G,modelNames="VII"),initial_V_z) - } else fitmc<-summary(EMclust(initial_V_z,G=G,modelNames="V"),initial_V_z) + fitmc<-summary(mclustBIC(initial_V_z,G=G,modelNames="VII"),initial_V_z) + } else fitmc<-summary(mclustBIC(initial_V_z,G=G,modelNames="V"),initial_V_z) } initial_V_eta<-t(fitmc$parameter$mean) initial_V_omega2<-c(t(fitmc$parameter$variance$sigmasq)) # for use with EII diff --git a/data/aids.rda b/data/aids.rda old mode 100755 new mode 100644 diff --git a/data/sampson.rda b/data/sampson.rda old mode 100755 new mode 100644 diff --git a/data/simulated.network.rda b/data/simulated.network.rda old mode 100755 new mode 100644 diff --git a/man/VBLPCM-package.Rd b/man/VBLPCM-package.Rd index 32ed1de..7befbb9 100644 --- a/man/VBLPCM-package.Rd +++ b/man/VBLPCM-package.Rd @@ -119,10 +119,10 @@ expand.grid(monks,monks)[Y==0,][order(probs[Y==0],decreasing=TRUE),][1,] ### find the least probable link that does in fact occur ### expand.grid(monks,monks)[Y==1,][order(probs[Y==1]),][1,] -### run a bigger example, using the likelihood sampler set to 0.2 ### +### run a bigger example, using the likelihood sampler set to 0.1 ### data(aids,package="VBLPCM") -v.start<-vblpcmstart(aids.net,G=7,model="rsender") -v.fit<-vblpcmfit(v.start, STRAT=0.2) +v.start<-vblpcmstart(aids.net,G=7,model="rsender",LSTEPS=5e2) +v.fit<-vblpcmfit(v.start, STRAT=0.1,STEPS=20) ### plot the mean posterior positions ### plot(v.fit, R2=0.1,main="Aids Blogs with Sender Random Effects") diff --git a/man/sampson.Rd b/man/sampson.Rd index 1ff06c7..225e79c 100644 --- a/man/sampson.Rd +++ b/man/sampson.Rd @@ -41,9 +41,6 @@ literature, having been modeled by Holland and Leinhardt and Fienberg, Meyer, and Wasserman (1981), Hoff, Raftery, and Handcock (2002), etc. This is only a small piece of the data collected by Sampson. - -For additional examples of \code{network}s see the \code{netdata} -package which is part of the \code{statnet} package. } \usage{ data(sampson) diff --git a/src/fruchterman_reingold.c b/src/fruchterman_reingold.c old mode 100755 new mode 100644