version 2.1

cran · Jul 10, 2012 · 0f6b20b · 0f6b20b
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diff --git a/CHANGELOG b/CHANGELOG
@@ -0,0 +1 @@
+2012/07    changed to mclustBIC in vblpcmstart function for compatibility with mclust 4
diff --git 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 <michael.salter-townshend@ucd.ie>
 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
@@ -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
diff --git 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
diff --git a/data/sampson.rda b/data/sampson.rda
diff --git a/data/simulated.network.rda b/data/simulated.network.rda
diff --git 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
@@ -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