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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,17 +1,17 @@ | ||
| Package: VBLPCM | ||
| Type: Package | ||
| Title: Variational Bayes Latent Position Cluster Model for networks. | ||
| Version: 1.3 | ||
| Date: 2012-01-30 | ||
| Version: 2.0 | ||
| Date: 2012-02-08 | ||
| Author: Michael Salter-Townshend | ||
| Maintainer: Michael Salter-Townshend <michael.salter-townshend@ucd.ie> | ||
| Description: A package to fit and simulate latent position and cluster | ||
| models for statistical networks using a Variational Bayes | ||
| approximation. | ||
| Depends: MASS, boot, mclust, network, sna, ergm | ||
| Depends: MASS, boot, mclust, network, ergm, sna | ||
| SystemRequirements: Gnu Scientific Library version >= 1.12 | ||
| License: GPL (>= 2) | ||
| LazyLoad: yes | ||
| Packaged: 2012-01-30 14:59:12 UTC; saltertm | ||
| Packaged: 2012-02-15 15:40:36 UTC; ripley | ||
| Repository: CRAN | ||
| Date/Publication: 2012-01-30 16:10:41 | ||
| Date/Publication: 2012-02-15 15:44:03 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,12 +1,3 @@ | ||
| # Export all names | ||
| exportPattern(".") | ||
| # Export everything | ||
| exportPattern("*") | ||
|
|
||
| # Import all packages listed as Imports or Depends | ||
| import( | ||
| MASS, | ||
| boot, | ||
| mclust, | ||
| network, | ||
| sna, | ||
| ergm | ||
| ) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,58 +1,33 @@ | ||
| vblpcmcovs<-function(N, model, Y, edgecovs=NULL,nodecovs=NULL) | ||
| { | ||
| XX<-matrix(rep(1,N^2),ncol=1) # all get the intercept term | ||
| P=ncol(XX) | ||
| if (model=="receiver") | ||
| XX_n<-NULL | ||
| XX_e<-matrix(rep(1,N^2),ncol=1) # all get the intercept term | ||
| if (model=="rreceiver") | ||
| { | ||
| # receiver random effects | ||
| #P=P+N | ||
| #XX<-cbind(XX,t(matrix(rep(diag(1,N),N),N))) | ||
| P=P+1 | ||
| tmp<-apply(Y,2,sum,na.rm=1) | ||
| tmp<-(tmp-mean(tmp))/sd(tmp) | ||
| XX<-cbind(XX,rep(tmp,N)) | ||
| XX_n<-cbind(XX_n,rep(1,N)) | ||
| } | ||
|
|
||
| if (model=="sender") | ||
| if (model=="rsender") | ||
| { | ||
| # sender random effects | ||
| #XX<-cbind(XX,matrix(0,N^2,N)) | ||
| #for (i in 1:N) | ||
| # XX[((i-1)*N+1):(i*N),i+P]<-1 | ||
| #P=P+N | ||
| P=P+1 | ||
| tmp<-apply(Y,1,sum,na.rm=1) | ||
| tmp<-(tmp-mean(tmp))/sd(tmp) | ||
| XX<-cbind(XX,c(t(matrix(rep(tmp,N),N)))) | ||
| XX_n<-cbind(XX_n,rep(1,N)) | ||
| } | ||
|
|
||
| if (model=="social") | ||
| if (model=="rsocial") | ||
| { | ||
| # sender random effects | ||
| #XX<-cbind(XX,matrix(0,N^2,N)) | ||
| #for (i in 1:N) | ||
| # XX[((i-1)*N+1):(i*N),i+P]<-1 | ||
| #P=P+N | ||
| #XX[,(P-N+1):P]<-XX[,(P-N+1):P]+t(matrix(rep(diag(1,N),N),N)) | ||
| #XX[,(P-N+1):P][XX[,(P-N+1):P]>1]<-1 | ||
| tmp1<-apply(Y,1,sum,na.rm=1) | ||
| tmp1<-(tmp1-mean(tmp1))/sd(tmp1) | ||
| tmp2<-apply(Y,2,sum,na.rm=1) | ||
| tmp2<-(tmp2-mean(tmp2))/sd(tmp2) | ||
| P=P+2 | ||
| XX<-cbind(XX,c(t(matrix(rep(tmp1,N),N))),rep(tmp2,N)) | ||
| XX_n<-cbind(XX_n,rep(1,N),rep(1,N)) | ||
| } | ||
| if (!is.null(nodecovs)) | ||
| if (!is.null(nodecovs)) # include option to not model nodecovs as edgecovs? | ||
| { | ||
| tmp<-expand.grid(1:N,1:N) | ||
| nodecovs<-as.matrix(nodecovs) | ||
| nodeedgecovs<-nodecovs[tmp[,1],]-nodecovs[tmp[,2],] | ||
| } | ||
| if (!is.null(nodecovs)) | ||
| XX<-cbind(XX,nodeedgecovs) | ||
| XX_n<-cbind(XX_n,nodeedgecovs) | ||
| if (!is.null(edgecovs)) | ||
| XX<-cbind(XX,edgecovs) | ||
| return(as.matrix(XX)) | ||
| XX_e<-cbind(XX_e,edgecovs) | ||
| return(list("XX_n"=XX_n,"XX_e"=XX_e)) | ||
| } | ||
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