version 2.4.9

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: VBLPCM
 Type: Package
 Title: Variational Bayes Latent Position Cluster Model for Networks
-Version: 2.4.8
-Date: 2021-10-06
+Version: 2.4.9
+Date: 2023-03-22
 Author: Michael Salter-Townshend
 Maintainer: Michael Salter-Townshend <mike.saltertownshend@gmail.com>
 Description: Fit and simulate latent position and cluster models for network data, using a fast Variational Bayes approximation developed in Salter-Townshend and Murphy (2013) <doi:10.1016/j.csda.2012.08.004>.
@@ -13,6 +13,6 @@ URL: https://www.r-project.org, https://mststats.github.io/#software
 License: GPL (>= 2)
 LazyLoad: yes
 NeedsCompilation: yes
-Packaged: 2021-10-06 09:37:25 UTC; mst
+Packaged: 2023-03-22 15:36:25 UTC; mst
 Repository: CRAN
-Date/Publication: 2021-10-06 11:30:16 UTC
+Date/Publication: 2023-03-22 16:10:02 UTC

MD5

@@ -1,13 +1,13 @@
-f0fa7bc5a911baef4e7544ac79973a3f *CHANGELOG
-bf5ba392c2695ae95fc507dafd9905db *DESCRIPTION
+da58a6ef3a05730d790b1928d9d7d564 *DESCRIPTION
 1d69d4741adbf48761e664579cf6b9ee *NAMESPACE
-01d48538efa577a3b1d341d06c097bea *R/KL.R
-59018b906a56eadb7f679bce30658b81 *R/VBLPCM.R
-912ab6f8dffb1ccc32485d43cc0c7ac9 *R/adjacency_to_edges.R
+18c8f25668b8db1334dd6b9cc673ca67 *NEWS.md
+18f699564ffd5acf7c55c941388b6996 *R/KL.R
+71fc7bed8d0f0c2b107c5720333a69e7 *R/VBLPCM.R
+f3fcd0fa87afe63a1e21a30acba6430a *R/adjacency_to_edges.R
 124931b1ae2da9856a9bed1beb43047d *R/covs.R
-c37a1721e1022d3894d1ff487a0f6829 *R/fruchterman_reingold.R
+5c5d0d589c865ad25bbc5d191697f416 *R/fruchterman_reingold.R
 cf57d570a3892125e33517728de7664b *R/gof.vblpcm.R
-8c56de4663246b2207ade78a50a52ba1 *R/log_like_forces.R
+93c2e234555761bad9494b767d6be9df *R/log_like_forces.R
 9fc252b68a6dc43a2bc8d97ab3f07f53 *R/plot_network.R
 6d0b56049f54c59dbe71754983a9a80d *R/predict.R
 203861162888e86a84e9b20d62f2d8ba *R/print.vblpcm.R
@@ -16,17 +16,17 @@ f2399d5414a7daef462ea7f027bab6bb *R/start.R
 4f69c86b26fbc64b90e83eb39a6ac450 *R/summarise_groups.R
 054e8f388ac9c8373ab5b6e66818754e *R/summary.vblpcm.R
 31c8ccdf29df94b0f5f9508fcb1a7e9e *R/vb_bic.R
-31cf9d5d81f03b2dd6cf446936301a3b *R/zzz.R
+41a2dc869b99e0cc97d104891504d121 *R/zzz.R
 4cda533c9aac1b3aa6d890381c4dd46c *cleanup
 7b0797ae9bdf1a440fef9986bfc3f6b0 *configure
 230471d9e64e9216efae1ab64933a57d *configure.ac
 013778ff539b989141783da07f3ddd03 *data/aids.rda
 375a6d94bfb6ff8b879de44250fff5d3 *data/sampson.rda
 1276843b63a1602933616b872ee9317f *data/simulated.network.rda
-9beed6138652a9e4ebedd2cb1f270acb *inst/CITATION
+de46b485251bd27fc99e78d4b0761c28 *inst/CITATION
 4ccabdb12a6c7592d26cceab34755ee0 *man/E_to_Y.Rd
 62b220ff6a4b95449f21d7eabbbd5848 *man/VBLPCM-internal.Rd
-947bed8ddafc3495d5be6a2ea23d5af3 *man/VBLPCM-package.Rd
+6fe271e0efa8e92c70139c8b559be67e *man/VBLPCM-package.Rd
 1d21ac5b8c3d8909d4782465e94cec14 *man/Y_to_E.Rd
 0eb794fe9b2faea92c95f0146560ac1a *man/Y_to_M.Rd
 a3d9e7566f96741ba738afda6cade6d7 *man/Y_to_nonE.Rd
@@ -58,6 +58,6 @@ b64c69878f210fcd2b8a05890f9046d1 *src/bb.c
 61a39c5900a8b02859418ac8e209e974 *src/fruchterman_reingold.c
 c762448b2281f5119d26973664245846 *src/funcs.c
 c650981e26f8f648c6683057bcf8234b *src/headers.h
-26182edc32dd38686277085e02ff5716 *src/init.c
+4479cb25085b79fe3d92e36bf643a879 *src/init.c
 58af03653b50ae580943f91e0301adf7 *src/likelihoods.c
 e98595aa0e3f407d16e37832b92f7449 *src/ll_layout.c

NEWS.md

@@ -0,0 +1,49 @@
+# VBLPCM 2.4.9
+
+* Added a `NEWS.md` file to track changes to the package.
+
+* fixed issue of "DLL requires the use of native symbols" by changing strings to symbols and using  .fixes="C_" in useDynLib _2023/03_    
+
+# VBLPCM 2.4.8
+
+* mirroring on github _2022/05_    
+
+* updated configure script using autoupdate _2021/10_    
+
+* removed use of externs in src .c files, now passing pointers to structs _2020/12_    
+
+* using useDynLib now for compatibility with new R versions _2020/12_    
+
+* had to change name of log_like_forces.c to ll_layout.c as was not compiling. Odd error resolved but not understood.  _2020/10_    
+
+* changed use of deprecated plot.gofobject function from ergm to plot.gof and added cleanup script. _2018/10_    
+
+* updated GSL requirements; added imports of 'sna' functions; added network to depends; shortened BIC example.  _2015/12_    
+
+* removed inv_sigma02 term from omega2 update (thanks to Robin Gong).  _2014/01_    
+
+* fixed bug in use of start function when using largest connected component only and edge covariates. _2014/01_    
+
+* checked for leaks using AddressSanitizer, moved some Depends to Imports. _2013/10_    
+
+* now if mclust fails Fruchterman-Reingold is (re)called until mclust can find clusters.  _2013/05_    
+
+* changed setting of seed. A single set.seed is now used.  _2013/05_    
+
+* plugged memory leak due do diagonal of sociomatrix and corrected case-control usage. _2013/04_    
+
+* fixed bug in convergence check for V_xi_* and V_psi2_* (thanks for Triona Ryan). _2013/04_    
+
+* fixed bug in random effects updates and tweaked plot function. _2013/02_    
+
+* fixed bug in predict function for random effects models. _2013/02_    
+
+* changed onAttach to onLoad in zzz.R _2013/01_    
+
+* fixed bugs in handling of nodal covariates and cast same as sender, receiver or social.  _2012/08_    
+
+* working startup message.  _2012/08_    
+
+* fixed V_xi_e and V_psi2_e update bug (thanks to Sebastian Leist).  _2012/08_    
+
+* changed to mclustBIC in vblpcmstart function for compatibility with mclust 4.  _2012/07_    

R/KL.R

@@ -40,7 +40,7 @@ vblpcmKL<-function(x)
   NC=x$NC
   KL=0
   imodel=switch(model, plain=0, rsender=1, rreceiver=2, rsocial=3)
-  final_KL<-.C("KL_total", NAOK=TRUE, 
+  final_KL<-.C(C_KL_total, NAOK=TRUE, 
 	       imodel=as.integer(imodel), P_n=as.integer(P_n),P_e=as.integer(P_e),D=as.integer(d), N=as.integer(N), 
 	       NE=as.integer(NE), NnonE=as.integer(NnonE), NM=as.integer(NM),
 	       G=as.integer(G), Y=as.numeric(t(Y)), E=as.integer(t(E)), nonE=as.integer(t(nonE)), M=as.integer(t(M)),

R/VBLPCM.R

@@ -52,7 +52,7 @@ vblpcmfit<-function(variational.start, STEPS=50, maxiter=100, tol=1e-6, NC=NULL,
   inv_sigma02<-variational.start$inv_sigma02
   imodel=switch(model, plain=0, rsender=1, rreceiver=2, rsocial=3)
   conv=0 # not converged to start with
-  out<-.C("Rf_VB_bbs", NAOK=TRUE, imodel=as.integer(imodel), steps=as.integer(STEPS), max_iter=as.integer(maxiter), P_n=as.integer(P_n), 
+  out<-.C(C_Rf_VB_bbs, NAOK=TRUE, imodel=as.integer(imodel), steps=as.integer(STEPS), max_iter=as.integer(maxiter), P_n=as.integer(P_n), 
            P_e=as.integer(P_e), D=as.integer(d), N=as.integer(N), NE=as.integer(NE), NnonE=as.integer(NnonE), NM=as.integer(NM),
            G=as.integer(G), Y=as.numeric(t(Y)), E=as.integer(t(E)), nonE=as.integer(t(nonE)), M=as.integer(t(M)),
   	   numedges=as.integer(t(numedges)), EnonE=as.integer(t(EnonE)), diam=as.integer(diam),

R/adjacency_to_edges.R

@@ -1,28 +1,28 @@
 Y_to_E<-function(N, NE, directed, Y)
   {
   E<-matrix(NaN,NE,2)
-  ans<-.C("Y_to_E", NAOK=TRUE, N=as.integer(N),  
+  ans<-.C(C_Y_to_E, NAOK=TRUE, N=as.integer(N),  
           directed=as.integer(directed), Y=as.numeric(t(Y)), E=as.integer(t(E)))
   return(t(matrix(ans$E,2)))
   }
 Y_to_nonE<-function(N, NnonE, directed, Y)
   {
   nonE<-matrix(0, NnonE, 2)
-  ans<-.C("Y_to_nonE", NAOK=TRUE, N=as.integer(N), directed=as.integer(directed), 
+  ans<-.C(C_Y_to_nonE, NAOK=TRUE, N=as.integer(N), directed=as.integer(directed), 
           Y=as.numeric(t(Y)), nonE=as.integer(t(nonE)))
   return(t(matrix(ans$nonE,2)))
   }
 Y_to_M<-function(N, NM, directed, Y)
   {
   M<-matrix(0, NM, 2)
-  ans<-.C("Y_to_M", NAOK=TRUE, N=as.integer(N), directed=as.integer(directed), 
+  ans<-.C(C_Y_to_M, NAOK=TRUE, N=as.integer(N), directed=as.integer(directed), 
           Y=as.numeric(t(Y)), M=as.integer(t(M)))
   return(t(matrix(ans$M,2)))
   }
 E_to_Y<-function(N, NE, directed, E)
   {
   Y<-matrix(0,N,N)
-  ans<-.C("E_to_Y", NAOK=TRUE, N=as.integer(N), NE=as.integer(NE), 
+  ans<-.C(C_E_to_Y, NAOK=TRUE, N=as.integer(N), NE=as.integer(NE), 
           directed=as.integer(directed), E=as.integer(t(E)), Y=as.numeric(t(Y)))
   return(matrix(ans$Y,N))
   }

R/fruchterman_reingold.R

@@ -5,7 +5,7 @@ fruchterman_reingold<-function(net, D=2, steps=1000, repulserad=N^D, m=N*(D-1),
   Y<-as.sociomatrix(net)
   X<-matrix(runif(N*D,-D^2,D^2),ncol=D)
   # update X
-  out<-.C("fruchterman_reingold", NAOK=TRUE, directed=as.integer(directed), N=as.integer(N), 
+  out<-.C(C_fruchterman_reingold, NAOK=TRUE, directed=as.integer(directed), N=as.integer(N), 
 	  D=as.integer(D), steps=as.integer(steps), Y=as.double(t(Y)), X=as.numeric(t(X)), 
 	  repulserad=as.double(repulserad), m=as.numeric(m), volume=as.numeric(volume))
   X<-t(matrix(out$X,ncol=N))

R/log_like_forces.R

@@ -20,7 +20,7 @@ log_like_forces<-function(net, D, X, B, m=network.size(net), steps=1e3)
     if (doB==1)
       B<-optim(B, loglike, x=tmpx, y=y, method="BFGS", control=list(fnscale=-1))$par
     # update X
-    out<-.C("log_like_forces", NAOK=TRUE, directed=as.integer(directed), N=as.integer(N), 
+    out<-.C(C_log_like_forces, NAOK=TRUE, directed=as.integer(directed), N=as.integer(N), 
 	    D=as.integer(D), steps=as.integer(steps), Y=as.double(t(Y)), X=as.numeric(t(X)), 
 	    B=as.numeric(B), m=as.numeric(N))
     out$X<-t(matrix(out$X,ncol=N))

R/zzz.R

@@ -1,17 +1,19 @@
 .onLoad <- function(lib,pkg) {
-    library.dynam("VBLPCM", pkg, lib)
-    }
+  library.dynam("VBLPCM", pkg, lib)
+  invisible()
+}
 
 .onAttach <- function(lib,pkg) {
-    packageStartupMessage("\n\n")
-    packageStartupMessage(paste("\n", "Variational Bayes Latent Position Cluster Model for networks.","\n"),
-        paste("VBLPCM", "Version", "2.4.7", 
-        "Created on", "2014-01-29"), paste("\n Created and maintained by ", "Michael Salter-Townshend"), "\n")
-    packageStartupMessage('For citation information type \'citation("VBLPCM")\'\n')
-    packageStartupMessage('Type \'help(VBLPCM)\' to get started.\n')
-    packageStartupMessage('Some worked examples are given by \'example(VBLPCM)\' \n')
+  packageStartupMessage("\n\n")
+  packageStartupMessage(paste("\n", "Variational Bayes Latent Position Cluster Model for networks.","\n"),
+			paste("VBLPCM", "Version", "2.4.9", 
+			      "Created on", "2023-03-22"), paste("\n Created and maintained by ", "Michael Salter-Townshend"), "\n")
+  packageStartupMessage('For citation information type \'citation("VBLPCM")\'\n')
+  packageStartupMessage('Type \'help(VBLPCM)\' to get started.\n')
+  packageStartupMessage('Some worked examples are given by \'example(VBLPCM)\' \n')
 } 
 
-.onUnload <- function(libpath){
-  library.dynam.unload("VBLPCM", libpath)
-} 
+#.onUnload <- function(libpath){
+#  library.dynam.unload("VBLPCM", libpath)
+#  invisible()
+#} 

inst/CITATION

@@ -1,8 +1,8 @@
 citHeader("To cite package 'VBLPCM' in publications use:")
 
-     citEntry(entry="Article",
+     bibentry(bibtype="Article",
               title = "Variational Bayesian Inference for the Latent Position Cluster Model",
-              author = personList(as.person("Michael Salter-Townshend"),
+              author = c(as.person("Michael Salter-Townshend"),
                                   as.person("Thomas Brendan Murphy")),
               year = "2013",
               journal = "Computational Statistics and Data Analysis",     

man/VBLPCM-package.Rd

@@ -11,8 +11,8 @@
   \tabular{ll}{
     Package: \tab VBLPCM\cr
     Type: \tab Package\cr
-    Version: \tab 2.4.8\cr
-    Date: \tab 2021-10-06\cr
+    Version: \tab 2.4.9\cr
+    Date: \tab 2023-03-22\cr
     License: \tab GPL (>=2) \cr
     LazyLoad: \tab yes\cr
   }

src/init.c

@@ -23,7 +23,7 @@ static const R_CMethodDef CEntries[] = {
 void R_init_VBLPCM(DllInfo *dll)
 {
     R_registerRoutines(dll, CEntries, NULL, NULL, NULL);
-    R_useDynamicSymbols(dll, FALSE);
+    R_useDynamicSymbols(dll, TRUE);
     R_forceSymbols(dll, TRUE);
 }