Merge pull request #50 from bmreilly/master

NMreadExt was incorrectly calculating blocksize for OMEGAs, I proposed a fix

R/NMreadExt.R

@@ -207,14 +207,16 @@ NMreadExt <- function(file,return,as.fun,modelname,col.model,auto.ext,tableno="m
         ## est is just a copy of value for backward compatibility
         pars[,est:=value]
 
-### add OMEGA block information based on off diagonal values
-        tab.blocks <- rbind(pars[par.type%in%c("OMEGA","SIGMA"),.(par.type,i=i,j=j,value)],
-                            pars[par.type%in%c("OMEGA","SIGMA"),.(par.type,i=j,j=i,value)])[
-            abs(value)>1e-9,.(iblock=min(i,j),blocksize=max(abs(j-i))+1),by=.(par.type,i)]
+        ### add OMEGA block information based on off diagonal values
+        tab.i <- rbind(pars[par.type%in%c("OMEGA","SIGMA"),.(par.type,i=i,j=j,value)],
+                       pars[par.type%in%c("OMEGA","SIGMA"),.(par.type,i=j,j=i,value)])[
+                # include i==j so that if an OMEGA is fixed to zero it is still assigned an iblock
+                                i==j|abs(value)>1e-9,.(iblock=min(i,j)),by=.(par.type,i)]
+        tab.i[,blocksize:=.N,by=.(par.type,iblock)]
 
         ## pars0 <- copy(pars)
         ## tab.blocks
-        pars <- mergeCheck(pars,tab.blocks,by=cc(par.type,i),all.x=T,quiet=TRUE)
+        pars <- mergeCheck(pars,tab.i,by=cc(par.type,i),all.x=T,quiet=TRUE)
 
         ## pars[par.type%in%c("OMEGA","SIGMA"),.(i,j,iblock,blocksize,value)]