[Pomp-commits] r967 - pkg/pomp/R

[noreply at r-forge.r-project.org]

Author: kingaa
Date: 2014-06-09 18:30:30 +0200 (Mon, 09 Jun 2014)
New Revision: 967

Modified:
   pkg/pomp/R/bsmc.R
   pkg/pomp/R/minim.R
   pkg/pomp/R/nlf-guts.R
   pkg/pomp/R/nlf.R
   pkg/pomp/R/spect-match.R
Log:
- remove unneeded explicit namespace references

Modified: pkg/pomp/R/bsmc.R
===================================================================
--- pkg/pomp/R/bsmc.R	2014-05-24 15:59:19 UTC (rev 966)
+++ pkg/pomp/R/bsmc.R	2014-06-09 16:30:30 UTC (rev 967)
@@ -223,12 +223,12 @@
 
     ## sample new parameter vector as per L&W AGM (3) and Liu & West eq(3.2)
     pvec <- try(
-                mvtnorm::rmvnorm(
-                                 n=Np,
-                                 mean=rep(0,npars.est),
-                                 sigma=hsq*params.var,
-                                 method="svd"
-                                 ),
+                rmvnorm(
+                        n=Np,
+                        mean=rep(0,npars.est),
+                        sigma=hsq*params.var,
+                        method="svd"
+                        ),
                 silent=FALSE
                 )
     if (inherits(pvec,"try-error"))

Modified: pkg/pomp/R/minim.R
===================================================================
--- pkg/pomp/R/minim.R	2014-05-24 15:59:19 UTC (rev 966)
+++ pkg/pomp/R/minim.R	2014-06-09 16:30:30 UTC (rev 967)
@@ -32,7 +32,7 @@
     opts <- list(...)
 
     if (method == 'subplex') {
-      opt <- subplex::subplex(par=guess,fn=objfun,control=opts)
+      opt <- subplex(par=guess,fn=objfun,control=opts)
     } else if (method=="sannbox") {
       opt <- sannbox(par=guess,fn=objfun,control=opts)
     } else if (method=="nloptr") {

Modified: pkg/pomp/R/nlf-guts.R
===================================================================
--- pkg/pomp/R/nlf-guts.R	2014-05-24 15:59:19 UTC (rev 966)
+++ pkg/pomp/R/nlf-guts.R	2014-06-09 16:30:30 UTC (rev 967)
@@ -185,7 +185,7 @@
     LQL <- dnorm(prediction.errors[,1],mean=0,sd=sigma.model,log=TRUE)
   } else {
     sigma.model <- cov(model.residuals)
-    LQL <- mvtnorm::dmvnorm(prediction.errors,sigma=sigma.model,log=TRUE) ## NOTE: This could be improved using GLS.
+    LQL <- dmvnorm(prediction.errors,sigma=sigma.model,log=TRUE) ## NOTE: This could be improved using GLS.
   }  
   
   LQL

Modified: pkg/pomp/R/nlf.R
===================================================================
--- pkg/pomp/R/nlf.R	2014-05-24 15:59:19 UTC (rev 966)
+++ pkg/pomp/R/nlf.R	2014-06-09 16:30:30 UTC (rev 967)
@@ -96,26 +96,26 @@
   }
 
   if (method == 'subplex') {
-    opt <- subplex::subplex(
-                            par=guess,
-                            fn=nlf.objfun,
-                            object=object,
-                            params=params,
-                            par.index=par.index, 
-                            transform.params=transform.params,
-                            times=times,
-                            t0=t0,
-                            lags=lags,
-                            period=period,
-                            tensor=tensor,
-                            seed=seed,
-                            transform=transform,
-                            nrbf=nrbf, 
-                            verbose=verbose,
-                            bootstrap=bootstrap,
-                            bootsamp=bootsamp,
-                            control=list(...)
-                            )
+    opt <- subplex(
+                   par=guess,
+                   fn=nlf.objfun,
+                   object=object,
+                   params=params,
+                   par.index=par.index, 
+                   transform.params=transform.params,
+                   times=times,
+                   t0=t0,
+                   lags=lags,
+                   period=period,
+                   tensor=tensor,
+                   seed=seed,
+                   transform=transform,
+                   nrbf=nrbf, 
+                   verbose=verbose,
+                   bootstrap=bootstrap,
+                   bootsamp=bootsamp,
+                   control=list(...)
+                   )
   } else {
     opt <- optim(
                  par=guess,

Modified: pkg/pomp/R/spect-match.R
===================================================================
--- pkg/pomp/R/spect-match.R	2014-05-24 15:59:19 UTC (rev 966)
+++ pkg/pomp/R/spect-match.R	2014-06-09 16:30:30 UTC (rev 967)
@@ -168,23 +168,23 @@
     msg <- "no optimization performed"
   } else {
     if (method == 'subplex') {
-      opt <- subplex::subplex(
-                              par=guess,
-                              fn=obj.fn,
-                              est=par.index,
-                              object=object,
-                              params=params,
-                              vars=vars,
-                              ker=ker,
-                              nsim=nsim,
-                              seed=seed,
-                              transform=transform,
-                              detrend=detrend,
-                              weights=weights,
-                              data.spec=ds,
-                              fail.value=fail.value,
-                              control=list(...)
-                              )
+      opt <- subplex(
+                     par=guess,
+                     fn=obj.fn,
+                     est=par.index,
+                     object=object,
+                     params=params,
+                     vars=vars,
+                     ker=ker,
+                     nsim=nsim,
+                     seed=seed,
+                     transform=transform,
+                     detrend=detrend,
+                     weights=weights,
+                     data.spec=ds,
+                     fail.value=fail.value,
+                     control=list(...)
+                     )
     } else {
       opt <- optim(
                    par=guess,