[Depmix-commits] r650 - in pkg/depmixS4: . R man

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

Author: ingmarvisser
Date: 2016-02-12 08:50:14 +0100 (Fri, 12 Feb 2016)
New Revision: 650

Modified:
   pkg/depmixS4/DESCRIPTION
   pkg/depmixS4/NAMESPACE
   pkg/depmixS4/R/allGenerics.R
   pkg/depmixS4/R/depmixfit.R
   pkg/depmixS4/man/depmix.fit.Rd
Log:
=test stuff from development version

Modified: pkg/depmixS4/DESCRIPTION
===================================================================
--- pkg/depmixS4/DESCRIPTION	2016-02-10 17:25:34 UTC (rev 649)
+++ pkg/depmixS4/DESCRIPTION	2016-02-12 07:50:14 UTC (rev 650)
@@ -6,7 +6,8 @@
 Maintainer: Ingmar Visser <i.visser at uva.nl>
 Depends: R (>= 3.0.1), nnet, MASS, Rsolnp
 Imports: stats, stats4, methods
-Suggests: gamlss, gamlss.dist
+Suggests: gamlss, gamlss.dist, Rdonlp2
+Additional_repositories: http://R-Forge.R-project.org
 Description: Fits latent (hidden) Markov models on mixed categorical and continuous (time series) data, otherwise known as dependent mixture models.
 License: GPL (>=2)
 URL: http://depmix.r-forge.r-project.org/

Modified: pkg/depmixS4/NAMESPACE
===================================================================
--- pkg/depmixS4/NAMESPACE	2016-02-10 17:25:34 UTC (rev 649)
+++ pkg/depmixS4/NAMESPACE	2016-02-12 07:50:14 UTC (rev 650)
@@ -2,6 +2,12 @@
 
 importFrom(stats, predict, simulate)
 
+importFrom("stats", "cov", "cov.wt", "dbinom", "dgamma", "dmultinom",
+             "dnorm", "dpois", "gaussian", "glm.fit", "lm.fit",
+             "lm.wfit", "mahalanobis", "make.link", "model.frame",
+             "model.matrix", "model.response", "pchisq", "rbinom",
+             "rgamma", "rmultinom", "rnorm", "rpois", "sd")
+
 importFrom(stats4, AIC, BIC, logLik, nobs, summary)
 
 export(	

Modified: pkg/depmixS4/R/allGenerics.R
===================================================================
--- pkg/depmixS4/R/allGenerics.R	2016-02-10 17:25:34 UTC (rev 649)
+++ pkg/depmixS4/R/allGenerics.R	2016-02-12 07:50:14 UTC (rev 650)
@@ -14,6 +14,8 @@
     library.dynam.unload("depmixS4",libpath)
 }
 
+utils::globalVariables(c("donlp2", "donlp2Control"))
+
 # Guess what: all generics
 
 setGeneric("depmix", function(response,data=NULL,nstates,transition=~1,family=gaussian(),prior=~1,initdata=NULL,

Modified: pkg/depmixS4/R/depmixfit.R
===================================================================
--- pkg/depmixS4/R/depmixfit.R	2016-02-10 17:25:34 UTC (rev 649)
+++ pkg/depmixS4/R/depmixfit.R	2016-02-12 07:50:14 UTC (rev 650)
@@ -125,7 +125,7 @@
 	    }
 	    
 	    if(method=="donlp") {
-		
+				
 		if(!(require(Rdonlp2,quietly=TRUE))) stop("Method 'donlp' requires package 'Rdonlp2'")
 				
 		mycontrol <- function(info) {
@@ -133,7 +133,7 @@
 		}
 		
 		# optimize the parameters
-		result <- donlp2(pars,logl,
+		result <- Rdonlp2::donlp2(pars,logl,
 		    par.upper=par.u[!fixed],
 		    par.lower=par.l[!fixed],
 		    A=lincon,

Modified: pkg/depmixS4/man/depmix.fit.Rd
===================================================================
--- pkg/depmixS4/man/depmix.fit.Rd	2016-02-10 17:25:34 UTC (rev 649)
+++ pkg/depmixS4/man/depmix.fit.Rd	2016-02-12 07:50:14 UTC (rev 650)
@@ -197,7 +197,7 @@
 # get parameters from estimated model
 modNew <- setpars(modNew,getpars(fmod1))
 # check the state sequence and probabilities
-viterbi(modeNew)
+viterbi(modNew)
 
 # same model, now with missing data
 \dontrun{