[Depmix-commits] r585 - in pkg/depmixS4: . R man

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

Author: ingmarvisser
Date: 2013-09-11 20:38:32 +0200 (Wed, 11 Sep 2013)
New Revision: 585

Modified:
   pkg/depmixS4/NEWS
   pkg/depmixS4/R/depmixfit.R
   pkg/depmixS4/man/depmix.fit.Rd
Log:
Minor changes in argument donlpcntrl

Modified: pkg/depmixS4/NEWS
===================================================================
--- pkg/depmixS4/NEWS	2013-09-04 09:21:17 UTC (rev 584)
+++ pkg/depmixS4/NEWS	2013-09-11 18:38:32 UTC (rev 585)
@@ -2,22 +2,27 @@
 
 Major changes
 
-	o The EM algorithm has gained an extra argument 'classification',
-		passed from the 'fit' function using argument 'emcontrol', to allow a
-		choice between maximising the regular (classification="soft", the
-		default) or classification (classification="hard") likelihood. 
-		WARNING: using the classification likelihood combined with random 
-		starting values may easily lead to unstable results; use with 
-		caution. 
+  o The EM algorithm has gained an extra argument 'classification',
+	passed from the 'fit' function using argument 'emcontrol', to allow a
+	choice between maximising the regular (classification="soft", the
+	default) or classification (classification="hard") likelihood. 
+	WARNING: using the classification likelihood combined with random 
+	starting values may easily lead to unstable results; use with 
+	caution. 
 
-	o Parameters are now given proper names, following the glm() scheme
-		(e.g. '(Intercept)', 'x1', et cetera); with this, the show and summary
-		methods have changed considerably and now produce more compact and more
-		readable output.  The summary method (for both fitted and unfitted
-		models) now has an argument 'compact' (TRUE by default) that controls
-		the presentation of the repsonse model parameters.  The prior and
-		transition models are now presented more compactly when there are no
-		covariates.
+  o Parameters are now given proper names, following the glm() scheme
+  	(e.g. '(Intercept)', 'x1', et cetera); with this, the show and summary
+	methods have changed considerably and now produce more compact and more
+	readable output.  The summary method (for both fitted and unfitted
+	models) now has an argument 'compact' (TRUE by default) that controls
+	the presentation of the repsonse model parameters.  The prior and
+	transition models are now presented more compactly when there are no
+	covariates.
+	
+  o The fit function has gained two arguments: solnpcntrl and donlpcntrl 
+    which can be used to fine tune optimization using packages Rsolnp and 
+	Rdonlp2; the latter is not on CRAN, and the version that depmixS4 is 
+	compatible with is from r-forge (note the licence from the package). 
 
 Minor changes
 
@@ -29,17 +34,12 @@
     the show method for these models.  
 
   o Added function getmodel(object) to select submodels of a full mix or 
-    depmix model, eg to use in deriving predictions, getting at parameter 
-    values, et cetera. 
+	depmix model, eg to use in deriving predictions, getting at parameter 
+	values, et cetera. 
 
   o Small parameter values in multinomial response models and the initial
-    probabilities and transition models (with identity link) are now set to
-    zero to speed-up convergence.  Current threshold is 1e-6.
-  
-  o Updated the EM routines to make local copies of objects slots to 
-    avoid repeatedly copying large objects. Thanks to Robert McGehee for 
-    this suggestion.
-    
+	probabilities and transition models (with identity link) are now set to
+	zero to speed-up convergence.  Current threshold is 1e-6. 
 
 Changes in depmixS4 version 1.2-2
 
@@ -47,7 +47,7 @@
 
   o Fixed a bug in the fit method of depmix models: linear inequality 
     constraints were not passed on to rsolnp (thanks to Peiming Wang for 
-	  bringing this to my attention). 
+	bringing this to my attention). 
 
 Changes in depmixS4 version 1.2-1
 

Modified: pkg/depmixS4/R/depmixfit.R
===================================================================
--- pkg/depmixS4/R/depmixfit.R	2013-09-04 09:21:17 UTC (rev 584)
+++ pkg/depmixS4/R/depmixfit.R	2013-09-11 18:38:32 UTC (rev 585)
@@ -6,13 +6,8 @@
 				conrows=NULL,conrows.upper=0,conrows.lower=0,
 				method=NULL,verbose=TRUE,
 				emcontrol=em.control(),
-				solnpcntrl=list(rho = 1, outer.iter = 400, inner.iter = 800, delta = 1e-5, tol = 1e-6),
-				donlpcntrl=list(iterma = 4000, nstep = 20, fnscale = 1, report = TRUE, 
-        	rep.freq = 1, tau0 = 1, tau = 0.1, del0 = 1, epsx = 1e-06, 
-					delmin = 0.1, epsdif = 1e-08, nreset.multiplier = 1, 
-					difftype = 2, epsfcn = 1e-16, taubnd = 1, hessian = FALSE, 
-					te0 = TRUE, te1 = FALSE, te2 = FALSE, te3 = FALSE, silent = TRUE, 
-					intakt = TRUE),		
+				solnpcntrl=list(rho = 1, outer.iter = 400, inner.iter = 800, delta = 1e-7, tol = 1e-8),
+				donlpcntrl=donlp2Control(),		
 				...) {
 	
 		fi <- !is.null(fixed)
@@ -122,7 +117,7 @@
 				allpars[!fixed] <- pars
 				object <- setpars(object,allpars)
 				ans = -as.numeric(logLik(object))
-				if(is.na(ans)) ans = 100000 # remove magic number here
+				if(is.na(ans)) ans = 100000 # remove magic number here!!!!!!!
 				ans
 			}
 			

Modified: pkg/depmixS4/man/depmix.fit.Rd
===================================================================
--- pkg/depmixS4/man/depmix.fit.Rd	2013-09-04 09:21:17 UTC (rev 584)
+++ pkg/depmixS4/man/depmix.fit.Rd	2013-09-11 18:38:32 UTC (rev 585)
@@ -35,12 +35,7 @@
 		method=NULL, verbose=TRUE,
 		emcontrol=em.control(),
 		solnpcntrl=list(rho = 1, outer.iter = 400, inner.iter = 800, delta = 1e-5, tol = 1e-6),
-		donlpcntrl=list(iterma = 4000, nstep = 20, fnscale = 1, report = TRUE, 
-        rep.freq = 1, tau0 = 1, tau = 0.1, del0 = 1, epsx = 1e-06, 
-        delmin = 0.1, epsdif = 1e-08, nreset.multiplier = 1, 
-        difftype = 2, epsfcn = 1e-16, taubnd = 1, hessian = FALSE, 
-        te0 = TRUE, te1 = FALSE, te2 = FALSE, te3 = FALSE, silent = TRUE, 
-        intakt = TRUE),
+		donlpcntrl=donlp2Control(),
 		...)
 	
 	\S4method{summary}{mix.fitted}(object,which="all")