version 0.1-9

ChangeLog

@@ -246,3 +246,11 @@ to c. 30 seconds of ellapsed time!)
 Thanks to Martin Ellis for drawing the problem of slowness
 of the simulation procedure to my attention, and indicating
 the solution of the problem.
+
+Version 0.1-8 --> 0.1-9
+=======================
+
+4 April 2013
+
+Fixed up the dimensioning of Fortran arrays so that they
+no longer use dummy 1's as the final dimension.

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: hmm.discnp
-Version: 0.1-8
-Date: 2012-03-02
+Version: 0.1-9
+Date: 2013-04-17
 Title: Hidden Markov models with discrete non-parametric observation
         distributions.
 Author: Rolf Turner <r.turner@auckland.ac.nz> and Limin Liu.
@@ -14,6 +14,7 @@ Description: Fits hidden Markov models with discrete non-parametric
         model.
 License: GPL (>= 2)
 URL: http://www.math.unb.ca/~rolf/
-Packaged: 2012-03-02 07:14:09 UTC; rolf
+Packaged: 2013-04-18 02:02:12 UTC; rolf
+NeedsCompilation: yes
 Repository: CRAN
-Date/Publication: 2012-03-02 14:13:09
+Date/Publication: 2013-04-18 07:29:04

MD5

@@ -1,7 +1,7 @@
-c58feb0f679b94b28d42f2a23f2b4c0f *ChangeLog
-411eef55a024abf99e801d6548058be9 *DESCRIPTION
+2221e8fd8f99f8070a0e96dfd981edb2 *ChangeLog
+1099d89012367c9dc0781cfe97decb3f *DESCRIPTION
 e97c7b6e0d7f0eb3b8e1303451431001 *NAMESPACE
-b2d13c9ca9fcdabeeb09db8998ecdd81 *R/First.R
+bb6f6344934b965a455a21347756e847 *R/First.R
 184809b9344434a680bbc30dc96d3bb9 *R/RCS/First.R,v
 1ea360172ada98073415122f3e5b73e4 *R/RCS/check.yval.R,v
 bd6a8531b5bb39645fbdcda423465ca0 *R/RCS/ffun.R,v
@@ -28,37 +28,37 @@ eb22d9be687321b5243b12879f272cee *R/init.all.R
 de0b8ed3091fa489ada6c6e5355b1856 *R/mat2list.R
 b92e3051eafb9511f4cae92645158ba8 *R/mps.R
 0dfefa748fd129b0dbe03289e8c45f35 *R/pr.R
-2ad359d1c282e91675fb00a1bccb9b29 *R/recurse.R
+b3453ba428bdb359f61e253cc01e23f2 *R/recurse.R
 1386236c29748ec48a8e4cc6a41649d8 *R/revise.ispd.R
 453a3658f3432a9b1b1feda4400134d7 *R/revise.rho.R
 f180f9d05c14a25f746e32f579875ff1 *R/revise.tpm.R
 1343dfe5864d155602c1457e62891944 *R/sim.hmm.R
 4c2d789f7ee7157a3f4c66fadbe74a7a *R/sp.R
 dab163b5304bd23f35e2f7f9a3ec0f3a *R/viterbi.R
 2656ac33803f83f5d131053efc7c4b6b *inst/READ_ME
-1cf8101749a8a99d30cd34fdc241c1d5 *inst/Ratfor/RCS/afun.r,v
-64d12988d748ac0aaf6e39ff355e5e61 *inst/Ratfor/RCS/bfun.r,v
-592f6e2ad146095e6523e4187414e809 *inst/Ratfor/RCS/gfun.r,v
+dd41961396b612dbb4afc7fdcf73e55e *inst/Ratfor/RCS/afun.r,v
+75869a842561e24d282d8ed2fc73eab8 *inst/Ratfor/RCS/bfun.r,v
+f1d36db9f8e9fda32f12221e55c6dbdd *inst/Ratfor/RCS/gfun.r,v
 7241424b21f65ca2f10e4dc859d31741 *inst/Ratfor/RCS/makefor,v
-216262f918bfc3a9e5d2a2c9f966e93a *inst/Ratfor/RCS/recurse.r,v
-d80e12de754a73bf8cc8eec9465207bb *inst/Ratfor/RCS/xfun.r,v
-b7c61bd8b7581485fd3363daadc1db87 *inst/Ratfor/afun.r
-db10a350fc50f2632e848bbdc72239dc *inst/Ratfor/bfun.r
-55d2f08888295e7d5a4721ac02ac0777 *inst/Ratfor/gfun.r
+c7a6fbf28f918754d33b796e71d553fb *inst/Ratfor/RCS/recurse.r,v
+770ae0f29b53d84c091de81fae008445 *inst/Ratfor/RCS/xfun.r,v
+41f0e806077d282c98851bc544b9a5ea *inst/Ratfor/afun.r
+17f9bbea01421df7e8c303a1fb5cbb95 *inst/Ratfor/bfun.r
+5cbc32129adddcfc60272834a794ca4a *inst/Ratfor/gfun.r
 40201e8652101f856140d17279cf3f4c *inst/Ratfor/makefor
-66dcf313cea6a0a481e46e7e0a65e94d *inst/Ratfor/recurse.r
-61fdccfeb2762053b21b96562ca7987e *inst/Ratfor/xfun.r
+d7c843cbee516d00dcc489c08cb9d069 *inst/Ratfor/recurse.r
+b97264d24cd7880ce7fbad579da6953b *inst/Ratfor/xfun.r
 41aaa76a3bd7b5413aac29fe8cbb6bf2 *man/fitted.hmm.discnp.Rd
-9cb0f691156f3ae2dfbcdbcb2c09ff92 *man/hmm.Rd
+80e4f4b78b7a476a41a9f37db05a8b65 *man/hmm.Rd
 3c143ea6632f17fe683cc2114326b16b *man/hmm.discnp-internal.Rd
 8361273b18a9243c78bf1b8792166a51 *man/logLikHmm.Rd
 f0b59556b361b40f21fb7373256de26d *man/mps.Rd
 aaaaf6989cb369e176840ad9b1d8f3f9 *man/pr.Rd
 8a65682cafd13e70cedb5b9d44fe8e46 *man/sim.hmm.Rd
 d477c7563a021ac09adc74dfba50a4ca *man/sp.Rd
 3a961815a3f7872928c7984a76c57d00 *man/viterbi.Rd
-bad8f38090026cf76ec89c84fe6fdc97 *src/afun.f
-66adac3b888ebebcd71435cff3b6aff8 *src/bfun.f
-3b912084f8680d2c005b1b570851a15a *src/gfun.f
-b802f92e3401bcf4c27a70bb46e06847 *src/recurse.f
-56390e2a9f3258e65ffb9e73178e9fb5 *src/xfun.f
+f1f57c6a20eb0a28ffd79efb0f8b1816 *src/afun.f
+ee174ec13251743ea33ccbc6f9009291 *src/bfun.f
+25ef80dc0168437aafd15bd0fd9974d8 *src/gfun.f
+36f16d5a97248e7040e2fd9c59921377 *src/recurse.f
+dc1264652e18b677e558425ce8bd9aa2 *src/xfun.f

R/First.R

@@ -1,12 +1,14 @@
 .onLoad <- function(lib, pkg) {
 	library.dynam("hmm.discnp", pkg, lib)
+}
+
+.onAttach <- function(lib, pkg) {
 	ver <- read.dcf(file.path(lib, pkg, "DESCRIPTION"), "Version")
         packageStartupMessage(paste(pkg, ver))
-	packageStartupMessage(
-            paste("\n     PLEASE NOTE:  The package has changed substantially",
-                  "\n     from the 0.0-x versions.  New functions have been",
-                  "\n     added and both the argument lists and the returned",
-                  "\n     values from old functions have new forms.  Please",
-                  "\n     read the ChangeLog and the documentation.\n")
-        )
+	msg <- paste("\n     PLEASE NOTE:  The package has changed substantially",
+                     "\n     from the 0.0-x versions.  New functions have been",
+                     "\n     added and both the argument lists and the returned",
+                     "\n     values from old functions have new forms.  Please",
+                     "\n     read the ChangeLog and the documentation.\n")
+	packageStartupMessage(msg)
 }

R/recurse.R

@@ -10,8 +10,10 @@ K  <- nrow(tpm)
 K2 <- K*K
 L  <- ncol(fy)
 M  <- K*L
-N  <- K*M - K2
 nreps <- length(lns)
+nxi   <- L - nreps
+#N  <- K*M - K2
+N <- K*K*nxi
 epsilon <- sqrt(.Machine$double.eps)
 
 # Recursive probabilities:
@@ -27,6 +29,8 @@ epsilon <- sqrt(.Machine$double.eps)
                 nstate=as.integer(K),
                 wrk=double(K2),
 		xlc=double(L),
+                ntot=as.integer(L),
+                nxi=as.integer(nxi),
                 alpha=double(M),
                 beta=double(M),
                 gamma=double(M),

inst/Ratfor/RCS/afun.r,v

@@ -1,11 +1,16 @@
-head	1.1;
+head	1.2;
 access;
 symbols;
 locks
-	rturner:1.1; strict;
+	rolf:1.2; strict;
 comment	@# @;
 
 
+1.2
+date	2013.04.17.02.30.39;	author rolf;	state Exp;
+branches;
+next	1.1;
+
 1.1
 date	2009.09.23.03.39.00;	author rturner;	state Exp;
 branches;
@@ -17,15 +22,15 @@ desc
 @
 
 
-1.1
+1.2
 log
-@Initial revision
+@Adjusted the dimensioning --- no more 1's.
 @
 text
 @subroutine afun(fy,xispd,tpm,epsilon,n,nstate,wrk,xlc,alpha)
 implicit double precision(a-h,o-z)
-dimension wrk(1), xispd(1), xlc(1)
-dimension fy(nstate,1), tpm(nstate,1), alpha(nstate,1)
+dimension wrk(nstate), xispd(nstate), xlc(n)
+dimension fy(nstate,n), tpm(nstate,nstate), alpha(nstate,n)
 
 # Set some constants
 one  = 1.d0
@@ -34,7 +39,7 @@ zero = 0.d0
 # Set the value to give to ``log-likelihood constant'', xlc(...)
 # if this is indeterminate --- i.e. less than epsilon.
 # Possible choices: -1, 1, or epsilon.
-dummy = -one
+dummy = epsilon
 
 # Update the initial alpha.
 tsum = zero
@@ -85,3 +90,18 @@ do kt = 2,n {
 return
 end
 @
+
+
+1.1
+log
+@Initial revision
+@
+text
+@d3 2
+a4 2
+dimension wrk(1), xispd(1), xlc(1)
+dimension fy(nstate,1), tpm(nstate,1), alpha(nstate,1)
+d13 1
+a13 1
+dummy = -one
+@

inst/Ratfor/RCS/bfun.r,v

@@ -1,11 +1,16 @@
-head	1.1;
+head	1.2;
 access;
 symbols;
 locks
-	rturner:1.1; strict;
+	rolf:1.2; strict;
 comment	@# @;
 
 
+1.2
+date	2013.04.17.02.31.28;	author rolf;	state Exp;
+branches;
+next	1.1;
+
 1.1
 date	2009.09.23.03.39.36;	author rturner;	state Exp;
 branches;
@@ -17,15 +22,15 @@ desc
 @
 
 
-1.1
+1.2
 log
-@Initial revision
+@Adjusted the dimensioning --- no more 1's.
 @
 text
 @subroutine bfun(fy,xispd,tpm,epsilon,n,nstate,wrk,beta)
 implicit double precision(a-h,o-z)
-dimension wrk(1), xispd(1)
-dimension fy(nstate,1), tpm(nstate,1), beta(nstate,1)
+dimension wrk(nstate), xispd(nstate)
+dimension fy(nstate,n), tpm(nstate,nstate), beta(nstate,n)
 
 # Set some constants.
 one  = 1.d0
@@ -64,3 +69,15 @@ do ktb = 2,n {
 return
 end
 @
+
+
+1.1
+log
+@Initial revision
+@
+text
+@d3 2
+a4 2
+dimension wrk(1), xispd(1)
+dimension fy(nstate,1), tpm(nstate,1), beta(nstate,1)
+@

inst/Ratfor/RCS/gfun.r,v

@@ -1,11 +1,16 @@
-head	1.1;
+head	1.2;
 access;
 symbols;
 locks
-	rturner:1.1; strict;
+	rolf:1.2; strict;
 comment	@# @;
 
 
+1.2
+date	2013.04.17.02.32.02;	author rolf;	state Exp;
+branches;
+next	1.1;
+
 1.1
 date	2009.09.23.03.40.08;	author rturner;	state Exp;
 branches;
@@ -17,15 +22,15 @@ desc
 @
 
 
-1.1
+1.2
 log
-@Initial revision
+@Adjusted the dimensioning --- no more 1's.
 @
 text
 @subroutine gfun(alpha,beta,epsilon,n,nstate,wrk,gamma)
 implicit double precision(a-h,o-z)
-dimension alpha(nstate,1), beta(nstate,1), gamma(nstate,1)
-dimension wrk(1)
+dimension alpha(nstate,n), beta(nstate,n), gamma(nstate,n)
+dimension wrk(nstate)
 
 zero = 0.d0
 ook  = 1.d0/dble(nstate)
@@ -51,3 +56,15 @@ do kt = 1,n {
 return
 end
 @
+
+
+1.1
+log
+@Initial revision
+@
+text
+@d3 2
+a4 2
+dimension alpha(nstate,1), beta(nstate,1), gamma(nstate,1)
+dimension wrk(1)
+@