version 1.4

cran · Dec 3, 2014 · e731e9c · e731e9c
1 parent b4d2362
commit e731e9c
Show file tree

Hide file tree

Showing 36 changed files with 73 additions and 73 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,15 +1,15 @@
 Package: conting
 Type: Package
 Title: Bayesian analysis of contingency tables
-Version: 1.3
-Date: 2014-06-11
+Version: 1.4
+Date: 2014-12-03
 Author: Antony M. Overstall
-Maintainer: Antony M. Overstall <antony@mcs.st-and.ac.uk>
+Maintainer: Antony M. Overstall <Antony.Overstall@glasgow.ac.uk>
 Description: Bayesian analysis of complete and incomplete contingency tables.
 Depends: R (>= 2.15.0)
 Imports: mvtnorm, BMS, gtools, tseries, coda
 License: GPL-2
-Packaged: 2014-06-11 09:38:34 UTC; antony
+Packaged: 2014-12-03 11:06:13 UTC; ao35j
 NeedsCompilation: no
 Repository: CRAN
-Date/Publication: 2014-06-11 11:57:55
+Date/Publication: 2014-12-03 13:47:17
diff --git a/MD5 b/MD5
@@ -1,4 +1,4 @@
-b02e7c92da807c5b9225862ddef08a42 *DESCRIPTION
+a6967f8172d6f9eb3d73e0b5150ebfbf *DESCRIPTION
 4eb234dfaf800c03afa81c02796821bd *NAMESPACE
 9071b89c46380a7af6be8fae2db00948 *R/RJ_update.R
 def339b59e64204e9db01335b77ac9e8 *R/accept_rate.R
@@ -39,42 +39,42 @@ ebd49330a88bba6d4cc5cbfe048379ea *R/print.submod.R
 a87c0874595f4b0e9c82c46433a2d942 *R/summary.bcct.R
 25d8d4dc32f86840812605ab3a2068c5 *R/summary.bict.R
 84ed36115620defbe585207a53a9c951 *R/total_pop.R
-b091506c11211bf150355f66524064ac *data/AOH.rda
-6b2eeb5eff0c2a126a0fdf3b3aa27c52 *data/ScotPWID.rda
-4ca8cd66e7e86991d1a52e7c86c7ae67 *data/heart.rda
-d875c73b09fd354b3b8d3a95150ab136 *data/spina.rda
+fcd0b8818ba678d708f10995250373b7 *data/AOH.rda
+9964486cb43abcb218e141366acec5b3 *data/ScotPWID.rda
+df0a075ec145b58833564aa0b9b0e3ba *data/heart.rda
+57c75ad48d80847eae9924d06770a3bc *data/spina.rda
 551b319d5c059d2714af405e6e005df9 *inst/CITATION
 da54c697af3c2d465145cf4d78f89732 *man/AOH.Rd
-0a5a484e02127cf8fe005869e68dae73 *man/RJ_update.Rd
+a7ef0b144b430f86d7c57de815e75698 *man/RJ_update.Rd
 f69405e0f5c86bc4982591e783e46a7c *man/ScotPWID.Rd
-c633c0bd4d3059bacb739eb6690558c6 *man/accept_rate.Rd
-0fde5dcba1d9a916048e573b19f66037 *man/add_term.Rd
-18594edc00e81777f213ab9f0a5f47a5 *man/bayespval.Rd
-c28f3705b1ee2b09c4ea3a18dce92bcc *man/bcct.Rd
-6abf82116016f3d799baca6ff4a2188f *man/bcct.fit.Rd
-18fc77bf191358dcaf5e1435a80e70ac *man/beta_mode.Rd
-5a90be904101f86ad01f8811245ead19 *man/bict.Rd
-5be20dec531bf7eefd9e416bd24ff7e7 *man/bict.fit.Rd
-04dadc7e220975fd5a5fb17b33da082f *man/conting-package.Rd
-7e10d412a6a8eae85cab511e2851a6d3 *man/find_cens.Rd
-f6cc7a2d7c7becac9d042db3d8221ace *man/formula2index.Rd
+1044fd6d23c1183a784e00d558a1aaf4 *man/accept_rate.Rd
+47b7907303f60bfaa9518b157ec5ad0a *man/add_term.Rd
+c8963bf5b265a82694f7cdcb58a89f73 *man/bayespval.Rd
+7e41612b324eef0f24819a764448922a *man/bcct.Rd
+ad4407056e82e020f0f404382f97c9da *man/bcct.fit.Rd
+2066618b2c7e1a2de0768407d486f2fa *man/beta_mode.Rd
+9670f314af585ad547c00c072772a831 *man/bict.Rd
+ba14f4d22009d53888b7b26a043c7a9a *man/bict.fit.Rd
+cb5fe47d65abb68336846692d9bf5516 *man/conting-package.Rd
+e7a8084279cee2c8cadc2a660d05c5ea *man/find_cens.Rd
+6335a3dcae17b4f64942f74ec5214e77 *man/formula2index.Rd
 8ac844d7f724081448928f8630adace5 *man/heart.Rd
-8060a294901b371a30a2f0a551913088 *man/index2model.Rd
-f40863dfc8288243eaa49bcb5372d423 *man/inter_probs.Rd
-a94c8c784b04c87d639ba044987fa9f0 *man/inter_stats.Rd
-d23581a11f3b675beb822cc9e01cd445 *man/iwls_mh.Rd
-8e0d38c90ac23045edf28e171e0ee0aa *man/mod_probs.Rd
-732cda659f9946674392863686a9079d *man/plot.pval.Rd
-bfc260d840ef3e7f8e82b8d16a1920d5 *man/plot.totpop.Rd
-9ed357ad8d7163b645444077cbc4923d *man/print.acceptrate.Rd
-267005e2b39e4e415b485684abe00297 *man/print.bcct.Rd
-ee7d8c4af0498ac0d8961620a6489bdd *man/print.interprob.Rd
-89cd4a32bd9360ce7dede89f90ef6678 *man/print.interstat.Rd
-65186af8295b7ec97edf37a5c4db3071 *man/print.modprobs.Rd
-7c83cc1f2520f5758a7a7a99175cde0a *man/print.pval.Rd
-070698f8fe7d331958ef2654b9ad5a1a *man/print.submod.Rd
-cc0e7661d4000e4f6265fee7c47c384f *man/print.totpop.Rd
+a23d5956100a6fb27f9858fe238fa115 *man/index2model.Rd
+f50b7c3621a429ba4c57951d900c2c89 *man/inter_probs.Rd
+a6edb1960da54e36b76e061c8e32ac15 *man/inter_stats.Rd
+29382133157eb0c74cf8e4d42667fbc3 *man/iwls_mh.Rd
+da98e83d91295fabb16142c7af497e32 *man/mod_probs.Rd
+9cf2c35c9a01151bcf0c5455090f4b55 *man/plot.pval.Rd
+957d31b3019560d6dfb9710152fcda30 *man/plot.totpop.Rd
+305758a3df578087fa9fe9f547f6e9b5 *man/print.acceptrate.Rd
+e73060dd2ce4016d1472b2c89bd170f6 *man/print.bcct.Rd
+09ff6774c99c00de7ae5ce369f13cd64 *man/print.interprob.Rd
+9710c237d28e26ed3464726782d5f0d2 *man/print.interstat.Rd
+e71f894293e3c49bed041549f4178332 *man/print.modprobs.Rd
+bc85fbe299f31c976f746de6496afc58 *man/print.pval.Rd
+3e931d97e008f06feba602feb3a820ba *man/print.submod.Rd
+a765000f5df8362c890475710e153a7e *man/print.totpop.Rd
 1cdd84e1c6050c775559904e230162a9 *man/spina.Rd
-3f199197d54dbae5b00fa134efd2c983 *man/sub_model.Rd
-09620d66702dc4a7485f3632e4c5deae *man/summary.bcct.Rd
-ab7afab726bcb2996df79820f45c9184 *man/total_pop.Rd
+c2e53f8a245cb4fdd98a52af7e6c75aa *man/sub_model.Rd
+378736f8ee3fe210906db640b320f7be *man/summary.bcct.Rd
+a0156c27e007fb88b9329901c690c476 *man/total_pop.Rd
diff --git a/data/AOH.rda b/data/AOH.rda
diff --git a/data/ScotPWID.rda b/data/ScotPWID.rda
diff --git a/data/heart.rda b/data/heart.rda
diff --git a/data/spina.rda b/data/spina.rda
diff --git a/man/RJ_update.Rd b/man/RJ_update.Rd
@@ -65,7 +65,7 @@ complete and incomplete contingency tables. \emph{Journal of Statistical Softwar
 1--27. \url{http://www.jstatsoft.org/v58/i07/}
 }
 \author{
-Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.
+Antony M. Overstall \email{Antony.Overstall@glasgow.ac.uk}.
 }
 \note{
 This function will not typically be called by the user.

diff --git a/man/accept_rate.Rd b/man/accept_rate.Rd
@@ -33,7 +33,7 @@ Markov chain Monte Carlo proposal distributions. \emph{Journal of the Royal Stat
 Society, Series B}, \bold{65 (1)}, 3--55.
 }
 \author{
-Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.
+Antony M. Overstall \email{Antony.Overstall@glasgow.ac.uk}.
 }
 
 \seealso{

diff --git a/man/add_term.Rd b/man/add_term.Rd
@@ -66,7 +66,7 @@ Forster, J.J., Gill, R.C. & Overstall, A.M. (2012) Reversible jump methods for g
 linear mixed models. \emph{Statistics and Computing}, \bold{22 (1)}, 107--120.
 }
 \author{
-Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.
+Antony M. Overstall \email{Antony.Overstall@glasgow.ac.uk}.
 }
 \note{
 This function will not typically be called by the user.

diff --git a/man/bayespval.Rd b/man/bayespval.Rd
@@ -66,7 +66,7 @@ complete and incomplete contingency tables. \emph{Journal of Statistical Softwar
 1--27. \url{http://www.jstatsoft.org/v58/i07/}
 }
 \author{
-Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.
+Antony M. Overstall \email{Antony.Overstall@glasgow.ac.uk}.
 }
 
 \seealso{

diff --git a/man/bcct.Rd b/man/bcct.Rd
@@ -166,7 +166,7 @@ complete and incomplete contingency tables. \emph{Journal of Statistical Softwar
 1--27. \url{http://www.jstatsoft.org/v58/i07/}
 }
 \author{
-Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.
+Antony M. Overstall \email{Antony.Overstall@glasgow.ac.uk}.
 }
 \note{
 These functions are wrappers for \code{\link{bcct.fit}}.

diff --git a/man/bcct.fit.Rd b/man/bcct.fit.Rd
@@ -91,7 +91,7 @@ complete and incomplete contingency tables. \emph{Journal of Statistical Softwar
 }
 
 \author{
-Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.
+Antony M. Overstall \email{Antony.Overstall@glasgow.ac.uk}.
 }
 \note{
 This function will not typically be called by the user.

diff --git a/man/beta_mode.Rd b/man/beta_mode.Rd
@@ -71,7 +71,7 @@ complete and incomplete contingency tables. \emph{Journal of Statistical Softwar
 }
 
 \author{
-Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.
+Antony M. Overstall \email{Antony.Overstall@glasgow.ac.uk}.
 }
 \note{
 This function will not typically be called by the user.

diff --git a/man/bict.Rd b/man/bict.Rd
@@ -229,7 +229,7 @@ tables with censored cells with application to estimating the number of people w
 in Scotland. \emph{Statistics in Medicine}, \bold{33 (9)}, 1564--1579.
 }
 \author{
-Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.
+Antony M. Overstall \email{Antony.Overstall@glasgow.ac.uk}.
 }
 \note{
 These functions are wrappers for \code{\link{bict.fit}}.

diff --git a/man/bict.fit.Rd b/man/bict.fit.Rd
@@ -105,7 +105,7 @@ complete and incomplete contingency tables. \emph{Journal of Statistical Softwar
 }
 
 \author{
-Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.
+Antony M. Overstall \email{Antony.Overstall@glasgow.ac.uk}.
 }
 \note{
 This function will not typically be called by the user.

diff --git a/man/conting-package.Rd b/man/conting-package.Rd
@@ -15,8 +15,8 @@ populations.
 \tabular{ll}{
 Package: \tab conting\cr
 Type: \tab Package\cr
-Version: \tab 1.3\cr
-Date: \tab 2014-06-11\cr
+Version: \tab 1.4\cr
+Date: \tab 2014-12-03\cr
 License: \tab GPL-2\cr
 }
 For the Bayesian analysis of complete contingency tables the key function is \code{\link{bcct}} 
@@ -33,9 +33,9 @@ and computational methods, as well as detailed examples.
 
 }
 \author{
-Antony M. Overstall \email{antony@mcs.st-and.ac.uk}
+Antony M. Overstall \email{Antony.Overstall@glasgow.ac.uk}
 
-Maintainer: Antony M. Overstall \email{antony@mcs.st-and.ac.uk}
+Maintainer: Antony M. Overstall \email{Antony.Overstall@glasgow.ac.uk}
 }
 \references{
 Overstall, A.M. & King, R. (2014) conting: An R package for Bayesian analysis of

diff --git a/man/find_cens.Rd b/man/find_cens.Rd
@@ -58,7 +58,7 @@ complete and incomplete contingency tables. \emph{Journal of Statistical Softwar
 1--27. \url{http://www.jstatsoft.org/v58/i07/}
 }
 \author{
-Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.
+Antony M. Overstall \email{Antony.Overstall@glasgow.ac.uk}.
 }
 
 \seealso{

diff --git a/man/formula2index.Rd b/man/formula2index.Rd
@@ -46,7 +46,7 @@ the argument \code{index}.
 }
 
 \author{
-Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.
+Antony M. Overstall \email{Antony.Overstall@glasgow.ac.uk}.
 }
 \note{
 This function will not typically be called by the user.

diff --git a/man/index2model.Rd b/man/index2model.Rd
@@ -34,7 +34,7 @@ in the maximal model, indicating which parameters are present in the model conve
 }
 
 \author{
-Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.
+Antony M. Overstall \email{Antony.Overstall@glasgow.ac.uk}.
 }
 \note{
 This function will not typically be called by the user.

diff --git a/man/inter_probs.Rd b/man/inter_probs.Rd
@@ -54,7 +54,7 @@ The function will only return elements in the above list if \code{prob} > \code{
 }
 
 \author{
-Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.
+Antony M. Overstall \email{Antony.Overstall@glasgow.ac.uk}.
 }
 
 \seealso{

diff --git a/man/inter_stats.Rd b/man/inter_stats.Rd
@@ -62,7 +62,7 @@ The function will only return elements in the above list if \code{prob} > \code{
 }
 
 \author{
-Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.
+Antony M. Overstall \email{Antony.Overstall@glasgow.ac.uk}.
 }
 \seealso{
 \code{\link{bcct}},

diff --git a/man/iwls_mh.Rd b/man/iwls_mh.Rd
@@ -45,7 +45,7 @@ complete and incomplete contingency tables. \emph{Journal of Statistical Softwar
 1--27. \url{http://www.jstatsoft.org/v58/i07/}
 }
 \author{
-Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.
+Antony M. Overstall \email{Antony.Overstall@glasgow.ac.uk}.
 }
 \note{
 This function will not typically be called by the user.

diff --git a/man/mod_probs.Rd b/man/mod_probs.Rd
@@ -61,7 +61,7 @@ and \code{prob}; giving the posterior model probability.}
 }
 
 \author{
-Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.
+Antony M. Overstall \email{Antony.Overstall@glasgow.ac.uk}.
 }
 
 \seealso{

diff --git a/man/plot.pval.Rd b/man/plot.pval.Rd
@@ -25,7 +25,7 @@ gives the Bayesian p-value.
 }
 
 \author{
-Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.
+Antony M. Overstall \email{Antony.Overstall@glasgow.ac.uk}.
 }
 \note{For an example see \code{\link{bayespval}}.}
 

diff --git a/man/plot.totpop.Rd b/man/plot.totpop.Rd
@@ -26,7 +26,7 @@ total population size.
 }
 
 \author{
-Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.
+Antony M. Overstall \email{Antony.Overstall@glasgow.ac.uk}.
 }
 
 \note{For an example see \code{\link{total_pop}}.}

diff --git a/man/print.acceptrate.Rd b/man/print.acceptrate.Rd
@@ -30,7 +30,7 @@ algorithms.
 }
 
 \author{
-Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.
+Antony M. Overstall \email{Antony.Overstall@glasgow.ac.uk}.
 }
 
 \note{For an example see \code{\link{accept_rate}}.}

diff --git a/man/print.bcct.Rd b/man/print.bcct.Rd
@@ -35,7 +35,7 @@ censored cells.
 }
 
 \author{
-Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.
+Antony M. Overstall \email{Antony.Overstall@glasgow.ac.uk}.
 }
 
 \note{For examples see \code{\link{bcct}} and \code{\link{bict}}.}

diff --git a/man/print.interprob.Rd b/man/print.interprob.Rd
@@ -29,7 +29,7 @@ to the argument \code{cutoff}).
 }
 
 \author{
-Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.
+Antony M. Overstall \email{Antony.Overstall@glasgow.ac.uk}.
 }
 \note{For an example see \code{\link{inter_probs}}.}
 

diff --git a/man/print.interstat.Rd b/man/print.interstat.Rd
@@ -29,7 +29,7 @@ log-linear parameter (subject to the argument \code{cutoff}).
 }
 
 \author{
-Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.
+Antony M. Overstall \email{Antony.Overstall@glasgow.ac.uk}.
 }
 \note{For an example see \code{\link{inter_stats}}.}
 

diff --git a/man/print.modprobs.Rd b/man/print.modprobs.Rd
@@ -29,7 +29,7 @@ This function will print out the posterior model probability of the
 }
 
 \author{
-Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.
+Antony M. Overstall \email{Antony.Overstall@glasgow.ac.uk}.
 }
 \note{For an example see \code{\link{mod_probs}}.}
 

diff --git a/man/print.pval.Rd b/man/print.pval.Rd
@@ -30,7 +30,7 @@ Bayesian p-value.
 }
 
 \author{
-Antony M. Overstall (\email{antony@mcs.st-and.ac.uk}).
+Antony M. Overstall (\email{Antony.Overstall@glasgow.ac.uk}).
 }
 
 \note{For an example see \code{\link{bayespval}}.}

diff --git a/man/print.submod.Rd b/man/print.submod.Rd
@@ -34,7 +34,7 @@ population size, conditional on the model of interest.
 
 }
 \author{
-Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.
+Antony M. Overstall \email{Antony.Overstall@glasgow.ac.uk}.
 }
 \note{For an example see \code{\link{sub_model}}.}
 

diff --git a/man/print.totpop.Rd b/man/print.totpop.Rd
@@ -29,7 +29,7 @@ density interval for the total population size.
 }
 
 \author{
-Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.
+Antony M. Overstall \email{Antony.Overstall@glasgow.ac.uk}.
 }
 \note{For an example see \code{\link{total_pop}}.}
 

diff --git a/man/sub_model.Rd b/man/sub_model.Rd
@@ -101,7 +101,7 @@ complete and incomplete contingency tables. \emph{Journal of Statistical Softwar
 1--27. \url{http://www.jstatsoft.org/v58/i07/}
 }
 \author{
-Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.
+Antony M. Overstall \email{Antony.Overstall@glasgow.ac.uk}.
 }
 
 \seealso{

diff --git a/man/summary.bcct.Rd b/man/summary.bcct.Rd
@@ -153,7 +153,7 @@ complete and incomplete contingency tables. \emph{Journal of Statistical Softwar
 }
 
 \author{
-Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.
+Antony M. Overstall \email{Antony.Overstall@glasgow.ac.uk}.
 }
 \note{
 For examples see the help files for \code{\link{bcct}} and \code{\link{bict}}.

diff --git a/man/total_pop.Rd b/man/total_pop.Rd
@@ -49,7 +49,7 @@ total population size.}
 }
 
 \author{
-Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.
+Antony M. Overstall \email{Antony.Overstall@glasgow.ac.uk}.
 }
 \seealso{
 \code{\link{bict}},