version 1.3

cran · Jun 11, 2014 · b4d2362 · b4d2362
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,15 +1,15 @@
 Package: conting
 Type: Package
 Title: Bayesian analysis of contingency tables
-Version: 1.2
-Date: 2014-05-19
+Version: 1.3
+Date: 2014-06-11
 Author: Antony M. Overstall
 Maintainer: Antony M. Overstall <antony@mcs.st-and.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: 2014-05-19 08:56:34 UTC; antony
+Packaged: 2014-06-11 09:38:34 UTC; antony
 NeedsCompilation: no
 Repository: CRAN
-Date/Publication: 2014-05-19 11:18:31
+Date/Publication: 2014-06-11 11:57:55
diff --git a/MD5 b/MD5
@@ -1,4 +1,4 @@
-b706038d52fabc00a28a51380c5e6d4d *DESCRIPTION
+b02e7c92da807c5b9225862ddef08a42 *DESCRIPTION
 4eb234dfaf800c03afa81c02796821bd *NAMESPACE
 9071b89c46380a7af6be8fae2db00948 *R/RJ_update.R
 def339b59e64204e9db01335b77ac9e8 *R/accept_rate.R
@@ -43,25 +43,26 @@ b091506c11211bf150355f66524064ac *data/AOH.rda
 6b2eeb5eff0c2a126a0fdf3b3aa27c52 *data/ScotPWID.rda
 4ca8cd66e7e86991d1a52e7c86c7ae67 *data/heart.rda
 d875c73b09fd354b3b8d3a95150ab136 *data/spina.rda
-65f7771242c0423d7968d4ff8d836981 *man/AOH.Rd
-c59a0d8ebdd0d551f7f5c96bcf66fbae *man/RJ_update.Rd
-ec37a3af3820a28b104d311b558dd1ea *man/ScotPWID.Rd
-39ccf0125b327337c0550ae7fc737457 *man/accept_rate.Rd
-d9f447355a532354e2f8b41e5d2acac9 *man/add_term.Rd
-66b5f4ce685bfce8509391c7791a4eff *man/bayespval.Rd
-6d6426f9c6d00294c9b1b6f90f530994 *man/bcct.Rd
-40bef9490edf703b71b921d14aa849b8 *man/bcct.fit.Rd
-734403917fcaea4abb4e0ed3347f492f *man/beta_mode.Rd
-36fe5ee7bf4d00652521f54743f5d95a *man/bict.Rd
-08e933c468edb53191deb60138e13361 *man/bict.fit.Rd
-911ba39fb1098b331b84f5562e57f49d *man/conting-package.Rd
-75dfa510d06fc4f833c0307efbebb630 *man/find_cens.Rd
+551b319d5c059d2714af405e6e005df9 *inst/CITATION
+da54c697af3c2d465145cf4d78f89732 *man/AOH.Rd
+0a5a484e02127cf8fe005869e68dae73 *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
-e89273d5b42fdd52f75e0c3975b83d6d *man/heart.Rd
+8ac844d7f724081448928f8630adace5 *man/heart.Rd
 8060a294901b371a30a2f0a551913088 *man/index2model.Rd
 f40863dfc8288243eaa49bcb5372d423 *man/inter_probs.Rd
 a94c8c784b04c87d639ba044987fa9f0 *man/inter_stats.Rd
-9fa8bd4d2e20a0a749734eb7b3236a6b *man/iwls_mh.Rd
+d23581a11f3b675beb822cc9e01cd445 *man/iwls_mh.Rd
 8e0d38c90ac23045edf28e171e0ee0aa *man/mod_probs.Rd
 732cda659f9946674392863686a9079d *man/plot.pval.Rd
 bfc260d840ef3e7f8e82b8d16a1920d5 *man/plot.totpop.Rd
@@ -73,7 +74,7 @@ ee7d8c4af0498ac0d8961620a6489bdd *man/print.interprob.Rd
 7c83cc1f2520f5758a7a7a99175cde0a *man/print.pval.Rd
 070698f8fe7d331958ef2654b9ad5a1a *man/print.submod.Rd
 cc0e7661d4000e4f6265fee7c47c384f *man/print.totpop.Rd
-8bdd02d37df143d803db2227eef9a7a1 *man/spina.Rd
-6115857f543682fa084d355feb874718 *man/sub_model.Rd
-c3c11c8fdf2e521ae48db9168c74840f *man/summary.bcct.Rd
+1cdd84e1c6050c775559904e230162a9 *man/spina.Rd
+3f199197d54dbae5b00fa134efd2c983 *man/sub_model.Rd
+09620d66702dc4a7485f3632e4c5deae *man/summary.bcct.Rd
 ab7afab726bcb2996df79820f45c9184 *man/total_pop.Rd
diff --git a/inst/CITATION b/inst/CITATION
@@ -0,0 +1,20 @@
+citHeader("To cite conting in publications use:")
+
+citEntry(entry = "Article",
+  title        = "{conting}: An {R} Package for Bayesian Analysis of Complete and Incomplete Contingency Tables",
+  author       = personList(as.person("Antony M. Overstall"),
+                   as.person("Ruth King")),
+  journal      = "Journal of Statistical Software",
+  year         = "2014",
+  volume       = "58",
+  number       = "7",
+  pages        = "1--27",
+  url          = "http://www.jstatsoft.org/v58/i07/",
+
+  textVersion  =
+  paste("Antony M. Overstall, Ruth King (2014).",
+        "conting: An R Package for Bayesian Analysis of Complete and Incomplete Contingency Tables.",
+        "Journal of Statistical Software, 58(7), 1-27.",
+        "URL http://www.jstatsoft.org/v58/i07/.")
+)
+
diff --git a/man/AOH.Rd b/man/AOH.Rd
@@ -36,12 +36,12 @@ For details on the function \code{\link{bcct}} applied to these data, see Overst
 }
 \source{
 Knuiman, M.W. & Speed, T.P. (1988) Incorporating Prior Information into the 
-Analysis of Contingency Tables. \emph{Biometrics}, \bold{44}, 1061--1071. 
+Analysis of Contingency Tables. \emph{Biometrics}, \bold{44 (4)}, 1061--1071. 
 }
 \references{
 Overstall, A.M. & King, R. (2014) conting: An R package for Bayesian analysis of
-complete and incomplete contingency tables. \emph{Technical Report}, University 
-of St Andrews, UK.
+complete and incomplete contingency tables. \emph{Journal of Statistical Software}, \bold{58 (7)}, 
+1--27. \url{http://www.jstatsoft.org/v58/i07/}
 }
 \examples{
 data(AOH)

diff --git a/man/RJ_update.Rd b/man/RJ_update.Rd
@@ -58,11 +58,11 @@ The function will return a list with the following components:
 }
 \references{
 Forster, J.J., Gill, R.C. & Overstall, A.M. (2012) Reversible jump methods for generalised linear models and generalised 
-linear mixed models. \emph{Statistics and Computing}, \bold{22}, 107--120.
+linear mixed models. \emph{Statistics and Computing}, \bold{22 (1)}, 107--120.
 
 Overstall, A.M. & King, R. (2014) conting: An R package for Bayesian analysis of
-complete and incomplete contingency tables. \emph{Technical Report}, University 
-of St Andrews, UK.
+complete and incomplete contingency tables. \emph{Journal of Statistical Software}, \bold{58 (7)}, 
+1--27. \url{http://www.jstatsoft.org/v58/i07/}
 }
 \author{
 Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.

diff --git a/man/ScotPWID.Rd b/man/ScotPWID.Rd
@@ -55,16 +55,16 @@ For details on the function \code{\link{bict}} applied to this data, see Oversta
 \source{
 King, R., Bird, S. M., Overstall, A. M., Hay, G. & Hutchinson, S. J. (2013) Injecting drug
 users in Scotland, 2006: Listing, number, demography, and opiate-related death-rates.
-\emph{Addiction Research and Theory}, \bold{21}, 235-246.
+\emph{Addiction Research and Theory}, \bold{21 (3)}, 235-246.
 }
 \references{
 Overstall, A.M., King, R., Bird, S.M., Hutchinson, S.J. & Hay, G. (2014) Incomplete contingency 
 tables with censored cells with application to estimating the number of people who inject drugs 
-in Scotland. \emph{Statistics in Medicine}, \bold{33}, 1564--1579.
+in Scotland. \emph{Statistics in Medicine}, \bold{33 (9)}, 1564--1579.
 
 Overstall, A.M. & King, R. (2014) conting: An R package for Bayesian analysis of
-complete and incomplete contingency tables. \emph{Technical Report}, University 
-of St Andrews, UK.
+complete and incomplete contingency tables. \emph{Journal of Statistical Software}, \bold{58 (7)}, 
+1--27. \url{http://www.jstatsoft.org/v58/i07/}
 }
 \examples{
 data(ScotPWID)

diff --git a/man/accept_rate.Rd b/man/accept_rate.Rd
@@ -30,7 +30,7 @@ following components.
 \references{
 Brooks, S.P., Giudici, P., & Roberts, G.O. (2003) Efficient construction of reversible jump 
 Markov chain Monte Carlo proposal distributions. \emph{Journal of the Royal Statistical 
-Society, Series B}, \bold{65}, 3--55.
+Society, Series B}, \bold{65 (1)}, 3--55.
 }
 \author{
 Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.

diff --git a/man/add_term.Rd b/man/add_term.Rd
@@ -63,7 +63,7 @@ depending on the type of move proposed.}
 }
 \references{
 Forster, J.J., Gill, R.C. & Overstall, A.M. (2012) Reversible jump methods for generalised linear models and generalised 
-linear mixed models. \emph{Statistics and Computing}, \bold{22}, 107--120.
+linear mixed models. \emph{Statistics and Computing}, \bold{22 (1)}, 107--120.
 }
 \author{
 Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.

diff --git a/man/bayespval.Rd b/man/bayespval.Rd
@@ -62,8 +62,8 @@ and their means.}
 Gelman, A., Carlin, J.B., Stern, H.S. & Rubin, D.B. (2004) \emph{Bayesian Data Analysis}, 2nd edition, Chapman & Hall.
 
 Overstall, A.M. & King, R. (2014) conting: An R package for Bayesian analysis of
-complete and incomplete contingency tables. \emph{Technical Report}, University 
-of St Andrews, UK.
+complete and incomplete contingency tables. \emph{Journal of Statistical Software}, \bold{58 (7)}, 
+1--27. \url{http://www.jstatsoft.org/v58/i07/}
 }
 \author{
 Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.

diff --git a/man/bcct.Rd b/man/bcct.Rd
@@ -149,21 +149,21 @@ The argument \code{b}.
 }
 \references{
 Sabanes-Bove, D. & Held, L. (2011) Hyper-g priors for generalized linear models. \emph{Bayesian
-Analysis}, \bold{6}, 387--410.
+Analysis}, \bold{6 (3)}, 387--410.
 
 Forster, J.J., Gill, R.C. & Overstall, A.M. (2012) Reversible jump methods for generalised linear models and generalised 
-linear mixed models. \emph{Statistics and Computing}, \bold{22}, 107--120.
+linear mixed models. \emph{Statistics and Computing}, \bold{22 (1)}, 107--120.
 
 Gamerman, D. (1997) Sampling from the posterior distribution in generalised linear mixed
-models. \emph{Statistics and Computing}, \bold{7}, 57--68.
+models. \emph{Statistics and Computing}, \bold{7 (1)}, 57--68.
 
 Nztoufras, I., Dellaportas, P. & Forster, J.J. (2003) Bayesian variable and link 
 determination for generalised linear models. \emph{Journal of Statistical Planning and 
-Inference}, \bold{111}, 165--180.
+Inference}, \bold{111 (1)}, 165--180.
 
 Overstall, A.M. & King, R. (2014) conting: An R package for Bayesian analysis of
-complete and incomplete contingency tables. \emph{Technical Report}, University 
-of St Andrews, UK.
+complete and incomplete contingency tables. \emph{Journal of Statistical Software}, \bold{58 (7)}, 
+1--27. \url{http://www.jstatsoft.org/v58/i07/}
 }
 \author{
 Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.

diff --git a/man/bcct.fit.Rd b/man/bcct.fit.Rd
@@ -85,8 +85,9 @@ that the proposal was rejected, and a 1 that the proposal was accepted.}
 }
 
 \references{
-Overstall, A.M. & King, R. (2014) conting: An R package for the Bayesian analysis of 
-complete and incomplete contingency tables. \emph{Technical Report}, University of St Andrews.
+Overstall, A.M. & King, R. (2014) conting: An R package for Bayesian analysis of
+complete and incomplete contingency tables. \emph{Journal of Statistical Software}, \bold{58 (7)}, 
+1--27. \url{http://www.jstatsoft.org/v58/i07/}
 }
 
 \author{

diff --git a/man/beta_mode.Rd b/man/beta_mode.Rd
@@ -55,19 +55,21 @@ linear parameters.}
 
 \references{
 Sabanes-Bove, D. & Held, L. (2011) Hyper-g priors for generalized linear models. \emph{Bayesian
-Analysis}, \bold{6}, 387--410.
+Analysis}, \bold{6 (3)}, 387--410.
 
 Forster, J.J., Gill, R.C. & Overstall, A.M. (2012) Reversible jump methods for 
 generalised linear models and generalised linear mixed models. \emph{Statistics and Computing}, 
-\bold{22}, 107--120.
+\bold{22 (1)}, 107--120.
 
 Nztoufras, I., Dellaportas, P. & Forster, J.J. (2003) Bayesian variable and link 
 determination for generalised linear models. \emph{Journal of Statistical Planning and 
-Inference}, \bold{111}, 165--180.
+Inference}, \bold{111 (1)}, 165--180.
 
-Overstall, A.M. & King, R. (2014) conting: An R package for the Bayesian analysis of 
-complete and incomplete contingency tables. \emph{Technical Report}, University of St Andrews.
+Overstall, A.M. & King, R. (2014) conting: An R package for Bayesian analysis of
+complete and incomplete contingency tables. \emph{Journal of Statistical Software}, \bold{58 (7)}, 
+1--27. \url{http://www.jstatsoft.org/v58/i07/}
 }
+
 \author{
 Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.
 }

diff --git a/man/bict.Rd b/man/bict.Rd
@@ -208,25 +208,25 @@ The argument \code{b}.
 }
 \references{
 Sabanes-Bove, D. & Held, L. (2011) Hyper-g priors for generalized linear models. \emph{Bayesian
-Analysis}, \bold{6}, 387--410.
+Analysis}, \bold{6 (3)}, 387--410.
 
 Forster, J.J., Gill, R.C. & Overstall, A.M. (2012) Reversible jump methods for generalised linear models and generalised 
-linear mixed models. \emph{Statistics and Computing}, \bold{22}, 107--120.
+linear mixed models. \emph{Statistics and Computing}, \bold{22 (1)}, 107--120.
 
 Gamerman, D. (1997) Sampling from the posterior distribution in generalised linear mixed
-models. \emph{Statistics and Computing}, \bold{7}, 57--68.
+models. \emph{Statistics and Computing}, \bold{7 (1)}, 57--68.
 
 Nztoufras, I., Dellaportas, P. & Forster, J.J. (2003) Bayesian variable and link 
 determination for generalised linear models. \emph{Journal of Statistical Planning and 
-Inference}, \bold{111}, 165--180.
+Inference}, \bold{111 (1)}, 165--180.
 
 Overstall, A.M. & King, R. (2014) conting: An R package for Bayesian analysis of
-complete and incomplete contingency tables. \emph{Technical Report}, University 
-of St Andrews, UK.
+complete and incomplete contingency tables. \emph{Journal of Statistical Software}, \bold{58 (7)}, 
+1--27. \url{http://www.jstatsoft.org/v58/i07/}
 
 Overstall, A.M., King, R., Bird, S.M., Hutchinson, S.J. & Hay, G. (2014) Incomplete contingency 
 tables with censored cells with application to estimating the number of people who inject drugs 
-in Scotland. \emph{Statistics in Medicine}, \bold{33}, 1564--1579.
+in Scotland. \emph{Statistics in Medicine}, \bold{33 (9)}, 1564--1579.
 }
 \author{
 Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.

diff --git a/man/bict.fit.Rd b/man/bict.fit.Rd
@@ -99,9 +99,11 @@ that the proposal was rejected, and a 1 that the proposal was accepted.}
 }
 
 \references{
-Overstall, A.M. & King, R. (2014) conting: An R package for the Bayesian analysis of 
-complete and incomplete contingency tables. \emph{Technical Report}, University of St Andrews.
+Overstall, A.M. & King, R. (2014) conting: An R package for Bayesian analysis of
+complete and incomplete contingency tables. \emph{Journal of Statistical Software}, \bold{58 (7)}, 
+1--27. \url{http://www.jstatsoft.org/v58/i07/}
 }
+
 \author{
 Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.
 }

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 1.2\cr
-Date: \tab 2013-05-19\cr
+Version: \tab 1.3\cr
+Date: \tab 2014-06-11\cr
 License: \tab GPL-2\cr
 }
 For the Bayesian analysis of complete contingency tables the key function is \code{\link{bcct}} 
@@ -39,8 +39,8 @@ Maintainer: Antony M. Overstall \email{antony@mcs.st-and.ac.uk}
 }
 \references{
 Overstall, A.M. & King, R. (2014) conting: An R package for Bayesian analysis of
-complete and incomplete contingency tables. \emph{Technical Report}, University 
-of St Andrews, UK.
+complete and incomplete contingency tables. \emph{Journal of Statistical Software}, \bold{58 (7)}, 
+1--27. \url{http://www.jstatsoft.org/v58/i07/}
 }
 
 \keyword{ package }

diff --git a/man/find_cens.Rd b/man/find_cens.Rd
@@ -51,10 +51,11 @@ used by the \code{\link{bict}} and \code{\link{bictu}} functions.
 \references{
 Overstall, A.M., King, R., Bird, S.M., Hutchinson, S.J. & Hay, G. (2014) Incomplete contingency 
 tables with censored cells with application to estimating the number of people who inject drugs 
-in Scotland. \emph{Statistics in Medicine}, \bold{33}, 1564--1579.
+in Scotland. \emph{Statistics in Medicine}, \bold{33 (9)}, 1564--1579.
 
-Overstall, A.M. & King, R. (2014) conting: An R package for the Bayesian analysis of 
-complete and incomplete contingency tables. \emph{Technical Report}, University of St Andrews.
+Overstall, A.M. & King, R. (2014) conting: An R package for Bayesian analysis of
+complete and incomplete contingency tables. \emph{Journal of Statistical Software}, \bold{58 (7)}, 
+1--27. \url{http://www.jstatsoft.org/v58/i07/}
 }
 \author{
 Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.

diff --git a/man/heart.Rd b/man/heart.Rd
@@ -47,12 +47,12 @@ For details on the function \code{\link{bcct}} applied to this data, see Oversta
 
 \source{
 Edwards, D. & Havranek, T. (1985) A fast procedure for model search 
-in multidimensional contingency tables. \emph{Biometrika}, \bold{72}, 339--351.
+in multidimensional contingency tables. \emph{Biometrika}, \bold{72 (2)}, 339--351.
 }
 \references{
 Overstall, A.M. & King, R. (2014) conting: An R package for Bayesian analysis of
-complete and incomplete contingency tables. \emph{Technical Report}, University 
-of St Andrews, UK.
+complete and incomplete contingency tables. \emph{Journal of Statistical Software}, \bold{58 (7)}, 
+1--27. \url{http://www.jstatsoft.org/v58/i07/}
 }
 \examples{
 data(heart)

diff --git a/man/iwls_mh.Rd b/man/iwls_mh.Rd
@@ -38,11 +38,11 @@ parameters.
 }
 \references{
 Gamerman, D. (1997) Sampling from the posterior distribution in generalised linear mixed
-models. \emph{Statistics and Computing}, \bold{7}, 57--68.
+models. \emph{Statistics and Computing}, \bold{7 (1)}, 57--68.
 
 Overstall, A.M. & King, R. (2014) conting: An R package for Bayesian analysis of
-complete and incomplete contingency tables. \emph{Technical Report}, University 
-of St Andrews, UK.
+complete and incomplete contingency tables. \emph{Journal of Statistical Software}, \bold{58 (7)}, 
+1--27. \url{http://www.jstatsoft.org/v58/i07/}
 }
 \author{
 Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.

diff --git a/man/spina.Rd b/man/spina.Rd
@@ -40,12 +40,12 @@ For details on the function \code{\link{bict}} applied to this data, see Oversta
 }
 \source{
 Madigan, D. & York, J.C. (1997) Methods for Estimation of the Size of a Closed Population. 
-\emph{Biometrika}, \bold{84}, 19--31.
+\emph{Biometrika}, \bold{84 (1)}, 19--31.
 }
 \references{
 Overstall, A.M. & King, R. (2014) conting: An R package for Bayesian analysis of
-complete and incomplete contingency tables. \emph{Technical Report}, University 
-of St Andrews, UK.
+complete and incomplete contingency tables. \emph{Journal of Statistical Software}, \bold{58 (7)}, 
+1--27. \url{http://www.jstatsoft.org/v58/i07/}
 }
 \examples{
 data(spina)

diff --git a/man/sub_model.Rd b/man/sub_model.Rd
@@ -97,8 +97,8 @@ cell counts, where k is the total number of missing and censored cell counts.}
 }
 \references{
 Overstall, A.M. & King, R. (2014) conting: An R package for Bayesian analysis of
-complete and incomplete contingency tables. \emph{Technical Report}, University 
-of St Andrews, UK.
+complete and incomplete contingency tables. \emph{Journal of Statistical Software}, \bold{58 (7)}, 
+1--27. \url{http://www.jstatsoft.org/v58/i07/}
 }
 \author{
 Antony M. Overstall \email{antony@mcs.st-and.ac.uk}.