version 1.2

DESCRIPTION

@@ -1,14 +1,15 @@
 Package: conting
 Type: Package
 Title: Bayesian analysis of contingency tables
-Version: 1.1
-Date: 2013-08-13
+Version: 1.2
+Date: 2014-05-19
 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), mvtnorm, BMS, gregmisc, tseries, coda
+Depends: R (>= 2.15.0)
+Imports: mvtnorm, BMS, gtools, tseries, coda
 License: GPL-2
-Packaged: 2013-08-13 11:52:03 UTC; antony
+Packaged: 2014-05-19 08:56:34 UTC; antony
 NeedsCompilation: no
 Repository: CRAN
-Date/Publication: 2013-08-13 14:14:11
+Date/Publication: 2014-05-19 11:18:31

MD5

@@ -1,5 +1,5 @@
-4ecc9b3e72f4d4e72ce87929714b8b95 *DESCRIPTION
-df390c53434517b304ac5db487184641 *NAMESPACE
+b706038d52fabc00a28a51380c5e6d4d *DESCRIPTION
+4eb234dfaf800c03afa81c02796821bd *NAMESPACE
 9071b89c46380a7af6be8fae2db00948 *R/RJ_update.R
 def339b59e64204e9db01335b77ac9e8 *R/accept_rate.R
 e3f610f6d31b1bc65164baf540514209 *R/add_term.R
@@ -39,30 +39,30 @@ ebd49330a88bba6d4cc5cbfe048379ea *R/print.submod.R
 a87c0874595f4b0e9c82c46433a2d942 *R/summary.bcct.R
 25d8d4dc32f86840812605ab3a2068c5 *R/summary.bict.R
 84ed36115620defbe585207a53a9c951 *R/total_pop.R
-541e8cea9e1c1b3919e280b55fc0185d *data/AOH.rda
-fe4c3af9426730958d340e3a9e4400bc *data/ScotPWID.rda
-7b7dc8fe033b801beca671e7c5f72337 *data/heart.rda
-8d82254257848f88f486321ede4abe5a *data/spina.rda
-1f1432e37f4e9b009cad01ce9b9d1b7f *man/AOH.Rd
-213c01a6d0c2eda18869d55bb9489176 *man/RJ_update.Rd
-eb248dd9d75ec07f249a3d9403a1ac7a *man/ScotPWID.Rd
+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
-e414ba53354f2e22e65b8a48cb592d44 *man/bayespval.Rd
-3cd1591981bd2dfbb69846962e1b8621 *man/bcct.Rd
-49f48422e6cad93fd0309cda5cbcf061 *man/bcct.fit.Rd
-fabbfb35ff261d407257a4c8fb5e0860 *man/beta_mode.Rd
-2b817c028950d352cc737fe3b996fde0 *man/bict.Rd
-7c302aa7411c09aa71574b950ab61b55 *man/bict.fit.Rd
-c4106ef24cac2505ef2fa4237864bcb8 *man/conting-package.Rd
-f1bc003c01ce0b21671db5d8d9479802 *man/find_cens.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
 f6cc7a2d7c7becac9d042db3d8221ace *man/formula2index.Rd
-2221b75f9fdd3e39f988b9925c4c5ea4 *man/heart.Rd
-e6e39adb2e2bef63009f4de08cc40a99 *man/index2model.Rd
-8d884af41b1f9e433a627e15242d5c86 *man/inter_probs.Rd
-578541bf41f1641963dffcd5c7fed62c *man/inter_stats.Rd
-007795c85baa92565e801c8d72c05989 *man/iwls_mh.Rd
-ebb168549c6e0e235a9c0e9eed74e81f *man/mod_probs.Rd
+e89273d5b42fdd52f75e0c3975b83d6d *man/heart.Rd
+8060a294901b371a30a2f0a551913088 *man/index2model.Rd
+f40863dfc8288243eaa49bcb5372d423 *man/inter_probs.Rd
+a94c8c784b04c87d639ba044987fa9f0 *man/inter_stats.Rd
+9fa8bd4d2e20a0a749734eb7b3236a6b *man/iwls_mh.Rd
+8e0d38c90ac23045edf28e171e0ee0aa *man/mod_probs.Rd
 732cda659f9946674392863686a9079d *man/plot.pval.Rd
 bfc260d840ef3e7f8e82b8d16a1920d5 *man/plot.totpop.Rd
 9ed357ad8d7163b645444077cbc4923d *man/print.acceptrate.Rd
@@ -73,7 +73,7 @@ ee7d8c4af0498ac0d8961620a6489bdd *man/print.interprob.Rd
 7c83cc1f2520f5758a7a7a99175cde0a *man/print.pval.Rd
 070698f8fe7d331958ef2654b9ad5a1a *man/print.submod.Rd
 cc0e7661d4000e4f6265fee7c47c384f *man/print.totpop.Rd
-8ad0a3bc241a44368ea4109efaa24059 *man/spina.Rd
-2c90630b4d84febacadd76e7e666e9d2 *man/sub_model.Rd
-57191c0694a0b6b4f55a04009433641c *man/summary.bcct.Rd
-e0b076dd277b6dc3fc20959fb1715570 *man/total_pop.Rd
+8bdd02d37df143d803db2227eef9a7a1 *man/spina.Rd
+6115857f543682fa084d355feb874718 *man/sub_model.Rd
+c3c11c8fdf2e521ae48db9168c74840f *man/summary.bcct.Rd
+ab7afab726bcb2996df79820f45c9184 *man/total_pop.Rd

NAMESPACE

@@ -1 +1,5 @@
+import(mvtnorm, tseries, coda)
+importFrom(gtools, combinations)
+importFrom(BMS, bin2hex)
+importFrom(BMS, hex2bin)
 exportPattern("^[[:alpha:]]+")

man/AOH.Rd

@@ -32,14 +32,14 @@ A factor with levels \code{yes} \code{no} indicating the classification of hyper
 These data are from a study in Western Australia. The study copied a larger study 
 from USA. See Knuiman & Speed (1988) for more details.
 
-For details on the function \code{\link{bcct}} applied to these data, see Overstall & King (2013).
+For details on the function \code{\link{bcct}} applied to these data, see Overstall & King (2014).
 }
 \source{
 Knuiman, M.W. & Speed, T.P. (1988) Incorporating Prior Information into the 
 Analysis of Contingency Tables. \emph{Biometrics}, \bold{44}, 1061--1071. 
 }
 \references{
-Overstall, A.M. & King, R. (2013) conting: An R package for Bayesian analysis of
+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.
 }

man/RJ_update.Rd

@@ -49,7 +49,7 @@ A matrix giving the inverse of the prior variance matrix for the log-linear para
 }
 \details{
 For the original algorithm see Forster et al (2012). For details on its application to log-linear models 
-see Overstall & King (2013), and the references therein.
+see Overstall & King (2014), and the references therein.
 }
 \value{
 The function will return a list with the following components:
@@ -60,7 +60,7 @@ The function will return a list with the following components:
 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.
 
-Overstall, A.M. & King, R. (2013) conting: An R package for Bayesian analysis of
+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.
 }

man/ScotPWID.Rd

@@ -46,23 +46,23 @@ A factor with levels \code{Young} \code{Old} indicating age (\code{Young} = <35
 Note that the PWID observed by source \code{S4}, the HCV database, are not necessarily current 
 PWID. They are people who have a history of drug use. Therefore the count in the cell 
 corresponding to only being observed by the HCV database is an overcount. Overstall et al 
-(2013) use a modelling approach whereby the count in the cell corresponding to only being 
+(2014) use a modelling approach whereby the count in the cell corresponding to only being 
 observed by the HCV database is missing and the observed value acts as an upper bound. For 
 more details on the dataset see King et al (2013).
 
-For details on the function \code{\link{bict}} applied to this data, see Overstall & King (2013).
+For details on the function \code{\link{bict}} applied to this data, see Overstall & King (2014).
 }
 \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.
 }
 \references{
-Overstall, A.M., King, R., Bird, S.M., Hutchinson, S.J. & Hay, G. (2013) Incomplete contingency 
+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{Technical Report}, University of St Andrews. 
+in Scotland. \emph{Statistics in Medicine}, \bold{33}, 1564--1579.
 
-Overstall, A.M. & King, R. (2013) conting: An R package for Bayesian analysis of
+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.
 }

man/bayespval.Rd

@@ -28,20 +28,20 @@ thinning.
 }
   \item{statistic}{
 An optional argument giving the discrepancy statistic to use for calculating the Bayesian p-value. It can be one of 
-\code{c("deviance","X2","FreemanTukey")} which correspond to the different statistics: 
-\code{"deviance"} = deviance statistic, \code{"X2"} = Chi-squared statistic, 
-\code{"FreemanTukey"} = Freeman-Tukey statistic. See Overstall & King (2013), and references 
+\code{c("X2","FreemanTukey","deviance")} which correspond to the different statistics: 
+\code{"X2"} = Chi-squared statistic, \code{"FreemanTukey"} = Freeman-Tukey statistic, 
+\code{"deviance"} = deviance statistic. See Overstall & King (2014), and references 
 therein, for descriptions of these statistics.
 }
 }
 
 \details{See Gelman et al (2004, Chapter 6) for more details on Bayesian p-values and see 
-Overstall & King (2013), and references therein, for details of their application to 
+Overstall & King (2014), and references therein, for details of their application to 
 contingency tables.
 
 The use of thinning is recommended when the number of MCMC iterations and/or the number of 
 log-linear parameters in the maximal model are/is large, which may cause problems with 
-computer memory storage.
+comuter memory storage.
 }
 
 \value{
@@ -61,7 +61,7 @@ and their means.}
 \references{
 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. (2013) conting: An R package for Bayesian analysis of
+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.
 }

man/bcct.Rd

@@ -4,7 +4,6 @@
 \title{
 Bayesian Analysis of Complete Contingency Tables
 }
-\encoding{UTF-8}
 \description{
 These functions implement a Bayesian analysis of complete contingency tables. This is 
 accomplished using an MCMC algorithm where the null moves are performed using 
@@ -37,7 +36,7 @@ model. If the model variables are not found in \code{data}, the variables are ta
 A numeric scalar giving the number of (additional, in the case of \code{bcctu}) MCMC iterations to perform.
 }
   \item{prior}{An optional argument giving the prior to be used in the analysis. It can be one of 
-\code{c("UIP","SBH")}, where \code{"UIP"} = unit information prior; and \code{"SBH"} = Sabanes-Bové & Held prior. The 
+\code{c("UIP","SBH")}, where \code{"UIP"} = unit information prior; and \code{"SBH"} = Sabanes-Bove & Held prior. The 
 default value is \code{"SBH"}.
 }
 
@@ -53,7 +52,7 @@ implied by the argument \code{start.formula}. If \code{NULL} (the default) the s
 posterior mode under the maximal model.
 }
   \item{start.sig}{
-An optional argument giving the starting value of sigma^2 (under the Sabanes-Bové & Held prior) for the 
+An optional argument giving the starting value of sigma^2 (under the Sabanes-Bove & Held prior) for the 
 MCMC algorithm when the argument of prior is \code{"SBH"}. If \code{NULL} (the default) the starting 
 value will be one.
 }
@@ -79,11 +78,11 @@ An optional scalar argument giving the probability of performing a null move in
 algorithm, i.e. proposing a move to the current model. The default value is 0.5.
 }
   \item{a}{
-The shape hyperparameter of the Sabanes-Bové & Held prior, see Overstall & King (2013). The default value 
+The shape hyperparameter of the Sabanes-Bove & Held prior, see Overstall & King (2014). The default value 
 is 0.001.
 }
   \item{b}{
-The scale hyperparameter of the Sabanes-Bové & Held prior, see Overstall & King (2013). The default value 
+The scale hyperparameter of the Sabanes-Bove & Held prior, see Overstall & King (2014). The default value 
 is 0.001.
 }
   \item{progress}{
@@ -93,15 +92,15 @@ Logical argument. If \code{TRUE}, then a progress bar will be displayed. The def
 }
 \details{
 For identifiability, the parameters are constrained. The \code{\link{conting-package}} uses sum-to-zero constraints. 
-See Overstall & King (2013), and the references therein, for more details. 
+See Overstall & King (2014), and the references therein, for more details. 
 
 The Metropolis-Hastings algorithm employed is the iterated weighted least squares method for 
 generalised linear models (GLMs) proposed by Gamerman (1997). The reversible jump algorithm employed is 
 that orthogonal projections method for GLMs proposed by Forster et al (2012). For details on these 
-methods applied to log-linear models see Overstall & King (2013), and the references therein. 
+methods applied to log-linear models see Overstall & King (2014), and the references therein. 
 
-For details on the unit information and Sabanes-Bové & Held priors for generalised linear models see Ntzoufras 
-et al (2003) and Sabanes-Bové & Held (2011), respectively. See Overstall & King (2013), and the references therein, 
+For details on the unit information and Sabanes-Bove & Held priors for generalised linear models see Ntzoufras 
+et al (2003) and Sabanes-Bove & Held (2011), respectively. See Overstall & King (2014), and the references therein, 
 for their application to log-linear models and contingency tables.
 
 }
@@ -114,7 +113,7 @@ to a log-linear parameter which is not present for the current model a zero is r
 
 \item{MODEL}{A vector of length \code{n.sample} giving the sampled model indicators in hexadecimal format.}
 
-\item{SIG}{A vector of length \code{n.sample} giving the sampled values for sigma^2 under the Sabanes-Bové & Held prior. If the 
+\item{SIG}{A vector of length \code{n.sample} giving the sampled values for sigma^2 under the Sabanes-Bove & Held prior. If the 
 unit information prior is used then the components of this vector will be one.}
 
 \item{rj_acc}{A binary vector of the same length as the number of reversible jump moves attempted. A 0 indicates 
@@ -149,7 +148,7 @@ The argument \code{b}.
 }
 }
 \references{
-Sabanes-Bové, D. & Held, L. (2011) Hyper-g priors for generalized linear models. \emph{Bayesian
+Sabanes-Bove, D. & Held, L. (2011) Hyper-g priors for generalized linear models. \emph{Bayesian
 Analysis}, \bold{6}, 387--410.
 
 Forster, J.J., Gill, R.C. & Overstall, A.M. (2012) Reversible jump methods for generalised linear models and generalised 
@@ -162,7 +161,7 @@ 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.
 
-Overstall, A.M. & King, R. (2012) conting: An R package for Bayesian analysis of
+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.
 }
@@ -250,7 +249,7 @@ summary(test1)
 #
 #Bayesian p-value =  0.28
 
-## For more examples see Overstall & King (2013).
+## For more examples see Overstall & King (2014).
 
 
 }

man/bcct.fit.Rd

@@ -4,7 +4,6 @@
 \title{
 Bayesian Analysis of Complete Contingency Tables
 }
-\encoding{UTF-8}
 \description{
 This function is the workhorse behind \code{\link{bcct}} and \code{\link{bcctu}}.
 }
@@ -54,10 +53,10 @@ A scalar argument giving the probability of performing a null move, i.e. proposi
 current model.
 }
   \item{a}{
-The shape hyperparameter of the Sabanes-Bové & Held prior, see Overstall & King (2013).
+The shape hyperparameter of the Sabanes-Bove & Held prior, see Overstall & King (2014).
 }
   \item{b}{
-The scale hyperparameter of the Sabanes-Bové & Held prior, see Overstall & King (2013).
+The scale hyperparameter of the Sabanes-Bove & Held prior, see Overstall & King (2014).
 }
   \item{progress}{
 Logical argument. If \code{TRUE}, then a progress bar will be displayed.
@@ -74,7 +73,7 @@ to a log-linear parameter which is not present for the current model a zero is r
 
 \item{MODEL}{A vector of length \code{iters} giving the sampled model indicators in hexadecimal form.}
 
-\item{SIG}{A vector of length \code{iters} giving the sampled values for sigma^2 under the Sabanes-Bové & Held prior. If the 
+\item{SIG}{A vector of length \code{iters} giving the sampled values for sigma^2 under the Sabanes-Bove & Held prior. If the 
 unit information prior is used then the components of this vector will be one.}
 
 \item{rj_acc}{A binary vector of the same length as the number of reversible jump moves attempted. A 0 indicates 
@@ -86,7 +85,7 @@ that the proposal was rejected, and a 1 that the proposal was accepted.}
 }
 
 \references{
-Overstall, A.M. & King, R. (2013) conting: An R package for the Bayesian analysis of 
+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.
 }