changes in diagnostics due to changes in bayesTFR

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: bayesLife
 Type: Package
 Title: Bayesian Projection of Life Expectancy
-Version: 5.0-1
-Date: 2021-03-04
+Version: 5.0-1.9001
+Date: 2021-09-09
 Author: Hana Sevcikova, Adrian Raftery, Jennifer Chunn 
 Maintainer: Hana Sevcikova <[email protected]>
 Description: Making probabilistic projections of life expectancy for all countries of the world, using a Bayesian hierarchical model <doi:10.1007/s13524-012-0193-x>. Subnational projections are also supported.

R/diagnostics.R

@@ -1,13 +1,13 @@
 e0.raftery.diag <- function(mcmc = NULL, 
 							 sim.dir = file.path(getwd(), 'bayesLife.output'),
 							 burnin = 0, country = NULL,
-							 par.names = NULL, par.names.cs = NULL,
+							 par.names = NA, par.names.cs = NA,
 							 country.sampling.prop = 1,
 							 verbose = TRUE, ...) {
     mcmc.set <- if (is.null(mcmc)) get.e0.mcmc(sim.dir = sim.dir, low.memory = TRUE) else mcmc
-    if(is.null(par.names)) 
+    if(bayesTFR:::is.missing(par.names))
         par.names <- e0.parameter.names(mcmc.set$meta$mcmc.options)
-    if(is.null(par.names.cs)) 
+    if(bayesTFR:::is.missing(par.names.cs)) 
         par.names.cs <- e0.parameter.names.cs(mcmc.set$meta$mcmc.options)
 
     return(bayesTFR::tfr.raftery.diag(mcmc = mcmc.set, sim.dir = sim.dir, burnin = burnin,

man/e0.raftery.diag.Rd

@@ -8,7 +8,7 @@ Raftery Diagnostics for Parameters of the Life Expectancy
 The function computes the Raftery diagnostics for each parameter in the same way as \code{\link[bayesTFR]{tfr.raftery.diag}} of the \pkg{bayesTFR} package.}
 \usage{
 e0.raftery.diag(mcmc = NULL, sim.dir = file.path(getwd(), "bayesLife.output"), 
-    burnin = 0, country = NULL, par.names = NULL, par.names.cs = NULL,
+    burnin = 0, country = NULL, par.names = NA, par.names.cs = NA,
     country.sampling.prop = 1, verbose = TRUE, \dots)
 }
 
@@ -25,9 +25,9 @@ Burnin.
   \item{country}{Name or code of a country. If it is given, only country-specific parameters parameters of that country are considered.}
   \item{par.names}{
 Names of country-independent parameters for which the Raftery diagnostics should be computed. By default all parameters are used.
-}
+ If it is \code{NULL}, no country-independent parameters are used.}
   \item{par.names.cs}{
-Names of country-specific parameters for which the Raftery diagnostics should be computed. By default all parameters are used.
+Names of country-specific parameters for which the Raftery diagnostics should be computed. By default all parameters are used. If it is \code{NULL}, no country-specific parameters are used.
 }
 \item{country.sampling.prop}{Proportion of countries that are included in the diagnostics. It should be between 0 and 1. If it is smaller than 1, the countries are randomly sampled. It is only relevant if \code{par.names.cs} is not \code{NULL}. }
 \item{verbose}{Logical switching log messages on and off.}