version 0.1-12

cran · Nov 19, 2023 · 2c22636 · 2c22636
1 parent 8bf2a40
commit 2c22636
Show file tree

Hide file tree

Showing 18 changed files with 59 additions and 56 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,20 +1,20 @@
 Package: INLABMA
-Version: 0.1-11
-Date: 2018-07-26
-Encoding: latin1
+Version: 0.1-12
+Date: 2023-11-17
+Encoding: UTF-8
 Title: Bayesian Model Averaging with INLA
-Author: Virgilio G�mez-Rubio <virgilio.gomez@uclm.es>, Roger Bivand <Roger.Bivand@nhh.no>
-Maintainer: Virgilio G�mez-Rubio <virgilio.gomez@uclm.es>
+Author: Virgilio Gómez-Rubio <virgilio.gomez@uclm.es>, Roger Bivand <Roger.Bivand@nhh.no>
+Maintainer: Virgilio Gómez-Rubio <virgilio.gomez@uclm.es>
 Depends: R(>= 2.15.0), parallel, sp
-Imports: Matrix, spdep
+Imports: Matrix, spdep, methods
 Suggests: INLA
 Description: Fit Spatial Econometrics models using Bayesian model averaging 
   on models fitted with INLA. The INLA package can be obtained from 
-  <http://www.r-inla.org>. 
+  <https://www.r-inla.org>. 
 License: GPL (>= 2)
 Additional_repositories: https://inla.r-inla-download.org/R/stable/
 RoxygenNote: 6.0.1
 NeedsCompilation: no
-Packaged: 2018-07-26 08:37:52 UTC; virgiliogomezgislab
+Packaged: 2023-11-17 20:54:25 UTC; virgil
 Repository: CRAN
-Date/Publication: 2018-07-26 22:10:06 UTC
+Date/Publication: 2023-11-18 14:20:05 UTC
diff --git a/MD5 b/MD5
@@ -1,20 +1,21 @@
-fab8cb3bd22e34dbd417ce8da61496dd *DESCRIPTION
-67d4ad58c745526e171b5edebd6b8f40 *NAMESPACE
+635ed034fef8f02b85d1713e32f62010 *DESCRIPTION
+6c90ea8ba339f92c37b6e72075b94367 *NAMESPACE
 e732fab3d0996e4cc221b7be3c792819 *R/BMArho.R
-b7f4d3d0932b259376e98cbf5b33aae8 *R/INLAMH.R
+da2beeb5856abdf2d14066ecabe638bf *R/INLAMH.R
 9770042bbcd031588531e09472a3eabc *R/SAC.R
 072bb1b56f7e5562a57b845db96ec8ee *R/SE-utils.R
 5855c97d0b73ad7c8d20e95eab75dfd5 *R/leroux.R
-176ccd894f1bb9d9f8a5953159bc1c92 *inst/CITATION
-c4b99dec6bd03be7898317d73189d046 *man/BMA2.Rd
-415194a38807dc78f5583ad02a0a99d2 *man/BMArho.Rd
-02c9389c46d8c1a5b3d80d8b20558f46 *man/INLAMH.Rd
-9d0a2d3960c4900ff25de005d2b78157 *man/fitmarg.Rd
-e01ddd8f763c02bec7bb12a29f38c602 *man/fitmargBMA.Rd
-42034b79cdb898bd4aaaeafeb946662e *man/leroux.Rd
-98b442e9d2c0934facf6316af1192c09 *man/logprrho.Rd
-56e9b1cb8daa634e0ae3be54b04ffd3c *man/mysplinefun.Rd
-b9b53e3712948efee16de1e1905f0268 *man/recompute.impacts.Rd
-8b7be27a8f31e427f57024a486a677f5 *man/rescalemarg.Rd
-14137ea3c0b26263fb915bbf5321d76b *man/sem.Rd
-ef553c7e01dde2f3a1e39c5b341e7e4b *man/trIrhoWinv.Rd
+8faf250d78a120ba4c7ea2186efddd24 *build/partial.rdb
+790b6ab8c3e8c065c0a388af84bf1cd5 *inst/CITATION
+97ce55be27ecf9aa48548688abe50d4a *man/BMA2.Rd
+ae73926a7e555bcf328156b133b1152b *man/BMArho.Rd
+18359f39f80d45912e4b7dc6fd736c32 *man/INLAMH.Rd
+e4d31f27b13d9c15825225da34473fde *man/fitmarg.Rd
+30afc3be3ef494765d8da9e120b06650 *man/fitmargBMA.Rd
+bd4dbcd4d5bce2bf71eb2f4fc31c4142 *man/leroux.Rd
+6e9046314704e5b2c5ce01f9f058096b *man/logprrho.Rd
+9d38199338e160b7dc20b1caab1ac076 *man/mysplinefun.Rd
+8cb1085acfb83e846b48b866a85eb9bb *man/recompute.impacts.Rd
+d68655ade8f3672fbee7a55e664741d4 *man/rescalemarg.Rd
+1846e157a6f5b0439ad7acc1bb8808bd *man/sem.Rd
+2ec6d9f645e8465fa89a70adab6e6b80 *man/trIrhoWinv.Rd
diff --git a/NAMESPACE b/NAMESPACE
@@ -12,3 +12,5 @@ import(spdep)
 
 importFrom("stats", "as.formula", "dnorm", "integrate", "model.matrix",
              "runif", "splinefun", "update", "quantile")
+
+importFrom("methods", "is")
diff --git a/R/INLAMH.R b/R/INLAMH.R
@@ -43,7 +43,7 @@ while (i <= n.sim.tot) {
    #Fit model using try to handle possible errors in INLA
    model.new <- try(fit.inla(d, b.new))
 
-   if(class(model.new) == "try-error") {
+   if(is(model.new, "try-error")) {
      #Update number of errors
      n.err.idx <- n.err.idx + 1
 

diff --git a/build/partial.rdb b/build/partial.rdb
diff --git a/inst/CITATION b/inst/CITATION
@@ -1,21 +1,21 @@
 citHeader("To cite INLABMA in publications use:")
 
-citEntry(entry = "Article",
+bibentry(bibtype = "Article",
   title        = "Spatial Data Analysis with {R}-{INLA} with Some Extensions",
-  author       = personList(as.person("Roger S. Bivand"),
+  author       = c(as.person("Roger S. Bivand"),
                    as.person("Virgilio G\\'omez-Rubio"),
                    as.person("H{\\aa}vard Rue")),
   journal      = "Journal of Statistical Software",
   year         = "2015",
   volume       = "63",
   number       = "20",
   pages        = "1--31",
-  url          = "http://www.jstatsoft.org/v63/i20/",
+  url          = "https://www.jstatsoft.org/v63/i20/",
 
   textVersion  =
   paste("Roger S. Bivand, Virgilio Gomez-Rubio, Havard Rue (2015).",
         "Spatial Data Analysis with R-INLA with Some Extensions.",
         "Journal of Statistical Software, 63(20), 1-31.",
-        "URL http://www.jstatsoft.org/v63/i20/.")
+        "URL https://www.jstatsoft.org/v63/i20/.")
 )
 
diff --git a/man/BMA2.Rd b/man/BMA2.Rd
@@ -45,7 +45,7 @@ summary information.
 %% ~put references to the literature/web site here ~
 %%}
 \author{
-Virgilio Gómez-Rubio <virgilio.gomez@uclm.es>
+Virgilio Gómez-Rubio <virgilio.gomez@uclm.es>
 }
 %%\note{
 %%  ~~further notes~~
@@ -60,11 +60,11 @@ Virgilio G
 %%}
 
 \references{
-  Roger S. Bivand, Virgilio Gómez-Rubio, Håvard Rue (2014). Approximate 
+  Roger S. Bivand, Virgilio Gómez-Rubio, Hĺvard Rue (2014). Approximate 
   Bayesian inference for spatial econometrics models. Spatial Statistics, 
   Volume 9, 146-165.
 
-  Roger S. Bivand, Virgilio Gómez-Rubio, Håvard Rue (2015). Spatial
+  Roger S. Bivand, Virgilio Gómez-Rubio, Hĺvard Rue (2015). Spatial
   Data Analysis with R-INLA with Some Extensions. Journal of
   Statistical Software, 63(20), 1-31. URL http://www.jstatsoft.org/v63/i20/.
 }

diff --git a/man/BMArho.Rd b/man/BMArho.Rd
@@ -35,7 +35,7 @@ Vector of averaged fitted values.
 %% ~put references to the literature/web site here ~
 %%}
 \author{
-Virgilio Gómez-Rubio <virgilio.gomez@uclm.es>
+Virgilio Gómez-Rubio <virgilio.gomez@uclm.es>
 }
 %%\note{
 %%  ~~further notes~~
@@ -50,11 +50,11 @@ Virgilio G
 % R documentation directory.
 
 \references{
-  Roger S. Bivand, Virgilio Gómez-Rubio, Håvard Rue (2014). Approximate 
+  Roger S. Bivand, Virgilio Gómez-Rubio, Hĺvard Rue (2014). Approximate 
   Bayesian inference for spatial econometrics models. Spatial Statistics, 
   Volume 9, 146-165.
 
-  Roger S. Bivand, Virgilio Gómez-Rubio, Håvard Rue (2015). Spatial
+  Roger S. Bivand, Virgilio Gómez-Rubio, Hĺvard Rue (2015). Spatial
   Data Analysis with R-INLA with Some Extensions. Journal of
   Statistical Software, 63(20), 1-31. URL http://www.jstatsoft.org/v63/i20/.
 }

diff --git a/man/INLAMH.Rd b/man/INLAMH.Rd
@@ -64,10 +64,10 @@ has been accepted or not. This is useful to compute the acceptance rate.}
 a list beacuse the sampled values can be vectors.}
 }
 \references{
-Virgilio Gómez-Rubio and Håvard Rue (2017).  Markov Chain Monte Carlo with the Integrated Nested Laplace Approximation. \url{https://arxiv.org/abs/1210.4908}.
+Virgilio Gómez-Rubio and Haavard Rue (2017).  Markov Chain Monte Carlo with the Integrated Nested Laplace Approximation. \doi{10.1007/s11222-017-9778-y}.
 }
 \author{
-Virgilio Gómez-Rubio.
+Virgilio Gómez-Rubio.
 }
 
 %%\examples{

diff --git a/man/fitmarg.Rd b/man/fitmarg.Rd
@@ -40,7 +40,7 @@ A function with the fitted marginal is returned.
 %% ~put references to the literature/web site here ~
 %%}
 \author{
-Virgilio Gómez-Rubio <virgilio.gomez@uclm.es>
+Virgilio Gómez-Rubio <virgilio.gomez@uclm.es>
 }
 %%\note{
 %%  ~~further notes~~

diff --git a/man/fitmargBMA.Rd b/man/fitmargBMA.Rd
@@ -68,7 +68,7 @@ distribution.
 %% ~put references to the literature/web site here ~
 %%}
 \author{
-Virgilio Gómez-Rubio <virgilio.gomez@uclm.es>
+Virgilio Gómez-Rubio <virgilio.gomez@uclm.es>
 }
 %%\note{
 %%  ~~further notes~~

diff --git a/man/leroux.Rd b/man/leroux.Rd
@@ -49,7 +49,7 @@ The marginal log-likelihood is corrected to add half the log-determinant of the
 An INLA object.
 }
 \author{
-Virgilio Gómez-Rubio <virgilio.gomez@uclm.es>
+Virgilio Gómez-Rubio <virgilio.gomez@uclm.es>
 }
 %%\note{
 %%  ~~further notes~~
@@ -67,11 +67,11 @@ Virgilio G
   (eds.), Statistical Models in Epidemiology, the Environment and Clinical
   Trials, pp. 135-178. Springer-Verlag, New York.
 
-  Roger S. Bivand, Virgilio Gómez-Rubio, Håvard Rue (2014). Approximate 
+  Roger S. Bivand, Virgilio Gómez-Rubio, Hĺvard Rue (2014). Approximate 
   Bayesian inference for spatial econometrics models. Spatial Statistics, 
   Volume 9, 146-165.
 
-  Roger S. Bivand, Virgilio Gómez-Rubio, Håvard Rue (2015). Spatial
+  Roger S. Bivand, Virgilio Gómez-Rubio, Hĺvard Rue (2015). Spatial
   Data Analysis with R-INLA with Some Extensions. Journal of
   Statistical Software, 63(20), 1-31. URL http://www.jstatsoft.org/v63/i20/.
 }

diff --git a/man/logprrho.Rd b/man/logprrho.Rd
@@ -28,7 +28,7 @@ Numerical.
 %% ~put references to the literature/web site here ~
 %%}
 \author{
-Virgilio Gómez-Rubio <virgilio.gomez@uclm.es>
+Virgilio Gómez-Rubio <virgilio.gomez@uclm.es>
 }
 %%\note{
 %%  ~~further notes~~

diff --git a/man/mysplinefun.Rd b/man/mysplinefun.Rd
@@ -37,7 +37,7 @@ Returns a function with \code{x} and \code{deriv} arguments.  See \code{\link{sp
 %% ~put references to the literature/web site here ~
 %%}
 \author{
-Virgilio Gómez-Rubio <virgilio.gomez@uclm.es>
+Virgilio Gómez-Rubio <virgilio.gomez@uclm.es>
 }
 %%\note{
 %%  ~~further notes~~

diff --git a/man/recompute.impacts.Rd b/man/recompute.impacts.Rd
@@ -32,7 +32,7 @@ Original object with the updated summary statistics of the impacts.
 Bivand et al. (2013)
 }
 \author{
-Virgilio Gómez-Rubio <virgilio.gomez@uclm.es>
+Virgilio Gómez-Rubio <virgilio.gomez@uclm.es>
 }
 %%\note{
 %%  ~~further notes~~

diff --git a/man/rescalemarg.Rd b/man/rescalemarg.Rd
@@ -31,7 +31,7 @@ probability densities. This is also an object of classes \code{inla.marginal}.
 INLA
 }
 \author{
-Virgilio Gómez-Rubio <virgilio.gomez@uclm.es>
+Virgilio Gómez-Rubio <virgilio.gomez@uclm.es>
 }
 %%\note{
 %%  ~~further notes~~

diff --git a/man/sem.Rd b/man/sem.Rd
@@ -89,19 +89,19 @@ the variance-covariance matrix of the error term or random effects.
 An \code{inla} object.
 }
 \references{
-  Roger S. Bivand, Virgilio Gómez-Rubio, Håvard Rue (2014). Approximate 
+  Roger S. Bivand, Virgilio Gómez-Rubio, Hĺvard Rue (2014). Approximate 
   Bayesian inference for spatial econometrics models. Spatial Statistics, 
   Volume 9, 146-165.
 
-  Roger S. Bivand, Virgilio Gómez-Rubio, Håvard Rue (2015). Spatial
+  Roger S. Bivand, Virgilio Gómez-Rubio, Hĺvard Rue (2015). Spatial
   Data Analysis with R-INLA with Some Extensions. Journal of
   Statistical Software, 63(20), 1-31. URL http://www.jstatsoft.org/v63/i20/.
 
-  Virgilio Gómez-Rubio and Francisco-Palmí Perales (2016).  Spatial Models with the Integrated Nested Laplace Approximation within Markov Chain Monte Carlo. Submitted.
+  Virgilio Gómez-Rubio and Francisco-Palmí Perales (2016).  Spatial Models with the Integrated Nested Laplace Approximation within Markov Chain Monte Carlo. Submitted.
 
 }
 \author{
-Virgilio Gómez-Rubio <virgilio.gomez@uclm.es>
+Virgilio Gómez-Rubio <virgilio.gomez@uclm.es>
 }
 %%\note{
 %%  ~~further notes~~

diff --git a/man/trIrhoWinv.Rd b/man/trIrhoWinv.Rd
@@ -2,10 +2,10 @@
 \alias{trIrhoWinv}
 
 \title{
-Compute trace of (I-rho*W)^{-1} matrix
+Compute trace of (I-rho*W)^\{-1\} matrix
 }
 \description{
-This function computes (or estimates) the trace of matrix (I-rho*W)^{-1},
+This function computes (or estimates) the trace of matrix (I-rho*W)^\{-1\},
 which is often needed when computing impacts in some spatial econometrics 
 models.
 }
@@ -21,7 +21,7 @@ Adjacency matrix. Usually, it is row-standardised.
 Value of spatial autocorrelation parameter \code{rho}.
 }
   \item{offset}{
-Number of times (I-rho*W)^{-1} is multiplied by W (for sdm model).
+Number of times (I-rho*W)^\{-1\} is multiplied by W (for sdm model).
 }
   \item{order}{
 Order of Taylor expansion used in the approximation of the trace.
@@ -35,7 +35,7 @@ only used if direct=TRUE.
 }
 }
 \details{
-This function computes the trace of (I-rho*W)^{-1}, which is later used
+This function computes the trace of (I-rho*W)^\{-1\}, which is later used
 to computed the impacts. This is an internal function.
 }
 \value{
@@ -46,7 +46,7 @@ LeSage and Page (2008)
 Bivand et al. (2013)
 }
 \author{
-Virgilio Gómez-Rubio <virgilio.gomez@uclm.es>
+Virgilio Gómez-Rubio <virgilio.gomez@uclm.es>
 }
 %%\note{
 %%  ~~further notes~~