Release version 3.1.3

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: abn
 Title: Modelling Multivariate Data with Additive Bayesian Networks
-Version: 3.1.2
-Date: 2024-08-07
+Version: 3.1.3
+Date: 2024-09-18
 Authors@R: c(
     person("Matteo", "Delucchi", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-9327-1496")),

NEWS.md

@@ -1,4 +1,11 @@
 
+# abn 3.1.3
+[diff](https://github.com/furrer-lab/abn/compare/3.1.2...3.1.3)
+
+> 2024-09-18
+
+* JOSS paper final edits ([#152](https://github.com/furrer-lab/abn/issues/152))
+
 # abn 3.1.2
 [diff](https://github.com/furrer-lab/abn/compare/3.1.1...3.1.2)
 

R/abn-package.R

@@ -21,13 +21,15 @@
 #' See also the files provided in the package directories \code{inst/bootstrapping_example} and \code{inst/old_vignette} for more details.
 #'
 #' @references
-#' Kratzer, Gilles, Fraser Lewis, Arianna Comin, Marta Pittavino, and Reinhard Furrer. “Additive Bayesian Network Modeling with the R Package Abn.” Journal of Statistical Software 105 (January 28, 2023): 1–41. https://doi.org/10.18637/jss.v105.i08.
+#' Kratzer G, Lewis F, Comin A, Pittavino M, Furrer R (2023). “Additive Bayesian Network Modeling with the R Package abn.” Journal of Statistical Software, 105(8), 1-41. https://doi.org/10.18637/jss.v105.i08.
 #'
-#' Kratzer, G., Lewis, F.I., Comin, A., Pittavino, M. and Furrer, R. (2019). "Additive Bayesian Network Modelling with the R Package abn". arXiv preprint arXiv:1911.09006.
+#' Delucchi M, Liechti J, Spinner G, Furrer R (2024). “abn: Additive Bayesian Networks.” Journal of Open Source Software, Accepted for publication. R package version 3.1.3, https://joss.theoj.org/papers/1bbc43a2be86f5d3f831cedb5cf81812.
 #'
 #' Lewis, F. I., and Ward, M. P. (2013). "Improving epidemiologic data analyses through multivariate regression modeling". Emerging themes in epidemiology, 10(1), 4.
 #'
-#' Kratzer, G., Pittavino, M, Lewis, F. I., and Furrer, R., (2017). "abn: an R package for modelling multivariate data using additive Bayesian networks". R package version 2.2.  https://CRAN.R-project.org/package=abn
+#' Kratzer, G., Lewis, F.I., Willi, B., Meli, M.L., Boretti, F.S., Hofmann-Lehmann, R., Torgerson, P., Furrer, R. and Hartnack, S. (2020). "Bayesian Network Modeling Applied to Feline Calicivirus Infection Among Cats in Switzerland". Frontiers in Veterinary Science, 7, 73.
+#'
+#' Delucchi M, Furrer R, Kratzer G, Lewis F, Liechti J, Pittavino M, Cherneva K (2024). "abn: Modelling Multivariate Data with Additive Bayesian Networks". R package version 3.1.3, https://CRAN.R-project.org/package=abn.
 #'
 #' @examples
 #' ## Citations:

README.md

@@ -5,7 +5,7 @@
 <!-- WARNING: -->
 <!-- The ?branch=release-x.y.y is updated automatically by the initiate_version_release workflow -->
 [![status](https://joss.theoj.org/papers/1bbc43a2be86f5d3f831cedb5cf81812/status.svg)](https://joss.theoj.org/papers/1bbc43a2be86f5d3f831cedb5cf81812)
-[![On Label CRAN Checks](https://github.com/furrer-lab/abn/actions/workflows/onlabel_CRAN_checks.yml/badge.svg?branch=release-3.1.2)](https://github.com/furrer-lab/abn/actions/workflows/onlabel_CRAN_checks.yml)
+[![On Label CRAN Checks](https://github.com/furrer-lab/abn/actions/workflows/onlabel_CRAN_checks.yml/badge.svg?branch=release-3.1.3)](https://github.com/furrer-lab/abn/actions/workflows/onlabel_CRAN_checks.yml)
 [![Codecov](https://img.shields.io/codecov/c/github/furrer-lab/abn)](https://app.codecov.io/gh/furrer-lab/abn)
 [![GitHub R package version](https://img.shields.io/github/r-package/v/furrer-lab/abn)](https://github.com/furrer-lab/abn/tags)
 ![cran](https://www.r-pkg.org/badges/version-ago/abn) 
@@ -161,7 +161,7 @@ All you need for the installation is to have the R-package [pak](https://pak.r-l
   brew install [email protected]
   ```
 
-  #### Dependencies
+  <ins>**Dependencies**</ins>
 
   On MacOS we need to install some system dependencies separately:
 
@@ -230,7 +230,7 @@ All you need for the installation is to have the R-package [pak](https://pak.r-l
   ```
 
 
-  #### Dependencies
+  <ins>**Dependencies**</ins>
 
   On Windows we need to install some system dependencies separately:
 
@@ -243,7 +243,7 @@ All you need for the installation is to have the R-package [pak](https://pak.r-l
     In Windows `GSL` is available a.o. through [cygwin](https://cygwin.com/index.html), which has a straight forward installation process.
     Either head over to the website, download and install the `setup-x86_64.exe` file or use PowerShell:
 
-    ```
+    ```powershell
     Import-Module bitstransfer
     New-Item -ItemType Directory -Force -Path "C:\Program Files\cygwin"
     start-bitstransfer -source https://cygwin.com/setup-x86_64.exe "C:\Program Files\cygwin\setup-x86_64.exe"
@@ -259,7 +259,7 @@ All you need for the installation is to have the R-package [pak](https://pak.r-l
     You can either head over to the [JAGS download page](https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Windows/), download and execute the installable, or use PowerShell.
     The following instructions will download and install `JAGS 4.3.1` in PowerShell:
 
-    ```
+    ```powershell
     Import-Module bitstransfer
     New-Item -ItemType Directory -Force -Path "C:\Program Files\JAGS\JAGS-4.3.1"
     start-bitstransfer -source https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Windows/JAGS-4.3.1.exe/download  "C:\Program Files\JAGS\JAGS-4.3.1\JAGS-4.3.1.exe"

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.71 for abn 3.1.2.
+# Generated by GNU Autoconf 2.71 for abn 3.1.3.
 #
 #
 # Copyright (C) 1992-1996, 1998-2017, 2020-2021 Free Software Foundation,
@@ -607,8 +607,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='abn'
 PACKAGE_TARNAME='abn'
-PACKAGE_VERSION='3.1.2'
-PACKAGE_STRING='abn 3.1.2'
+PACKAGE_VERSION='3.1.3'
+PACKAGE_STRING='abn 3.1.3'
 PACKAGE_BUGREPORT=''
 PACKAGE_URL=''
 
@@ -1212,7 +1212,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures abn 3.1.2 to adapt to many kinds of systems.
+\`configure' configures abn 3.1.3 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1274,7 +1274,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of abn 3.1.2:";;
+     short | recursive ) echo "Configuration of abn 3.1.3:";;
    esac
   cat <<\_ACEOF
 
@@ -1342,7 +1342,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-abn configure 3.1.2
+abn configure 3.1.3
 generated by GNU Autoconf 2.71
 
 Copyright (C) 2021 Free Software Foundation, Inc.
@@ -1379,7 +1379,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by abn $as_me 3.1.2, which was
+It was created by abn $as_me 3.1.3, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   $ $0$ac_configure_args_raw
@@ -2368,7 +2368,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by abn $as_me 3.1.2, which was
+This file was extended by abn $as_me 3.1.3, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -2423,7 +2423,7 @@ ac_cs_config_escaped=`printf "%s\n" "$ac_cs_config" | sed "s/^ //; s/'/'\\\\\\\\
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config='$ac_cs_config_escaped'
 ac_cs_version="\\
-abn config.status 3.1.2
+abn config.status 3.1.3
 configured by $0, generated by GNU Autoconf 2.71,
   with options \\"\$ac_cs_config\\"
 

configure.ac

@@ -1,4 +1,4 @@
-AC_INIT([abn],[3.1.2])
+AC_INIT([abn],[3.1.3])
 
 ## Use gsl-config to find arguments for compiler and linker flags
 ##

inst/CITATION

@@ -1,3 +1,18 @@
+bibentry(bibtype = "Manual",
+    title = "abn: Modelling Multivariate Data with Additive Bayesian Networks",
+    author = c(person(given = "Matteo", family = "Delucchi", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9327-1496")),
+               person(given = "Reinhard", family = "Furrer", email = "[email protected]", role = "aut", comment = c(ORCID = "0000-0002-6319-2332")),
+               person(given = "Gilles", family = "Kratzer", email = "[email protected]", role = "aut", comment = c(ORCID = "0000-0002-5929-8935")),
+               person(given = "Fraser Iain", family = "Lewis", email = "[email protected]", role = "aut", comment = c(ORCID = "0000-0003-4580-2712")),
+               person(given = "Jonas I.", family = "Liechti", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0003-3447-3060")),
+               person(given = "Marta", family = "Pittavino", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0002-1232-1034")),
+               person(given = "Kalina", family = "Cherneva", email = "[email protected]", role = "ctb")),
+    year = "2024",
+    note = "R package version 3.1.3",
+    url = "https://CRAN.R-project.org/package=abn",
+    header = "To cite the software implementation of the R package 'abn' use:"
+)
+
 bibentry(bibtype = "Article",
   title        = "Additive Bayesian Network Modeling with the R Package abn",
   author       = c(person(given = "Gilles", family = "Kratzer"),
@@ -14,6 +29,20 @@ bibentry(bibtype = "Article",
   header       = "To cite the methodology of the R package 'abn' use:"
 )
 
+bibentry(bibtype = "Article",
+         title = "abn: Additive Bayesian Networks",
+         author = c(person(given = "Matteo", family = "Delucchi", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9327-1496")),
+                    person(given = "Jonas I.", family = "Liechti", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0003-3447-3060")),
+                    person(given = "Georg G.", family = "Spinner", role = "fnd", comment = c(ORCID = "0000-0001-9640-8155")),
+                    person(given = "Reinhard", family = "Furrer", email = "[email protected]", role = "aut", comment = c(ORCID = "0000-0002-6319-2332"))),
+          year = "2024",
+          journal = "Journal of Open Source Software",
+          volume = "Accepted for publication",
+          note = "R package version 3.1.3",
+          url = "https://joss.theoj.org/papers/1bbc43a2be86f5d3f831cedb5cf81812",
+          header = "To cite the application of mixed-effects ABN use:"
+)
+
 bibentry(bibtype = "Article",
   title        = "Bayesian Network Modeling Applied to Feline Calicivirus Infection Among Cats in Switzerland",
   author       = c(person(given = "Gilles", family = "Kratzer"),
@@ -31,17 +60,3 @@ bibentry(bibtype = "Article",
   textVersion  =
   paste("Kratzer, G., Lewis, F.I., Willi, B., Meli, M.L., Boretti, F.S., Hofmann-Lehmann, R., Torgerson, P., Furrer, R. and Hartnack, S. (2020). Bayesian Network Modeling Applied to Feline Calicivirus Infection Among Cats in Switzerland. Frontiers in Veterinary Science, 7, 73")
 )
-
-bibentry(bibtype = "Manual",
-    title = "abn: Modelling Multivariate Data with Additive Bayesian Networks",
-    author = c(person(given = "Reinhard", family = "Furrer"),
-                person(given = "Gilles", family = "Kratzer"),
-                person(given = "Fraser Iain", family = "Lewis")),
-    year = "2023",
-    note = "R package version 2.7-2",
-    url = "https://CRAN.R-project.org/package=abn",
-    header       = "To cite the software implementation of the R package 'abn' use:",
-  textVersion  =
-  paste("Furrer, R., Kratzer, G. and Lewis, F.I. (2023). abn: Modelling Multivariate Data with Additive Bayesian Networks. R package version 2.7-2.
-  https://CRAN.R-project.org/package=abn")
-)