added citations for bayesnec

open-AIMS · Aug 8, 2024 · 42f8b31 · 42f8b31
1 parent c06e59a
commit 42f8b31
Show file tree

Hide file tree

Showing 17 changed files with 102 additions and 14 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: bayesnec
 Title: A Bayesian No-Effect- Concentration (NEC) Algorithm
-Version: 2.1.2.0
-Authors@R: c(person("Rebecca", "Fisher", email = "r.fisher@aims.gov.au", role = c("aut", "cre")), person("Diego","Barneche",role="aut"), person("Gerard","Ricardo",role="aut"), person("David","Fox",role="aut"))
-Description: Implementation of No-Effect-Concentration estimation that uses 'brms' (see Burkner (2017)<doi:10.18637/jss.v080.i01>; Burkner (2018)<doi:10.32614/RJ-2018-017>; Carpenter 'et al.' (2017)<doi:10.18637/jss.v076.i01> to fit concentration(dose)-response data using Bayesian methods for the purpose of estimating 'ECx' values, but more particularly 'NEC' (see Fox (2010)<doi:10.1016/j.ecoenv.2009.09.012>), 'NSEC' (see Fisher and Fox (2023)<doi:10.1002/etc.5610>), and 'N(S)EC (see Fisher et al. 2023<doi:10.1002/ieam.4809>). This package expands and supersedes an original version implemented in R2jags, see Fisher, Ricardo and Fox (2020)<doi:10.5281/ZENODO.3966864>.
+Version: 2.1.3.0
+Authors@R: c(person("Rebecca", "Fisher", email = "r.fisher@aims.gov.au", role = c("aut", "cre")), person("Diego R.","Barneche",role="aut"), person("Gerard F.","Ricardo",role="aut"), person("David R.","Fox",role="aut"))
+Description: Implementation of No-Effect-Concentration estimation that uses 'brms' (see Burkner (2017)<doi:10.18637/jss.v080.i01>; Burkner (2018)<doi:10.32614/RJ-2018-017>; Carpenter 'et al.' (2017)<doi:10.18637/jss.v076.i01> to fit concentration(dose)-response data using Bayesian methods for the purpose of estimating 'ECx' values, but more particularly 'NEC' (see Fox (2010)<doi:10.1016/j.ecoenv.2009.09.012>), 'NSEC' (see Fisher and Fox (2023)<doi:10.1002/etc.5610>), and 'N(S)EC (see Fisher et al. 2023<doi:10.1002/ieam.4809>). A full description of this package can be found in Fisher 'et al.' (2024)<doi:10.18637/jss.v110.i05>. This package expands and supersedes an original version implemented in R2jags (see Su and Yajima (2020)<https://CRAN.R-project.org/package=R2jags>; Fisher et al. (2020)<doi:10.5281/ZENODO.3966864>).
 Depends:
     R (>= 4.1),
     brms,

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# bayesnec 2.1.3.0
+
+- Added citation for JSS manuscript describing `bayesnec`.
+
 # bayesnec 2.1.2.0
 
 - Added `step` function to toolkit to allow for `brms` non-linear formula evaluation ([89edef72](https://github.com/open-AIMS/bayesnec/commit/89edef72)).

diff --git a/R/bayesmanecfit-class.R b/R/bayesmanecfit-class.R
@@ -54,6 +54,10 @@
 #'   \code{\link{bayesnecfit}}
 #'
 #' @references
+#' Fisher R, Barneche DR, Ricardo GF, Fox, DR (2024) An {R} Package for
+#' Concentration-Response Modeling and Estimation of Toxicity Metrics
+#' doi:10.18637/jss.v110.i05.
+#' 
 #' Fisher R, Fox DR (2023). Introducing the no significant effect concentration 
 #' (NSEC).Environmental Toxicology and Chemistry, 42(9), 2019–2028. 
 #' doi: 10.1002/etc.5610.

diff --git a/R/bayesnec-package.R b/R/bayesnec-package.R
@@ -3,11 +3,12 @@
 #' @description A No-Effect toxicity estimation package that uses brms (Bürkner 
 #' (2018), https://github.com/paul-buerkner/brms) to fit concentration
 #' (dose)-response data using Bayesian methods for the purpose of estimating
-#' both Effect Concentration (ECx) values, but more particularly NEC, but more 
-#' particularly 'NEC' (Fox 2010), 'NSEC' (Fisher and Fox 2023), and 'N(S)EC 
-#' (Fisher et al. 2023). Please see ?bnec
-#' for more details.
-#'
+#' both Effect Concentration (ECx) values, but more particularly 'NEC'
+#' (Fox 2010), 'NSEC' (Fisher and Fox 2023), and 'N(S)EC (Fisher et al. 2023).
+#' A full description of bayesnec can be found in Fisher et al. (2024).
+#' Please see ?bnec for more details. This package expands and supersedes an
+#' original version implemented in R2jags (Su and Yajima 2020), see Fisher et
+#  al. (2020).
 #' @docType package
 #' @name bayesnec-package
 #' @aliases bayesnec
@@ -18,6 +19,10 @@
 #' Bürkner P-C (2018) Advanced Bayesian Multilevel Modeling with the R Package
 #' brms. The R Journal, 10: 395-411. doi:10.32614/RJ-2018-017.
 #' 
+#' Fisher R, Barneche DR, Ricardo GF, Fox, DR (2024) An {R} Package for
+#' Concentration-Response Modeling and Estimation of Toxicity Metrics
+#' doi:10.18637/jss.v110.i05.
+#' 
 #' Fisher R, Fox DR (2023). Introducing the no significant effect concentration 
 #' (NSEC).Environmental Toxicology and Chemistry, 42(9), 2019–2028. 
 #' doi: 10.1002/etc.5610.
@@ -26,6 +31,12 @@
 #' estimating no-effect toxicity concentrations in ecotoxicology. Integrated 
 #' Environmental Assessment and Management. doi:10.1002/ieam.4809.
 #' 
+#' Fisher R, Ricardo GF, Fox, DR (2020) jagsNEC: A Bayesian No Effect
+#' Concentration (NEC) package. doi:10.5281/ZENODO.3966864.
+#' 
+#' Su Y, Yajima M (2020). R2jags: Using R to Run 'JAGS'. R package version
+#' 0.6-1, <https://CRAN.R-project.org/package=R2jags>.
+#' 
 #' Fox DR (2010). A Bayesian Approach for Determining the No Effect
 #' Concentration and Hazardous Concentration in Ecotoxicology. Ecotoxicology
 #' and Environmental Safety, 73(2), 123–131. doi: 10.1016/j.ecoenv.2009.09.012.

diff --git a/R/bayesnecfit-class.R b/R/bayesnecfit-class.R
@@ -56,6 +56,10 @@
 #'   \code{\link{bayesnecformula}}
 #'
 #' @references
+#' Fisher R, Barneche DR, Ricardo GF, Fox, DR (2024) An {R} Package for
+#' Concentration-Response Modeling and Estimation of Toxicity Metrics
+#' doi:10.18637/jss.v110.i05.
+#' 
 #' Fisher R, Fox DR (2023). Introducing the no significant effect concentration 
 #' (NSEC).Environmental Toxicology and Chemistry, 42(9), 2019–2028. 
 #' doi: 10.1002/etc.5610.

diff --git a/R/bnec.R b/R/bnec.R
@@ -177,6 +177,10 @@
 #'   \code{\link{show_params}}
 #'   
 #' @references
+#' Fisher R, Barneche DR, Ricardo GF, Fox, DR (2024) An {R} Package for
+#' Concentration-Response Modeling and Estimation of Toxicity Metrics
+#' doi:10.18637/jss.v110.i05.
+#'
 #' Fisher R, Fox DR (2023). Introducing the no significant effect concentration 
 #' (NSEC).Environmental Toxicology and Chemistry, 42(9), 2019–2028. 
 #' doi: 10.1002/etc.5610.

diff --git a/R/manecsummary-class.R b/R/manecsummary-class.R
@@ -46,6 +46,10 @@
 #'   \code{\link{necsummary}}
 #'
 #' @references
+#' Fisher R, Barneche DR, Ricardo GF, Fox, DR (2024) An {R} Package for
+#' Concentration-Response Modeling and Estimation of Toxicity Metrics
+#' doi:10.18637/jss.v110.i05.
+#' 
 #' Fisher R, Fox DR (2023). Introducing the no significant effect concentration 
 #' (NSEC).Environmental Toxicology and Chemistry, 42(9), 2019–2028. 
 #' doi: 10.1002/etc.5610.

diff --git a/R/necsummary-class.R b/R/necsummary-class.R
@@ -38,6 +38,10 @@
 #'   \code{\link{manecsummary}}
 #'
 #' @references
+#' Fisher R, Barneche DR, Ricardo GF, Fox, DR (2024) An {R} Package for
+#' Concentration-Response Modeling and Estimation of Toxicity Metrics
+#' doi:10.18637/jss.v110.i05.
+#' 
 #' Fisher R, Fox DR (2023). Introducing the no significant effect concentration 
 #' (NSEC).Environmental Toxicology and Chemistry, 42(9), 2019–2028. 
 #' doi: 10.1002/etc.5610.

diff --git a/README.Rmd b/README.Rmd
@@ -81,5 +81,5 @@ individual functions can be found on the
 ## Further Information
 
 `bayesnec` is provided by the
-[Australian Institute of Marine Science](https://www.aims.gov.au) under the
+[Australian Institute of Marine Science](https://www.aims.gov.au/) under the
 GPL-2 License ([GPL-2](https://opensource.org/license/gpl-2-0)).
diff --git a/README.md b/README.md
@@ -66,5 +66,5 @@ Further Information
 -------------------
 
 `bayesnec` is provided by the [Australian Institute of Marine
-Science](https://www.aims.gov.au) under the GPL-2 License
+Science](https://www.aims.gov.au/) under the GPL-2 License
 ([GPL-2](https://opensource.org/license/gpl-2-0)).
diff --git a/inst/CITATION b/inst/CITATION
@@ -0,0 +1,22 @@
+bibentry(bibtype = "Article",
+  title        = "{bayesnec}: An {R} Package for Concentration-Response Modeling and Estimation of Toxicity Metrics",
+  author       = c(person(given = "Rebecca",
+                          family = "Fisher",
+                          email = "r.fisher@aims.gov.au"),
+                   person(given = c("Diego", "R."),
+                          family = "Barneche",
+                          email = "d.barneche@aims.gov.au"),
+                   person(given = c("Gerard", "F."),
+                          family = "Ricardo",
+                          email = "g.ricardo@uq.edu.au"),
+                   person(given = c("David", "R."),
+                          family = "Fox",
+                          email = "david.fox@environmetrics.net.au")),
+  journal      = "Journal of Statistical Software",
+  year         = "2024",
+  volume       = "110",
+  number       = "5",
+  pages        = "1--41",
+  doi          = "10.18637/jss.v110.i05",
+  header       = "To cite bayesnec in publications use:"
+)
diff --git a/man/bayesmanecfit-class.Rd b/man/bayesmanecfit-class.Rd
diff --git a/man/bayesnec-package.Rd b/man/bayesnec-package.Rd
diff --git a/man/bayesnecfit-class.Rd b/man/bayesnecfit-class.Rd
diff --git a/man/bnec.Rd b/man/bnec.Rd
diff --git a/man/manecsummary-class.Rd b/man/manecsummary-class.Rd
diff --git a/man/necsummary-class.Rd b/man/necsummary-class.Rd