From 42f8b31021537aba7dfc238b88478a6f6fc58175 Mon Sep 17 00:00:00 2001 From: Diego Barneche Date: Thu, 8 Aug 2024 10:41:16 -0700 Subject: [PATCH] added citations for bayesnec --- DESCRIPTION | 6 +++--- NEWS.md | 4 ++++ R/bayesmanecfit-class.R | 4 ++++ R/bayesnec-package.R | 21 ++++++++++++++++----- R/bayesnecfit-class.R | 4 ++++ R/bnec.R | 4 ++++ R/manecsummary-class.R | 4 ++++ R/necsummary-class.R | 4 ++++ README.Rmd | 2 +- README.md | 2 +- inst/CITATION | 22 ++++++++++++++++++++++ man/bayesmanecfit-class.Rd | 4 ++++ man/bayesnec-package.Rd | 19 +++++++++++++++---- man/bayesnecfit-class.Rd | 4 ++++ man/bnec.Rd | 4 ++++ man/manecsummary-class.Rd | 4 ++++ man/necsummary-class.Rd | 4 ++++ 17 files changed, 102 insertions(+), 14 deletions(-) create mode 100644 inst/CITATION diff --git a/DESCRIPTION b/DESCRIPTION index 498805ab..082f3b28 100644 --- 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); Burkner (2018); Carpenter 'et al.' (2017) to fit concentration(dose)-response data using Bayesian methods for the purpose of estimating 'ECx' values, but more particularly 'NEC' (see Fox (2010)), 'NSEC' (see Fisher and Fox (2023)), and 'N(S)EC (see Fisher et al. 2023). This package expands and supersedes an original version implemented in R2jags, see Fisher, Ricardo and Fox (2020). +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); Burkner (2018); Carpenter 'et al.' (2017) to fit concentration(dose)-response data using Bayesian methods for the purpose of estimating 'ECx' values, but more particularly 'NEC' (see Fox (2010)), 'NSEC' (see Fisher and Fox (2023)), and 'N(S)EC (see Fisher et al. 2023). A full description of this package can be found in Fisher 'et al.' (2024). This package expands and supersedes an original version implemented in R2jags (see Su and Yajima (2020); Fisher et al. (2020)). Depends: R (>= 4.1), brms, diff --git a/NEWS.md b/NEWS.md index 49e3f215..8f8a7b45 100644 --- 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 index 3e05d130..60d74a99 100644 --- 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 index 3ad77989..be83a8f4 100644 --- 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, . +#' #' 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 index 060f3826..a7adf50d 100644 --- 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 index 82780671..3fb418f0 100644 --- 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 index dee3088c..83240345 100644 --- 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 index 937e9f48..50c4eef4 100644 --- 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 index c66c0d53..803777c0 100644 --- 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 index 6e29e739..965b6264 100644 --- 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 new file mode 100644 index 00000000..e4fd1347 --- /dev/null +++ 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 index d12e1da5..c06c115e 100644 --- a/man/bayesmanecfit-class.Rd +++ b/man/bayesmanecfit-class.Rd @@ -65,6 +65,10 @@ and NSEC estimates, and is reported as the \code{N(S)EC} }} \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/man/bayesnec-package.Rd b/man/bayesnec-package.Rd index 5e41f0f4..951dcae7 100644 --- a/man/bayesnec-package.Rd +++ b/man/bayesnec-package.Rd @@ -9,15 +9,20 @@ 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 } \references{ 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 @@ Fisher R, Fox DR, Negri AP, van Dam J, Flores F, Koppel D (2023). Methods for 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, \url{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/man/bayesnecfit-class.Rd b/man/bayesnecfit-class.Rd index e8066a57..f0d1ac50 100644 --- a/man/bayesnecfit-class.Rd +++ b/man/bayesnecfit-class.Rd @@ -74,6 +74,10 @@ a no-significant-effect-concentration (\code{NSEC}, see Fisher and Fox 2023).} }} \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/man/bnec.Rd b/man/bnec.Rd index 27d831e1..fd8a95a8 100644 --- a/man/bnec.Rd +++ b/man/bnec.Rd @@ -218,6 +218,10 @@ exmp_b <- bnec(y ~ crf(x, model = c("nec4param", "ecx4param")), } \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/man/manecsummary-class.Rd b/man/manecsummary-class.Rd index 0b91fedf..8472b97f 100644 --- a/man/manecsummary-class.Rd +++ b/man/manecsummary-class.Rd @@ -55,6 +55,10 @@ model exhibited convergence issues based on the Rhat evaluation.} }} \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/man/necsummary-class.Rd b/man/necsummary-class.Rd index ff5b2b6c..cf9568e1 100644 --- a/man/necsummary-class.Rd +++ b/man/necsummary-class.Rd @@ -42,6 +42,10 @@ should the user decide to calculate them (see the non-exported }} \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.