References updated to report v1.1, package version set to v1.0.0

DESCRIPTION

@@ -1,16 +1,17 @@
 Package: lemna
 Title: Lemna Ecotox Effect Model
-Version: 0.9.2
+Version: 1.0.0
 Authors@R: c(
     person("Nils", "Kehrein", , "[email protected]", c("aut", "cre")),
     person("SETAC Europe IG Effect Modeling", role="ccp")
     )
-Description: An implementation of model equations and default parameters for the
-    toxicokinetic-toxicodynamic (TKTD) model of the Lemna (duckweed) aquatic
-    plant. Lemna is a standard test macrophyte used in ecotox effect studies.
-    The model was described and published by the SETAC Europe Interest Group
-    Effect Modeling. It is a refined description of the Lemna TKTD model
-    published by Schmitt et al. (2013) <doi:10.1016/j.ecolmodel.2013.01.017>.
+Description: The reference implementation of model equations and default
+    parameters for the toxicokinetic-toxicodynamic (TKTD) model of the Lemna
+    (duckweed) aquatic plant. Lemna is a standard test macrophyte used in ecotox
+    effect studies. The model was described and published by the SETAC Europe
+    Interest Group Effect Modeling. It is a refined description of the Lemna
+    TKTD model published by Schmitt et al. (2013)
+    <doi:10.1016/j.ecolmodel.2013.01.017>.
 URL: https://github.com/nkehrein/lemna
 BugReports: https://github.com/nkehrein/lemna/issues
 License: MIT + file LICENSE

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2021
+YEAR: 2022
 COPYRIGHT HOLDER: Nils Kehrein

LICENSE.md

@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2021 Nils Kehrein
+Copyright (c) 2022 Nils Kehrein
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

NEWS.md

@@ -1,3 +1,14 @@
+# lemna 1.0.0
+
+* Documentation adapted to reference report version 1.1
+* Added a warning message in case removed parameter `BM_threshold` is used
+
+# lemna 0.9.2
+
+* Minor adaption of the biomass ODE according to the draft report version 1.1,
+  handling of low biomass densities was simplified to use only one parameter,
+  `BM_min`
+
 # lemna 0.9.1
 
 * Documentation improved and typos fixed

R/lemna.R

@@ -121,11 +121,12 @@
 #' @export
 #'
 #' @references
-#' Klein J., Cedergreen N., Heine S., Reichenberger S., Rendal C.,
-#'   Schmitt W., Hommen U., 2021: Refined description of the *Lemna* TKTD growth model
-#'   based on *Schmitt et al.* (2013) – equation system and default parameters.
+#' Klein J., Cedergreen N., Heine S., Kehrein N., Reichenberger S., Rendal C.,
+#'   Schmitt W., Hommen U., 2022: Refined description of the *Lemna* TKTD growth model
+#'   based on *Schmitt et al.* (2013) – equation system and default parameters,
+#'   implementation in R.
 #'   Report of the working group *Lemna* of the SETAC Europe Interest Group Effect
-#'   Modeling. Version 1, uploaded on 22. Sept. 2021.
+#'   Modeling. Version 1.1, uploaded on 09 May 2022.
 #'   <https://www.setac.org/group/SEIGEffectModeling>
 #'
 #' @examples

R/param.R

@@ -1,6 +1,6 @@
 #' Default parameters
 #'
-#' Returns the default Lemna model parameters as reported by Klein et al. (2021).
+#' Returns the default Lemna model parameters as reported by Klein *et al.* (2022).
 #'
 #' ## Model parameters
 #'
@@ -50,11 +50,12 @@
 #' @export
 #'
 #' @references
-#' Klein J., Cedergreen N., Heine S., Reichenberger S., Rendal C.,
-#'   Schmitt W., Hommen U., 2021: Refined description of the *Lemna* TKTD growth model
-#'   based on *Schmitt et al.* (2013) – equation system and default parameters.
+#' Klein J., Cedergreen N., Heine S., Kehrein N., Reichenberger S., Rendal C.,
+#'   Schmitt W., Hommen U., 2022: Refined description of the *Lemna* TKTD growth model
+#'   based on *Schmitt et al.* (2013) – equation system and default parameters,
+#'   implementation in R.
 #'   Report of the working group *Lemna* of the SETAC Europe Interest Group Effect
-#'   Modeling. Version 1, uploaded on 22. Sept. 2021.
+#'   Modeling. Version 1.1, uploaded on 09 May 2022.
 #'   <https://www.setac.org/group/SEIGEffectModeling>
 #'
 #' @examples

README.Rmd

@@ -26,8 +26,9 @@ It implements model equations and default parameters to simulate the
 toxicokinetic-toxicodynamic (TKTD) model of the *Lemna* aquatic plant.
 *Lemna* is a standard test macrophyte used in ecotox effect studies. The model
 was described and published by the *SETAC Europe Interest Group Effect Modeling*
-(Klein *et al.* 2021). It is a refined description of the *Lemna* TKTD model
-published by Schmitt *et al.* (2013).
+(Klein *et al.* 2022). It is a refined description of the *Lemna* TKTD model
+published by Schmitt *et al.* (2013). This package contains the model's reference
+implementation which is provided by the *SETAC* interest group.
 
 
 ## Installation
@@ -81,11 +82,12 @@ If you find any issues or bugs within the package, please create a
 
 ## References
 
-- Klein J., Cedergreen N., Heine S., Reichenberger S., Rendal C.,
-  Schmitt W., Hommen U., 2021: Refined description of the *Lemna* TKTD growth model
-  based on *Schmitt et al.* (2013) – equation system and default parameters.
+- Klein J., Cedergreen N., Heine S., Kehrein N., Reichenberger S., Rendal C.,
+  Schmitt W., Hommen U., 2022: Refined description of the *Lemna* TKTD growth model
+  based on *Schmitt et al.* (2013) – equation system and default parameters,
+  implementation in R.
   Report of the working group *Lemna* of the SETAC Europe Interest Group Effect
-  Modeling. Version 1, uploaded on 22. Sept. 2021.
+  Modeling. Version 1.1, uploaded on 09 May 2022.
   https://www.setac.org/group/SEIGEffectModeling
 - Schmitt W., Bruns E., Dollinger M., Sowig P., 2013: Mechanistic TK/TD-model
   simulating the effect of growth inhibitors on *Lemna* populations. Ecol Model

README.md

@@ -14,8 +14,10 @@ default parameters to simulate the toxicokinetic-toxicodynamic (TKTD)
 model of the *Lemna* aquatic plant. *Lemna* is a standard test
 macrophyte used in ecotox effect studies. The model was described and
 published by the *SETAC Europe Interest Group Effect Modeling* (Klein
-*et al.* 2021). It is a refined description of the *Lemna* TKTD model
-published by Schmitt *et al.* (2013).
+*et al.* 2022). It is a refined description of the *Lemna* TKTD model
+published by Schmitt *et al.* (2013). This package contains the model’s
+reference implementation which is provided by the *SETAC* interest
+group.
 
 ## Installation
 
@@ -80,12 +82,13 @@ issue](https://github.com/nkehrein/lemna/issues) on GitHub.
 
 ## References
 
--   Klein J., Cedergreen N., Heine S., Reichenberger S., Rendal C.,
-    Schmitt W., Hommen U., 2021: Refined description of the *Lemna* TKTD
-    growth model based on *Schmitt et al.* (2013) – equation system and
-    default parameters. Report of the working group *Lemna* of the SETAC
-    Europe Interest Group Effect Modeling. Version 1, uploaded on 22.
-    Sept. 2021. <https://www.setac.org/group/SEIGEffectModeling>
+-   Klein J., Cedergreen N., Heine S., Kehrein N., Reichenberger S.,
+    Rendal C., Schmitt W., Hommen U., 2022: Refined description of the
+    *Lemna* TKTD growth model based on *Schmitt et al.* (2013) –
+    equation system and default parameters, implementation in R. Report
+    of the working group *Lemna* of the SETAC Europe Interest Group
+    Effect Modeling. Version 1.1, uploaded on 09 May 2022.
+    <https://www.setac.org/group/SEIGEffectModeling>
 -   Schmitt W., Bruns E., Dollinger M., Sowig P., 2013: Mechanistic
     TK/TD-model simulating the effect of growth inhibitors on *Lemna*
     populations. Ecol Model 255, pp. 1-10. DOI:

dev/release.R

@@ -14,7 +14,7 @@ devtools::document()
 devtools::install(upgrade="never", quick=TRUE)
 devtools::build_vignettes(quiet=FALSE, install=FALSE)
 if(!dir.exists("docs")) dir.create("docs")
-file.copy(list.files("doc", pattern="*.html", full.names=TRUE), "docs")
+file.copy(list.files("doc", pattern="\\.html$", full.names=TRUE), "docs", recursive=TRUE)
 unlink("doc", recursive = TRUE)
 
 # build package files