MindTheGap-ERC · NiklasHohmann · Aug 26, 2024 · Jul 17, 2024 · Jul 18, 2024 · Aug 26, 2024
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: admtools
 Title: Estimate and Manipulate Age-Depth Models
-Version: 0.3.0.9000
+Version: 0.3.0
 Authors@R: 
     person("Niklas", "Hohmann", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-1559-1838"))

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,7 @@
 # admtools (development version)
 
+# admtools 0.3.0
+
 * removed dependency from `ape` package
 
 * defined S3 class `timelist` and `stratlist` for data assiciated with time/height

diff --git a/R/CarboCatLite_data.R b/R/CarboCatLite_data.R
@@ -2,7 +2,7 @@
 #' @title Example data from CarboCATLite
 #' 
 #' @description
-#' Data exported from CarboCATLite model run
+#' Data exported from CarboCATLite model run, equivalent to scenario A from Hohmann et al. (2024). See therein for details.
 #' 
 #' @format A list with the following fields:
 #'  * _time_myr_ : time points in Myr from the model run
@@ -20,6 +20,8 @@
 #' @references
   #' * Burgess, Peter. "CarboCAT: A cellular automata model of heterogeneous carbonate strata." Computers & geosciences 53 (2013): 129-140. \doi{10.1016/j.cageo.2011.08.026}
   #' * Burgess, Peter. (2023). CarboCATLite (v1.0.1). Zenodo. \doi{10.5281/zenodo.8402578}
+  #' * Hohmann, Niklas; Koelewijn, Joël R.; Burgess, Peter; Jarochowska, Emilia. 2024. "Identification of the mode of evolution in incomplete carbonate successions." BMC Ecology and Evolution 24, 113. \doi{10.1186/s12862-024-02287-2}.
+#' * Hohmann, Niklas, Koelewijn, Joël R.; Burgess, Peter; Jarochowska, Emilia. 2023. “Identification of the Mode of Evolution in Incomplete Carbonate Successions - Supporting Data.” Open Science Framework. \doi{10.17605/OSF.IO/ZBPWA}, published under the [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) license.
 
 
 "CarboCATLite_data"
diff --git a/README.md b/README.md
@@ -13,7 +13,7 @@ R package to estimate age-depth models from stratigraphic and sedimentological d
 
 __Niklas Hohmann__  
 Utrecht University  
-email: n.hohmann [at] uu.nl  
+email: n.h.hohmann [at] uu.nl  
 Web page: [uu.nl/staff/NHohmann](https://www.uu.nl/staff/NHHohmann)  
 Orcid: [0000-0003-1559-1838](https://orcid.org/0000-0003-1559-1838)
 
@@ -90,12 +90,24 @@ To cite the package, use
 or run
 
 ```R
-citation("admtools)
+citation("admtools")
 ```
 
 in R. Alternatively, you can use the information in the CITATION.cff file, or generate it using the "cite this repository" button on GitHub.
 
+## References
+
+This package uses data from
+
+-   Hohmann, Niklas; Koelewijn, Joël R.; Burgess, Peter; Jarochowska, Emilia. 2024. "Identification of the mode of evolution in incomplete carbonate successions." BMC Ecology and Evolution, **24**, 113. [DOI: 10.1186/s12862-024-02287-2](https://doi.org/10.1186/s12862-024-02287-2).
+
+-   Hohmann, Niklas, Koelewijn, Joël R.; Burgess, Peter; Jarochowska, Emilia. 2023. "Identification of the Mode of Evolution in Incomplete Carbonate Successions - Supporting Data." Open Science Framework. <https://doi.org/10.17605/OSF.IO/ZBPWA>, published under the [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) license.
+
 ## Funding information
 
+The authors acknowledge the contribution of the CycloNet project, funded by the Research Foundation Flanders (FWO, grant no. W000522N)
+
 Funded by the European Union (ERC, MindTheGap, StG project no 101041077). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them.
 ![European Union and European Research Council logos](https://erc.europa.eu/sites/default/files/2023-06/LOGO_ERC-FLAG_FP.png)
+
+
diff --git a/inst/CITATION b/inst/CITATION
@@ -1,7 +1,10 @@
 bibentry(
   bibtype  = "Misc",
-  title    = "admtools package for R",
+  title    = "admtools: R package for estimating age-depth models and transform data",
   author   = "Niklas Hohmann",
-  year     = "2023",
-  doi      ="10.5281/zenodo.10213587"
+  year     = "2024",
+  doi      ="10.5281/zenodo.12761132",
+  publisher = "Zenodo",
+  version = "v0.3.0",
+  url = "https://zenodo.org/records/12761132"
 )
diff --git a/man/CarboCATLite_data.Rd b/man/CarboCATLite_data.Rd
diff --git a/vignettes/adm_plotting.Rmd b/vignettes/adm_plotting.Rmd
@@ -2,7 +2,7 @@
 title: "Plotting Age-Depth Models"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{adm_plotting}
+  %\VignetteIndexEntry{Plotting Age-Depth Models}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---

diff --git a/vignettes/admtools.Rmd b/vignettes/admtools.Rmd
@@ -27,6 +27,14 @@ This vignette is an introduction to the *admtools* package.
 
 ### From GitHub
 
+### From CRAN
+
+To install the package from *CRAN*, run
+
+```{r, eval=FALSE}
+install.packages("admtools")
+```
+
 To install the package from *GitHub*, first install the *remotes* package:
 
 ```{r, eval=FALSE}
@@ -43,22 +51,7 @@ remotes::install_github(repo = "MindTheGap-ERC/admtools",
                         dependencies = TRUE)
 ```
 
-to install the latest stable release. To install the version under development, use
-
-```{r, eval=FALSE}
-remotes::install_github(repo = "MindTheGap-ERC/admtools",
-                        build_vignettes = TRUE,
-                        ref = "dev",
-                        dependencies = TRUE)
-```
-
-### From CRAN
-
-To install the package from CRAN, run
-
-```{r, eval=FALSE}
-install.packages("admtools")
-```
+to install the latest stable version.
 
 ## Loading the package
 
@@ -104,12 +97,14 @@ In contrast to its name, the *admtools* package currently deals with time and he
 
 ## Example
 
-This example explains the construction and application of `adm` objects. As example data we use outputs from CarboCAT Lite, a model of carbonate platform growth (Burgess 2013, 2023). This data is automatically loaded in the background by the package. To get some info of the data use
+This example explains the construction and application of `adm` objects. As example data we use outputs from CarboCAT Lite, a model of carbonate platform growth [(Burgess 2013, 2023)](#References). This data is automatically loaded in the background by the package. To get some info of the data use
 
 ```{r, eval=FALSE}
 ?CarboCATLite_data
 ```
 
+This data is identical to scenario A from [Hohmann et al. (2024)](#References) as published in [Hohmann et al. (2023)](#References). See therein for details on the simulation, reproducibility, and a chronostratigraphic chart and a figure showing a transect through the carbonate platform.
+
 ### Defining age-depth models
 
 The standard constructor for age-depth models is `tp_to_adm` ("tiepoint to age-depth model"). It returns an objecto of class `adm`. This object combines information of stratigraphic heights and times and erosive interval. It allows to transform data between the stratigraphic and the time domain, and identify which data is destroyed due to hiatuses.
@@ -167,7 +162,7 @@ plot_sed_rate_t(my_adm)
 
 For more information on the extraction of sedimentation rates xin the time domain see the functions `sed_rate_t` and `sed_rate_t_fun`. Sedimentation rates in the length domain can be extracted using `sed_rate_l` and `sed_rate_l_fun` and plotted via `plot_sed_rate_l`. In addition, condensation (time preserved per stratigraphic increment) can be examined using the functions `condensation`, `condensation_fun` and `plot_condensation`.
 
-### Extracting data from age-depth models
+## Extracting data from age-depth models
 
 Use the functions `get_total_duration`, `get_total_thickness`, `get_completeness`, and `get_hiat_no` to extract information:
 
@@ -234,6 +229,8 @@ get_height(my_adm,
            destructive = FALSE)
 ```
 
+Alternatively, you can also use the wrappers `strat_to_time` and `time_to_strat` for the transformation. For expanded modeling features please use the `StratPal` package ([Github](https://github.com/MindTheGap-ERC/StratPal) | [Webpage](https://mindthegap-erc.github.io/StratPal/) |  [CRAN](https://cran.r-project.org/package=StratPal)). It provides more biological context and utility functions to build modeling pipelines that include ecological, taphonomic, stratigraphic, and evolutionary effects.
+
 #### Phylogenetic trees
 
 The `admtools` package can transform complex objects between the time and stratigraphic domain. This is done using the functions `strat_to_time` and `time_to_strat`.
@@ -257,7 +254,7 @@ tree_in_strat_domain = time_to_strat(obj = timetree,
                                      x = my_adm)
 ```
 
-Plotting the resulting tree along the tratigraphic column shows how the evolutinoary relationships would be preserved 2 km offshore in the simulated carbonate platform:
+Plotting the resulting tree along the tratigraphic column shows how the evolutionary relationships would be preserved 2 km offshore in the simulated carbonate platform:
 
 ```{r}
 ape::plot.phylo(tree_in_strat_domain, direction = "upwards")
@@ -269,7 +266,7 @@ mtext("Stratigraphic Height [m]",
 
 #### Lists and time/stratigraphic series
 
-*admtools* can transfrom lists from the time to the height domain and vice versa given they have elements with names `h` or `t`. These lists can be interpreted as time/stratigraphic series, where times and stratigraphic positions are associated with measured values. Note that these are not `t` objects as used by the `stats` package, as they will be generally heterodistant due to hte irregular nature of the age-depth transformation.
+*admtools* can transfrom lists from the time to the height domain and vice versa given they have elements with names `h` or `t`. These lists can be interpreted as time/stratigraphic series, where times and stratigraphic positions are associated with measured values. Note that these are not `ts` objects as used by the `stats` package, as they will be generally heterodistant due to the irregular nature of the age-depth transformation.
 
 As example, we simulate trait evolution over 2 Myr using a Brownian motion, and transform the simulation into the stratigraphic domain.
 
@@ -300,7 +297,9 @@ plot(x = strat_list,
      main = "Trait Evolution 2 km Offshore")
 ```
 
-Note the jump in traits generated by the erosional interval in `my_adm`. Both `time_to_strat` and `strat_to_time` return `stratlist` and `timelist` objects when applied to lists. These are like ordinary lists, but come with simplified plotting optinality, see `?plot.stratlist` and `plot.timelist` for details.
+Note the jump in traits generated by the erosional interval in `my_adm`. Both `time_to_strat` and `strat_to_time` return `stratlist` and `timelist` objects when applied to lists. These are like ordinary lists, but come with simplified plotting optionality, see `?plot.stratlist` and `?plot.timelist` for details.
+
+For expanded modeling features with biological context, please use the `StratPal` package ([Github](https://github.com/MindTheGap-ERC/StratPal) | [Webpage](https://mindthegap-erc.github.io/StratPal/) |  [CRAN](https://cran.r-project.org/package=StratPal)). It provides light wrappers around `admtools` and out of the box modeling of trait evolution.
 
 #### Numeric vectors
 
@@ -332,7 +331,12 @@ For information on estimating age-depth models from tracer contents of rocks and
 vignette("adm_from_trace_cont")
 ```
 
-## References
+## References {#References}
 
 -   Burgess, Peter. "CarboCAT: A cellular automata model of heterogeneous carbonate strata." Computers & geosciences 53 (2013): 129-140. [DOI: 10.1016/j.cageo.2011.08.026](https://doi.org/10.1016/j.cageo.2011.08.026)
+
 -   Burgess, Peter. "CarboCAT Lite v1.0.1". Zenodo 2023. [DOI: 10.5281/zenodo.8402578](https://doi.org/10.5281/zenodo.8402578)
+
+-   Hohmann, Niklas; Koelewijn, Joël R.; Burgess, Peter; Jarochowska, Emilia. 2024. "Identification of the mode of evolution in incomplete carbonate successions." BMC Ecology and Evolution 24, 113. <https://doi.org/10.1186/s12862-024-02287-2>.
+
+-   Hohmann, Niklas, Koelewijn, Joël R.; Burgess, Peter; Jarochowska, Emilia. 2023. "Identification of the Mode of Evolution in Incomplete Carbonate Successions - Supporting Data." Open Science Framework. <https://doi.org/10.17605/OSF.IO/ZBPWA>, published under the [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) license.
diff --git a/vignettes/admtools_doc.Rmd b/vignettes/admtools_doc.Rmd
@@ -3,7 +3,7 @@ title: "Structure and classes of the admtools package"
 output: rmarkdown::html_vignette
 author: "Niklas Hohmann"
 vignette: >
-  %\VignetteIndexEntry{admtools_doc}
+  %\VignetteIndexEntry{Structure and classes of the admtools package}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---