Merge pull request #4 from MindTheGap-ERC/dev

Dev

README.md

@@ -10,7 +10,7 @@ R package for stratigraphic paleobiology modeling pipelines.
 
 __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)
 
@@ -35,7 +35,7 @@ remotes::install_github(repo = "MindTheGap-ERC/StratPal",
                         dependencies = TRUE)
 ```
 
-to install the lastest stable version of the package.
+to install the latest stable version of the package.
 
 ## Usage
 
@@ -53,6 +53,10 @@ browseVignettes(package = "StratPal")
 
 to view the available vignettes (long form documentation) with use cases or visit the package webpage ([mindthegap-erc.github.io/StratPal](https://mindthegap-erc.github.io/StratPal/)) to get started.
 
+## Contribution
+
+For contribution guidelines see the CONTRIBUTING.md file
+
 ## License
 
 Apache 2.0, see LICENSE file for license text.

vignettes/StratPal.Rmd

@@ -21,49 +21,62 @@ library(admtools)
 
 ## Overview
 
-Welcome to the `StratPal` package. This vignette provides an overview of the structure of the package and preliminaries needed to efficiently use it. We go through _dependencies_, _piping_, and working with _age-depth models_.
+Welcome to the `StratPal` package. This vignette provides an overview of the structure of the package and preliminaries needed to efficiently use it. We go through _installation_, _dependencies_, provide an overview of the available _example data_, _piping_, and working with _age-depth models_.
 
 If you want to skip the introduction, go to
 
 ```{r, eval=FALSE}
-vignette("fossil_occ")
+vignette("phenotypic_evolution")
 ```
 
-for details on how to model stratigraphic paleobiology of events such as fossil occurrences and first/last occurrences. Go to 
+for details on how to model stratigraphic paleobiology of phenotypic evolution. Go to
 
 ```{r, eval=FALSE}
-vignette("trait_evolution")
+vignette("event_data")
 ```
 
-for details on how to model stratigraphic paleobiology of trait evolution.
+for details on how to model stratigraphic paleobiology of event data such as individual fossils and first/last occurrences of taxa.
 
-## Dependencies
+## Installation
 
-The `StratPal` heavily relies on the age-depth modelling tools provided by the `admtools` package. To make sure you have the latest version of the package installed, first install the `remotes` package by running
+To install the `StratPal` package, first install the `remotes` package by running
 
-```{r, eval=FALSE}
+```R
 install.packages("remotes")
 ```
 
-in your console. Then you can install the latest version of `admtools` from _GitHub_ by running
+in the R console. Then, run
 
-```{r, eval=FALSE}
-remotes::install_github(repo = "MindTheGap-ERC/admtools",
+```R
+remotes::install_github(repo = "MindTheGap-ERC/StratPal",
                         build_vignettes = TRUE,
                         ref = "HEAD",
                         dependencies = TRUE)
 ```
 
-This will also ask you to update all dependent packages.
+to install the latest stable version of the package and all its dependencies.
+
+## Dependencies
+
+The `StratPal` heavily relies on the age-depth modelling tools provided by the `admtools` package, which is _automatically_ installed when you install `StratPal`.
 
-Below we provide a brief overview of the functionality of the `admtools` package we need. If you want more information, you can browse through the package vignettes using
+To use its functionality, you need to run
+
+```{r}
+library(admtools)
+```
+
+
+before running any of the provided examples. Below we provide a brief overview of the functionality of the `admtools` package we need. If you want more information, you can browse through the package vignettes using
 
 ```{r, eval=FALSE}
 browseVignettes(package = "admtools") # opens in Browser
 ```
 
 or by visiting the package website at https://mindthegap-erc.github.io/admtools/.
 
+## Example data
+
 ## Piping
 
 In the `StratPal` package and its vignettes, we make heavy use of the base R _pipe_ operator `|>`. While this is not required to run the package, it simplifies the code and makes the underlying logic of a modeling _pipeline_ clearer.
@@ -182,13 +195,13 @@ In `admtools`, the transformation of data is done by the functions `time_to_stra
 With the preliminaries out of the way, you can go to go to
 
 ```{r, eval=FALSE}
-vignette("fossil_occ")
+vignette("event_data")
 ```
 
 for details on how to model stratigraphic paleobiology of events such as fossil occurrences and first/last occurrences. Go to 
 
 ```{r, eval=FALSE}
-vignette("trait_evolution")
+vignette("phenotypic_evolution")
 ```
 
 for details on how to model stratigraphic paleobiology of trait evolution.

vignettes/fossil_occ.Rmd → vignettes/event_data.Rmd

@@ -1,8 +1,8 @@
 ---
-title: "Stratigraphic Paleobiology for fossil occurrences"
+title: "Stratigraphic Paleobiology for Event Data"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{Stratigraphic Paleobiology for fossil occurrences}
+  %\VignetteIndexEntry{Stratigraphic Paleobiology for Event Data}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---

vignettes/trait_evolution.Rmd → vignettes/phenotypic_evolution.Rmd

@@ -1,8 +1,8 @@
 ---
-title: "trait_evolution"
+title: "Stratigraphic Paleobiology for Phenotypic Evolution"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{trait_evolution}
+  %\VignetteIndexEntry{Stratigraphic Paleobiology for Phenotypic Evolution}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---