From 92fb90a2b46bcff607e638d4de4d9fcbb506f5cb Mon Sep 17 00:00:00 2001 From: Niklas Hohmann <67792281+NiklasHohmann@users.noreply.github.com> Date: Thu, 18 Jul 2024 09:13:16 +0200 Subject: [PATCH 1/5] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 38ff199..ca66696 100644 --- a/README.md +++ b/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) From 5518c9ffd353a2522d959b15ed402a31818c279e Mon Sep 17 00:00:00 2001 From: Niklas Hohmann <67792281+NiklasHohmann@users.noreply.github.com> Date: Fri, 19 Jul 2024 07:52:19 +0200 Subject: [PATCH 2/5] Change vignette names and titles --- vignettes/{fossil_occ.Rmd => event_data.Rmd} | 4 ++-- vignettes/{trait_evolution.Rmd => phenotypic_evolution.Rmd} | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) rename vignettes/{fossil_occ.Rmd => event_data.Rmd} (98%) rename vignettes/{trait_evolution.Rmd => phenotypic_evolution.Rmd} (97%) diff --git a/vignettes/fossil_occ.Rmd b/vignettes/event_data.Rmd similarity index 98% rename from vignettes/fossil_occ.Rmd rename to vignettes/event_data.Rmd index 3d9f622..67af56b 100644 --- a/vignettes/fossil_occ.Rmd +++ b/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} --- diff --git a/vignettes/trait_evolution.Rmd b/vignettes/phenotypic_evolution.Rmd similarity index 97% rename from vignettes/trait_evolution.Rmd rename to vignettes/phenotypic_evolution.Rmd index 1d23539..7c2f9e3 100644 --- a/vignettes/trait_evolution.Rmd +++ b/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} --- From 98cd710607027f686b7c63ece7b5d4e68cf3f915 Mon Sep 17 00:00:00 2001 From: Niklas Hohmann <67792281+NiklasHohmann@users.noreply.github.com> Date: Fri, 19 Jul 2024 08:07:03 +0200 Subject: [PATCH 3/5] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index ca66696..05fe0b8 100644 --- a/README.md +++ b/README.md @@ -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 From 9bb7369ba07ebb5fa514ad825d1c90c316de8dbf Mon Sep 17 00:00:00 2001 From: Niklas Hohmann <67792281+NiklasHohmann@users.noreply.github.com> Date: Fri, 19 Jul 2024 08:08:34 +0200 Subject: [PATCH 4/5] add contribution guidelines --- README.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/README.md b/README.md index 05fe0b8..b2e34fe 100644 --- a/README.md +++ b/README.md @@ -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. From 366fff6500e46be3e37e8b8fb1f373d9c4ed94bd Mon Sep 17 00:00:00 2001 From: Niklas Hohmann <67792281+NiklasHohmann@users.noreply.github.com> Date: Fri, 19 Jul 2024 08:09:28 +0200 Subject: [PATCH 5/5] Update StratPal.Rmd adjust vignette names, add section on example data --- vignettes/StratPal.Rmd | 43 +++++++++++++++++++++++++++--------------- 1 file changed, 28 insertions(+), 15 deletions(-) diff --git a/vignettes/StratPal.Rmd b/vignettes/StratPal.Rmd index 068c2d7..38798f5 100644 --- a/vignettes/StratPal.Rmd +++ b/vignettes/StratPal.Rmd @@ -21,42 +21,53 @@ 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 @@ -64,6 +75,8 @@ 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.