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current_workshop's Introduction

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lifecycle NSF-1948926

Neotoma Current R Workshop

A repository to host interactive R workshops. This repository will always be set up for the most recent/current Neotoma Workshop. All past workshops will be archived in the Neotoma Workshops repository.

This repository is built with the structure required to serve the content through an interactive, online RStudio session using Binder (and Docker). Clicking the Binder link will open RStudio in the user's browser.

Currently, this repo hosts the Workshop to be delivered in Aarhus about Species Distribution Modelling with pollen data.

To access the content for this Workshop, click the badge below:

Binder

Contributors

This is an open project and contributions are welcome from any individual. All contributors to this project are bound by a code of conduct. Please review and follow this code of conduct as part of your contribution.

Translations

How to use this repository

This repository contains two different R workflows, a complex workflow that shows how to manage and modify chronologies with the R package, and a simple workflow that shows how to access data and perform relatively simple analysis. These workflows may be modified for content (e.g., focusing on different dataset types or geospatial contexts).

Users may clone this workshop and modify the content, but be aware that the Binder links are specific to this repository, and must be modified through the users' own Binder setup.

  • apt.txt defines a set of packages required by Binder/Docker to enable the spatial tools in the neotoma2 R package.
  • install.R defines the R packages that are to be loaded by the Binder environment at runtime.

current_workshop's People

Contributors

jessicablois avatar noraschlenker avatar sedv8808 avatar simongoring avatar

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current_workshop's Issues

Aarhus Workshop debrief

Overall

  • Provide guidance for versioning &cetera for folks prior to the workshop to identify the current software requirements.

Simple Workflow

  • Concepts about pollen, taxonomy & "occurrence" are critical, how and when are they addressed in the workshop?
  • Introduction material in the complex workflow is also relevant for the simple workflow.
  • For non-experts, age depth models are complicated. Can provide a simple description.
  • Need an explanation of how pollen actually works.
  • Taxonomic Harmonization is discussed in the introduction but wasn't explicitly in the workshop (is now in the repository)

Complex Workflow

  • Neotoma2 package wasn't working because of the error neotoma2 is not available for your version of R.
    • Can be installed using devtools/install_github()
  • The filter() function on the europe_ready variable (line 250) times out on binder.
  • The case_when() function used is from a relatively new version of dplyr and so meant that from a personal computer people needed to update dplyr.

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