Skip to content

Repo for storing scripts related to Hmsc-INCLINE manuscript in preparation

License

Notifications You must be signed in to change notification settings

evalieungh/hmsc_incline

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

19 Commits
 
 
 
 
 
 
 
 

Repository files navigation

traits and species co-occurrences with Hmsc and INCLINE data

This repository contains scripts for a manuscript about traits and species co-occurrences, using Hmsc and INCLINE data.

NB! this is a work in progress. The scripts are not 100% clean and finished, and results may not be reproducible. Some scripts have been heavily inspired by other sources.

This readme file was generated on [2023-01-13] by Eva Lieungh

Contact: Eva Lieungh, https://orcid.org/0000-0003-4009-944X, Natural History Museum, University of Oslo, eva.lieungh[at]nhm.uio.no / evaleriksen[at]gmail.com

Related resources:

  • Otso Ovaskainen, & Eva Lieungh. (2023). Model output for five Hmsc models of alpine grassland communities (1.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.8064101
  • INCLINE data repository will be published on OSF along with a data paper by Gya et al. (in prep): https://osf.io/zhk3m/
  • HMSC pipeline example scripts that follow the book. Scripts available from the hmsc webpage. Book: Ovaskainen, O., & Abrego, N. (2020). Joint Species Distribution Modelling (1st ed.). Cambridge University Press. ISBN: 9781108716789.

Contents

This is the folder structure in my local copy of the directory. Most of these folders are listed in .gitignore and will not be uploaded to GitHub. See Related resources list above for the necessary data.

Folder or file name Description
archive/ files made redundant, old versions
data/ raw and input data
data_processed/ modified data, intermediate files
writing manuscript drafts and backups, other texts
results output files, models, figures etc.
resources external resources not to be uploaded (add to .gitignore)
src scripts/code/notebooks
.gitignore file specifying folders and files Git should not track or upload
README.md this file, read as the front page of GitHub repository

Funding sources that supported this project

PhD project funded by the Norwegian Ministry of Education and Research, through the Natural History Museum, University of Oslo. Vascular plant community data were collected for the INCLINE project, Research Council of Norway FRIMEDBIO project 274712. PI: Vandvik, Töpper. 2018–2021.

Sharing and access

See license. Copy snippets freely, but please refer to this repository if you use large parts of several scripts (that is, if you are doing most of the same analyses and your starting point is a copy of these scripts). See for instance the ICMJE authorship guidelines (Vancouver convention) to help you decide which kind of acknowledgement is appropriate.

Help and useful tricks

Questions? Contact me, or post an issue in this repository.

A neat trick to find the answer to questions like "what script creates and saves the important_data.Rds file?" is to open a terminal in the ´/src´ folder and enter this command to search (grep) inside all files (-e) inside that folder and subfolders (-r): ´grep -r -e "important_data.Rds"´

About

Repo for storing scripts related to Hmsc-INCLINE manuscript in preparation

Resources

License

Stars

Watchers

Forks

Packages

No packages published

Languages