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volumodel's Introduction

voluModel

R-CMD-check Project Status: Active – The project has reached a stable, usable state and is being actively developed. Codecov test coverage cran version DOI rstudio mirror downloads

Summary

This package is designed to facilitate modeling species' ecological niches and geographic distributions based on occurrences and environments that have a vertical as well as horizontal component, and projecting models into three-dimensional geographic space. Working in three dimensions is useful in an aquatic context when the organisms one wishes to model can be found across a wide range of depths in the water column.

Please cite voluModel. Run the following to get the appropriate citation for the version you’re using:

citation(package = "voluModel")
## Owens H, Rahbek C (2024). _voluModel: Modeling Species Distributions in Three Dimensions_. doi:
## 10.5281/zenodo.7813394  (URL: https://doi.org/10.5281/zenodo.7813394), R package version 0.2.2, <URL:
## http://CRAN.R-project.org/package=voluModel>.
##
## A BibTeX entry for LaTeX users is
##
##  @Manual{,
##    title = {{voluModel}: Modeling Species Distributions in Three Dimensions},
##    author = {Hannah L. Owens and Carsten Rahbek},
##    year = {2024}
##    note = {R package version 0.2.2},
##    url = {http://CRAN.R-project.org/package=voluModel},
##    doi = {10.5281/zenodo.5792654},
##  }

Installation

install.packages("voluModel")

Or, install GitHub development version (version 0.2.1):

devtools::install_github("hannahlowens/voluModel", build_vignettes = TRUE)

Getting Started

  1. Introduction
  2. Processing Rasters
  3. Sampling Environtmental Data in 3D
  4. Visualization Tools
  5. Generalized Linear Model Workflow

Meta

  • Please report any issues or bugs.
  • License: GPL-3
  • Get citation information for voluModel in R using citation(package = 'voluModel')

Acknowledgements

EU flag

  • This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 891702.

volumodel's People

Contributors

hannahlowens avatar

Stargazers

Santiago J.E. Velazco avatar Mireia Valle avatar Lillian Fleming avatar Ali GUNCAN avatar François Guilhaumon avatar Adam B. Smith avatar Shelly Gaynor avatar Francisco Rodriguez-Sanchez avatar

Watchers

James Cloos avatar  avatar Mireia Valle avatar

volumodel's Issues

"Fish Tank" visualization

What about plotting suitability so it looks like one is looking through a fishtank? That is, plot longitude versus depth. Or latitude versus depth. Furthermore, it would be great to have an inset latitude x longitude map with the relative position of the "fishtank plot".

"Fish Tank" Visualization

New visualization for 3D distributions and diversity estimates coming soon, which plots vertical transects through the data.

introduction vignette possible mistake

In line 294, is it supposed to be envelopeModelBottom being masked, since envelopeModelSurface was already masked earlier in the script?:

Put it all together, bottom

envelopeModelBottom <- temperaturePresence * AOUpresence
envelopeModelSurface <- mask(crop(envelopeModelSurface, studyRegion), mask = studyRegion)

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