<i>tidysdm</i> : Leveraging the flexibility of <i>tidymodels</i> for species distribution modelling in R

Abstract In species distribution modelling (SDM), it is common practice to explore multiple machine learning (ML) algorithms and combine their results into ensembles. In R, many implementations of different ML algorithms are available but, as they were mostly developed independently, they often use inconsistent syntax and data structures. For this reason, repeating an analysis with multiple algorithms and combining their results can be challenging. Specialised SDM packages solve this problem by providing a simpler, unified interface by wrapping the original functions to tackle each specific requirement. However, creating and maintaining such interfaces is time‐consuming, and with this approach, the user cannot easily integrate other methods that may become available. Here, we present tidysdm , an R package that solves this problem by taking advantage of the tidymodels universe. tidymodels provide standardised grammar, data structures and modelling interfaces, and a well‐documented infrastructure to integrate new algorithms and metrics. The wide adoption of tidymodels means that most ML algorithms and metrics are already integrated, and the user can add additional ones. Moreover, because of the broad adoption of tidymodels , new statistical approaches tend to be implemented quickly, making them easily integrated into existing pipelines and analyses. tidysdm takes advantage of the tidymodels universe to provide a flexible and fully customisable pipeline to fit SDM. It includes SDM‐specific algorithms and metrics, and methods to facilitate the use of spatial data within tidymodels . Additionally, tidysdm is the first software that natively allows SDM to be performed using data from different periods, expanding the availability of SDM for scholars working in palaeontology, archaeology, palaeobiology, palaeoecology and other disciplines focussing on the past.

Authors

Institutions

Publication Details

Journal
Methods in Ecology and Evolution
Published
2024-09-09
DOI
https://doi.org/10.1111/2041-210x.14406
Citations
9
Primary Topic
Species Distribution and Climate Change
Type
article
Field-Weighted Citation Impact
8.28

Funders

Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
OCT
article

tidysdm : Leveraging the flexibility of tidymodels for species distribution modelling in R

Andrea Manica, Margherita Colucci, Michela Leonardi, Eleanor M. L. Scerri et al.
9 citations
Methods in Ecology and Evolution
Species Distribution and Climate Change
8.28
article

tidysdm : Leveraging the flexibility of tidymodels for species distribution modelling in R

Andrea Manica, Margherita Colucci, Michela Leonardi, Eleanor M. L. Scerri, Andrea Vittorio Pozzi
article en
9 citations

Abstract

Abstract In species distribution modelling (SDM), it is common practice to explore multiple machine learning (ML) algorithms and combine their results into ensembles. In R, many implementations of different ML algorithms are available but, as they were mostly developed independently, they often use inconsistent syntax and data structures. For this reason, repeating an analysis with multiple algorithms and combining their results can be challenging. Specialised SDM packages solve this problem by providing a simpler, unified interface by wrapping the original functions to tackle each specific requirement. However, creating and maintaining such interfaces is time‐consuming, and with this approach, the user cannot easily integrate other methods that may become available. Here, we present tidysdm , an R package that solves this problem by taking advantage of the tidymodels universe. tidymodels provide standardised grammar, data structures and modelling interfaces, and a well‐documented infrastructure to integrate new algorithms and metrics. The wide adoption of tidymodels means that most ML algorithms and metrics are already integrated, and the user can add additional ones. Moreover, because of the broad adoption of tidymodels , new statistical approaches tend to be implemented quickly, making them easily integrated into existing pipelines and analyses. tidysdm takes advantage of the tidymodels universe to provide a flexible and fully customisable pipeline to fit SDM. It includes SDM‐specific algorithms and metrics, and methods to facilitate the use of spatial data within tidymodels . Additionally, tidysdm is the first software that natively allows SDM to be performed using data from different periods, expanding the availability of SDM for scholars working in palaeontology, archaeology, palaeobiology, palaeoecology and other disciplines focussing on the past.

Methods in Ecology and EvolutionVol. 15(10)
University of Cologne (DE), University of Malta (MT), University of Cambridge (GB), Max Planck Institute for the Science of Human History (DE), Max Planck Institute of Geoanthropology
Leverhulme Trust, Natural Environment Research Council
Industry, innovation and infrastructure
Openalex Percentile: Top 3%
Species Distribution and Climate Change
8.28
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.