tidysdm - Species Distribution Models with Tidymodels

Fit species distribution models (SDMs) using the 'tidymodels' framework, which provides a standardised interface to define models and process their outputs. 'tidysdm' expands 'tidymodels' by providing methods for spatial objects, models and metrics specific to SDMs, as well as a number of specialised functions to process occurrences for contemporary and palaeo datasets. The full functionalities of the package are described in Leonardi et al. (2024) <doi:10.1111/2041-210X.14406>.

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species-distribution-modellingtidymodels

8.91 score 37 stars 124 scripts 507 downloads

tidypopgen - Tidy Population Genetics

We provide a tidy grammar of population genetics, facilitating the manipulation and analysis of data on biallelic single nucleotide polymorphisms (SNPs). 'tidypopgen' scales to very large genetic datasets by storing genotypes on disk, and performing operations on them in chunks, without ever loading all data in memory. The full functionalities of the package are described in Carter et al. (2025) <doi:10.1111/2041-210x.70204>.

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openblaszlibcppopenmp

8.81 score 13 stars 1 dependents 46 scripts 370 downloads

admixtools - Inferring demographic history from genetic data

admixtools is a set of methods used to infer demographic history from genetic data using f-statistics. It was originally implemented as a command line program in C. This is a new implementation of the programs qpDstat, qpAdm, qpGraph, and contains several new features. It is efficient because it precomputes f2-statistics which can be re-used for many analyses.

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openblascpp

8.34 score 96 stars 253 scripts

pastclim - Manipulate Time Series of Climate Reconstructions

Methods to easily extract and manipulate climate reconstructions for ecological and anthropological analyses, as described in Leonardi et al. (2023) <doi:10.1111/ecog.06481>. The package includes datasets of palaeoclimate reconstructions, present observations, and future projections from multiple climate models.

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climate-datapaleoclimatespecies-distribution-modelling

7.97 score 41 stars 65 scripts 868 downloads

crstools - Tools to Work with Projections

Choose the appropriate map projection for a given application, visualise the resulting distortion, and georeference data from unknown projections. The full functionalities of the package are described in Pozzi et al. (2026) <doi:10.31223/X5K17P> (pre-print).

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5.00 score 2 stars 4 scripts 529 downloads

geoGraph - Walking through the geographic space using graphs

Classes and methods for spatial graphs interfaced with support for GIS shapefiles.

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3.40 score 5 stars 2 scripts

tidygenclust - Clustering for Population Genetics in R

A tidy interface to clustering in population genetics. This package provides a set of functions to perform clustering on genetic data, and to visualize the results, both for single runs and for multiple repeats of the same analysis. 'tidygenclust' ports the 'fastmixture' and 'clumppling' python modules to R, and it is built on top of the 'tidypopgen' package. Currently it works only on Linux and OSX (you can use the WSL on Windows).

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3.30 score 1 stars 5 scripts