phyf - Phylogenetic Flow Objects for Easy Manipulation and Modelling of Data on Phylogenetic Trees and Graphs

The {phyf} package implements a tibble and vctrs based object for storing phylogenetic trees along with data. It is fast and flexible and directly produces data structures useful for phylogenetic modelling in the {fibre} package.

Last updated 3 months ago

4.49 score 1 stars 1 packages 51 scripts

fibre - Fast Evolutionary Trait Modelling on Phylogenies using Branch Regression Models

Implements Phylogenetic Branch Regression models which allow for flexible and versatile models of evolution along a phylogeny. The model can be used to detect shifts in rates of evolution along branches. The model uses a continuous and linear model structure and so can be easily combined with other non-phylogenetic statistical structures, as long as they are implemented using the R package INLA. One major uses of this are to condition on phylogeny in a standard regression between two traits, thus 'accounting' for phylogenetic structure in the response variable, similar to how pgls is used but allowing for a more flexible phylogenetic model. This also allows the phylogenetic model to be combined with the spatial models that INLA excels at (and with comparable flexibility to those spatial models).

Last updated 12 months ago

4.18 score 3 stars 34 scripts

trampoline - Make Functions that Can Recurse Infinitely

Implements a trampoline algorithm for R that let's users write recursive functions that get around R's stack call limitations, enabling theoretically infinite recursion. The algorithm is based around generator function as implemented in the 'coro' package, and is based almost completely on the 'trampoline' module from Python <https://gitlab.com/ferreum/trampoline>.

Last updated 3 years ago

4.02 score 21 stars 8 scripts 113 downloads

tidysdm - Sprecies Distribution Modelling with Tidymodels

Provides functions and classes to help create Species Distribution Models (SDMs) within the {tidymodels} framework. Provides new {parsnip} models, new {recipes} steps, and {yardstick} metrics. This package provides access to the powerful {tidymodels} ecosystem for SDMs, especially the package {spatialsample} for spatially aware cross validation and model evaluation, as well as opening up all classification models implemented in {parsnip} for presence-only SDMs, using the pseudo-absence approach.

Last updated 1 years ago

3.32 score 1 stars 42 scripts 380 downloads

slimr - Create, Run and Post-Process 'SLiM' Population Genetics Forward Simulations

Lets you write 'SLiM' scripts (population genomics simulation) using your favourite R IDE, using a syntax as close as possible to the original 'SLiM' language. It offer many tools to manipulate those scripts, as well as run them in the 'SLiM' software from R, as well as capture and post-process their output, after or even during a simulation.

Last updated 11 months ago

2.95 score 7 stars 42 scripts

impac - Make packed image mosaics

impac takes a list of images or a function that generates images and packs them onto a canvas using a greedy algorithm, while respecting transparency.

Last updated 1 years ago

2.85 score 14 stars 4 scripts

rbff - R Interface to Boundary First Flattening Software (BFF)

Flatten 3D meshes into arbitrary 2D shapes using boundary first flattening (<https://github.com/GeometryCollective/boundary-first-flattening>).

Last updated 3 years ago

2.40 score 5 stars 6 scripts

sdmpack - FIU SDM Course Package

Course material for FIU course on SDM

Last updated 1 years ago

2.08 score 24 scripts