smatr - (Standardised) Major Axis Estimation and Testing Routines

Methods for fitting bivariate lines in allometry using the major axis (MA) or standardised major axis (SMA), and for making inferences about such lines. The available methods of inference include confidence intervals and one-sample tests for slope and elevation, testing for a common slope or elevation amongst several allometric lines, constructing a confidence interval for a common slope or elevation, and testing for no shift along a common axis, amongst several samples. See Warton et al. 2012 <doi:10.1111/j.2041-210X.2011.00153.x> for methods description.

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allometric-linesinference

7.34 score 2 stars 5 dependents 312 scripts 1.6k downloads

plant - A Package for Modelling Forest Trait Ecology and Evolution

Solves trait, size and patch structured model from (Falster et al. 2016) using either method of characteristics or as stochastic, finite-sized population.

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c-plus-plusdemographydynamicecologyevolutionforestsplant-physiologyscience-researchsimulationtraitcpp

6.90 score 54 stars 47 scripts

APCalign - Resolving Plant Taxon Names Using the Australian Plant Census

The process of resolving and updating taxon names is necessary when working with biodiversity data. 'APCalign' uses the Australian Plant Census (APC) and the Australian Plant Name Index (APNI) to align and update plant taxon names to current, accepted standards. 'APCalign' also supplies information about the establishment status (i.e. native or introduced) of plant taxa across different states/territories.

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6.79 score 5 stars 1 dependents 34 scripts 695 downloads

hmde - Hierarchical Methods for Differential Equations

Wrapper for 'Stan' that offers a number of in-built models to implement a hierarchical Bayesian longitudinal model for repeat observation data. Model choice selects the differential equation that is fit to the observations. Single and multi-individual models are available. O'Brien et al. (2024) <doi:10.1111/2041-210X.14463>.

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bayesian-inverse-problemsbayesian-methodsdifferential-equationshierarchical-modelsrstanstancpp

6.56 score 5 stars 12 scripts 241 downloads

austraits - Helpful functions to access the AusTraits database and wrangle data from other traits.build databases

`austraits` allow users to **access, explore and wrangle data** from traits.build relational databases. It is also an R interface to AusTraits, the Australian plant trait database. This package contains functions for joining data from various tables, filtering to specific records, combining multiple databases and visualising the distribution of the data. We expect this package will assist users in working with `traits.build` databases.

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australiadatabaseplantstraits

6.20 score 23 stars 1 dependents 57 scripts

datastorr - Simple Data Versioning

Simple dataversioning using GitHub to store data.

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5.70 score 67 stars 5 dependents 3 scripts

litterfitter - Fits a Collection of Curves to Single-Cohort Decomposition Data

Fit different model forms to single-cohort litter decomposition data (mass remaining through time) using likelihood-based estimation. Models span simple empirical to process-motivated forms with differing numbers of free parameters. Provides parameter estimates, uncertainty, and tools for model comparison/selection. Based on Cornwell & Weedon (2013) <doi:10.1111/2041-210X.12138>.

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carboncarboncycledecompositionecology-modellingsoil

5.69 score 5 stars 22 scripts 145 downloads

fungaltraits - A dynamically-updating versioned trait database for fungi

A functional trait database for fungi.

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databasefungitraits

4.54 score 86 stars 40 scripts

infinitylists - A Shiny-Based Application for Generating Place-Based Species Lists

This shiny-based application allows users to extract species occurrence records from the Atlas of Living Australia or GBIF and generate a species list for a defined area. All records associated with either a physical voucher (stored in herbaria or museums) or a photographic or audio voucher (stored in iNaturalist) are extracted. For each species within the defined area, the application will return voucher type, number of vouchers, date of the most recent voucher, spatial coordinates, voucher location, and the voucher collector. Records are displayed both in a table and on a map, and are downloadable as a CSV.

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4.45 score 14 stars 6 scripts

earthtones - Derive a Color Palette from a Particular Location on Earth

Downloads a satellite image via ESRI and maptiles (these are originally from a variety of aerial photography sources), translates the image into a perceptually uniform color space, runs one of a few different clustering algorithms on the colors in the image searching for a user-supplied number of colors, and returns the resulting color palette.

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4.20 score 32 stars 4 scripts 236 downloads

taxonlookup - A dynamically-updating versioned taxonomic resource for vascular plants

This is a taxon lookup table for land plants. It is built from a set of scripts that dynamically build a versioned genus-family-order-higher taxa lookup table from canonical sources on the web. It uses semantic versioning to keep track of changes.

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4.01 score 33 stars 62 scripts

traits.build - A workflow for harmonising trait data from diverse sources into a documented standard structure

The `traits.build` package provides a workflow to harmonise trait data from diverse sources. A description of the data model, workflow, and R package are presented in Wenk et al, 2024, <doi:10.1016/j.ecoinf.2024.102773>. The code was originally built to support AusTraits (see Falster et al 2021, <doi:10.1038/s41597-021-01006-6>, <https://github.com/traitecoevo/autraits.build>) and has been generalised here to support construction of other trait databases. For detailed instructions and examples see <https://traitecoevo.github.io/traits.build-book/>.

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3.56 score 11 stars 33 scripts

bmsma - Bayesian Multilevel fits of Standardise Major Axis lines to bivariate data

Allows fitting of Standardise Major Axis lines to bivariate data via MCMC with random effects.

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cpp

3.18 score 3 stars 3 scripts

baad.data - Retrieve Data From the 'BAAD' (Biomass And Allometry Database)

Retrieves data from the Biomass And Allometry Database ('baad'). This simplifies the task of keeping a consistently referenceable set of data on a computer without having to manually cache it.

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3.12 score 7 stars 19 scripts

phyndr - Matches Tip and Trait Data

Use topological or taxonomic information to maximize the overlap of phylogenetic and comparative data.

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3.03 score 9 stars 12 scripts 2 downloads

growthform - Global Plant Growth Form: a dynamically-updating versioned growth form data for vascular plants

A growth form database for >145,000 species of vascular plants.

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2.98 score 19 stars 4 scripts

leaf13C - a global dataset of leaf D13C data

These are data from bulk leaf D13C data collected on many different species from across the world.

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carbonisotopesleafphysiologyplantwaterrelations

2.48 score 6 stars 4 scripts

ksi - Phylogeny-based Komogorov-Smirnov Importance Statistic

Package underlying Cornwell et al. 2014 J. Ecology.

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2.00 score 2 stars 3 scripts