APCalign - Resolving Plant Taxon Names Using the Australian Plant Census

The process of resolving 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 established status of plant taxa across different states/territories.

Last updated 10 days ago

7.33 score 4 stars 1 dependents 23 scripts 377 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.

Last updated 1 months ago

australiadatabaseplantstraits

5.93 score 22 stars 1 dependents 43 scripts

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.

Last updated 8 days ago

bayesian-inverse-problemsbayesian-methodsdifferential-equationshierarchical-modelsrstanstancpp

5.53 score 3 stars 10 scripts

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

There is a long tradition of studying the flux of carbon from the biosphere to the atmosphere by following a particular cohort of litter (wood, leaves, roots, or other organic material) through time. The resulting data are mass remaining and time. A variety of functional forms may be used to fit the resulting data. Some work better empirically. Some are better connected to a process-based understanding. Some have a small number of free parameters; others have more. This package matches decomposition data to a family of these curves using likelihood--based fitting. This package is based on published research by Cornwell & Weedon (2013) <doi:10.1111/2041-210X.12138>.

Last updated 1 years ago

5.05 score 5 stars 15 scripts 209 downloads

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

This shiny-based application allows users to extract plant occurrence data from the Atlas of Living Australia and generate a species list for any defined area in New South Wales. All records associated with either a physical voucher (stored in Australian herbaria) or a photographic 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.

Last updated 2 days ago

4.86 score 3 stars 7 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. 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/>.

Last updated 2 months ago

3.40 score 10 stars 25 scripts