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. https://doi.org/10.1071/BT24014

Last updated 5 days ago

7.33 score 4 stars 1 dependents 23 scripts 589 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 3 months ago

australiadatabaseplantstraits

5.93 score 22 stars 1 dependents 43 scripts

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.

Last updated 23 days ago

c-plus-plusdemographydynamicecologyevolutionforestsplant-physiologyscience-researchsimulationtraitcpp

5.87 score 53 stars

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.

Last updated 3 years ago

allometric-linesinference

5.65 score 2 stars 5 dependents 879 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.

Last updated 8 days ago

bayesian-inverse-problemsbayesian-methodsdifferential-equationshierarchical-modelsrstanstancpp

5.56 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 2 years ago

5.05 score 5 stars 15 scripts 169 downloads

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.

Last updated 16 hours ago

5.02 score 4 stars 7 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.

Last updated 20 hours ago

4.48 score 30 stars 162 downloads

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 12 days ago

3.70 score 10 stars 25 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.

Last updated 8 days ago

cpp

3.48 score 2 stars

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.

Last updated 13 days ago

2.78 score 6 stars