Kar, F. | bioRxiv Science

bioRxiv2025

hmde: Hierarchical Methods for Differential Equations

AbstractRepeat observations of size are a common tool for understanding growth across taxa, and are used to estimate parameters for functions that describe growth rates. Recent advances in estimating differential equation parameters with a hierarchical longitudinal model have gone beyond available software. Custom implementation of such models is a barrier to use particularly for people who are not familiar with statistical programming. We introduce a new R package implementing a hierarchical Bayesian longitudinal model for repeat observation data with three growth models from ecological case studies. The package provides tools for model fitting and estimate extraction, example data, and case studies to demonstrate the use-case for each of the example models.

bioinformatics↗

bioRxiv2024

APCalign: an R package workflow and app for aligning and updating flora names to the Australian Plant Census

Here we present "APCalign", an R package and accompanying browser-sourced application to align and update scientific names for Australian vascular plants to the most likely currently accepted name using the Australian Plant Census (APC) or a name in the Australian Plant Names Index (APNI). Scientific names are the label assigned to unique taxon concepts by the scientific community, but this common terminology is most useful if a taxon concept is consistently referred to by the same name. These links can be broken due to either spelling mistakes or taxonomic changes. Automated tools are required to resolve taxon lists, aligning and updating long lists of possibly erroneous scientific names to the most likely currently accepted names. It is essential that tools specific to the APC/APNI be developed, as these lists specify an endorsed national-level nomenclature used in government legislation and include the uniquely Australian concept of phrase names, absent in global taxonomic datasets. To align input names to names within the APC or APNI, "APCalign" works progressively through a sequence of checks that combine different permutations of the input name, exact versus fuzzy matches, matches that consider the entire name input versus a subset of words, and character strings that indicate a name can only be resolved to a genus or family. The aligned names are then, when possible, updated to a currently accepted taxon concept within the APC. This package should facilitate all research outputs that require diverse scientific name lists to be merged or outdated lists to be updated.

plant biology↗