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Robust Exponential Decreasing Index
Implementation of the Robust Exponential Decreasing Index (REDI), proposed in the article by Issa Moussa, Arthur Leroy et al. (2019) < https://bmjopensem.bmj.com/content/bmjosem/5/1/e000573.full.pdf>. The REDI represents a measure of cumulated workload, robust to missing data, providing control of the decreasing influence of workload over time. Various functions are provided to format data, compute REDI, and visualise results in a simple and convenient way.
Parse 'Tableau' Workbooks into Functional Data
High-performance parsing of 'Tableau' workbook files into tidy data frames and dependency graphs for other visualization tools like R 'Shiny' or 'Power BI' replication.
Load 'Overture' Datasets as 'dbplyr' and 'sf'-Ready Data Frames
An integrated R interface to the 'Overture' API (< https://docs.overturemaps.org/>). Allows R users to return 'Overture' data as 'dbplyr' data frames or materialized 'sf' spatial data frames.
Soundscape Background Noise, Power, and Saturation
Accessible and flexible implementation of three ecoacoustic indices that are less commonly available in existing R frameworks: Background Noise, Soundscape Power and Soundscape Saturation. The functions were design to accommodate a variety of sampling designs. Users can tailor calculations by specifying spectrogram time bin size, amplitude thresholds and normality tests. By simplifying computation and standardizing reproducible methods, the package aims to support ecoacoustics studies. For more details about the indices read Towsey (2017) < https://eprints.qut.edu.au/110634/> and Burivalova (2017)
Classify Occurrences by Confidence Levels in the Species ID
Classify occurrence records based on confidence levels of species identification. In addition, implement tools to filter occurrences inside grid cells and to manually check for possibles errors with an interactive shiny application.
Analysing 'SNP' and 'Silicodart' Data - Basic Functions
Facilitates the import and analysis of 'SNP' (single nucleotide 'polymorphism') and 'silicodart' (presence/absence) data. The main focus is on data generated by 'DarT' (Diversity Arrays Technology), however, data from other sequencing platforms can be used once 'SNP' or related fragment presence/absence data from any source is imported. Genetic datasets are stored in a derived 'genlight' format (package 'adegenet'), that allows for a very compact storage of data and metadata. Functions are available for importing and exporting of 'SNP' and 'silicodart' data, for reporting on and filtering on various criteria (e.g. 'callrate', 'heterozygosity', 'reproducibility', maximum allele frequency). Additional functions are available for visualization (e.g. Principle Coordinate Analysis) and creating a spatial representation using maps. 'dartR.base' is the 'base' package of the 'dartRverse' suits of packages. To install the other packages, we recommend to install the 'dartRverse' package, that supports the installation of all packages in the 'dartRverse'. If you want to cite 'dartR', you find the information by typing citation('dartR.base') in the console.
A Set of Methods for Longitudinal Data Objects
A very simple implementation of a class for longitudinal data.
Rank-Based Test to Evaluate a Surrogate Marker
Uses a novel rank-based nonparametric approach to evaluate a surrogate marker
in a small sample size setting. Details are described in Parast et al (2024)
Externally Studentized Midrange Distribution
Computes the studentized midrange distribution (pdf, cdf and quantile) and generates random numbers.
Flexible Population Dynamics Simulations
Simulate population dynamics from realistically complex matrix population models in a plug-and-play fashion. Supports aspatial and spatially implicit models with one or more species and time-varying covariates, stochasticity, density dependence, additions or removals of individuals, interspecific interactions, and metapopulations.