Working with Metabarcoding Data in a Tidy Format

A series of R functions that come in handy while working with metabarcoding data. The reasoning of doing this is to have the same functions we use all the time stored in a curated, reproducible way. In a way it is all about putting together the grammar of the 'tidyverse' from Wickham et al.(2019) with the functions we have used in community ecology compiled in packages like 'vegan' from Dixon (2003) and 'phyloseq' McMurdie & Holmes (2013) . The package includes functions to read sequences from FAST(A/Q) into a tibble ('fasta_reader' and 'fastq_reader'), to process 'cutadapt' Martin (2011) 'info-file' output. When it comes to sequence counts across samples, the package works with the long format in mind (a three column 'tibble' with Sample, Sequence and counts ), with functions to move from there to the wider format.

Tidy Up Date/Time Ranges

Collapse, partition, combine, fill gaps in and expand date/time ranges.

A Tidy Interface to the 'Walk Score' API

Easily collect walk scores, bike scores, and transit scores (where available) from the 'Walk Score' API < https://www.walkscore.com/professional/api.php>, a proprietary API that assigns locations a walkability score between 0 and 100.

A Tidy Interface for Simulating Multivariate Data

Provides pipe-friendly (%>%) wrapper functions for MASS::mvrnorm() to create simulated multivariate data sets with groups of variables with different degrees of variance, covariance, and effect size.

Operations Designed for Tidy Strength Data

Mappings for estimated one rep max from commonly used formulas. Convenience functions for turning mass/rep/set data into useful derived quantities.

A Tidy Toolbox for Climate Extreme Indices

Calculate Expert Team on Climate Change Detection and Indices (ETCCDI) <-- (acronym) climate indices from daily or hourly temperature and precipitation data. Provides flexible data handling.

Tidy Intensive Longitudinal Data Analysis

A reproducible, tidyverse-style framework for intensive longitudinal data analysis in R, with built-in methodological safeguards, provenance tracking, and reporting tools. Encodes time structure, enforces within-between decomposition, provides spacing-aware lags, and integrates diagnostics and visualization. Use ild_prepare(), ild_center(), ild_lag(), and related functions for a unified pipeline from raw EMA/diary data to interpretable models.

Tidy Tools for Joinpoint Regression Models

Provides tools to fit joinpoint regression models with a log-linear specification by levels of a categorical variable. The package acts as a wrapper around the 'segmented' package, facilitating model fitting, selection, and interpretation. It includes functions to estimate the Annual Percent Change (APC) and the Average Annual Percent Change (AAPC), along with their 95% confidence intervals, and to generate formatted summary tables and plots of results.

A Tidy Format Datasets of Dengue by Country

Provides a weekly, monthly, yearly summary of dengue cases by state/ province/ country.

Diverse Datasets for 'tsibble'

Provides diverse datasets in the 'tsibble' data structure. These datasets are useful for learning and demonstrating how tidy temporal data can tidied, visualised, and forecasted.