Small-Sample Adjustments for Wald Tests Using Sandwich Estimators

Tests coefficients with sandwich estimator of variance and with small samples. Regression types supported are gee, linear regression, and conditional logistic regression.

An R Interface to the JBrowse 2 Genome Browser

Provides an R interface to the JBrowse 2 genome browser. Enables embedding a JB2 genome browser in a Shiny app or R Markdown document. The browser can also be launched from an interactive R console. The browser can be loaded with a variety of common genomics data types, and can be used with a custom theme.

Exact Binary Sequential Designs and Analysis

For a series of binary responses, create stopping boundary with exact results after stopping, allowing updating for missing assessments.

Agnostic Fay-Herriot Model for Small Area Statistics

Implements the Agnostic Fay-Herriot model, an extension of the traditional small area model. In place of normal sampling errors, the sampling error distribution is estimated with a Gaussian process to accommodate a broader class of distributions. This flexibility is most useful in the presence of bounded, multi-modal, or heavily skewed sampling errors.

Scans R Projects for Vulnerable Third Party Dependencies

Collects a list of your third party R packages, and scans them with the 'OSS' Index provided by 'Sonatype', reporting back on any vulnerabilities that are found in the third party packages you use.

Process CBASS-Derived PAM Data

Tools to process CBASS-derived PAM data efficiently. Minimal requirements are PAM-based photosynthetic efficiency data (or data from any other continuous variable that changes with temperature, e.g. relative bleaching scores) from 4 coral samples (nubbins) subjected to 4 temperature profiles of at least 2 colonies from 1 coral species from 1 site. Please refer to the following CBASS (Coral Bleaching Automated Stress System) papers for in-depth information regarding CBASS acute thermal stress assays, experimental design considerations, and ED5/ED50/ED95 thermal parameters: Nicolas R. Evensen et al. (2023) Christian R. Voolstra et al. (2020) Christian R. Voolstra et al. (2025) .

An API Client for the Environmental Data Initiative Repository

A client for the Environmental Data Initiative repository REST API. The 'EDI' data repository < https://portal.edirepository.org/nis/home.jsp> is for publication and reuse of ecological data with emphasis on metadata accuracy and completeness. It is built upon the 'PASTA+' software stack < https://pastaplus-core.readthedocs.io/en/latest/index.html#> and was developed in collaboration with the US 'LTER' Network < https://lternet.edu/>. 'EDIutils' includes functions to search and access existing data, evaluate and upload new data, and assist other data management tasks common to repository users.

Random Survival Forest for Recurrent Events

Analyze recurrent events with right-censored data and the potential presence of a terminal event (that prevents further occurrences, like death). 'recofest' extends the random survival forest algorithm, adapting splitting rules and node estimators to handle complexities of recurrent events. The methodology is fully described in Murris, J., Bouaziz, O., Jakubczak, M., Katsahian, S., & Lavenu, A. (2024) (< https://hal.science/hal-04612431v1/document>).

Processing Linear Features

Assists in the manipulation and processing of linear features with the help of the 'sf' package. Makes use of linear referencing to extract data from most shape files. Reference for this packages methods: Albeke, S.E. et al. (2010) .

Beyond the Border - Kernel Density Estimation for Urban Geography

The kernelSmoothing() function allows you to square and smooth geolocated data. It calculates a classical kernel smoothing (conservative) or a geographically weighted median. There are four major call modes of the function. The first call mode is kernelSmoothing(obs, epsg, cellsize, bandwidth) for a classical kernel smoothing and automatic grid. The second call mode is kernelSmoothing(obs, epsg, cellsize, bandwidth, quantiles) for a geographically weighted median and automatic grid. The third call mode is kernelSmoothing(obs, epsg, cellsize, bandwidth, centroids) for a classical kernel smoothing and user grid. The fourth call mode is kernelSmoothing(obs, epsg, cellsize, bandwidth, quantiles, centroids) for a geographically weighted median and user grid. Geographically weighted summary statistics : a framework for localised exploratory data analysis, C.Brunsdon & al., in Computers, Environment and Urban Systems C.Brunsdon & al. (2002) , Statistical Analysis of Spatial and Spatio-Temporal Point Patterns, Third Edition, Diggle, pp. 83-86, (2003) .