Tools for 'Box Geometry Model' (BGM) Files and Topology for the Atlantis Ecosystem Model

Facilities for working with Atlantis box-geometry model (BGM) files. Atlantis is a deterministic, biogeochemical, whole-of-ecosystem model. Functions are provided to read from BGM files directly, preserving their internal topology, as well as helper functions to generate spatial data from these mesh forms. This functionality aims to simplify the creation and modification of box and geometry as well as the ability to integrate with other data sources.

Tidy Tools for 'Raster' Data

Facilities to work with vector and raster data in efficient repeatable and systematic work flow. Missing functionality in existing packages is included here to allow extraction from raster data with 'simple features' and 'Spatial' types and to make extraction consistent and straightforward. Extract cell numbers from raster data and return the cells as a data frame rather than as lists of matrices or vectors. The functions here allow spatial data to be used without special handling for the format currently in use.

Quadrangle Mesh

Create surface forms from matrix or 'raster' data for flexible plotting and conversion to other mesh types. The functions 'quadmesh' or 'triangmesh' produce a continuous surface as a 'mesh3d' object as used by the 'rgl' package. This is used for plotting raster data in 3D (optionally with texture), and allows the application of a map projection without data loss and many processing applications that are restricted by inflexible regular grid rasters. There are discrete forms of these continuous surfaces available with 'dquadmesh' and 'dtriangmesh' functions.

Tools for Standardizing Variables for Regression in R

Tools which allow regression variables to be placed on similar scales, offering computational benefits as well as easing interpretation of regression output.

Raster Georeferencing, Grid Affine Transforms, Cell Abstraction

Tools for raster georeferencing, grid affine transforms, and general raster logic. These functions provide converters between raster specifications, world vector, geotransform, 'RasterIO' window, and 'RasterIO window' in 'sf' package list format. There are functions to offset a matrix by padding any of four corners (useful for vectorizing neighbourhood operations), and helper functions to harvesting user clicks on a graphics device to use for simple georeferencing of images. Methods used are available from < https://en.wikipedia.org/wiki/World_file> and < https://gdal.org/user/raster_data_model.html>.

Spatial Extent Tools

Functions to produce a fully fledged 'geo-spatial' object extent as a 'SpatialPolygonsDataFrame'. Also included are functions to generate polygons from raster data using 'quadmesh' techniques, a round number buffered extent, and general spatial-extent and 'raster-like' extent helpers missing from the originating packages. Some latitude-based tools for polar maps are included.

Constrained Triangulation for Simple Features

Build a constrained high quality Delaunay triangulation from simple features objects, applying constraints based on input line segments, and triangle properties including maximum area, minimum internal angle. The triangulation code in 'RTriangle' uses the method of Cheng, Dey and Shewchuk (2012, ISBN:9781584887300). For a low-dependency alternative with low-quality path-based constrained triangulation see < https://CRAN.R-project.org/package=decido> and for high-quality configurable triangulation see < https://github.com/hypertidy/anglr>. Also consider comparison with the 'GEOS' lib which since version 3.10.0 includes a low quality polygon triangulation method that starts with ear clipping and refines to Delaunay.

Tools for 'ROMS' the Regional Ocean Modeling System

Helper functions for working with Regional Ocean Modeling System 'ROMS' output. See < https://www.myroms.org/> for more information about 'ROMS'.

Southern Ocean Frontal Distributions (Orsi)

A data set package with the "Orsi" and "Park/Durand" fronts as 'SpatialLinesDataFrame' objects. The Orsi et al. (1995) fronts are published at the Southern Ocean Atlas Database Page, and the Park et al. (2019) fronts are published at the 'SEANOE' Altimetry-derived Antarctic Circumpolar Current fronts page, please see package CITATION for details.

Principal Component Analysis Applied to Ridit Scoring

Implements the 'PRIDIT' (Principal Component Analysis applied to 'RIDITs') scoring system described in Brockett et al. (2002) . Provides functions for ridit scoring originally developed by Bross (1958) , calculating 'PRIDIT' weights, and computing final 'PRIDIT' scores for multivariate analysis of ordinal data.