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permute - Functions for Generating Restricted Permutations of Data

A set of restricted permutation designs for freely exchangeable, line transects (time series), and spatial grid designs plus permutation of blocks (groups of samples) is provided. 'permute' also allows split-plot designs, in which the whole-plots or split-plots or both can be freely-exchangeable or one of the restricted designs. The 'permute' package is modelled after the permutation schemes of 'Canoco 3.1' (and later) by Cajo ter Braak.

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permutationrestricted-permutations

14.00 score 24 stars 509 dependents 708 scripts 96k downloads

gratia - Graceful 'ggplot'-Based Graphics and Other Functions for GAMs Fitted Using 'mgcv'

Graceful 'ggplot'-based graphics and utility functions for working with generalized additive models (GAMs) fitted using the 'mgcv' package. Provides a reimplementation of the plot() method for GAMs that 'mgcv' provides, as well as 'tidyverse' compatible representations of estimated smooths.

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distributional-regressiongamgammgeneralized-additive-mixed-modelsgeneralized-additive-modelsggplot2glmlmmgcvpenalized-splinerandom-effectssmoothingsplinesopenblascpp

13.59 score 233 stars 6 dependents 3.1k scripts 3.9k downloads

analogue - Analogue and Weighted Averaging Methods for Palaeoecology

Fits Modern Analogue Technique and Weighted Averaging transfer function models for prediction of environmental data from species data, and related methods used in palaeoecology.

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8.41 score 14 stars 4 dependents 183 scripts 1.1k downloads

ggvegan - 'ggplot2' Plots for the 'vegan' Package

Functions to produce 'ggplot2'-based plots of objects produced by functions in the 'vegan' package. Provides fortify(), autoplot(), and tidy() methods for many of 'vegan''s functions. The aim of 'ggvegan' is to make it easier to work within the 'tidyverse' with 'vegan'.

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7.87 score 126 stars 422 scripts 761 downloads

coenocliner - Coenocline Simulation

Simulate species occurrence and abundances (counts) along gradients.

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6.61 score 12 stars 1 dependents 14 scripts 400 downloads

cocorresp - Co-Correspondence Analysis Methods

Fits predictive and symmetric co-correspondence analysis (CoCA) models to relate one data matrix to another data matrix. More specifically, CoCA maximises the weighted covariance between the weighted averaged species scores of one community and the weighted averaged species scores of another community. CoCA attempts to find patterns that are common to both communities.

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5.56 score 6 stars 40 scripts 674 downloads

MRFtools - Tools for Constructing and Plotting Markov Random Fields in R for Graphical Data

Utility functions for using Markov Random Field smooths in Generalized Additive Models fitted with the 'mgcv' package.

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quarto

3.68 score 16 scripts

temporalEF - Temporal Eigenfunctions

Build sets of (asymmetric) one-dimensional, temporal eigenfunctions. The set of eigenfunctions are orthogonal patterns of temporal variation at a range of scales. Two types of temporal eigenfunctions are implemented; i) asymmetric temporal eigenfunctions (ATEs), based on the Asymmetric Eigenvector Map (AEM) method of Blanchet et al (2008), and ii) principal coordinates of temporal neighbour matrices (PCTNs), based on the concept of principal coordinates of neighbour matrices.

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2.30 score 4 stars

analogueExtra - Additional Functions for Use with the 'analogue' Package

Provides additional functionality for the analogue package that is not required by all users of the main package.

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1.70 score 1 stars 1 scripts 31 downloads