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fuzzySim (version 3.0)

Fuzzy Similarity in Species Distributions

Description

Functions to calculate fuzzy versions of species' occurrence patterns based on presence-absence data (including inverse distance interpolation, trend surface analysis and prevalence-independent favourability GLM), and pair-wise fuzzy similarity (based on fuzzy versions of commonly used similarity indices) among those occurrence patterns. Includes also functions for model comparison (overlap and fuzzy similarity, loss or gain), and for data preparation, such as obtaining unique abbreviations of species names, converting species lists (long format) to presence-absence tables (wide format), transposing part of a data frame, assessing the false discovery rate, or analysing and dealing with multicollinearity among variables. Includes also sample datasets for providing practical examples.

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Version

Install

install.packages('fuzzySim')

Monthly Downloads

1,184

Version

3.0

License

GPL-3

Maintainer

A. Barbosa

Last Published

February 4th, 2020

Functions in fuzzySim (3.0)

fuzzyOverlay

Row-wise overlay operations based on fuzzy logic
bioThreat

Biotic threat of a stronger over a weaker species based on their favourability values
fuzzySim-package

Fuzzy Similarity in Species Distributions
favClass

Classify favourability into 3 categories (low, intermediate, high)
fuzzyRangeChange

Range change based on continuous (fuzzy) values
fuzSim

Fuzzy similarity
FDR

False Discovery Rate
Fav

Favourability
distPres

(Inverse) distance to the nearest presence
corSelect

Select among correlated variables based on a given criterion
pairwiseRangemaps

Pairwise intersection (and union) of range maps
simMat

Pair-wise (fuzzy) similarity matrix
gridRecords

Grid point occurrence records onto a raster
getPreds

Get model predictions
modOverlap

Overall overlap between model predictions
multicol

Analyse multicollinearity in a dataset, including VIF
splist2presabs

Convert a species list to a presence-absence table
modelTrim

Trim off non-significant variables from a model
spCodes

Obtain unique abbreviations of species names
multConvert

Multiple conversion
rotif.env

Rotifers and environmental variables on TDWG level 4 regions of the world
multTSA

Trend Surface Analysis for multiple species
multGLM

GLMs with variable selection for multiple species
timer

Timer
integerCols

Classify integer columns
rotifers

Rotifer species on TDWG level 4 regions of the world
triMatInd

Triangular matrix indices
percentTestData

Percent test data
transpose

Transpose (part of) a matrix or dataframe
rangemapSim

Pairwise similarity between rangemaps
stepByStep

Analyse and compare stepwise model predictions
simFromSetOps

Calculate similarity from set operations
sharedFav

Shared favourability for two competing species