fuzzySim: Fuzzy similarity in species distributions

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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.

Author
Barbosa A.M.
Date of publication
2016-09-30 11:21:15
Maintainer
A. Marcia Barbosa <barbosa@uevora.pt>
License
GPL-3
Version
1.7.8

View on R-Forge

Man pages

corSelect
Select among correlated variables based on their relationship...
distPres
(Inverse) distance to the nearest presence
Fav
Favourability
FDR
False Discovery Rate
fuzSim
Fuzzy similarity
fuzzyOverlay
Row-wise overlay operations based on fuzzy logic
fuzzyRangeChange
Range change based on continuous (fuzzy) values
fuzzySim-package
Fuzzy similarity in species distributions
getPreds
Get model predictions
integerCols
Classify integer columns
modelTrim
Trim off non-significant variables from a model
modOverlap
Overall overlap between model predictions
multConvert
Multiple conversion
multGLM
GLMs for multiple species with multiple options
multicol
Analyse multicollinearity in a dataset, including VIF
multTSA
Trend Surface Analysis for multiple species
pairwiseRangemaps
Pairwise intersection (and union) of range maps
percentTestData
Percent test data
rangemapSim
Pairwise similarity between rangemaps
rotif.env
Rotifers and environmental variables on TDWG level 4 regions...
rotifers
Rotifer species on TDWG level 4 regions of the world
simFromSetOps
Calculate similarity from set operations
simMat
Pair-wise (fuzzy) similarity matrix
spCodes
Obtain unique abbreviations of species names
splist2presabs
Convert a species list to a presence-absence table
stepByStep
Analyse and compare stepwise model predictions
timer
Timer
transpose
Transpose (part of) a matrix or dataframe
triMatInd
Triangular matrix indices

Files in this package

fuzzySim/DESCRIPTION
fuzzySim/NAMESPACE
fuzzySim/NEWS
fuzzySim/R
fuzzySim/R/FDR.R
fuzzySim/R/Fav.R
fuzzySim/R/corSelect.R
fuzzySim/R/distPres.R
fuzzySim/R/fuzSim.R
fuzzySim/R/fuzzyOverlay.R
fuzzySim/R/fuzzyRangeChange.R
fuzzySim/R/fuzzySim-internal.R
fuzzySim/R/getPreds.R
fuzzySim/R/integerCols.R
fuzzySim/R/modOverlap.R
fuzzySim/R/modelTrim.R
fuzzySim/R/multConvert.R
fuzzySim/R/multGLM.R
fuzzySim/R/multTSA.R
fuzzySim/R/multicol.R
fuzzySim/R/onAttach.R
fuzzySim/R/pairwiseRangemaps.R
fuzzySim/R/percentTestData.R
fuzzySim/R/rangemapSim.R
fuzzySim/R/simFromSetOps.R
fuzzySim/R/simMat.R
fuzzySim/R/spCodes.R
fuzzySim/R/splist2presabs.R
fuzzySim/R/stepByStep.R
fuzzySim/R/timer.R
fuzzySim/R/transpose.R
fuzzySim/R/triMatInd.R
fuzzySim/data
fuzzySim/data/rotif.env.rda
fuzzySim/data/rotifers.rda
fuzzySim/dummyfile
fuzzySim/man
fuzzySim/man/FDR.Rd
fuzzySim/man/Fav.Rd
fuzzySim/man/corSelect.Rd
fuzzySim/man/distPres.Rd
fuzzySim/man/fuzSim.Rd
fuzzySim/man/fuzzyOverlay.Rd
fuzzySim/man/fuzzyRangeChange.Rd
fuzzySim/man/fuzzySim-package.Rd
fuzzySim/man/getPreds.Rd
fuzzySim/man/integerCols.Rd
fuzzySim/man/modOverlap.Rd
fuzzySim/man/modelTrim.Rd
fuzzySim/man/multConvert.Rd
fuzzySim/man/multGLM.Rd
fuzzySim/man/multTSA.Rd
fuzzySim/man/multicol.Rd
fuzzySim/man/pairwiseRangemaps.Rd
fuzzySim/man/percentTestData.Rd
fuzzySim/man/rangemapSim.Rd
fuzzySim/man/rotif.env.Rd
fuzzySim/man/rotifers.Rd
fuzzySim/man/simFromSetOps.Rd
fuzzySim/man/simMat.Rd
fuzzySim/man/spCodes.Rd
fuzzySim/man/splist2presabs.Rd
fuzzySim/man/stepByStep.Rd
fuzzySim/man/timer.Rd
fuzzySim/man/transpose.Rd
fuzzySim/man/triMatInd.Rd