# fuzzySim: Fuzzy similarity in species distributions

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

## 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 |