Package: fuzzySim 4.26

A. Marcia Barbosa

fuzzySim: Fuzzy Similarity in Species Distributions

Functions to compute fuzzy versions of species occurrence patterns based on presence-absence data (including inverse distance interpolation, trend surface analysis, and prevalence-independent favourability obtained from probability of presence), as well as pair-wise fuzzy similarity (based on fuzzy logic versions of commonly used similarity indices) among those occurrence patterns. Includes also functions for model consensus and comparison (overlap and fuzzy similarity, loss or gain), and for data preparation, such as obtaining unique abbreviations of species names, cleaning and gridding (thinning) point occurrence data onto raster maps, selecting absences under specified criteria, converting species lists (long format) to presence-absence tables (wide format), transposing part of a data frame, selecting relevant variables for models, assessing the false discovery rate, or analysing and dealing with multicollinearity. Initially described in Barbosa (2015) <doi:10.1111/2041-210X.12372>.

Authors:A. Marcia Barbosa [aut], Paul Melloy [ctb], Jose Carlos Guerrero [fnd], A. Marcia Barbosa [cre]

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fuzzySim.pdf |fuzzySim.html
fuzzySim/json (API)
NEWS

# Install 'fuzzySim' in R:
install.packages('fuzzySim', repos = c('https://r-forge.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://r-forge.r-project.org/projects/fuzzysim

Datasets:
  • rotif.env - Rotifers and environmental variables on TDWG level 4 regions of the world
  • rotifers - Rotifer species on TDWG level 4 regions of the world

On CRAN:

5.05 score 2 stars 139 scripts 658 downloads 4 mentions 42 exports 4 dependencies

Last updated 1 days agofrom:a014c158bf. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winOKOct 31 2024
R-4.5-linuxOKOct 31 2024
R-4.4-winOKOct 31 2024
R-4.4-macOKOct 31 2024
R-4.3-winOKOct 31 2024
R-4.3-macOKOct 31 2024

Exports:appendDatabioThreatcleanCoordscorSelectdistPresdms2decentropyFavfavClassFDRfuzSimfuzzyConsensusfuzzyOverlayfuzzyRangeChangegetPredsgetRegiongridRecordsintegerColsmodelTrimmodOverlapmultConvertmultGLMmulticolmultTSApairwiseRangemapspercentTestDataprevalencerangemapSimrarityselectAbsencessharedFavsimFromSetOpssimMatspCodessplist2presabsstepByStepstepwisesummaryWaldtimertransposetriMatIndvulnerability

Dependencies:modEvARcppstringiterra

Readme and manuals

Help Manual

Help pageTopics
Fuzzy Similarity in Species DistributionsfuzzySim-package fuzzySim
Append dataappendData
Biotic threat of a stronger over a weaker species based on their favourability valuesbioThreat
Clean coordinatescleanCoords
Select among correlated variables based on a given criterioncorSelect
(Inverse) distance to the nearest presencedistPres
Degree-minute-second to decimal degree coordinatesdms2dec
(Fuzzy) entropyentropy
Favourability (probability without the effect of sample prevalence)Fav
Classify favourability into 3 categories (low, intermediate, high)favClass
False Discovery RateFDR
Fuzzy similarityfuzSim
Fuzzy consensus among model predictionsfuzzyConsensus
Overlay operations based on fuzzy logicfuzzyOverlay
Range change based on continuous (fuzzy) valuesfuzzyRangeChange
Get model predictionsgetPreds
Get regiongetRegion
Grid (or thin) point occurrence records to the resolution of a raster mapgridRecords
Classify integer columnsintegerCols
Trim off non-significant variables from a modelmodelTrim
Overall overlap between model predictionsmodOverlap
Multiple conversionmultConvert
GLMs with variable selection for multiple speciesmultGLM
Analyse multicollinearity in a dataset, including VIFmulticol
Trend Surface Analysis for multiple speciesmultTSA
Pairwise intersection (and union) of range mapspairwiseRangemaps
Percent test datapercentTestData
Prevalenceprevalence
Pairwise similarity between rangemapsrangemapSim
(Fuzzy) rarityrarity
Rotifers and environmental variables on TDWG level 4 regions of the worldrotif.env
Rotifer species on TDWG level 4 regions of the worldrotifers
Select (spatially biased) absence rows.selectAbsences
Shared favourability for two competing speciessharedFav
Calculate similarity from set operationssimFromSetOps
Pair-wise (fuzzy) similarity matrixsimMat
Obtain unique abbreviations of species namesspCodes
Convert a species list to a presence-absence tablesplist2presabs
Compare model predictions along a stepwise variable selection processstepByStep
Stepwise regressionstepwise
Model summary with Wald (instead of z) test statisticssummaryWald
Timertimer
Transpose (part of) a matrix or dataframetranspose
Triangular matrix indicestriMatInd
(Fuzzy) vulnerabilityvulnerability