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.


News

TO DO:

  • stepByStep:
  • implement 'direction = both'

============================================ fuzzySim v2.0 (committed 2018-12-05)

Modified functions:

  • multTSA:
  • resulting model object now named 'models' rather than 'TSA.models'
  • corrected bug in coordinate polynomial names (if save.models = TRUE)

============================================ fuzzySim v1.9 (committed 2018-11-20)

Modified functions:

  • distPres
  • 'inv' now subtracts from 1 (after standardizing) rather than dividing by 1
  • multTSA:
  • added 'criterion' argument, which can be 'AIC' (to use 'step') or 'significance' (to use 'modelTrim')
  • added '...' argument to pass to modelTrim
  • introduced more informative coordinate polynomial names (visible if 'save.models = TRUE')
  • added 'simple = TRUE' to 'poly' for speedup
  • modelTrim:
  • added 'data' argument to 'update', to avoid 'attach'
  • multGLM:
  • added arguments 'verbosity', 'TSA' and 'coord.cols'
  • added 'data = train.data' to 'step', and 'with(train.data' to 'model.formula', so finally got rid of 'attach'
  • "Building model 1..." 'message' instances replaced with 'cat' so that they are saved if 'sink' is used

============================================ fuzzySim v1.8.3 (committed 2018-07-06)

Modified functions:

  • multTSA:
  • added argument 'type' which can be "Y", "P" (the default, for back-compatibility) or "F" (which substitutes the deprecated argument below)
  • deprecated argument 'Favourability = FALSE'

Modified .Rd files:

  • multTSA:
  • documented argument changes described above
  • pairwiseRangemaps:
  • updated literature reference

webpage:

  • added additional article citing fuzzySim

============================================ fuzzySim v1.8.2 (committed 2018-05-23)

Modified functions:

  • getPreds:
  • 'data' can now be a RasterStack

============================================ fuzzySim v1.8.1 (committed 2018-05-15)

Modified functions:

  • multTSA:
  • fixed bug when only one species was used

webpage:

  • added articles citing fuzzySim

============================================ fuzzySim v1.8.0 (committed 2017-07-07)

Modified functions:

  • corSelect:
  • included 'VIF' criterion

============================================ fuzzySim v1.7.9 (committed 2017-03-27)

Modified functions:

  • multGLM:
  • fixed bug when only one variabe passed to corSelect
  • corSelect:
  • added check that 'data' is not missing and is a data frame
  • help file now states that corSelect is included as option in multGLM
  • added 'use = "pairwise.complete.obs"' to examples
  • PDF manual:
  • reduced several code line lengths to avoid overboard

============================================ fuzzySim v1.7.8 (committed 2016-09-15)

Removed empty sections from .Rd files

Modified functions:

  • fuzzyRangeChange:
  • underscore replaced with space in measure names
  • x axis labels plotted instead of legend
  • 'col' no longer supplied by default

============================================ fuzzySim v1.7.7 (committed 2016-08-01)

Modified functions:

  • pairwiseRangemaps:
  • argument 'chunks' replaced with 'nchunks' for operative reasons
  • added 'subchunks' argument for continuing interrupted runs

============================================ fuzzySim v1.7.6 (committed 2016-05-05)

Modified functions:

  • corSelect:
  • removed error when no corrs above threshold
  • sp.cols now NULL by default (to avoid error when missing)
  • multGLM:
  • FDR correction reverted to "fdr" by default

============================================ fuzzySim v1.7.5 (committed 2016-04-26)

Modified functions:

  • FDR:
  • BIC now also provided
  • corSelect:
  • BIC now included as selection criterion
  • multGLM:
  • added "select" argument (for 'step') - AIC or BIC

============================================ fuzzySim v1.7.4 (committed 2016-04-15)

Modified functions:

  • multGLM:
  • FDR correction now "BY" by default

============================================ fuzzySim v1.7.3 (committed 2016-04-12)

Modified functions:

  • corSelect:
  • error message when length(sp.cols) > 1
  • message about excluded missing data
  • added option sp.cols=NULL to get only high.cor.mat
  • multGLM:
  • added 'correction' argument to pass to 'FDR'

============================================ fuzzySim v1.7.2 (committed 2016-03-22)

Modified functions:

  • fuzzyRangeChange:
  • user can now choose which measures to calculate
  • 'loss' now reported as originally negative
  • results provided also as a barplot

============================================ fuzzySim v1.7.1 (committed 2016-03-17)

Modified functions:

  • multTSA:
  • eliminated call to 'attach'

============================================ fuzzySim v1.7 (committed 2016-02-12)

New functions:

  • pairwiseRangemaps (calculate area of pairwise intersection and union between rangemaps)

  • rangemapSim (calculate rangemap similarity using common similarity indices)

============================================ fuzzySim v1.6.3 (committed 2015-12-02)

Modified functions:

  • FDR:
  • now uses only finite sp.col values

============================================ fuzzySim v1.6.2 (committed 2015-11-23)

Modified functions:

  • fuzzyRangeChange:
  • corrected proportional changes to be relative to reference range size, not total study area
  • replaced "stable" with "stable presence" and added (fuzzy equivalent of) "stable absence"
  • replaced "change" with "balance" (overall loss/gain, not amount of changed cells)
  • result is now data frame, not named vector
  • distPres:
  • now allows NA values

============================================ fuzzySim v1.6.1 (committed 2015-11-13)

Modified functions:

  • fuzzyOverlay:
  • added arguments 'prop = TRUE' and 'overlay.cols = 1:ncol(data)'
  • result now includes 4 (not 8) values, either sum or proportion
  • result is now a named vector instead of a list
  • 'na.rm' now TRUE by default
  • fuzSim:
  • added argument 'na.rm = TRUE'
  • multGLM:
  • bug corrected in corSelect (was reporting but not really eliminating variables)
  • suppressMessages in corSelect

Modified help files:

  • fuzzyOverlay: modifications reflecting function changes

  • modOverlap: example now provided

  • fuzzyOverlay, fuzzyRangeChange, modOverlap:

  • examples containing 'jitter' corrected to avoid values outside the [0, 1] interval
  • fuzSim:
  • examples now provided also for similarity between fuzzy data
  • tables of significance for Jaccard and Baroni's indices now referred

============================================ fuzzySim v1.6 (committed 2015-11-03)

New functions:

  • fuzzyOverlay (calculate row-wise intersection, union, expansion, contraction or consensus among continuous model predictions)

  • fuzzyRangeChange (calculate overal loss, gain, and maintenance of favourability between models)

============================================ fuzzySim v1.5 (committed 2015-10-29)

New functions:

  • corSelect (select among correlated variables based on their bivariate relationship with the response)

  • modOverlap (asses the total overlap between model predictions using niche comparison metrics)

Modified functions:

  • multGLM:
  • 'corSelect' now included as additional option for variable selection
  • FDR:
  • AIC now also calculated
  • 'model.type' deprecated
  • 'family = "auto"' by default
  • 'simplif' argument added

============================================ previous edits (that I can remember)

Modified functions:

  • multicol:
  • 'model' argument added (user can provide a model object instead of a set of variables)
  • variables in output are now ordered according to VIF
  • simFromSetOps:
  • the similarity index used is now mentioned in a message
  • FDR:
  • data input format changed, with former parameters 'response' and 'predictors' replaced with 'data', 'sp.cols' and 'var.cols' (for coherence and compatibility with 'multGLM' function)

Reference manual

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install.packages("fuzzySim")

2.0 by A. Marcia Barbosa, 8 months ago


Browse source code at https://github.com/cran/fuzzySim


Authors: Barbosa A.M.


Documentation:   PDF Manual  


GPL-3 license


Suggests maptools, parallel, PBSmapping, sp, tools, raster


See at CRAN