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