
============================================
fuzzySim v3.7 (committed 2022-01-21)
============================================

## Modified functions:

* corSelect
- fixed new CRAN check error (with 'all.equal' in 'corSelect') on r-devel-linux-x86_64-fedora-clang and r-devel-linux-x86_64-fedora-gcc (by manually setting the 'tolerance' argument for 'all.equal')

* Fav
- added import modEvA::mod2obspred


## Other modified files:

* fuzsim.Rd
- updated Sorensen wikipedia link with 'https'


============================================
fuzzySim v3.6 (committed 2021-09-29)
============================================

## Modified functions:

* Fav
- 'model' argument can now be of class 'glm', 'gam', 'gbm', 'randomForest' or 'bart'
- 'pred' can now also be a 'SpatRaster' ('terra' pkg) object

* gridRecords
- 'rst' can now also be a 'SpatRaster' ('terra' pkg) object
- Raster* 'rst' coerced to SpatRaster if 'terra' pkg is installed


============================================
fuzzySim v3.5 (committed 2021-09-04)
============================================

## Modified functions:

* FDR
- fixed bug when using 'pvalues' as input (following bug report by Stephen via modTools contact form)


============================================
fuzzySim v3.4 (committed 2021-09-02)
============================================

## Modified functions:

* gridRecords
- fixed bug when only one raster layer [ , drop = FALSE]


============================================
fuzzySim v3.3 (committed 2021-04-24)
============================================

## Modified functions:

* simMat
- added 'verbosity' argument
- replaced "25%-50%-75% done" with 'utils::txtProgressBar'

* multTSA
- added 'verbosity' argument

* getPreds
- added 'verbosity' argument
- 'data' can now also be a RasterBrick (not only dataframe or a RasterStack)

* Fav
- added 'verbosity' argument
- 'pred' can now also be a RasterLayer (not only a numeric vector)


============================================
fuzzySim v3.2 (committed 2020-12-12)
============================================

## Modified functions:

* favClass (benefitting also bioThreat)
- added 'is.na(fav) | ' to 'stopifnot' to avoid NA fail


## Other changes:

- added Linero et al. (2020) to references of papers using fuzzySim


============================================
fuzzySim v3.1 (committed 2020-09-18)
============================================

## Modified functions:

* gridRecords
- added 'absences' logical argument


============================================
fuzzySim v3.0 (committed 2020-02-03) -> CRAN
============================================

## Modified functions:

* gridRecords
- added 'na.rm' argument (default TRUE)
- fixed bug when no gridded absences (i.e. no absence AND not presence)


## Other changes:

-  clarifications and typo/format corrections in the manual


============================================
fuzzySim v2.5 (committed 2020-01-31)
============================================

## Modified files:

* gridRecords.Rd
- added examples


============================================
fuzzySim v2.2.4 (committed 2020-01-30)
============================================

## New functions:

* gridRecords


## Modified functions:

* getPreds:
- replaced 'if("raster" %in% class(data))' (no longer working) with 'if (is(data, "RasterStack"))'
- added 'Imports: methods' to DESCRIPTION and 'importFrom("methods", "is")' to NAMESPACE
- if 'data' are raster, added 'raster::' before 'stack'


============================================
fuzzySim v2.2.3 (committed 2020-01-06)
============================================

## Modified functions:

* multGLM:
- fixed id.col name in 'predictions' when id.col input as character

## Other changes:

- added 'inst' folder with article citation information
- removed 'onAttach' function with citation message on load
- added package URLs to DESCRIPTION file


============================================
fuzzySim v2.2.2 (committed 2020-01-03)
============================================

## Modified functions:

* multGLM:
- output now includes list of selected variables per model
- sp.cols, var.cols and id.col can now optionally be input as column names rather than index numbers


## Other changes:

- fixed length of some lines along the PDF manual


============================================
fuzzySim v2.2.1 (committed 2019-10-18)
============================================

## Modified functions:

* modOverlap:
- corrected typo in na.rm closing parentheses (reported by Heidi Mod)

* Fav:
- slightly reduced probabilities of exactly 1, which would cause division by zero (resulting Fav is still 1)


============================================
fuzzySim v2.2 (committed 2019-03-10)
============================================

## New functions:

* sharedFav


============================================
fuzzySim v2.1 (committed 2019-03-07)
============================================

## New functions:

* favClass
* bioThreat


## Modified functions:

* multGLM:
- spatial_trend variable in models (when TSA=TRUE and the spatial trend is selected) now named after the response variable (e.g. 'sptrend_giraffe')

* getPreds:
- fixed new bug by replacing 'if (class(data) == "RasterStack")' with 'if ("RasterStack" %in% class(data))'


## Modified .Rd files:

* multGLM:
- added example with TSA=TRUE


## Other changes:

- updated maintainer e-mail address


============================================
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)

## package sent to CRAN


============================================
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)


