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fuzzySim v3.0 (committed 2020-02-03) -> CRAN
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## 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
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fuzzySim v2.5 (committed 2020-01-31)
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## Modified files:
* gridRecords.Rd
- added examples
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fuzzySim v2.2.4 (committed 2020-01-30)
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## 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'
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fuzzySim v2.2.3 (committed 2020-01-06)
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## 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
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fuzzySim v2.2.2 (committed 2020-01-03)
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## 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
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fuzzySim v2.2.1 (committed 2019-10-18)
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## 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)
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fuzzySim v2.2 (committed 2019-03-10)
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## New functions:
* sharedFav
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fuzzySim v2.1 (committed 2019-03-07)
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## 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
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fuzzySim v2.0 (committed 2018-12-05)
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## 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
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fuzzySim v1.9 (committed 2018-11-20)
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## 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
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fuzzySim v1.8.3 (committed 2018-07-06)
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## 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
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fuzzySim v1.8.2 (committed 2018-05-23)
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## Modified functions:
* getPreds:
- 'data' can now be a RasterStack
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fuzzySim v1.8.1 (committed 2018-05-15)
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## Modified functions:
* multTSA:
- fixed bug when only one species was used
## webpage:
- added articles citing fuzzySim
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fuzzySim v1.8.0 (committed 2017-07-07)
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## Modified functions:
* corSelect:
- included 'VIF' criterion
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fuzzySim v1.7.9 (committed 2017-03-27)
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## 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
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fuzzySim v1.7.8 (committed 2016-09-15)
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## 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
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fuzzySim v1.7.7 (committed 2016-08-01)
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## Modified functions:
* pairwiseRangemaps:
- argument 'chunks' replaced with 'nchunks' for operative reasons
- added 'subchunks' argument for continuing interrupted runs
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fuzzySim v1.7.6 (committed 2016-05-05)
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## 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
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fuzzySim v1.7.5 (committed 2016-04-26)
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## Modified functions:
* FDR:
- BIC now also provided
* corSelect:
- BIC now included as selection criterion
* multGLM:
- added "select" argument (for 'step') - AIC or BIC
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fuzzySim v1.7.4 (committed 2016-04-15)
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## Modified functions:
* multGLM:
- FDR correction now "BY" by default
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fuzzySim v1.7.3 (committed 2016-04-12)
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## 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'
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fuzzySim v1.7.2 (committed 2016-03-22)
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## Modified functions:
* fuzzyRangeChange:
- user can now choose which measures to calculate
- 'loss' now reported as originally negative
- results provided also as a barplot
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fuzzySim v1.7.1 (committed 2016-03-17)
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## Modified functions:
* multTSA:
- eliminated call to 'attach'
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fuzzySim v1.7 (committed 2016-02-12)
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## New functions:
* pairwiseRangemaps (calculate area of pairwise intersection and union between rangemaps)
* rangemapSim (calculate rangemap similarity using common similarity indices)
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fuzzySim v1.6.3 (committed 2015-12-02)
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## Modified functions:
* FDR:
- now uses only finite sp.col values
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fuzzySim v1.6.2 (committed 2015-11-23)
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## 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
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fuzzySim v1.6.1 (committed 2015-11-13)
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## 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
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fuzzySim v1.6 (committed 2015-11-03)
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## 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)
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fuzzySim v1.5 (committed 2015-10-29)
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## 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
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previous edits (that I can remember)
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## 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)