                        Changes in version 3.48                         

(Committed 2026-10-07)

Modified functions:

  - plotGLM
    
      - change plot colours to match other functions

  - multModEv
    
      - add plot=FALSE to HLfit() call

Other modified files:

  - DESCRIPTION
    
      - add package DOI (CRAN)
      - add GitHub URL besides R-Forge

  - CITATION
    
      - replace URL with package DOI

                  Changes in version 3.47 (2026-09-25)                  

(Committed 2026-09-25)

Modified functions:

  - varImp
    
      - fix bugs when horiz = TRUE

  - predPlot, predDensity, varImp
    
      - semi-transparent legend background, in case of overlap

                  Changes in version 3.46 (2026-08-28)                  

(Committed 2026-08-04)

Modified functions:

  - varImp
    
      - implement "each" for GAM (with warning)

  - HLfit
    
      - include 'HLI' in output also when simplif = TRUE

  - plotCoeffs
    
      - add dashed dark-red abline() where coefficients = 0

Other modified files:

  - plotCoeffs.Rd
    
      - improve 'model' argument description to reflect that it
        accommodates more classes
      - add confint() to SeeAlso

  - mod2obspred.Rd
    
      - mention use by fuzzySim::clampVars()

                  Changes in version 3.45 (2026-05-21)                  

(Committed 2026-04-21)

Modified functions:

  - Miller
    
      - add "MCA" output (inverse standardized slope difference)
      - change 'plot.values' shown
      - add 'values.col' argument

  - getBins
    
      - show also empty bins

  - HLfit
    
      - add 'HLI' output (inverse standardized HL index)
      - fix error when empty bins
      - change 'plot.values' shown
      - add 'values.col' argument
      - move 'simplif' code to after 'plot', so that both can be TRUE
      - bin size red for small bins
      - reduce bin size cex, and add transparency for overlaps
      - change plot colours, par('mgp') and axis limits to better match
        other functions

  - Boyce
    
      - add "xlim" and "ylim" arguments

  - AUC, Boyce, Miller
    
      - format plot value to show 3 decimals even if 0

  - poMeasures
    
      - accommodate 'pred' values outside [0, 1] (with warning)

                        Changes in version 3.44                         

(Committed 2026-04-29)

Modified functions:

  - evaluate (benefiting threshMeasures)
    
      - fix bug in SEDI computation

  - threshMeasures
    
      - add SEDI to (optionally) standardized measures
      - non-finite measures also in plot

Other modified files:

  - threshMeasures.Rd
      - list, define and cite output measures

                        Changes in version 3.43                         

(Committed 2026-04-17)

Modified functions:

  - getBins
    
      - fix bug (extra bin at the end) when bin.method="mov.bins" &
        !is.na(n.bins)

  - predDensity
    
      - add 'bw' arg to pass to density()
      - add wilcox.test() and ks.test() of pred1 vs pred0 (if
        separate=TRUE)

  - Boyce
    
      - red-flag small bins under 15 (not 30) values, as per biblio now
        cited in help file

  - Boyce, poMeasures
    
      - add 'simplif' argument
      - improve plot value placement

  - several functions producing plots
    
      - change colours to steel blues and slate greys

Other modified files:

  - most .Rd files
    
      - explicitly add "optional" at the beginning of the 'model'
        argument descriptions

  - AUC.Rd
    
      - mention AUC-PR flaw and add reference to the alternative
        Precision-Recall-Gain curve

                        Changes in version 3.42                         

(Committed 2026-02-27)

New functions:

  - poMeasures
      - experimental, under review

Modified functions:

  - MillerCalib
      - renamed to Miller

Other modified files:

  - CITATION
      - add citation of package with self-updating version and year

                  Changes in version 3.41 (2026-01-09)                  

(Committed 2026-01-08)

Modified functions:

  - Boyce
    
      - fixed bug identified in 'ecospat' original code at
        https://github.com/ecospat/ecospat/issues/99#issue-2528136160

  - AUC
    
      - added Somer's D (= Gini coefficient) to outputs

Other modified files:

  - Boyce.Rd
      - added "See also" section

                  Changes in version 3.40 (2025-09-20)                  

(Committed 2025-09-19)

Modified functions:

  - varImp
    
      - add required 'n.trees' and 'newdata' args to predict() call for
        GBM models

  - Boyce
    
      - move 'r <-' upward to fix bug for edge cases with very few
        unique pred values

  - evaluate (benefiting threshMeasures)
    
      - convert a, b, c and d to numeric, to avoid kappa integer
        overflow when large numbers (seen in
        https://github.com/benjjneb/dada2/issues/1747#issuecomment-1579180381)

                  Changes in version 3.39 (2025-07-18)                  

(Committed 2025-07-03) -> CRAN

Modified functions:

  - MillerCalib
      - plot values: replace "slope - 1" with "slopeDiff"
      - include 'slopeDiff' in console output

Other modified files:

  - varImp.Rd
      - mention Shapley values in See Also

                        Changes in version 3.38                         

(Committed 2025-06-29)

Modified functions:

  - MillerCalib
    
      - move intercept value on plot back to just after slope

  - pseudoRsq
    
      - improved Tjur NA message, and show it only when verbosity > 1

Other modified files:

  - RsqGLM.Rd, pseudoRsq.Rd
      - removed duplicated info to avoid future mismatches; slightly
        improved text

                        Changes in version 3.37                         

(Committed 2025-06-21)

Modified functions:

  - varImp
    
      - replaced instances of methods::is() with inherits()
      - check if class 'Gam' or 'gam', in which case 'imp.type'
        automatically set to 'permutation' (as 'maxnet' already did)
      - warning (not just message if verbosity) when 'imp.type'
        automatically changed
      - changed 'col' argument defaults to named colours
      - help file mentions 'Gam' and 'gam' classes also implemented

  - mod2obspred
    
      - replaced instances of methods::is() with inherits()

  - prevalence
    
      - replaced if (!is(obs, "vector") && !is(obs, "factor")) with if
        (!is.vector(obs) && !is.factor(obs)) to remove dependency on
        {methods}

Other modified files:

  - NAMESPACE
    
      - removed importFrom("methods", "is")

  - DESCRIPTION
    
      - removed "methods" from Imports

                        Changes in version 3.36                         

(Committed 2025-06-09)

Modified functions:

  - RsqGLM
    
      - renamed to pseudoRsq

  - MillerCalib
    
      - changed colour of slope-1 value on plot, from red (too dramatic)
        to dark red
      - moved slope-1 value on plot to just after slope, before
        intercept

  - optiThresh
    
      - added '...' which was missing in 'plot(all.thresholds, )'

                        Changes in version 3.35                         

(Committed 2025-05-12)

Modified functions:

  - confusionLabel
      - vector output now also ordered factor rather than character (as
        for raster inputs)

Other modified files:

  - AUC.Rd
    
      - mention Swets AUC-ROC interpretation thresholds

  - RsqGLM.Rd

  - mention McFadden R-squared interpretation thresholds

  - threshMeasures.Rd
    
      - mention prevalence dependence and add reference on TSS

  - VarImp.Rd
    
      - mention {vip} and other packages in See Also and References

                  Changes in version 3.34 (2025-04-29)                  

(Committed 2025-04-29) -> CRAN

Modified functions:

  - confusionLabel
    
      - reordered output categories, low to high rather than
        alphabetical
      - removed colour table for rasters

  - RsqGLM
    
      - implemented for raster inputs

  - MillerCalib
    
      - plot text now grey for intercept
      - plot text now includes 1-slope (in red)

                  Changes in version 3.33 (2025-03-20)                  

(Committed 2025-03-19) -> CRAN

Modified functions:

  - AUC
    
      - interval="auto" now 0.01 or 0.001 depending on 'pred' coverage
      - added cex.lab argument
      - improved axis labels

  - MillerCalib, lollipop
    
      - slightly changed default colours

Other modified files:

  - NEWS
      - reformatted and converted to .md to work with news()

                        Changes in version 3.32                         

(Committed 2025-03-18)

Modified functions:

  - plotCoeffs
      - return also data frame with the results
      - improve Details section

                        Changes in version 3.31                         

(Committed 2025-03-05)

Modified functions:

  - varImp
    
      - added option "permutation" for argument 'imp.type' (pending
        implementation for BART models)
      - added partial argument matching
      - added arguments 'n.per', 'data' and 'n.trees' for some model
        classes when imp.type="permutation"
      - implemented also for 'maxnet' models if imp.type = "permutation"

  - mod2obspred
    
      - added option x.only = FALSE; if TRUE, the values of the
        predictors are returned instead (for varImp if imp.type =
        "permutation")

  - AUC
    
      - 'interval' new default "auto", to make it smaller as 'pred' mean
        departs from 0.5

                  Changes in version 3.30 (2025-02-21)                  

(Committed 2025-02-21) -> CRAN

Modified functions:

  - AUC, Boyce, lollipop (affecting threshMeasures), optiPair
      - fixed opar() reset bug: reset only the changed parameter 'mgp'

                  Changes in version 3.29 (2025-02-16)                  

(Committed 2025-02-14) -> CRAN

Modified functions:

  - lollipop (-> varImp, ploCoeffs, threshMeasures, similarity, RsqGLM)
      - removed 'axis.lab' argument for back-compatibility issues
      - improved handling of plot arguments provided under \dots, namely
        xlab and ylab when horiz is either TRUE or FALSE

                        Changes in version 3.28                         

(Committed 2025-02-10)

Modified functions:

  - lollipop
    
      - better distribution between plot limits when two lollipops
      - renamed argument "horizontal" to "horiz", to match barplot()
      - added 'axis.lab' argument, to use as xlab or ylab depending on
        'horiz'

  - plotCoeffs
    
      - added 'labels' argument

  - varImp
    
      - fixed when horizontal = TRUE

  - threshMeasures, similarity
    
      - changed 'las' from 3 to 2

                        Changes in version 3.27                         

(Committed 2025-01-28)

Modified functions:

  - lollipop
    
      - 'bold' default FALSE, not NULL

  - plotCoeffs
    
      - empty plot if no variables in model

Other modified files:

  - lollipop.Rd, plotCoeffs.Rd, varImp.Rd
      - improved Description, Examples, and See also

                        Changes in version 3.26                         

(Committed 2025-01-27)

Modified functions:

  - lollipop
      - new argument "horizontal"
      - "sticks" can also be a matrix of confidence limits

New functions:

  - plotCoeffs
      - uses lollipop() with confidence intervals

Other modified files:

  - evaluate.Rd
      - improved definitions of a, b, c, and d, relating with TP, FP,
        TN, FN

                        Changes in version 3.25                         

(Committed 2024-12-27)

Modified functions:

  - AUC
    
      - new default line colour and diagonal line type
      - xlab closer to axis, to match 2nd line of ylab and fit in
        default margins
      - values also closer to axes

  - Boyce
    
      - labels and values closer to axes
      - new colours for points and for plot text
      - new position for plot text
      - new symbol (triangle) for red points

  - optiPair
    
      - plot values closer to axes
      - new arguments 'col1' and 'col2' for plot point colours

  - optiThresh
    
      - plot values and axis labels closer to axes
      - new plot arguments 'pch', 'cex' and 'col', with new default
        colours and symbols
      - plot margins adjusted also when fewer than 4 measures
      - fixed 'xlab' argument, which wasn't being considered

                        Changes in version 3.24                         

(Committed 2024-12-18)

Modified functions:

  - MillerCalib
      - changed default line colours to blues
      - lwd = 2 for calibration line
      - intercept in parentheses in plot text
      - help file now mentions Baquero et al.'s thresholds for a good
        slope

                  Changes in version 3.23 (2024-11-24)                  

(Committed 2024-11-24) -> CRAN

Modified functions:

  - lollipop
    
      - new argument ylim [to replace ymin, futurely deprecated],
        default "auto0"

  - threshMeasures, similarity
    
      - change default ymin to 0 (default ylim "auto0") when min value
        is >0, to avoid deceiving plots
      - allow plot=TRUE with simplif=FALSE

  - optiThresh, multModEv
    
      - added plot=FALSE to some threshMeasures() calls

                        Changes in version 3.22                         

(Committed 2024-11-19)

Modified functions:

  - varImp
      - new default "auto0" for 'ylim', to avoid deceiving plots

                        Changes in version 3.21                         

(Committed 2024-11-19)

Modified functions:

  - predDensity
    
      - in plot legend, changed "absences" to "background" if pbg = TRUE

  - optiThresh
    
      - added 'reset.par' argument
      - 'sep.plots' argument can be set to NA

  - Boyce, Dsquared, errorMeasures, getThreshold, logLike, MillerCalib,
    optiPair, plotGLM, predPlot, RMSE
    
      - added 'verbosity' argument and passed it to inputMunch()

  - confusionMatrix, getBins, HLfit, predDensity, similarity
    
      - passed 'verbosity' argument to inputMunch()

                  Changes in version 3.20 (2024-10-29)                  

(Committed 2024-10-28) -> CRAN

Modified functions:

  - inputMunch, applyThreshold, AUC, Boyce, Dsquared, getThreshold,
    optiPair, optiThresh, predPlot, similarity, threshMeasures (not
    confusionMatrix, confusionLabel, errorMeasures, getBins, HLfit,
    logLike, MillerCalib, plotGLM, RMSE)
    
      - added 'pbg' argument

  - predDensity
    
      - added also 'verbosity' argument
      - message when 'separate' automatically set to FALSE because 'ci'
        not NA

  - Boyce
    
      - changed colour of plot text to grey50, to increase visibility
        when overlapping points

                        Changes in version 3.19                         

(Committed 2024-10-02)

New functions:

  - errorMeasures (incl. RMSE, MSE, Brier score)

Modified functions:

  - RMSE
      - warning: function deprecated in favour of errorMeasures

Other modified files:

  - quantReclass.Rd
    
      - update Formoso-Freire ref with publication date

  - DESCRIPTION
    
      - added contributors

                 Changes in version 3.18.2 (2024-08-28)                 

(Committed 2024-08-28) -> CRAN

Modified functions:

  - predDensity
      - slightly improved plot colours for better contrast
      - added legend when CI not NA

Other modified files:

  - predDensity.Rd
      - slight improvements to increase clarity

                       Changes in version 3.18.1                        

(Committed 2024-08-09)

Modified functions:

  - mod2obspred
    
      - implemented class 'GBMFit' (pkg 'gbm3') when obs.only=FALSE

  - predDensity
    
      - adapted x-axis values for predictors outside range [0, 1] when
        type="histogram"
      - changed plot colours

Other modified files:

  - inputMuch.Rd
    
      - added mention to class 'GBMFit' for 'model'

  - predDensity.Rd
    
      - added mention to 'predictor' values

                        Changes in version 3.18                         

(Committed 2024-08-08)

Modified functions:

  - mod2obspred, varImp
      - implemented class 'GBMFit' from pkg 'gbm3'

                       Changes in version 3.17.1                        

(Committed 2024-06-07)

Modified files:

  - varImp.Rd
      - second example now uses new argument 'relative'
      - improved descriptions and Details

                  Changes in version 3.17 (2024-06-06)                  

(Committed 2024-06-06) -> CRAN

Modified functions:

  - varImp
      - 'relative' argument now applies also to BART and flexBART models
      - adapted to latest version of flexBART, which does carry variable
        names
      - informative error messages when model is BART and doesn't have
        the required info
      - added 'verbosity' argument

                        Changes in version 3.16                         

(Committed 2024-06-05)

Modified functions:

  - optiThresh
    
      - added 'verbosity' argument to pass to inputMunch()
      - abline() now plotted also if 'optimize' is a specific measure
        name, not necessarily "each"

  - AUC
    
      - added 'verbosity' argument to pass to inputMunch()

  - varImp
    
      - added 'relative' argument for z value (suggested by Alba
        Estrada)

                        Changes in version 3.15                         

(Committed 2024-03-25)

Modified functions:

  - threshMeasures, evaluate, modEvAmethods
      - added 'ORSS' and 'SEDI' metrics (Wunderlich et al. 2019)
        (suggested by Jose Carlos Guerrero)

                        Changes in version 3.14                         

(Committed 2024-02-01)

New functions:

  - logLike

Modified functions:

  - predDensity
      - added 'xlim' argument

                 Changes in version 3.13.3 (2024-01-19)                 

(Committed 2024-01-19) -> CRAN

Modified functions:

  - threshMeasures
    
      - set plot=FALSE on confusionMatrix() call

  - confusionMatrix
    
      - set default 'plot' to FALSE (for back-compatibility)

                       Changes in version 3.13.2                        

(Committed 2024-01-18)

Modified functions:

  - confusionMatrix
      - add arguments plot=TRUE, classes=FALSE and '...'

                       Changes in version 3.13.1                        

(Committed 2024-01-17)

Modified functions:

  - confusionLabel
      - assign consistent colours to output raster categories
      - add plot=TRUE and '...' arguments

                        Changes in version 3.13                         

(Committed 2024-01-16)

Modified functions:

  - confusionLabel
      - output SpatRaster (if input 'pred' is SpatRaster) now properly
        categorical

Other modified files:

  - AUC.Rd
      - not-yet-implemented argument 'FPR.limits' now suggests using
        'pROC::roc'

                        Changes in version 3.12                         

(Committed 2023-12-14)

Modified functions:

  - applyThreshold, inputMunch
    
      - added 'verbosity' argument to pass to ptsrast2obspred()

  - AUC
    
      - added 'grid.lty' argument (used e.g. in modevapp)
      - 'grid' now at 0.1 (not threshold) intervals

  - getThreshold
    
      - finished implementing 'maxF'
      - implemented maxJaccard, maxSorensen (= maxF)

  - optiThresh
    
      - replaced single with double ||, &&
      - added modEvAmethods("similarity") to default 'measures'
      - added maxJaccard and maxSorensen criteria

  - modEvAmethods
    
      - added Jaccard, Sorensen and their maximizations

  - arrangePlots
    
      - return c(1, 1) if n.plots <= 1

Other modified files:

  - Boyce.Rd
    
      - 'Note' now mentions that Boyce is designed for suitability or
        favourability, not probability

  - similarity.Rd
    
      - 'Description' and 'Details' now mention equivalence to Li &
        Guo's F-measures

                  Changes in version 3.11 (2023-11-25)                  

(Committed 2023-11-25) -> CRAN

Modified functions:

  - Dsquared
      - added dismo.version argument: if FALSE, uses the previous
        version of Dsquared, as the dismo version sometimes produces
        negative or NaN results

                  Changes in version 3.10 (2023-11-12)                  

(Committed 2023-11-10) -> CRAN

New functions:

  - quantReclass

  - similarity

Modified functions:

  - modEvAmethods
      - added methods for similarity()

                        Changes in version 3.9.6                        

(Committed 2023-10-04)

Modified functions:

  - Dsquared
    
      - warning emitted and Dsquared calculated correctly even when
        family binomial and response not binary (following bug report by
        Elic M. Weitzel)

  - varImp
    
      - metric reported in console result
      - absolute (rather than original) values now returned for z value
        (if model is glm)

  - AUC
    
      - added 'GiniCoefficient' to outputs when simplif=FALSE

                        Changes in version 3.9.5                        

(Committed 2023-01-02)

Modified functions:

  - varImp
      - barplot now also gets error bars replotted on top of points if
        plot.points=TRUE
      - implemented for models of class "lbart" and "pbart" of pkg
        'BART' (though not ideal for group.cats = TRUE)
      - group.cats default now FALSE
      - started implementation for flexBART models (still imperfect
        because object has no var names; issue submitted at
        https://github.com/skdeshpande91/flexBART/issues/8)

                        Changes in version 3.9.4                        

(Committed 2023-04-26)

Modified functions:

  - varImp
      - new argument group.cats=TRUE, for BART models, to sum up the
        contributions of (one-hot encoded) categorical variable levels

                 Changes in version 3.9.3 (2023-04-14)                  

(Committed 2023-04-14) -> CRAN

Modified functions:

  - AUC
      - 'method' default now NULL, to avoid unsolicited warning when
        curve="PR" because default method was "rank"

Other modified files:

  - varImp.Rd
      - improved info on parameters for different plot types (e.g.
        cex.axis for lollipop, cex.names for barplot)

                        Changes in version 3.9.2                        

(Committed 2023-03-19)

Modified functions:

  - Boyce
    
      - explicit warning instead of obscure error if 'obs' has no
        presences
      - warning also when 'obs' has only presences (Boyce = NA)

  - optiThresh
    
      - explicit warning (and results NA) instead of obscure error if
        'obs' has either no presences or no absences
      - empty plot instead of error for incalculable metrics

  - threshMeasures
    
      - explicit warning instead of obscure error if 'obs' has either no
        presences or no absences

                        Changes in version 3.9.1                        

(Committed 2023-02-26)

Modified functions:

  - varImp
    
      - error if family is not 'binomial', to avoid obscure error
        otherwise because no 'z-value' column in summary

  - confusionMatrix, confusionLabel
    
      - changed defaults 'interval = interval, quant = quant' to
        'interval = 0.01, quant = 0'

Other modified files:

  - CITATION
      - replaced old-style personList() with c(), and citEntry() with
        bibentry(), as per new CRAN requirements

                  Changes in version 3.9 (2023-01-13)                   

(Committed 2023-01-12) -> CRAN

Modified functions:

  - varImp
    
      - corrected point locations (accounting for space between bars)
        for barplot
      - error.bars in lollipop chart re-plotted on top to improve
        visibility
      - help file cites Weissgerber et al.

  - predDensity
    
      - 'ci' now plotted as semi-transparent rectangle (rather than just
        vertical ablines)
      - added 'ci' example to help file

                        Changes in version 3.8.9                        

(Committed 2023-01-11)

Modified functions:

  - varImp
    
      - implemented plot.points argument
      - arguments 'ci' and 'ci.type' replaced by argument 'error.bars'
      - 'error.bars' can also be a numeric for a x% confidence interval
      - added 'grid' argument
      - added "imp.type" argument (placeholder, so far only option
        "each")
      - set 'border' to NA in legend and barplot
      - fixed legend colour bug
      - added check for loaded 'gbm' when needed

  - predDensity
    
      - added 'ci' argument
      - added '...' for arguments to pass to 'hist'

                        Changes in version 3.8.8                        

(Committed 2023-01-05)

New functions:

  - RMSE

  - lollipop

Modified functions:

  - varImp
    
      - added "ylim" argument (default "auto"), and xpd=FALSE to
        'barplot' call
      - changed default positive colour for better contrast with CI
        lines in barplot
      - new default plot.type = "lollipop"

  - threshMeasures
    
      - "OddsRatio" removed from default 'measures'
      - 'ylim' argument removed (default 0,1 not needed after OddsRation
        removal; 'ylim' can still be used under '...')
      - new argument 'plot.type'
      - new default plot.type = "lollipop"

  - RsqGLM
    
      - new argument 'plot.type'
      - new default plot.type = "lollipop"

                        Changes in version 3.8.7                        

(Committed 2022-12-22)

New functions:

  - varImp

Modified functions:

  - mod2obspred
      - added supressMessages() when predicting with GBM

                        Changes in version 3.8.6                        

(Committed 2022-12-20)

Modified functions:

  - Dsquared
      - 'family' is now guessed from data (with message) if null
      - extended to models other than GLM

                        Changes in version 3.8.5                        

(Committed 2022-11-06)

Modified functions:

  - ptsrast2obspred
    
      - added (or 'rm.dup.points=TRUE' for 'Boyce' function) to warning,
        otherwise Boyce would say "argument X matches multiple formal
        arguments"

  - MilerCalib
    
      - added final empty line

                 Changes in version 3.8.4 (2022-10-30)                  

(Committed 2022-10-28) -> CRAN

Modified functions:

  - applyThreshold
      - added "as.numeric" to 'sort(tresh)', otherwise it was character
        if one of the input 'thresh' criteria was character, which
        generated errors downstream

                        Changes in version 3.8.3                        

(Committed 2022-10-27)

Modified functions:

  - predPlot
    
      - 'thresh' can now be set to NA or NULL
      - legend is also changed accordingly

  - optiThresh
    
      - warning emitted if obs are all 0 or all 1 (which may originate
        errorr) - propagates to optiPair

Other modified files:

  - MillerCalib.Rd
      - added explanations and examples on applicability to non-logit
        link models and non-probability predictions

                        Changes in version 3.8.2                        

(Committed 2022-07-21)

Modified functions:

  - varPart
      - added argument 'cor.method'
      - changed previous argument name 'method' to 'pred.type', to avoid
        confusion with the above

                        Changes in version 3.8.1                        

(Committed 2022-07-20)

Modified functions:

  - varPart
      - argument 'model' now accepts glms of any family (but properly
        tested only for binomial!)

                         Changes in version 3.8                         

(Committed 2022-07-20)

Modified functions:

  - varPart
      - new arguments 'model', 'groups', 'method', 'return.models'
      - output table now doesn't say "pure" or "overlap", just the
        factor names separated by "_"
      - argument 'coloured' changed to 'colr' to avoid English/American
        spelling issues

                         Changes in version 3.7                         

(Committed 2022-07-10)

Modified functions:

  - applyThreshold
      - 'thresh' can now be of length 2, for high, intermediate and low
        predictions

Other modified files:

  - DESCRIPTION
      - added reference about the method, as suggested by Uwe Ligges
        after previous CRAN submission

                         Changes in version 3.6                         

(Committed 2022-06-14)

New functions:

  - confusionMatrix

Modified functions:

  - confusionLabel
    
      - added 'getThreshold' to include all 'thresh' options
      - added 'interval' and 'quant' arguments for the above
      - 'rm.dup' now defaults to FALSE to assume less

  - threshMeasures
    
      - moved part of the code to new 'confusionMatrix' function, which
        is now called from here

                  Changes in version 3.5 (2022-06-01)                   

(Committed 2022-05-16) -> CRAN

New functions:

  - applyThreshold

Modified functions:

  - Boyce
    
      - warning emitted and points coloured red for bins with less
        than 30 values

  - standard01 (benefiting threshMeasures)
    
      - added is.finite(score) to avoid error when NAs produced by kappa
        integer overflow

  - getThreshold, inputMunch
    
      - 'obs' can be null if only 'pred' is needed

  - predPlot
    
      - added call to 'getThreshold' to include more threshold options
      - added 'cex' argument (default 0.5), plus 'interval' and 'quant'
        to pass to 'getThreshold'

  - confusionLabel
    
      - output is SpatRaster if input is too (as also implemented in
        'applyThreshold')

  - optiThresh
    
      - fixed bug: Precision and Recall were missing from
        'goodness.measures' and didn't get optimals

                         Changes in version 3.4                         

(Committed 2022-05-06)

Modified functions:

  - AUC, confusionLabel, Dsquared, getBins, HLfit, MillerCalib,
    optiPair, optiThresh, plotGLM, predDensity, predPlot, RsqGLM,
    threshMeasures
    
      - added arguments 'rm.dup' and 'na.rm' to pass to 'inputMunch' and
        cascade to 'ptsrast2obspred'

  - Boyce
    
      - renamed arguments 'rm.dupl.classes' and 'rm.dupl.points' to
        'rm.dup.classes' and 'rm.dup.points', for better coherence with
        'rm.dup' in other functions
      - added 'na.rm' argument

                         Changes in version 3.3                         

(Committed 2022-05-03)

New functions:

  - inputMunch
    
      - converts from model or point & raster inputs to obs & pred
        vectors

  - getThreshold
    
      - computes threshold based on any of a range of published criteria

Modified functions:

  - prevalence
    
      - added 'unlist' to avoid obscure error when input is one-column
        tibble instead of vector

  - confusionLabel, Dsquared, getBins, HLfit, MillerCalib, optiPair,
    optiThresh, plotGLM, predDensity, predPlot, RsqGLM, threshMeasures
    
      - 'obs' and 'pred' can also be presence coordinates and a
        SpatRaster, respectively

  - confusionLabel, getBins
    
      - added 'na.rm' argument

  - threshMeasures
    
      - 'thresh' argument now calls new 'getThreshold' function to
        include more options

  - ptsrast2obspred
    
      - checks for duplicates and shows message if there are (if rm.dup
        = FALSE)
      - 'rm.dup' now defaults to FALSE, to assume less and to match
        'ecospat.boyce'

  - Boyce
    
      - 'rm.dupl.points' now defaults to FALSE, to assume less and to
        match 'ecospat.boyce'

  - modEvAmethods
    
      - added error message when 'fun' not correctly specified (instead
        of silent empty result)
      - help file now provides all available values under 'fun' argument

  - getModEqn
    
      - 'round' replaced with 'signif' to avoid small coeffs becoming
        zeros (bug report by Jose Carlos Guerrero)

  - MESS
    
      - added 'verbosity' argument

                         Changes in version 3.2                         

(Committed 2022-03-13)

Modified functions:

  - AUC
    
      - 'obs' and 'pred' can be presence coordinates and a SpatRaster,
        respectively

  - Boyce
    
      - added argument '...', e.g. for plot 'main' or 'xlim'
      - argument name 'nclass' replaced with 'n.bins' to match other
        modEvA functions
      - argument name 'window.w' replaced with 'bin.width' to accomodate
        other modEvA functions
      - default 'nclass = 0' replaced with 'n.bins = NA', and all else
        accordingly
      - changed default 'rm.dupl.classes' to FALSE after some checks
        (e.g. Galpyr RF in SDMB course)

  - ptsrast2obspred
    
      - added argument 'na.rm' and set to TRUE by default
      - help file now uses 'elev' raster for more clarity

                         Changes in version 3.1                         

(Committed 2022-02-22)

New functions:

- Boyce

- ptsrast2obspred

Modified functions:

  - AUC
    
      - moved 'pred' range check to after NAs are removed to avoid error

  - predPlot
    
      - on exit, restores only 'par(mar)' (the only one changed) rather
        than all 'par'

  - RsqGLM
    
      - added las = 2 to 'barplot'

                  Changes in version 3.0 (2021-12-20)                   

(Committed 2021-12-20) -> CRAN

Modified functions:

  - AUC
    
      - warning if 'obs' contains only zeros or only ones (to explain
        result NaN and no curve on plot)
      - if the previous occurs, other warnings suppressed (PR curve
        interpolated past NaN precision, method changed to 'trapezoid',
        etc.)

  - MillerCalib
    
      - plot text elevated by 0.05 y-axis units, to avoid it being
        cropped in small plots

Other changes:

  - uniformized description of arguments "model", "obs" and "pred"
    across functions' help files

                         Changes in version 2.8                         

(Committed 2021-12-03)

Modified functions:

  - optiPair
      - message "'pred' must range between 0 and 1" changed from error
        to warning
      - added argument 'na.rm' (default TRUE) to avoid NaNs in result
        MinDiff, MaxSum, etc.
      - added argument 'exclude.zeros' (default TRUE) to avoid
        precision-recall "optimal" difference when both 0 or NaN

                         Changes in version 2.7                         

(Committed 2021-11-26)

New functions:

  - confusionLabel (to map the confusion matrix)

  - mod2obspred (to extract 'obs' and 'pred' from model objects)

Modified functions:

  - prevalence
    
      - message "'event' is not among of the values of 'obs'" changed
        from error to warning
      - 'mod2obspred' now used for extracting 'obs' if 'model' is
        provided

  - AUC, getBins, HLfit, MillerCalib, optiPair, optiThresh, predDensity,
    predPlot, threshMeasures
    
      - 'model' can now be of class "glm", "gam", "gbm", "randomForest"
        or "bart"
      - 'mod2obspred' now used for extracting 'obs' and 'pred' if
        'model' is provided

                         Changes in version 2.6                         

(Committed 2021-11-01)

Modified functions:

  - predDensity
    
      - added 'main' argument for plot title

  - predPlot
    
      - added 'pch' and 'col' arguments for the plot
      - legend.pos is now "n" by default (legend was ugly and needed box
        to distinguish from actual plot points)

  - RsqGLM
    
      - added "plot" argument (default TRUE)
      - added '...' for additional parameters for 'plot'

  - plotGLM
    
      - added 'plot=FALSE' to 'RsqGLM' (used if 'plot.values')

  - optiThresh
    
      - slightly changed plot margins so that bottom axis values are
        visible

Other modified files:

  - www/modEvA-tutorial.html
      - updated with these recent options

                         Changes in version 2.5                         

(Committed 2021-10-31)

Modified functions:

  - AUC
      - plot.preds=TRUE now plots filled circles with transparency
      - plot.preds=TRUE now defaults to plotting circles on the curve
        (rather than both curve and bottom)
      - size of circles if plot.preds=TRUE changed from 100prop.preds
        to 20sqrt(prop.preds)
      - x coordinates of circles if plot.preds=TRUE changed from
        'thresholds' to 'xx'
      - if plot.values=TRUE, value is now plotted on the middle bottom
        for ROC and middle top for PR curve
      - NaN precision values now coerced to the last non-NaN value
        (rather than 1), and warning emitted
      - interpolated (NaN precision) part of the PR curve now plotted
        besides the curve with actual precision values

                         Changes in version 2.4                         

(Committed 2021-10-30)

Modified functions:

  - AUC
    
      - fixed wrong PR area when last precision value(s) NaN, by
        coercing NaN precisions to 1 (thanks to bug report by Ying-Ju
        Tessa Chen)
      - deactivated option method = "integrate", which was providing
        somewhat inaccurate values
      - added / improved warning messages when 'method' changed to match
        chosen 'curve'
      - added warning when method = "trapezoid" and interval >= 0.01,
        noting result is more accurate with smaller intervals

  - threshMeasures
    
      - added 'ylim' argument with default c(0, 1) to avoid error when
        no selected measure has finite values

Other modified files:

  - inst/CITATION
      - corrected publication year of 'New measures' paper under
        'textVersion' of citation (thanks to bug report by Alba Estrada)

                         Changes in version 2.3                         

(Committed 2021-09-30)

Modified functions:

  - prevalence
      - added 'model' argument, which can now be provided instead of
        'obs'
      - help file includes examples with 'model' and with character
        'obs'
      - error message when 'obs' not a vector and when 'event' not in
        'obs'
      - warning when 'obs' ignored in favour of 'model'

                         Changes in version 2.2                         

(Committed 2021-09-08)

Modified functions:

  - MillerCalib
    
      - slope value now plotted before (above) intercept (if plot.values
        = TRUE)

  - varPart
    
      - fixed right margin in 2-factor plot and added option for
        colouring the circles, following suggestions by Oswald van
        Ginkel

  - MESS
    
      - bug fix e-mailed by Huijie Qiao

                         Changes in version 2.1                         

(Committed 2021-01-15)

New functions:

  - predPlot

Modified functions:

  - predDensity
    
      - like 'predPlot', 'legend.pos' now allows NA (for no legend)
        instead of throwing obscure error

  - optiThresh
    
      - added warning when any of 'measures' or 'optimize' not within
        implemented values

Other modified files:

  - MESS.Rd
      - removed mention that we will implement ExDet for dataframes;
        added 'ecospat.climan' to 'See also'

Other changes:

  - minor corrections to some 'man' files

                  Changes in version 2.0 (2020-01-21)                   

(Committed 2020-01-21) -> CRAN

Modified functions:

  - modEvA-internal
    
      - removed .Random.seed

  - multModEv, modEvAmethods, modEvA-internal
    
      - added "MeanPrecision", "AUCPR" and "F1score"

Other modified files:

  - multModEv.Rd
      - added "AUCPR" to one of the examples

(Committed 2020-01-20)

Modified functions:

  - AUC
    
      - added 'meanPrecision' to returned list (if simplif = FALSE)
      - "AUC[PR]" mentioned on plot when curve = "PR"

  - optiThresh
    
      - added "F1score" to goodness.measures in optimals.each
      - added Liu et al. 2005 reference to threshold criteria

  - threshMeasures, modEvAmethods
    
      - added "Precision" and "Recall" (even though synonyms with "PPP"
        and "Sensitivity")

  - optiPair
    
      - changed pch of measure 1 to 19 (slightly larger than pch 20) so
        it's still visible when overlapped by measure 2

  - multModEv
    
      - added 'plot = FALSE' to internal AUC call

Other modified files:

  - threshMeasures.Rd, optiThresh.Rd, optiPair.Rd
      - added "Note" saying sens=recall and PPP=precision, and defining
        F1score

                         Changes in version 1.8                         

(Committed 2020-01-17)

Modified functions:

  - AUC
      - removed artificial zeros (instead of NaN) when curve = "PR"
      - reversed the reference diagonal if curve = "PR"
      - value now placed higher on the plot if curve = "PR" to avoid
        superposition

Other changes:

  - added 'inst' folder with article citation information

                         Changes in version 1.7                         

(Committed 2020-01-16)

Modified functions:

  - AUC
    
      - implemented methods "trapezoid" and "integrate"
      - added area calculation for "PR" curve

  - threshMeasures, evaluate, modEvAmethods, (optiThresh, optiPair)
    
      - added "F1score" to available 'measures'

                         Changes in version 1.5                         

(Committed 2020-01-15)

New functions:

  - predDensity

Modified functions:

  - AUC
      - new 'method' argument, which in the future can be "rank",
        "trapezoid" or "integrate" (currently only "rank" is
        implemented)
      - new 'curve' argument which can be "ROC" or "PR"
        (precision-recall)
      - arguments 'roc.col', 'roc.lty' and 'roc.lwd' renamed to
        'curve.col', 'curve.lty' and 'curve.lwd'
      - 'xlab' and 'ylab' now default to "auto", to be generated
        according to 'curve'
      - removed 'main' argument (can be provided via '...')
      - 'plot.preds' can now be either a logical value as before, or a
        character "curve" and/or "bottom"
      - 'plot.preds' circles now plotted in darkgrey
      - title in .Rd file changed to "Area Under the Curve" (removed
        "ROC")

Other changes:

  - corrected some problems in .Rd files, to reduce LaTeX errors when
    creating PDF version of manual.

                        Changes in version 1.4.2                        

(Committed 2020-01-03)

Modified functions:

  - plotGLM
      - corrected to adj=1 when plotting values on the right of the plot

                        Changes in version 1.4.1                        

(Committed 2019-10-18)

Modified functions:

  - RsqGLM
      - added NA handling for 'cor'

                         Changes in version 1.4                         

(Committed 2018-11-28)

Modified functions:

  - AUC
    
      - added arguments diag, diag.col, diag.lty, roc.col, roc.lty,
        roc.lwd
      - 'simplif = TRUE' no longer overrides 'plot = TRUE'

  - MillerCalib
    
      - added arguments diag, line.col

Other modified files:

  - edited .Rd files (AUC, HLfit, evaluate, optiPair, threshMeasures,
    modEvA-package) to reflect difference between discrimination and
    classification
      - updated index.php

                        Changes in version 1.3.3                        

(Committed 2017-03-24)

Modified functions:

  - varPart:
      - bug fixed (with na.omit) when only two factors (A, B, AB)

                 Changes in version 1.3.2 (2016-07-15)                  

(Committed 2016-07-12)

Modified functions:

  - getBins (affecting HLfit):
    
      - bug fixed in "bin.method = size.bins", which was giving two
        different messages regarding ignored arguments

  - HLfit:
    
      - help file slightly clarified

                        Changes in version 1.3.1                        

(Committed 2016-06-27)

Modified functions:

  - getBins (affecting HLfit):
    
      - bug fixed in "bin.method = quantiles", now providing even-sized
        bins (=SPSS)
      - added argument 'quantile.type', to pass to 'quantile' function

  - HLfit:
    
      - added argument 'quantile.type', to pass to 'quantile' function
      - added argument 'verbosity'

  - multModEv:
    
      - removed default 'thresh' (must be user-specified)
      - replaced argument 'quiet' with 'verbosity' for coherence with
        other functions

  - threshMeasures:
    
      - removed default 'thresh' (must be user-specified)
      - replaced argument 'messages' with 'verbosity' for coherence with
        other functions

                         Changes in version 1.3                         

(Committed 2016-06-16)

Modified functions:

  - getBins (affecting HLfit):
    
      - bug fixed in "bin.method = quantiles", removing last additional
        bin of size 1
      - help file improved to better explain what each bin.method does
        and what arguments it ignores
      - added argument 'verbosity'

  - HLfit:
    
      - added examples to help file to illustrate differences in
        bin.methods

                        Changes in version 1.2.9                        

(Committed 2016-06-06)

Modified functions:

  - getBins (affecting HLfit):
    
      - bug fixed in "bin.method = n.bins, fixed.bin.size = TRUE"
      - help file updated to explain what each bin.method does
      - removed default bin.method (must be specified by user)

  - multModEv:
    
      - included '...' for additional arguments to pass to HLfit
      - removed default bin.method (must be specified if HL in measures)

  - modEvAmethods:
    
      - excluded "Miller.p" (previously eliminated from MillerCalib)

                        Changes in version 1.2.8                        

(Committed 2016-04-18)

Modified functions:

  - varPart:
    
      - 'plot.unexpl' now also rounded to 'plot.digits'
      - 'model.type' deprecated (message emitted)
      - AB or ABC now also mandatory, and unexplained var 0, for GLMs
      - help file updated

  - plotGLM:
    
      - warning on preds outside [0,1] now only emitted when appropriate

  - AUC, getBins, HLfit, MillerCalib, multModEv, optiPair, optiThresh,
    plotGLM, threshMeasures:
    
      - error when model(s) provided but not binomial logit glm

                        Changes in version 1.2.7                        

(Committed 2016-04-15)

Modified functions:

  - varPart:
      - added argument 'plot.unexpl = TRUE'
      - explicit error message for 3-factor LM with no ABC
      - help file now with both LM and GLM examples
      - help file now notes that wrong input = wrong result

                        Changes in version 1.2.6                        

(Committed 2016-04-13)

Modified functions:

  - AUC:
    
      - error replaced with warning when pred values outside the [0,1]
        interval
      - added argument plot.digits = 3 (for plot.values)

  - varPart:
    
      - added arguments 'main' and 'cex.main'
      - slightly increased default cex values
      - updated help file to make GLM use a bit clearer

  - plotGLM:
    
      - error replaced with warning when pred values outside the [0,1]
        interval
      - added pseudo-R-squared measures to plot.values
      - changed plot.values default to TRUE
      - added argument plot.digits = 3 (for plot.values)

                        Changes in version 1.2.5                        

(Committed 2016-03-30)

Modified functions:

  - getBins:
    
      - eliminated error when pred values outside the [0,1] interval

  - HLfit:
    
      - error replaced with warning on pred values outside the [0,1]
        interval
      - plot now stretches if pred values exceed [0,1] interval

  - MillerCalib:
    
      - error replaced with warning on pred values outside the [0,1]
        interval
      - default digits (for plot.values) lowered to 2
      - slope p-value removed (values looked wrong)
      - NaNs avoided by converting 0 and 1 in 'pred' to (1 -) 2e-16
      - increased plot ymax by 0.2
      - changed plot text location to bottom right

                        Changes in version 1.2.4                        

(Committed 2016-03-22)

Modified functions:

  - multModEv:
      - warning now emitted, and help file updated, about calibration
        measures being valid only for probability (when input is
        obs.data + pred.data)

                        Changes in version 1.2.3                        

(Committed 2015-12-10)

Modified functions:

  - prevalence:
      - 'na.rm = TRUE' added

                        Changes in version 1.2.2                        

(Committed 2015-11-27)

Modified functions:

  - Dsquared, RsqGLM, plotGLM:
      - NaN-caused errors avoided by converting 0 and 1 in 'pred' to (1
        -) 2e-16

                        Changes in version 1.2.1                        

(Committed 2015-11-26)

Modified functions:

  - Dsquared, RsqGLM:
      - NaN-caused errors avoided by converting 0 in 'pred' to smallest
        computable positive number

                         Changes in version 1.2                         

Modified functions:

  - AUC, Dsquared, RsqGLM, threshMeasures, optiPair, HLfit & MillerCalib
    now omit NAs

  - Dsquared based on obs&pred now available also for Poisson GLMs
