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Version 3.33 (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

Version 3.32 (committed 2025-03-18)

Modified functions:

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

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

Version 3.30 (committed 2025-02-21) -> CRAN

Modified functions:

• AUC, Boyce, lollipop (affecting threshMeasures), optiPair
  • fixed opar() reset bug: reset only the changed parameter ‘mgp’

Version 3.29 (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 , namely xlab and ylab when horiz is either TRUE or FALSE

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

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

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

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

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

Version 3.23 (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

Version 3.22 (committed 2024-11-19)

Modified functions:

• varImp
  • new default “auto0” for ‘ylim’, to avoid deceiving plots

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()

Version 3.20 (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

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

Version 3.18.2 (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

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

Version 3.18 (committed 2024-08-08)

Modified functions:

• mod2obspred, varImp
  • implemented class ‘GBMFit’ from pkg ‘gbm3’

Version 3.17.1 (committed 2024-06-07)

Modified files:

• varImp.Rd
  • second example now uses new argument ‘relative’
  • improved descriptions and Details

Version 3.17 (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

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)

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)

Version 3.14 (committed 2024-02-01)

New functions:

• logLike

Modified functions:

• predDensity
  • added ‘xlim’ argument

Version 3.13.3 (committed 2024-01-19) -> CRAN

Modified functions:

• threshMeasures
  • set plot=FALSE on confusionMatrix() call
• confusionMatrix
  • set default ‘plot’ to FALSE (for back-compatibility)

Version 3.13.2 (committed 2024-01-18)

Modified functions:

• confusionMatrix
  • add arguments plot=TRUE, classes=FALSE and …

Version 3.13.1 (committed 2024-01-17)

Modified functions:

• confusionLabel
  • assign consistent colours to output raster categories
  • add plot=TRUE and … arguments

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
  • unimplemented argument ‘FPR.limits’ now suggests using ‘pROC::roc’

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

Version 3.11 (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

Version 3.10 (committed 2023-11-10) -> CRAN

New functions:

• quantReclass

• similarity

Modified functions:

• modEvAmethods
  • added methods for similarity()

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

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)

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

Version 3.9.3 (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)

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

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

Version 3.9 (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

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’

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”

Version 3.8.7 (committed 2022-12-22)

New functions:

• varImp

Modified functions:

• mod2obspred
  • added supressMessages() when predicting with GBM

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

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

Version 3.8.4 (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

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

Version 3.82 (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

Version 3.81 (committed 2022-07-20)

Modified functions:

• varPart
  • argument ‘model’ now accepts glms of any family (but properly tested only for binomial!)

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

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

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

Version 3.5 (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 (benefitting 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

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

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

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

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’

Version 3.0 (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

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

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

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

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

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)

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’

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

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

Version 2.0 (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

Version 2.0 (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

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

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’

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.

Version 1.4.2 (committed 2020-01-03)

Modified functions:

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

Version 1.4.1 (committed 2019-10-18)

Modified functions:

• RsqGLM
  • added NA handling for ‘cor’

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

Version 1.3.3 (committed 2017-03-24)

Modified functions:

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

Version 1.3.2 (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

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

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

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)

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

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

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)

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

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)

Version 1.2.3 (committed 2015-12-10)

Modified functions:

• prevalence:
  • ‘na.rm = TRUE’ added

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

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

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

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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