Version 3.41 -> CRAN

(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

Version 3.40 -> CRAN

(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)

Version 3.39

(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

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

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

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, )’

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

Version 3.34

(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)

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 to work with news()

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 3.8.2

(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

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!)

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