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 - unimplemented 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 (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 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