==========================================
modEvA v3.0 (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


==========================================
modEvA v2.8 (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


==========================================
modEvA v2.7 (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


==========================================
modEvA v2.6 (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


==========================================
modEvA v2.5 (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 100*prop.preds to 20*sqrt(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


==========================================
modEvA v2.4 (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)


==========================================
modEvA v2.3 (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'


==========================================
modEvA v2.2 (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


==========================================
modEvA v2.1 (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


==========================================
modEvA v2.0 (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


==========================================
modEvA v2.0 (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 


==========================================
modEvA v1.8 (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


==========================================
modEvA v1.7 (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'


==========================================
modEvA v1.5 (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.


==========================================
modEvA v1.4.2 (committed 2020-01-03)
==========================================

## Modified functions:

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


==========================================
modEvA v1.4.1 (committed 2019-10-18)
==========================================

## Modified functions:

* RsqGLM
- added NA handling for 'cor'


==========================================
modEvA v1.4 (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


==========================================
modEvA v1.3.3 (committed 2017-03-24)
==========================================

## Modified functions:

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


==========================================
modEvA v1.3.2 (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


==========================================
modEvA v1.3.1 (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


==========================================
modEvA v1.3 (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


==========================================
modEvA v1.2.9 (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)


==========================================
modEvA v1.2.8 (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


==========================================
modEvA v1.2.7 (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


==========================================
modEvA v1.2.6 (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)


==========================================
modEvA v1.2.5 (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


==========================================
modEvA v1.2.4 (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)


==========================================
modEvA v1.2.3 (committed 2015-12-10)
==========================================

## Modified functions:

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


==========================================
modEvA v1.2.2 (committed 2015-11-27)
==========================================

## Modified functions:

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


==========================================
modEvA v1.2.1 (committed 2015-11-26)
==========================================

## Modified functions:

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


==========================================
modEvA v1.2
==========================================

## Modified functions:

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

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