Model Evaluation and Analysis

Analyses species distribution models and evaluates their performance. It includes functions for performing variation partitioning, calculating several measures of model discrimination and calibration, optimizing prediction thresholds based on a number of criteria, performing multivariate environmental similarity surface (MESS) analysis, and displaying various analytical plots.


News

========================================== 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

Reference manual

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install.packages("modEvA")

1.3.2 by A. Marcia Barbosa, 3 years ago


http://modeva.r-forge.r-project.org/


Browse source code at https://github.com/cran/modEvA


Authors: Barbosa A.M. , Brown J.A. , Jimenez-Valverde A. , Real R.


Documentation:   PDF Manual  


GPL-3 license


Imports graphics, stats


See at CRAN