Package: SDMtune
Type: Package
Title: Species Distribution Model Selection
Version: 0.1.0
Date: 2019-06-20
Authors@R: c(
	  person("Sergio", "Vignali",  email = "sergio.vignali@iee.unibe.ch",
	         role = c("aut", "cre"), comment = c(ORCID = "00000-0002-3390-5442")),
	  person("Arnaud", "Barras", role = "aut",
	         comment = c(ORCID = "0000-0003-0850-6965")),
	  person("Veronika", "Braunisch", role = "aut",
	         comment = c(ORCID = "00000-0001-7035-4662")),
	  person("Conservation Biology - University of Bern", role = "fnd")
	)
Description: User-friendly framework that enables the training and the
    evaluation of species distribution models (SDMs). The package implements
    functions for data driven variable selection and model tuning and includes
    numerous utilities to display the results. All the functions used to select
    variables or to tune model hyperparameters have an interactive real-time
    chart displayed in the 'RStudio' viewer pane during their execution. At the
    moment only the maximum entropy method is available using the 'Java'
    implementation, Phillips et al. (2006) <doi:10.1016/j.ecolmodel.2005.03.026>,
    through the 'dismo' package and the 'R' implementation through the 'maxnet'
    package, Phillips et al. (2017) <doi:10.1111/ecog.03049>. 'SDMtune' uses its
    own script to predict maxent models, resulting in much faster predictions
    for large datasets compared to native predictions from the use of the 'Java'
    software. This reduces considerably the computation time when tuning the
    model using the AICc.
License: GPL-3
URL: https://consbiol-unibern.github.io/SDMtune/
BugReports: https://github.com/ConsBiol-unibern/SDMtune/issues
Depends: R (>= 3.2.0)
Imports: cli (>= 1.1.0), crayon (>= 1.3.4), dismo (>= 1.1-4), ggplot2
        (>= 3.2.0), htmltools (>= 0.3.6), jsonlite (>= 1.6), kableExtra
        (>= 1.1.0), maxnet (>= 0.1.2), methods, progress (>= 1.2.2),
        raster (>= 2.9-5), rasterVis (>= 0.45), Rcpp (>= 1.0.1),
        reshape2 (>= 1.4.3), rgdal (>= 1.4-4), rJava (>= 0.9-11),
        rstudioapi (>= 0.10), scales (>= 1.0.0), stringr (>= 1.4.0),
        whisker (>= 0.3-2)
Encoding: UTF-8
LazyData: true
LinkingTo: Rcpp
RoxygenNote: 6.1.1
Suggests: covr, knitr (>= 1.23), maps (>= 3.3.0), pkgdown (>= 1.3.0),
        rmarkdown (>= 1.13), roxygen2 (>= 6.1.1), snow (>= 0.4-3),
        testthat (>= 2.1.1), zeallot (>= 0.1.0)
VignetteBuilder: knitr
Collate: 'Maxent_class.R' 'Maxnet_class.R' 'RcppExports.R'
        'SDMmodel2MaxEnt.R' 'SWD_class.R' 'SDMmodelCV.R'
        'SDMmodel_class.R' 'SDMtune.R' 'SDMtune_class.R' 'aicc.R'
        'auc.R' 'chart_utils.R' 'condor.R' 'confMatrix.R' 'corVar.R'
        'doJk.R' 'getSubsample.R' 'gridSearch.R' 'maxentTh.R'
        'maxentVarImp.R' 'mergeSWD.R' 'modelReport.R' 'optimizeModel.R'
        'plotCor.R' 'plotJk.R' 'plotPA.R' 'plotPred.R' 'plotROC.R'
        'plotResponse.R' 'plotVarImp.R' 'predict_Maxent.R'
        'predict_SDMmodel.R' 'prepareSWD.R' 'randomSearch.R'
        'reduceVar.R' 'swd2csv.R' 'thinData.R' 'thresholds.R' 'train.R'
        'trainMaxent.R' 'trainMaxnet.R' 'trainValTest.R' 'tss.R'
        'utils.R' 'varImp.R' 'varSel.R' 'zzz.R'
NeedsCompilation: yes
Packaged: 2019-06-20 07:08:49 UTC; vignali
Author: Sergio Vignali [aut, cre] (<https://orcid.org/00000-0002-3390-5442>),
  Arnaud Barras [aut] (<https://orcid.org/0000-0003-0850-6965>),
  Veronika Braunisch [aut] (<https://orcid.org/00000-0001-7035-4662>),
  Conservation Biology - University of Bern [fnd]
Maintainer: Sergio Vignali <sergio.vignali@iee.unibe.ch>
Repository: CRAN
Date/Publication: 2019-06-21 08:00:20 UTC
