## compiled code
useDynLib(analogue)

## Imports
##
## vegan
importFrom(vegan, pasteCall, eigenvals, tolerance, scores, ordirgl)
## mgcv
importFrom(mgcv, gam, s, smoothCon, mono.con, pcls, Predict.matrix)
## MASS
importFrom(MASS, dose.p)
## lattice
##   -- need here *only* those funs that we define S3 methods for
##      not the functions from lattice we use as they are covered
##      by Depends: lattice in DESCRIPTION
importFrom(lattice, densityplot, dotplot, histogram)
## stats
import(stats)
## utils
importFrom(utils, head, tail)
## graphics
import(graphics)
## grid
importFrom(grid,
           convertWidth,
           gpar,
           grid.layout,
           grobWidth,
           frameGrob,
           placeGrob,
           rectGrob,
           textGrob,
           unit,
           unit.c)
## brglm
importFrom(brglm,
           brglm,
           brglm.control)
## rgl
importFrom(rgl,
           plot3d,
           lines3d,
           decorate3d)
## princurve
importFrom(princurve,
           get.lam)

## Exports
export(analog,
       bayesF,
       bootstrap,
       caterpillar,
       caterpillarPlot,
       chooseTaxa,
       cma,
       crossval,
       deshrink,
       dissim,
       dissimilarities,
       distance, oldDistance, ## oldDistance is the original R-only code
       #distance3,
       #distanceX,
       fuse,
       getK,
       gradientDist,
       join,
       logitreg,
       mat,
       mcarlo,
       minDC,
       optima,
       panel.Loess,
       panel.Stratiplot,
       pcr,
       performance,
       prcurve, ##randomWA,
       reconPlot,
       residLen,
       RMSEP,
       splitSample,
       rankDC,
       roc,
       smoothSpline,
       smoothGAM,
       sppResponse,
       Stratiplot,
       stdError,
       timetrack,
       tran,
       varExpl,
       wa,
       weightedCor,
       "setK<-",
       Hellinger,
       ChiSquare)

### S3 Methods
##
## main user-visible functions
S3method(analog, default)
S3method(analog, distance)
S3method(bootstrap, default)
S3method(bootstrap, mat)
S3method(bootstrap, wa)
S3method(chooseTaxa, default)
S3method(cma, analog)
S3method(cma, default)
S3method(cma, predict.mat)
S3method(cma, mat)
S3method(crossval, pcr)
S3method(crossval, wa)
S3method(densityplot, residLen)
S3method(dissimilarities, analog)
S3method(dissimilarities, mat)
S3method(distance, default)
S3method(distance, join)
S3method(oldDistance, default)
S3method(oldDistance, join)
#S3method(distance3, default)
S3method(eigenvals, pcr)
S3method(fuse, dist)
S3method(fuse, matrix)
S3method(getK, default)
S3method(getK, mat)
S3method(getK, bootstrap.mat)
S3method(getK, predict.mat)
S3method(gradientDist, default)
S3method(gradientDist, cca)
S3method(gradientDist, prcurve)
S3method(head, join)
S3method(hist, residLen)
S3method(histogram, residLen)
S3method(logitreg, default)
S3method(logitreg, analog)
S3method(mat, default)
S3method(mat, formula)
S3method(mcarlo, default)
S3method(mcarlo, mat)
S3method(mcarlo, analog)
S3method(minDC, default)
S3method(minDC, predict.mat)
S3method(minDC, analog)
S3method(minDC, wa)
S3method(optima, default)
S3method(pcr, default)
S3method(pcr, formula)
S3method(performance, bootstrap.wa)
S3method(performance, predict.wa)
S3method(performance, pcr)
S3method(performance, wa)
S3method(RMSEP, default)
S3method(RMSEP, mat)
S3method(RMSEP, bootstrap.mat)
S3method(RMSEP, bootstrap.wa)
##S3method(randomWA, default)
S3method(roc, default)
S3method(roc, analog)
S3method(roc, mat)
S3method(scores, prcurve)
S3method(scores, timetrack)
S3method(sppResponse, prcurve)
S3method(stdError, mat)
S3method(stdError, predict.mat)
S3method("setK<-", default)
S3method("setK<-", mat)
S3method(tail, join)
S3method(tolerance, default)
S3method(tran, default)
S3method(tran, formula)
S3method(varExpl, default)
S3method(varExpl, cca)
S3method(varExpl, prcurve)
S3method(wa, default)
S3method(wa, formula)
S3method(weightedCor, default)
## fitted, predict, coef etc
S3method(coef, pcr)
S3method(coef, wa)
S3method(fitted, pcr)
S3method(fitted, bootstrap.mat)
S3method(fitted, logitreg)
S3method(fitted, mat)
S3method(fitted, timetrack)
S3method(fitted, wa)
S3method(predict, logitreg)
S3method(predict, mat)
S3method(predict, pcr)
S3method(predict, wa)
S3method(residuals, bootstrap.mat)
S3method(residuals, mat)
S3method(residuals, pcr)
S3method(residuals, prcurve)
## plotting
S3method(caterpillarPlot, default)
S3method(caterpillarPlot, data.frame)
S3method(caterpillarPlot, wa)
S3method(dotplot, rankDC)
S3method(plot, minDC)
S3method(plot, bayesF)
S3method(plot, cma)
S3method(plot, dissimilarities)
S3method(plot, gradientDist)
S3method(lines, gradientDist)
S3method(points, gradientDist)
S3method(plot, logitreg)
S3method(plot, mat)
S3method(plot, mcarlo)
S3method(plot, prcurve)
S3method(lines, prcurve)
S3method(plot, rankDC)
S3method(plot, residLen)
S3method(plot, roc)
S3method(plot, sppResponse)
S3method(plot, timetrack)
S3method(plot, wa)
S3method(plot, weightedCor)
S3method(plot3d, prcurve)
S3method(reconPlot, default)
S3method(reconPlot, predict.mat)
S3method(reconPlot, predict.wa)
S3method(screeplot, bootstrap.mat)
S3method(screeplot, mat)
S3method(screeplot, pcr)
S3method(Stratiplot, default)
S3method(Stratiplot, formula)
## print
S3method(print, analog)
S3method(print, bayesF)
S3method(print, bootstrap.mat)
S3method(print, bootstrap.wa)
S3method(print, cma)
S3method(print, crossval)
S3method(print, fitted.bootstrap.mat)
S3method(print, fitted.mat)
S3method(print, logitreg)
S3method(print, mat)
S3method(print, mcarlo)
S3method(print, minDC)
S3method(print, optima)
S3method(print, pcr)
S3method(print, performance)
S3method(print, prcurve)
S3method(print, predict.mat)
S3method(print, predict.wa)
S3method(print, rankDC)
S3method(print, residLen)
S3method(print, residuals.bootstrap.mat)
S3method(print, residuals.mat)
S3method(print, roc)
S3method(print, stdError)
S3method(print, summary.analog)
S3method(print, summary.bootstrap.mat)
S3method(print, summary.cma)
S3method(print, summary.logitreg)
S3method(print, summary.mat)
S3method(print, summary.predict.mat)
S3method(print, summary.roc)
S3method(print, timetrack)
S3method(print, tolerance)
S3method(print, wa)
S3method(print, weightedCor)
## summary
S3method(summary, analog)
S3method(summary, bootstrap.mat)
S3method(summary, cma)
S3method(summary, logitreg)
S3method(summary, mat)
S3method(summary, predict.mat)
S3method(summary, roc)
## utilities
S3method(as.data.frame, optima)
S3method(as.data.frame, tolerance)
