Running 'add.R' [14s]
  Running 'ade4-functions.R' [186s]
  Running 'adegraphics.R' [178s]
  Running 'nbgraph.R' [3s]
  Running 'panelSpatial.R' [163s]
  Running 'parameter.R' [167s]
  Running 's.arrow.R' [164s]
  Running 's.class.R' [2s]
  Running 's.corcircle.R' [152s]
  Running 's.density.R' [166s]
  Running 's.distri.R' [2s]
  Running 's.image.R' [157s]
  Running 's.label.R' [156s]
  Running 's.logo.R' [155s]
  Running 's.match.R' [166s]
  Running 's.traject.R' [2s]
  Running 's.value.R' [160s]
  Running 's1d.barchart.R' [2s]
  Running 's1d.boxplot.R' [153s]
  Running 's1d.class.R' [2s]
  Running 's1d.density.R' [2s]
  Running 's1d.distri.R' [159s]
  Running 's1d.gauss.R' [2s]
  Running 's1d.hist.R' [172s]
  Running 's1d.label.R' [2s]
  Running 's1d.match.R' [159s]
  Running 'table.image.R' [172s]
  Running 'table.value.R' [161s]
  Running 'triangle.R' [4s]
Running the tests in 'tests/ade4-functions.R' failed.
Complete output:
  > ## delete/remove this file when 'scatter' functions will be removed in ade4
  > 
  > library(adegraphics)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  > pdf("ade4-functions.pdf")
  > 
  > ##################### scatter.dudi
  > data(deug, package = "ade4")
  > dd1 <- ade4::dudi.pca(deug$tab, scannf = FALSE, nf = 4)
  > scatter(dd1, posieig = "bottomright")
  > scatter(dd1, posieig = "bottomright", plot = T, prop = TRUE)
  > scatter(dd1, posieig = "none", plot = T)
  > scatter(dd1, posieig = "bottomleft", plot = T)
  > scatter(dd1, posieig = "topright", plot = T)
  > scatter(dd1, posieig = "topleft", plot = T, eig.col = c("white", "blue", "red"))
  > 
  > data(rhone, package = "ade4")
  > dd1 <- ade4::dudi.pca(rhone$tab, nf = 4, scannf = FALSE)
  > g1 <- scatter(dd1, sub = "Principal component analysis", row = list(plabels.optim = TRUE), col.pla.boxes.alpha = 0.5)
  > g1[2, drop = TRUE]
  > scatter(dd1, row = list(sub = "Principal component analysis", plabels.optim = TRUE), col.pla.boxes.alpha = 0.5)
  > scatter(dd1, prop = TRUE, ppoints.cex = 0.2, density.plot = TRUE, row = list(threshold = 0.01))
  > 
  > scatter(dd1, posieig = "none")
  > scatter(dd1, posieig = "bottomright")
  > scatter(dd1, posieig = c(0.5, 0.5))
  > scatter(dd1, posieig = c(0.5, 0.5, 1, 1))
  > 
  > 
  > ##################### scatter.coa
  > data(housetasks, package = "ade4")
  > par(mfrow = c(2, 2))
  > dd2 <- ade4::dudi.coa(housetasks, scan = FALSE)
  > ade4::scatter(dd2, method = 1, sub = "1 / Standard", posieig = "none")
  > ade4::scatter(dd2, method = 2, sub = "2 / Columns -> averaging -> Rows", posieig = "none")
  > ade4::scatter(dd2, method = 3, sub = "3 / Rows -> averaging -> Columns ", posieig = "none")
  > par(mfrow = c(1, 1))
  > 
  > g1 <- scatter(dd2, method = 1, row.sub = "1 / Standard", posieig = "none", plot = FALSE)
  > g2 <- scatter(dd2, method = 2, col.sub = "2 / Columns -> averaging -> Rows", posieig = "none", plot = FALSE)
  > g3 <- scatter(dd2, method = 3, row.sub = "3 / Rows -> averaging -> Columns ", posieig = "none", plot = FALSE)
  > G <- ADEgS(list(g1, g2, g3), layout = c(2, 2), plot = TRUE)
  > 
  > scatter(dd2, posieig = "none")
  > scatter(dd2, posieig = "bottomright")
  > scatter(dd2, posieig = c(0.5, 0.5))
  > scatter(dd2, posieig = c(0.5, 0.5, 1, 1))
  > 
  > 
  > ##################### scatter.pco
  > data(yanomama, package = "ade4")
  > gen <- ade4::quasieuclid(as.dist(yanomama$gen))
  > gen1 <- ade4::dudi.pco(gen, scann = FALSE, nf = 3)
  > scatter(gen1, posieig = "none")
  > scatter(gen1, posieig = "bottomri")
  > scatter(gen1, posieig = c(0.5, 0.5))
  > scatter(gen1, posieig = c(0.5, 0.5, 1, 1))
  > 
  > 
  > ##################### scatter.nipals
  > data(doubs, package = "ade4")
  > acp1 <- ade4::dudi.pca(doubs$env, scannf = FALSE, nf = 2)
  > nip1 <- ade4::nipals(doubs$env)
  > scatter(nip1, posieig = "none")
  > scatter(nip1, posieig = "bottomri")
  > scatter(nip1, posieig = c(0.5, 0.5))
  > scatter(nip1, posieig = c(0.5, 0.5, 1, 1))
  > 
  > 
  > ##################### score.inertia - plot.inertia
  > data(housetasks, package = "ade4")
  > coa2 <- ade4::dudi.coa(housetasks, scann = FALSE)
  > res21 <- ade4::inertia(coa2, row = TRUE, col = FALSE)
  > plot(res21, posieig = "none")
  > plot(res21, posieig = "bottomri")
  > plot(res21, posieig = c(0.5,0.5))
  > plot(res21, posieig = c(0.5, 0.5, 1, 1))
  > score(res21, posieig = "none")
  > score(res21, posieig = "bottomri")
  > score(res21, posieig = c(0.5, 0.5))
  > score(res21, posieig = c(0.5, 0.5, 1, 1))
  > 
  > res22 <- ade4::inertia(coa2, row = FALSE, col = TRUE)
  > plot(res22, posieig = "none")
  > plot(res22, posieig = "bottomri")
  > plot(res22, posieig = c(0.5, 0.5))
  > plot(res22, posieig = c(0.5, 0.5, 1, 1))
  > score(res22, posieig = "none")
  > score(res22, posieig = "bottomri")
  > score(res22, posieig = c(0.5, 0.5))
  > score(res22, posieig = c(0.5, 0.5, 1, 1))
  > 
  > res23 <- ade4::inertia(coa2, row = TRUE, col = TRUE)
  > plot(res23, posieig = "none")
  > plot(res23, posieig = "bottomri")
  > plot(res23, posieig = c(0.5, 0.5))
  > plot(res23, posieig = c(0.5, 0.5, 1, 1))
  > score(res23, posieig = "none")
  > score(res23, posieig = "bottomri")
  > score(res23, posieig = c(0.5, 0.5))
  > score(res23, posieig = c(0.5, 0.5, 2, 2))
  > 
  > 
  > ##################### plot.acm
  > data(lascaux, package = "ade4")
  > 
  > acm1 <- ade4::dudi.acm(lascaux$ornem, sca = FALSE)
  > p1 <- proc.time()
  > ade4::scatter(acm1)
  > Tade4 <- proc.time() - p1
  > 
  > p2 <- proc.time()
  > plot(acm1, ppoints.cex = 0.3, plot = T)
  > Tadegraphics <- proc.time() - p2
  > ## faster calculus, longest display than for ade4
  > 
  > 
  > ##################### plot.fca
  > data(coleo, package = "ade4")
  > coleo.fuzzy <- ade4::prep.fuzzy.var(coleo$tab, coleo$col.blocks)
  2 missing data found in block 1 
  1 missing data found in block 3 
  2 missing data found in block 4 
  > 
  > fca1 <- ade4::dudi.fca(coleo.fuzzy, scannf = FALSE, nf = 3)
  > ade4::scatter(fca1)
  > plot(fca1)
  > 
  > proc.time()
     user  system elapsed 
    17.35    0.53   17.93 
Running the tests in 'tests/adegraphics.R' failed.
Complete output:
  > library(adegraphics)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  > pdf("adegraphics.pdf")
  > 
  > xy <- cbind.data.frame(runif(7), runif(7))
  > g1 <- s.label(xy)
  > 
  > data(olympic, package = "ade4")
  > pca <- ade4::dudi.pca(olympic$tab, scan = FALSE)
  > g2 <- s.corcircle(pca$co, lab = names(olympic$tab))
  > 
  > g3 <- ADEgS(list(g1, g2), rbind(c(0, 0, 0.5, 1), c(0.5, 0, 1, 1)))
  > g4 <- ADEgS(list(g1, g2), layout = c(1, 2)) ## the same as g3
  > g4b <- ADEgS(list(g1, g2)) ## the same as g3
  > g5 <- s.label(xy, plabels.cex = 0, paxes.draw = TRUE, ppoints.col = "red")
  > 
  > g6 <- superpose(g1, g5, plot = TRUE)
  > g6b <- s.density(xy)
  > g7 <- superpose(s.density(xy), g5, plot = TRUE)
  >  
  > g8 <- superpose(s.label(xy, plabels.boxes.col = "orange", plot = FALSE), 
  +                 s.label(xy, plabels.cex = 0, paxes.draw = TRUE, ppoints.col = "red", plot = FALSE), 
  +                 plot = TRUE)
  > 
  > g9 <- g8[1, drop = TRUE]
  > class(g9)
  [1] "S2.label"
  attr(,"package")
  [1] "adegraphics"
  > g10 <- g8[1, drop = FALSE]
  > class(g10)
  [1] "ADEgS"
  attr(,"package")
  [1] "adegraphics"
  > 
  > g11 <- ADEgS(list(g8, g3), positions = rbind(c(0, 0, 0.5, 1), c(0.5, 0, 1, 1)))
  > 
  > ## cbindADEgS - rbindADEgS
  > g12 <- cbindADEg(g1, g2, plot = TRUE) ## the same as g3
  > g13 <- cbindADEg(g8, g3, plot = TRUE) ## the same as g11
  > g14 <- rbindADEg(g8, g3, plot = TRUE)
  > 
  > data(banque, package = "ade4")
  > banque.acm <- ade4::dudi.acm(banque, scann = FALSE, nf = 3)
  > g15 <- score(banque.acm, which = which(banque.acm$cr[, 1] > 0.2), plot = FALSE)
  > g15 <- g15[[1]]
  > cbindADEg(g15[[1]], g15[[2]], plot = TRUE)   ## work on trellis object
  > 
  > 
  > proc.time()
     user  system elapsed 
     4.40    0.50    4.84 
Running the tests in 'tests/panelSpatial.R' failed.
Complete output:
  > library(ade4)
  > library(adegraphics)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  
  Attaching package: 'adegraphics'
  
  The following objects are masked from 'package:ade4':
  
      kplotsepan.coa, s.arrow, s.class, s.corcircle, s.distri, s.image,
      s.label, s.logo, s.match, s.traject, s.value, table.value,
      triangle.class
  
  > library(sp)
  > pdf("panelSpatial.pdf")
  > 
  > ## ex1
  > data(mafragh, package = "ade4")
  > dfxy1 <- coordinates(mafragh$Spatial)
  > g1 <- s.label(dfxy1, Sp = mafragh$Spatial, pSp.col = colorRampPalette(c("yellow", "blue"))(97), pgrid.draw = FALSE, plabels.cex = 0)
  > 
  > 
  > ## ex2
  > data(meuse, package = "sp")
  > coordinates(meuse) <- ~ x + y
  > data(meuse.grid, package = "sp")
  > m <- SpatialPixelsDataFrame(points = meuse.grid[c("x", "y")], data = meuse.grid)
  > data(meuse.riv)
  > meuse.sr <- SpatialPolygons(list(Polygons(list(Polygon(meuse.riv)), "meuse.riv")))
  > 
  > scale1 <- list("SpatialPolygonsRescale", offset = c(179900, 329600), scale = 500, fill = c("transparent", "black"), layout.scale.bar())
  > text11 <- list("sp.text", c(179900, 329700), "0")
  > text21 <- list("sp.text", c(180400, 329700), "500 m")
  > arrow1 <- list("SpatialPolygonsRescale", offset = c(178750, 332500), scale = 400, layout.north.arrow())
  > river <- list("sp.polygons", meuse.sr, fill = "lightblue")
  > dfxy2 <- as.data.frame(coordinates(meuse))
  > g2 <- s.value(dfxy2, z = meuse[, 1]$cadmium, sp.layout = list(scale1, text11, text21, arrow1, river), Sp = m)
  > 
  > fac <- meuse@data$ffreq
  > levels(fac)[1] <- "1 in 2 years"
  > levels(fac)[2] <- "1 in 10 years"
  > levels(fac)[3] <- "1 in 50 years"
  > arrow2 <- list("SpatialPolygonsRescale", layout.north.arrow(), offset = c(181750, 330000), scale = 400)
  > scale2 <- list("SpatialPolygonsRescale", layout.scale.bar(), offset =  c(178050, 333600), scale = 500, fill = c("transparent", "black"))
  > text12 <- list("sp.text", c(178050, 333700), "0")
  > text22 <- list("sp.text", c(178550, 333700), "500 m")
  > g3 <- s.class(dfxy2, fac = fac, sp.layout = list(scale2, text12, text22, arrow2, river), starSize = 1, col = c(1, 2, 4), pellipses.col = c(1, 2, 4), 
  +   pellipses.alpha = 0.7, plines.lty = 3, psub.text = "Flooding frequency \n near the Meuse river", psub.pos = c(0.2, 0.88), pgrid.text.cex = 0,
  +   porigin.include = FALSE, Sp = meuse.sr)
  > 
  > ## ex3
  > # if(require(Guerry)) {
  > #   data(gfrance85)
  > #   
  > #   dfxy4 <- coordinates(gfrance85)
  > #   region.names <- data.frame(gfrance85)[, 5]
  > #   col.region <- colors()[c(149, 254, 468, 552, 26)]
  > #   g4 <- s.class(dfxy4, region.names, ellip = 0, star = 0, col = col.region, Sp = gfrance85, pSp.col = col.region[region.names], porig.inclu = F)
  > # }
  > 
  > ## ex4
  > library(sp)
  > library(lattice)
  > 
  > data(elec88, package = "ade4")
  > sp <- elec88$Spatial
  > 
  > g5 <- xyplot(1 ~ 1, xlim = bbox(sp)[1, ], ylim = bbox(sp)[2, ], panel = function(...) {adeg.panel.Spatial(SpObject = sp, col = "black", border = "black")})
  > g6 <- xyplot(1 ~ 1, xlim = bbox(sp)[1, ], ylim = bbox(sp)[2, ], panel = function(...) {adeg.panel.Spatial(sp, col = 1:14, border = "black")})
  > g7 <- xyplot(1 ~ 1, xlim = bbox(sp)[1, ], ylim = bbox(sp)[2, ], aspect = "iso", panel = function(...) {sp.polygons(sp, col = "black", fill = 1:5)})
  > g8 <- xyplot(1 ~ 1, xlim = bbox(sp)[1, ], ylim = bbox(sp)[2, ], panel = function(...) {adeg.panel.Spatial(SpObject = sp, col = "black", border = "blue")})
  > g9 <- xyplot(1 ~ 1, xlim = bbox(sp)[1, ], ylim = bbox(sp)[2, ], panel = function(...) {adeg.panel.Spatial(SpObject = sp, col = "black", border = "blue")})
  > #g10 <- s.label(cbind(-80, 35), Sp = nc)
  > #g11 <- s.label(cbind(-80, 35), Sp = sp)
  > 
  > 
  > ## ex5
  > data(jv73, package = "ade4")
  > g12 <- s.label(jv73$xy, Sp = jv73$Spatial)
  > g13 <- s.label(jv73$xy, Sp = jv73$Spatial, pSp.col = "red")
  > 
  > spoints <- SpatialPoints(jv73$xy)
  > g14 <- s.label(jv73$xy, Sp = spoints, plab.cex = 0, ppoin.cex = 0, pSp.col = 1)
  > 
  > sgrid <- SpatialGrid(GridTopology(c(0, 0), c(1, 1), c(3, 5)))
  > xyplot(0:5 ~ 0:3, panel = function(...) sp.grid(sgrid, col = 1:2))
  > 
  > nc <- SpatialGridDataFrame(getGridTopology(sgrid), data = data.frame(matrix(1:15, ncol = 1)))
  > xyplot(0:5 ~ 0:3, panel = function(...) sp.grid(nc, col = 1, at = pretty(rnorm(15), 2), col.region = 2:3))
  > xyplot(0:5 ~ 0:3, panel = function(...) adeg.panel.Spatial(nc, col = 1:3))
  > xyplot(0:5 ~ 0:3, panel = function(...) adeg.panel.Spatial(nc, col = 1:2))
  > 
  > 
  > ## ex6
  > mysp <- SpatialPointsDataFrame(matrix(rnorm(20), 10), data.frame(matrix(rnorm(20), 10)))
  > s.Spatial(mysp)
  > s.Spatial(mysp, col = c("red", "blue"))
  > s.Spatial(mysp, ppoints.cex = 2)
  > s.Spatial(mysp, ppoints.alpha = 0.5)
  > s.Spatial(mysp, symbol = "circle")
  > s.Spatial(mysp, method = "color", ppalette.quanti = colorRampPalette(c("red", "white", "blue")))
  > 
  > proc.time()
     user  system elapsed 
     3.60    0.35    3.93 
Running the tests in 'tests/parameter.R' failed.
Complete output:
  > library(ade4)
  > library(adegraphics)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  
  Attaching package: 'adegraphics'
  
  The following objects are masked from 'package:ade4':
  
      kplotsepan.coa, s.arrow, s.class, s.corcircle, s.distri, s.image,
      s.label, s.logo, s.match, s.traject, s.value, table.value,
      triangle.class
  
  > pdf("parameter.pdf")
  > 
  > adegparold <- adegpar()
  > b1 <- length(adegraphics:::separation(plines = list(col = "blue"), plab.bo.dra = FALSE, plab = list(orien = F))$rest) == 0
  > b2 <- length(adegraphics:::separation(plines = list(col = "blue", lwd = c(1:5)), parr.end = NA, plab.boxes.dr = FALSE)$rest) == 0
  > b3 <- length(adegraphics:::separation(plot.li = list(col = "blue", lwd = c(1:5)), par.end = NA, pl.boxes.draw = FALSE, pattern = 1)$rest) == 2
  > b4 <- length(adegraphics:::separation(plot.li = list(col = "blue", lwd = c(1:5)), par.end = NA, pl.boxes.draw = FALSE, pattern = 0)$rest) == 2
  > b5 <- length(adegraphics:::separation()) == 2
  > b6 <- length(adegraphics:::separation(par.sub.text = list("lineheight" = 5), pattern = 1)$rest) == 0
  > b7 <- names(adegraphics:::separation(toto = "rienavoir!")$rest) == "toto"
  > b8 <- names(adegraphics:::separation(toto = "rienavoir!", pattern = 1)$rest) == "toto"
  > 
  > l1 <- list(parrow = list(col = "blue", lwd = c(1:5), end = NA), plboxes.draw = FALSE, pattern = 1)
  > sep1 <- adegraphics:::separation(l1)  ## no recognition of "pattern" in a list
  > 
  > l2 <- list("parrow.lwd", "plboxes.draw")
  > sep2 <- adegraphics:::separation(l2)
  > 
  > sep3 <- adegraphics:::separation("plboxes" = list("draw" = FALSE, "col"))
  > sep4 <- adegraphics:::separation("plboxes" = list("draw" = FALSE, "col" = 2))
  > sep5 <- adegraphics:::separation(pla.box = list(col = 1:5))
  > sep6 <- adegraphics:::separation(pla.box.col = c(1:5))
  > sep7 <- adegraphics:::separation(pla = list(box.col = 1:5))  ## don't match
  > 
  > 
  > ## adegpar test
  > ad1 <- adegpar()
  > ad2 <- adegpar("paxes.draw")
  > ad3 <- adegpar("paxes.draw", "psub.cex")
  > 
  > ad4 <- adegpar("psub.cex" = 5)
  > ad5 <- adegpar("psub.cex" = 5, paxes.draw = FALSE)
  > ad6 <- adegpar("psub")
  > ad7 <- adegpar("psub.cex", "plabe.boxes")
  > 
  > ad8 <- adegpar(ppoints = list(col = "yellow"), pgrid.space = 4, plines = list(lwd = c(1:5)))
  > ad9 <- adegpar(ppoints = list(col = "red"), pgrid = list(nint = 12), plines = list(lwd = c(1:5)))
  > ad10 <- adegpar("ppoints.col", "pgrid.nint", "plines")
  > 
  > ad11 <- adegpar(paxes = list("x"), pgrid = list("nint", "col"))
  > ad12 <- adegpar(list(pellip = list(col = "red"), grid.nint = 8, plines = list(lwd = c(1:5))))
  > ad13 <- adegpar(paxes = list("x"), pgrid = list("nint", "col"), "plines", "pellipse")
  > 
  > ad14 <- adegpar(plegend.drawKey = FALSE)
  > ad15 <- adegpar(list(paxes = list(col = "white"), pgrid.nint = 6, plines = list(lwd = c(1:5))))
  > ad16 <- adegpar(paxes = list(x = list(draw = TRUE)))
  > 
  > adegpar(adegparold)
  > 
  > ## merging list
  > l3 <- list(plabels = list(boxes = list(col = "white", alpha = 1)), plabels = list(cex = 2), plabels = list(col = "red"))
  > adegraphics:::.mergingList(l3)
  $plabels
  $plabels$boxes
  $plabels$boxes$col
  [1] "white"
  
  $plabels$boxes$alpha
  [1] 1
  
  
  $plabels$cex
  [1] 2
  
  $plabels$col
  [1] "red"
  
  
  > adegraphics:::.mergingList(list(plabels = list(cex = 3)))
  $plabels
  $plabels$cex
  [1] 3
  
  
  > 
  > 
  > ## update parameters in graphics
  > cha <- rep(LETTERS, length.out = 100)
  > xy <- cbind.data.frame(runif(length(cha)), runif(length(cha)))
  > g1 <- s.label(xy, labels = cha, paxes.draw = TRUE, plabels.cex = runif(length(cha), 0.5, 1.5))
  > update(g1, paxes = list(aspect = "fill", draw = TRUE, x = list(draw = FALSE)), 
  +   pgrid = list(col = "black", lwd = 2, lty = 5), 
  +   plabels = list(col = 1:4, alpha = 0.5, cex = 2, boxes = list(border = "blue", col = "antiquewhite", alpha = 0.2, lwd = 2.5, lty = 5))) 
  > 
  > g2 <- s.label(xy, labels = cha)
  > update(g2, paxes.draw = FALSE, pgrid = list(col = "blue", lwd = 2, lty = 5, text = list(pos = "bottomright", cex = 2, col = "green")))
  > update(g2, porigin = list(alpha = 0.5, col = "red", lty = 5 , lwd = 2, origin = c(0.6, 0.1)), pgrid.lwd = 0.5)
  > update(g2, psub = list(text = "parameters", cex = 2, col = "red", position = "topright"))
  > update(g2, plabels.cex = 0, ppoints = list(alpha = 0.4, cex = 2, col = "red", fill = "blue", pch = 21))
  > 
  > 
  > ## from tdr641
  > data(doubs, package = "ade4")
  > dudi1 <- ade4::dudi.pca(doubs$env, scale = T, scannf = F, nf = 3)
  > dudi2 <- ade4::dudi.pca(doubs$fish, scale = T, scannf = F, nf = 2)
  > coin1 <- ade4::coinertia(dudi1, dudi2, scannf = F, nf = 2)
  > g3 <- s.arrow(coin1$l1, plabels.cex = .87)
  > update(g3, plines = list(col = "blue", lwd = 2, lty = 3), parr.end = "both", parr = list(angle = 25, length = 0.5))
  > 
  > ## with spatial object
  > data(elec88, package = "ade4")
  > g4 <- s.label(elec88$xy, label = as.character(1:nrow(elec88$xy)), porigin.include = FALSE, Sp = elec88$Spatial, pSp.col = colorRampPalette(c("yellow", "blue"))(5), pgrid.draw = TRUE)
  > update(g4, pSp = list(col = "yellow", border = "blue", lwd = 2, lty = 5, alpha = 0.01)) ## don't match : to solve
  > 
  > ## plabels parameter
  > data(tortues, package = "ade4")
  > pturtles <- tortues
  > names(pturtles) <- c("length", "width", "height", "sex")
  > sex <- pturtles$sex
  > sexcol <- ifelse(sex == "M", "blue", "red")
  > measures <- pturtles[, 1:3]
  > pca1 <- ade4::dudi.pca(measures, scann = FALSE, nf = 3)
  > g5 <- scatter(pca1, row.plabel.cex = 0, col.plabel.cex = c(1, 2, 3), posieig = "none", col.plabel.col = c("red", "blue", "green"))
  > 
  > proc.time()
     user  system elapsed 
     3.79    0.32    4.09 
Running the tests in 'tests/s.arrow.R' failed.
Complete output:
  > library(adegraphics)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  > pdf("s.arrow.pdf")
  > 
  > ## ex1 : from tdr641
  > data(doubs, package = "ade4") 
  > dudi1 <- ade4::dudi.pca(doubs$env, scale = T, scan = F, nf = 3)
  > dudi2 <- ade4::dudi.pca(doubs$fish, scale = T, scan = F, nf = 2)
  > coin1 <- ade4::coinertia(dudi1, dudi2, scan = F, nf = 2)
  > g1 <- s.arrow(coin1$l1, plabels.cex = 0.87)
  > g2 <- s.arrow(coin1$c1, plabels.cex = 1)
  > 
  > ## ex2 : from bs81
  > data(granulo, package = "ade4")
  > w <- data.frame(t(apply(granulo$tab, 1, function(x) x / sum(x))))
  > g3 <- s.arrow(ade4::dudi.pca(data.frame(w), scan = F, nf = 2)$co)
  > 
  > wtr <- data.frame(t(w))
  > wmoy <- data.frame(matrix(apply(wtr, 1, mean), 1))
  > dudi3 <- ade4::dudi.pca(w, scal = FALSE, scan = FALSE)
  > wmoy <- ade4::suprow(dudi3, wmoy)$lisup
  > 
  > g4 <- s.arrow(dudi3$c1, plabels.cex = 1.5)
  > g4 <- s.distri(dudi3$c1, wtr, starSize = 0.33, ellipseSize = 0, add = TRUE, plabels.cex = 1)
  > g4 <- s.label(wmoy, ppoint.cex = 5, plabels.cex = 0, add = TRUE)
  > 
  > ## ex3
  > data(deug, package = "ade4")
  > pca1 <- ade4::dudi.pca(deug$tab, scal = FALSE, center = deug$cent, scan = FALSE)
  > g5 <- s.arrow(40 * pca1$c1)
  > 
  > ## ex4
  > xy <- cbind(rnorm(50), rnorm(50))
  > g6 <- s.arrow(xy, plabels.cex = 0.9, parrows = list(angle = 20))
  > 
  > proc.time()
     user  system elapsed 
     1.50    0.18    1.67 
Running the tests in 'tests/s.corcircle.R' failed.
Complete output:
  > library(adegraphics)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  > pdf("s.corcircle.pdf")
  > data(olympic, package = "ade4")
  > 
  > dudi1 <- ade4::dudi.pca(olympic$tab, scan = FALSE) # a normed PCA
  > g1 <- s.corcircle(dudi1$co, lab = names(olympic$tab))
  > 
  > g2 <- s.corcircle(dudi1$co, lab = names(olympic$tab), fullcircle = T)
  > g3 <- s.corcircle(dudi1$co, lab = names(olympic$tab), fullcircle = FALSE)
  > g4 <- s.corcircle(dudi1$co, lab = names(olympic$tab), pback.col = "red", pbackground.box = FALSE)
  > 
  > proc.time()
     user  system elapsed 
     1.14    0.17    1.29 
Running the tests in 'tests/s.density.R' failed.
Complete output:
  > library(adegraphics)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  > pdf("s.density.pdf")
  > 
  > xx1 <- rnorm(1000, 1, 2)
  > yy1 <- rnorm(1000, 1, 2)
  > 
  > g1 <- s.density(cbind(xx1, yy1), paxes.draw = T, gridsize = c(40, 40))
  > g2 <- s.density(cbind(xx1, yy1), paxes.draw = T, gridsize = c(80, 80), col = colorRampPalette(c("red", "blue"))(58), storeData = FALSE, region = TRUE)
  > g3 <- s.density(cbind(yy1 + 3, xx1 + 3), gridsize = c(400, 400))
  > g4 <- s.density(cbind(xx1, yy1), paxes.draw = T, gridsize = c(200, 200), add = TRUE)
  > g5 <- s.density(cbind(c(rnorm(50000, 1, 1), rnorm(50000, -1, 1)), c(rnorm(50000, -1, 0.5), rnorm(50000, 1, 0.5))), paxes.draw = T, gridsize = c(200, 200), region = TRUE, contour = TRUE, plabels.cex = 1, plabels.srt = "vertial")
  > g6 <- s.density(cbind(rnorm(300, 3, 0.3), rnorm(300, -2, 0.5)), gridsize = c(500, 500), thres = 0.01, nr = 10, regions = list(alpha = 0.5), col = colorRampPalette(c("red", "blue"))(108))
  > g7 <- s.density(cbind(c(rnorm(50000, 1, 1), rnorm(50000, -1, 1)), c(rnorm(50000, -1, 0.5), rnorm(50000, 1, 0.5))), paxes.draw = T, gridsize = c(100, 100), region = TRUE, contour = TRUE, plabels.cex = 1, nclass = 5)
  > 
  > proc.time()
     user  system elapsed 
     3.78    0.40    4.18 
Running the tests in 'tests/s.image.R' failed.
Complete output:
  > library(adegraphics)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  > library(sp)
  > pdf("s.image.pdf")
  > 
  > ## ex1
  > xy <- data.frame(expand.grid(-3:3, -3:3))
  > names(xy) <- c("x", "y")
  > z <- (1 / sqrt(2)) * exp(-(xy$x ^ 2 + xy$y ^ 2) / 2)
  > s.image(xy, z)
  > s.image(xy, z, grid = 20)
  > s.image(xy, z, grid = 500)
  > 
  > ## ex2
  > Sr1 <- Polygon(cbind(c(0, 1, 2, 1, 2, 0 , -2, -1, -2, -1, 0), c(2.5, 1.5, 2, 0, -2, -1, -2, 0, 2, 1.5, 2.5)))    
  > Srs1 <- Polygons(list(Sr1), ID = "stars")        
  > SPp1 <- SpatialPolygons(list(Srs1))
  > xy1 <- cbind(rnorm(100, 0, 1), rnorm(100, 0, 1.5))
  > g1 <- s.image(xy1, runif(100), outsideLimits = SPp1)
  > 
  > ## ex3
  > Sr2 <- Polygon(cbind(c(-0.5, 0.5, 0.5, -0.5, -0.5), c(0, 0, 1 ,1, 0)), hole = TRUE)
  > Srs2 <- Polygons(list(Sr1, Sr2), ID = "hole")
  > SPp2 <- SpatialPolygons(list(Srs2))
  > xy2 <- cbind(c(rnorm(2000, 1, 0.25), rnorm(3000, -1, 1.5)), c(rnorm(2000, 1, 0.5), rnorm(3000, -1, 3)))
  > z <- c(rnorm(2000, 12, 1), rnorm(3000, 1, 2))
  > g2 <- s.image(xy2, z, outsideLimits = SPp2, grid = 500, xlim = c(-2.5, 2.5), ylim = c(-2, 3))
  > 
  > proc.time()
     user  system elapsed 
     3.54    0.48    3.98 
Running the tests in 'tests/s.label.R' failed.
Complete output:
  > library(adegraphics)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  > library(grid)
  > pdf("s.label.pdf")
  > 
  > x0 <- runif(50, -2, 2)
  > y0 <- runif(50, -2, 2)
  > z <- x0 ^ 2 + y0 ^ 2
  > dfxy1 <- data.frame(x0, y0)
  > g1 <- s.label(dfxy1, label = as.character(z < 1), paxes.draw = TRUE, axis.text = list(col = "grey"))
  > g2 <- s.label(dfxy1[1, ])
  > g3 <- s.label(dfxy1[1, ], pori.incl = FALSE)
  > g4 <- s.label(dfxy1, labels = c("", "MM", "", NA, "ooo"), plabels.optim = TRUE)
  > g5 <- s.label(dfxy1, labels = as.character(z < 1), psub = list(text = "Subtitle", col = "blue", position = "topleft"), plabels.col = 1:5, pgrid.text.pos = c(unit(0.95, "npc"), unit(0.94, "npc")))
  > 
  > dfxy2 <- cbind(dfxy1, runif(50, -5, 5))
  > g6 <- s.label(dfxy2, xax = 1, yax = 2:3, paxes.draw = TRUE, paxes.aspectratio = 1.5, plabels.cex = 0.8)
  > 
  > l <- ls()
  > x1 <- runif(length(l))
  > x2 <- runif(100)
  > y1 <- runif(length(l))
  > y2 <- runif(100)
  > g7 <- s.label(cbind(x2, y2), labels = as.character((x2 * x2 + y2 * y2) < 1))
  > g8 <- s.label(cbind(x1, y1), labels = l, add = TRUE, plabels.col = "blue")
  > 
  > proc.time()
     user  system elapsed 
     1.82    0.15    2.01 
Running the tests in 'tests/s.logo.R' failed.
Complete output:
  > library(adegraphics)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  > pdf("s.logo.pdf")
  > 
  > ## ex1
  > data(ggtortoises, package = "ade4")
  > ico <- ggtortoises$ico[as.character(ggtortoises$pop$carap)]
  > g1 <- s.logo(ggtortoises$pop, ico, pori.incl = FALSE)
  Loading required package: pixmap
  > g2 <- s.label(ggtortoises$pop, add = TRUE, plabels = list(boxes = list(alpha = 0.4, border = "transparent")))
  > 
  > ## ex2
  > data(capitales, package = "ade4")
  > index <- unlist(lapply(1:15, function(i) which(names(capitales$logo) == tolower(rownames(capitales$xy)[i]))), use.names = FALSE)
  > g3 <- s.logo(capitales$xy, capitales$logo[index])
  > 
  > x <- c(0, max(capitales$area$x))
  > y <- c(0, max(capitales$area$y))
  > #g4 <- s.image(cbind(x, y), z = c(1, 2), outsideLimits = capitales$area, grid = 500, regions = list(col = "yellow", alpha = 0.9))
  > #s.logo(capitales$xy, capitales$logo[index], add = TRUE)
  > 
  > proc.time()
     user  system elapsed 
     1.15    0.25    1.35 
Running the tests in 'tests/s.match.R' failed.
Complete output:
  > library(adegraphics)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  > pdf("s.match.pdf")
  > 
  > X <- data.frame(x = runif(50, -1, 2), y = runif(50, -1, 2))
  > Y <- X + rnorm(100, sd = 0.3)
  > 
  > g1 <- s.match(X, Y, ppoints.cex = 0, col = c("blue", "red"))
  > g2 <- s.match(X, Y, arr = FALSE, ppoints.cex = 2, ppoints.col = c("blue", "green"))
  > g3 <- s.match(X, Y, arr = FALSE)
  > g4 <- s.match(X, Y, arrows = TRUE, plabels = list(alpha = 1, col = "black", cex = 1), plines = list(col = "red"), panel.background = list(col = "antiquewhite"))
  > 
  > proc.time()
     user  system elapsed 
     1.42    0.06    1.46 
Running the tests in 'tests/s.value.R' failed.
Complete output:
  > library(adegraphics)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  > pdf("s.value.pdf")
  > 
  > ## ex1
  > xy <- cbind.data.frame(x = runif(50, -1, 1), y = runif(50, 0, 2))
  > z <- rnorm(50)
  > z <- sapply(z, function(X) max(X, -3))
  > z <- sapply(z, function(X) min(X, 3))
  > val1 <- s.value(xy, z, method = "size", symbol = "square", plot = F)
  > val2 <- s.value(xy, z, method = "color", symbol = "square", plot = F)
  > val3 <- s.value(xy, z, method = "size", symbol = "circle", plot = F)
  > val4 <- s.value(xy, z, method = "color", symbol = "circle", plot = F)
  > g1 <- ADEgS(c(val1, val2, val3, val4), positions = layout2position(matrix(c(1, 2, 3, 4), 2, 2)), add = matrix(0, ncol = 4, nrow = 4))
  > g2 <- s.value(xy, z, method = "color", symbol = "square", breaks = c(-3, -1, -0.5, 0, 0.5, 1, 3))
  > g3 <- s.value(xy, z, method = "color", col = colorRampPalette(c("yellow", "blue"))(6))
  > g4 <- s.value(xy, z, method = "size", symbol = "circle", paxes.draw = FALSE)
  > 
  > ## ex2
  > xx <- runif(100) * 100
  > yy <- 1:100 
  > zz <- 1:100
  > breaks <- c(0, 25, 50, 75, 100)
  > g5 <- s.value(data.frame(xx, yy), zz, breaks = breaks, method = "color", paxes.draw = TRUE,  porigin.include = FALSE)
  > g6 <- s.value(data.frame(xx, yy), cbind(zz, rev(zz)), breaks = breaks, method = "color", col = c("blue", "red", "green", "yellow"), paxes.draw = TRUE)
  > g7 <- s.value(data.frame(xx, yy), cbind(zz, rev(zz)), nclass = c(2, 6), method = "color", col = c("blue", "red", "pink", "green", "yellow"), paxes.draw = TRUE)
  > 
  > ## ex3
  > data(rpjdl, package = "ade4")
  > fau.coa <- ade4::dudi.coa(rpjdl$fau, scan = FALSE, nf = 3)
  > val5 <- s.value(fau.coa$li, fau.coa$li[,3], plot = FALSE)
  > val6 <- s.value(fau.coa$li, fau.coa$li[, 3], center = 0, method = "size", symbol = "circle", col = c("yellow", "red"), plot = FALSE)
  > g8 <- ADEgS(c(val5, val6), positions = layout2position(matrix(c(1, 2), 1, 2)), add = matrix(0, ncol = 2, nrow = 2))
  > 
  > ## ex3
  > data(doubs, package = "ade4")
  > g9 <- s.value(doubs$xy, doubs$env[, 1:2])
  > g10 <- s.value(doubs$xy, doubs$env)
  > 
  > proc.time()
     user  system elapsed 
     2.95    0.31    3.21 
Running the tests in 'tests/s1d.boxplot.R' failed.
Complete output:
  > library(adegraphics)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  > pdf("s1d.boxplot.pdf")
  > 
  > ## ex1
  > x <- c(rnorm(10), rnorm(10))
  > fact <- factor(rep(c("A", "B"), 10))
  > g11 <- s1d.boxplot(x, fact)
  > g12 <- s1d.boxplot(x, fact, col = TRUE)
  > g12 <- s1d.boxplot(x, fact, col = 2:3)
  > g12 <- s1d.boxplot(x, fact, col = TRUE, plines.col = "black")
  > 
  > g2 <- s1d.boxplot(x, fact, ppolygon.border = c("red", "blue"), box.rectangle = list(alpha = 1, fill = "green"))
  > 
  > ## ex2
  > w1 <- rnorm(100, -1)
  > w2 <- rnorm(100)
  > w3 <- rnorm(100, 1)
  > f1 <- gl(3, 100)
  > f2 <- gl(30, 10)
  > g3 <- s1d.boxplot(c(w1, w2, w3), f1)
  > g4 <- s1d.boxplot(c(w1, w2, w3), f2)
  > g5 <- s1d.boxplot(c(w1, w2, w3), f2, p1d.rug.draw = FALSE)
  > 
  > mat <- matrix(0, ncol = 1, nrow = 8)
  > mat[c(2), ] <- 1
  > mat[c(3:8), ] <- 2
  > mat[1, ] <- 3
  > g6 <- ADEgS(c(g3, g4, s1d.label(c(w1, w2, w3), p1d = list(rug = list(tck = 0.8), rev = TRUE), ppoints.cex = 0, plabels.cex = 0, plot = F, pgrid.draw = F)), 
  +   layout = matrix((rev(mat)), ncol = 1))
  > g7 <- s1d.boxplot(c(w1, w2, w3), data.frame(f1, f2))
  > 
  > ## ex3
  > data(banque, package = "ade4")
  > banque.acm <- ade4::dudi.acm(banque, scan = FALSE, nf = 4)
  > s1d.boxplot(banque.acm$l1[, 1], banque[, 1:7], plabels.cex = 1.8)
  > 
  > 
  > proc.time()
     user  system elapsed 
     2.26    0.26    2.46 
Running the tests in 'tests/s1d.distri.R' failed.
Complete output:
  > library(adegraphics)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  > pdf("s1d.distri.pdf")
  > 
  > ## ex1
  > score <- rnorm(10)
  > df <- data.frame(matrix(rep(c(1, 2), 10), ncol = 2))
  > g1 <- s1d.distri(score, df)
  > 
  > ## ex2
  > set.seed(1)
  > w <- seq(-1, 1, le = 200)
  > distri <- data.frame(lapply(1:50, function(x) sample(200:1) * ((w >= (- x / 50)) & (w <= x / 50))))
  > names(distri) <- paste("w", 1:50, sep = "")
  > g2 <- s1d.distri(w, distri)
  > g3 <- s1d.distri(w, distri, yrank = TRUE, sdS = 1.5)
  > 
  > g4 <- s1d.distri(w, distri, p1d.rug.draw = FALSE)
  > g5 <- s1d.distri(w, distri, p1d.reverse = TRUE)
  > g6 <- s1d.distri(w, distri, p1d.hori = FALSE)
  > g7 <- s1d.distri(w, distri, p1d.hori = FALSE, p1d.reverse = TRUE)
  > 
  > update(g2, p1d.rug.draw = FALSE)
  > update(g5, p1d.rug.draw = FALSE)
  > 
  > proc.time()
     user  system elapsed 
     1.85    0.23    2.09 
Running the tests in 'tests/s1d.hist.R' failed.
Complete output:
  > library(ade4)
  > library(adegraphics)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  
  Attaching package: 'adegraphics'
  
  The following objects are masked from 'package:ade4':
  
      kplotsepan.coa, s.arrow, s.class, s.corcircle, s.distri, s.image,
      s.label, s.logo, s.match, s.traject, s.value, table.value,
      triangle.class
  
  > pdf("s1d.hist.pdf")
  > 
  > set.seed(40)
  > x1 <- rnorm(1000)
  > g11 <- s1d.hist(x1)
  > g12 <- s1d.hist(x1, col = 1:10)
  > g13 <- s1d.hist(x1, col = FALSE, ppoly.col = 1:10)
  > g14 <- s1d.hist(x1, col = TRUE, ppoly.col = "blue")
  > 
  > set.seed(50)
  > x1 <- rnorm(1000)
  > g21 <- s1d.hist(x1) # p1d.hori = TRUE and p1d.reverse = FALSE by default
  > # g22 <- s1d.hist(x1, p1d.hori = TRUE,  p1d.rev = TRUE)
  > g23 <- s1d.hist(x1, p1d.hori = FALSE, p1d.rev = FALSE)
  > # g24 <- s1d.hist(x1, p1d.hori = FALSE, p1d.rev = TRUE)
  > 
  > 
  > # randtest.pcaiv
  > data(rpjdl, package = "ade4")
  > millog <- log(rpjdl$mil + 1)
  > coa1 <- dudi.coa(rpjdl$fau, scann = FALSE)
  > caiv1 <- pcaiv(coa1, millog, scan = FALSE)
  > set.seed(50)
  > rd11 <- randtest(caiv1)
  > plot(rd11)
  > set.seed(50)
  > rd12 <- randtest(caiv1, output = "full")
  > plot(rd12, nclass = 15) # must be the same output as rd11
  > set.seed(50)
  > rd13 <- randtest(caiv1, output = "full")
  > plot(rd13, nclass = 8)
  > plot(rd13, nclass = 8, plines.col = "red")
  > plot(rd13, nclass = 8, obs.plines.col = "red")
  > plot(rd13, nclass = 8, sim.plines.col = "red")
  > 
  > # randtest.dpcoa
  > data(humDNAm, package = "ade4")
  > dpcoahum <- dpcoa(data.frame(t(humDNAm$samples)), sqrt(humDNAm$distances), scan = FALSE, nf = 2)
  > set.seed(50)
  > rd21 <- randtest(dpcoahum)
  > plot(rd21)
  > rd22 <- randtest(dpcoahum, output = "full")
  > plot(rd22)
  > 
  > # randtest.amova (plot.krandtest)
  > amovahum <- amova(humDNAm$samples, sqrt(humDNAm$distances), humDNAm$structures)
  > set.seed(50)
  > rd31 <- randtest(amovahum, 49)
  > plot(rd31)
  > plot(rd31, plines.col = "red")
  > plot(rd31, g1.plines.col = "red")
  > set.seed(50)
  > rd32 <- randtest(amovahum, 49, output = "full")
  > plot(rd32)
  > plot(rd32, plines.col = "red")
  > plot(rd32, g1.plines.col = "red")
  > plot(rd32, nclass = 30, g2.pback.col = "lightblue")
  > 
  > # randtest.coinertia
  > data(doubs, package = "ade4")
  > dudi1 <- dudi.pca(doubs$env, scale = TRUE, scan = FALSE, nf = 3)
  > dudi2 <- dudi.pca(doubs$fish, scale = FALSE, scan = FALSE, nf = 2)
  > coin1 <- coinertia(dudi1,dudi2, scan = FALSE, nf = 2)
  > set.seed(50)
  > rd4 <- randtest(coin1)
  > plot(rd4)
  > 
  > # randtest.pcaivortho
  > data(rpjdl, package = "ade4")
  > millog <- log(rpjdl$mil + 1)
  > coa1 <- dudi.coa(rpjdl$fau, scann = FALSE)
  > caiv1 <- pcaiv(coa1, millog, scan = FALSE)
  > set.seed(50)
  > rd5 <- randtest(caiv1)
  > plot(rd5)
  > 
  > # randtest.rlq (plot.krandtest)
  > data(aviurba, package = "ade4")
  > coa1 <- dudi.coa(aviurba$fau, scannf = FALSE, nf = 2)
  > dudimil <- dudi.hillsmith(aviurba$mil, scannf = FALSE, nf = 2, row.w = coa1$lw)
  > duditrait <- dudi.hillsmith(aviurba$traits, scannf = FALSE, nf = 2, row.w = coa1$cw)
  > rlq1 <- rlq(dudimil, coa1, duditrait, scannf = FALSE, nf = 2)
  > set.seed(50)
  > rd6 <- randtest(rlq1)
  > plot(rd6)
  > 
  > # randtest.between
  > data(meaudret, package = "ade4")
  > pca1 <- dudi.pca(meaudret$env, scan = FALSE, nf = 3)
  > set.seed(50)
  > rd7 <- randtest(bca(pca1, meaudret$design$season, scan = FALSE), 99)
  > plot(rd7, main = "Monte-Carlo test")
  > 
  > # randtest.discrimin
  > set.seed(50)
  > rd8 <- randtest(discrimin(pca1, meaudret$design$season, scan = FALSE), 99)
  > plot(rd8, main = "Monte-Carlo test")
  > 
  > proc.time()
     user  system elapsed 
     7.28    0.51    7.78 
Running the tests in 'tests/s1d.match.R' failed.
Complete output:
  > library(adegraphics)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  > pdf("s1d.match.pdf")
  > 
  > g1 <- s1d.match(-5:5, 2 * (-5:5))
  > g2 <- s1d.match(rnorm(10), runif(10), p1d.hor = FALSE)
  > g3 <- s1d.match(1:5, 7:11, p1d.hor = F, p1d.rev = T)
  > 
  > proc.time()
     user  system elapsed 
     1.20    0.23    1.39 
Running the tests in 'tests/table.image.R' failed.
Complete output:
  > library(adegraphics)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  > pdf("table.image.pdf")
  > 
  > ## ex1
  > x <- 1:4
  > y <- 1:4
  > df <- data.frame(as.matrix(cbind(x, y)))
  > g1 <- table.image(df, col = 2:4)
  > update(g1, plegend.drawColorKey = TRUE)
  > 
  > ## ex2
  > df <- matrix(0, 10, 10)
  > df[1:3, 1:3] <- 5        
  > g2 <- table.image(df)
  > g3 <- table.image(df, breaks = c(5, 2, 0))
  > 
  > ## ex3
  > data(rpjdl, package = "ade4")
  > X <- data.frame(t(rpjdl$fau))
  > Y <- data.frame(t(rpjdl$mil))
  > coa1 <- ade4::dudi.coa(X, scan = FALSE)
  > x <- rank(coa1$co[, 1])
  > y <- rank(coa1$li[, 1])
  > g4 <- table.image(Y, coordsx = x, coordsy = 1:8, axis.text = list(alpha = 0), pgrid.col = "black", pgrid.lwd = 0.8, col = c("white", "black"), plegend.drawKey = FALSE)
  > g5 <- table.image(X, coordsx = x, coordsy = y, ptable = list(x = list(tck = 0), y = list(tck = 4)), pleg.drawKey = FALSE, labelsy = paste(" ", row.names(X), sep = ""))
  > g6 <- ADEgS(list(g4, g5), positions = rbind(c(0, 0, 1, 0.3), c(0, 0.4, 1, 1)))
  > 
  > proc.time()
     user  system elapsed 
     1.37    0.25    1.61 
Running the tests in 'tests/table.value.R' failed.
Complete output:
  > library(adegraphics)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  > pdf("table.value.pdf")
  > 
  > 
  > ## ex1
  > data(olympic, package = "ade4")
  > tab1 <- data.frame(scale(olympic$tab))
  > pca <- ade4::dudi.pca(tab1, scann = FALSE)
  > g1 <- table.value(tab1, axis.line = list(col = "blue"), axis.text = list(col = "grey"))
  > g2 <- table.value(tab1, coordsx = c(1:5, 10:6))
  > g3 <- table.value(tab1, coordsx = c(1:5, 10:8))
  > g4 <- table.value(tab1, coordsy = rank(pca$li[, 1]), coordsx = rank(pca$co[, 1]), method = "color")
  > g5 <- table.value(tab1, coordsy = pca$li[, 1], coordsx = pca$co[, 1], ptable = list(x = list(srt = 90)))
  > 
  > ## ex2
  > data(eurodist)
  > g61 <- table.value(eurodist)
  > g62 <- table.value(eurodist, store = TRUE, symbol = "circle")
  > g63 <- table.value(eurodist, store = FALSE, psub.text = "eurodist", psub.position = c(0, -0.04))
  > g64 <- table.value(eurodist, ptable.margin = list(b = 17, t = 17, l = 17, r = 17))
  > g65 <- table.value(eurodist, ptable.x = list(pos = "bottom"),
  +                   ptable.margin = list(b = 17, t = 17, l = 17, r = 17))
  > 
  > ## ex3
  > data("doubs", package = "ade4")
  > tab2 <- as.table(as.matrix(doubs$fish))
  > g8 <- table.value(tab2)
  > 
  > ## ex4
  > data(chats, package = "ade4")
  > tab3 <- as.table(as.matrix(data.frame(t(chats))))
  > coa1 <- ade4::dudi.coa(data.frame(t(chats)), scann = FALSE)
  > adegparold <- adegpar()
  > adegpar(ptable = list(x = list(pos = "bottom", srt = 0), y = list(pos = "left")), plegend.drawKey = FALSE)
  > g9 <- table.value(tab3, meanX = TRUE, ablineX = TRUE)
  > g10 <- table.value(tab3, meanY = TRUE, ablineY = TRUE) 
  > g11 <- table.value(tab3, coordsx = coa1$c1[, 1], coordsy = coa1$l1[, 1], meanX = TRUE, ablineX = TRUE)
  > g12 <- table.value(tab3, coordsx = coa1$c1[, 1], coordsy = coa1$l1[, 1], meanY = TRUE, ablineY = TRUE)
  > g13 <- ADEgS(list(g9, g10, g11, g12), pos = rbind(c(0, 0.5, 0.5, 1), c(0.5, 0.5, 1, 1), c(0, 0, 0.5, 0.5), c(0.5, 0, 1, 0.5)))
  > adegpar(adegparold)
  > 
  > ## ex5
  > data(rpjdl, package = "ade4")
  > tab4 <- data.frame(t(rpjdl$fau))
  > coa2 <- ade4::dudi.coa(tab4, scann = FALSE)
  > g14 <- table.value(tab4, coordsx = coa2$c1[, 1], coordsy = rank(coa2$l1[, 1]), axis.text = list(cex = 0), labelsy = rpjdl$lalab, plot = F)
  > 
  > ## ex6
  > tab5 <- as.table(matrix(rep(0, 100), 10))
  > tab5[1:5, 1:5] <- 10
  > ade4::table.cont(tab5, abmean.x = T, y = 10:1)
  > g15 <- table.value(tab5, coordsy = 10:1, meanX = T)
  > g16 <- table.value(tab5, coordsy = 10:1, meanX = T, meanY = TRUE, ablineX = TRUE, ablineY = TRUE)
  > 
  > ## ex7
  > tab6 <- matrix(rep(0, 100), 10)
  > tab6[1:5, 1:5] <- 20
  > colnames(tab6) <- LETTERS[1:10]
  > rownames(tab6) <- LETTERS[1:10]
  > ade4::table.value(tab6, x = 1:10, y = 10:1)
  > g17 <- table.value(tab6, coordsx = 1:10, coordsy = 10:1)
  > g18 <- table.value(tab6, coordsx = 1:10, coordsy = c(1, 2, 5, 6, 8, 9, 10, 3, 4, 7))
  > 
  > 
  > ## ex8
  > d <- as.dist(matrix(rep(1:5, 5), 5), upper = TRUE)
  > attr(d, "Labels") <- c ("A", "B", "C", "D", "E")
  > g4 <- table.value(d)
  > 
  > ## ex9
  > data(irishdata, package = "ade4")
  > d.geo <- dist(irishdata$xy.utm)
  > g5 <- table.value(d.geo)
  > 
  > proc.time()
     user  system elapsed 
     2.67    0.23    2.87