This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository r-cran-adegraphics.
commit 4a60b62d6806f7c6f495b46ef384052d8a23492d Author: Andreas Tille <[email protected]> Date: Sat Sep 30 08:19:57 2017 +0200 New upstream version 1.0-8 --- DESCRIPTION | 8 +++--- MD5 | 62 ++++++++++++++++++++++----------------------- R/ADEg.C1.R | 18 ++++++------- R/ADEg.S1.R | 2 ++ R/ADEg.S2.R | 4 ++- R/ADEg.T.R | 2 ++ R/ADEg.Tr.R | 6 +++-- R/C1.barchart.R | 32 ++++++++++++++--------- R/C1.curve.R | 8 ++++-- R/C1.curves.R | 20 +++++++-------- R/C1.density.R | 4 +-- R/C1.dotplot.R | 10 ++++++-- R/C1.gauss.R | 5 ++-- R/C1.interval.R | 8 ++++-- R/ade4-plot.R | 9 ++++--- R/multiplot.R | 32 +++++++++++++++++------ build/vignette.rds | Bin 214 -> 214 bytes inst/doc/adegraphics.html | 27 +++++++++++--------- man/C1.barchart-class.Rd | 1 + man/adeg.panel.Spatial.Rd | 2 +- man/adeg.panel.hist.Rd | 2 +- man/adeg.panel.join.Rd | 2 +- man/adeg.panel.label.Rd | 4 +-- man/adeg.panel.nb.Rd | 8 +++--- man/adeg.panel.values.Rd | 4 +-- man/adegraphics-package.Rd | 6 ++--- man/changelatticetheme.Rd | 10 ++++---- man/s.Spatial.Rd | 2 +- man/s.image.Rd | 2 +- man/s.logo.Rd | 9 +++---- man/s1d.barchart.Rd | 6 +++-- vignettes/classes.png | Bin 756947 -> 763859 bytes 32 files changed, 184 insertions(+), 131 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 7a4c8be..acb328e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,8 +2,8 @@ Package: adegraphics Type: Package Title: An S4 Lattice-Based Package for the Representation of Multivariate Data -Version: 1.0-6 -Date: 2016-12-13 +Version: 1.0-8 +Date: 2017-04-11 Author: Stéphane Dray <[email protected]> and Aurélie Siberchicot <[email protected]>, with contributions from Jean Thioulouse. Based on earlier work by Alice Julien-Laferrière. Maintainer: Aurélie Siberchicot <[email protected]> Description: Graphical functionalities for the representation of multivariate data. It is a complete re-implementation of the functions available in the 'ade4' package. @@ -29,6 +29,6 @@ BugReports: https://github.com/sdray/adegraphics/issues Encoding: UTF-8 VignetteBuilder: knitr NeedsCompilation: no -Packaged: 2016-12-13 16:26:49 UTC; aurelie +Packaged: 2017-04-11 15:11:52 UTC; aurelie Repository: CRAN -Date/Publication: 2016-12-13 19:53:07 +Date/Publication: 2017-04-11 22:52:03 UTC diff --git a/MD5 b/MD5 index dd8b8be..935873f 100644 --- a/MD5 +++ b/MD5 @@ -1,20 +1,20 @@ -c9064e2cdb7d3561005682df1d9ae101 *DESCRIPTION +58c4805f83e7213e190aa2100144cec9 *DESCRIPTION b4088c0e1885d7be5a5dd041292c145d *NAMESPACE -df8836b16fe378a33be9f8a4ed3b6f77 *R/ADEg.C1.R +d3c4e289da7442520091536ada6f8d9d *R/ADEg.C1.R f9398e5cc9c57c5c4b6835dde14f7bc5 *R/ADEg.R -f66e5c9cf7175cf176069c5ad2ba7080 *R/ADEg.S1.R -56c4944df0f38bfc2ff1abc55855de58 *R/ADEg.S2.R -faef3f753ccb139fe60508736b784f5b *R/ADEg.T.R -be814ef56be814a617cee2e398627b69 *R/ADEg.Tr.R +b45d3c5e03d9d3ed080bd3bf7a523848 *R/ADEg.S1.R +c9f54ca4776bb33b4b0ab24b7977554c *R/ADEg.S2.R +2545695c9bb86d7dff7813f355bb224d *R/ADEg.T.R +11de1d5d11ee4e59d3c865b797092e92 *R/ADEg.Tr.R 7f50e188e2d69328b1b306fe5645ada9 *R/ADEgS.R -a9697051052b07eafeae670191b6d155 *R/C1.barchart.R -14cf56097d2a3477a34f91cac9dc1ade *R/C1.curve.R -1cbfe1cfa4facb3b8bf03bf6ec9a7b33 *R/C1.curves.R -1a18230d19f601760c1e49da814d7807 *R/C1.density.R -b22c962b6f85ec74c512817ab03b816b *R/C1.dotplot.R -5dfc1a965b5db9e39dcfc7d735f4ee60 *R/C1.gauss.R +49115ad780cba879d84a095b41613310 *R/C1.barchart.R +1f4103b624811d0b729c057dc6867bc7 *R/C1.curve.R +76136e17a4e5d68fe309c19edc1be83d *R/C1.curves.R +f58d5e80ed4b16001430899831efc550 *R/C1.density.R +f798f96b582b953940858322f83d8b7e *R/C1.dotplot.R +efdf344665030fa99b8f7c96d805eb79 *R/C1.gauss.R e2ed04a387365c8f28913a7f7a5f3843 *R/C1.hist.R -80879bed3d247f407f9b18103c2e9fe2 *R/C1.interval.R +1ca0f312a9aa8ae5be1e1e0845820d87 *R/C1.interval.R c13eb6e9a077eb3bd31f1714ba1fe863 *R/S1.boxplot.R 0d7eb82fe6783a5380dd2f2b6bcf936a *R/S1.class.R b7188f7d92e5986ec6c987188978d26d *R/S1.distri.R @@ -40,11 +40,11 @@ ff06fe70abb0e3218aaaa904f4f2d487 *R/Tr.match.R 212b2031be6b85efd371d270b56ea852 *R/Tr.traject.R 826e3790fd381de7f09e6f57e4cda593 *R/addtext.R 5c21e6a21545a45fbdbcea330b1d8c0d *R/ade4-kplot.R -cd420ae778a28028f906c737735de3de *R/ade4-plot.R +f6371078150b77ed42ce32212b0953b6 *R/ade4-plot.R 15650c713cbfefb6b2e4b5cc9da6ccfe *R/ade4-scatter.R 970d295db2936d608f06cbd2ece30b50 *R/adeGsenv.R 746e00372f84ac545a79667e09908efa *R/genericMethod.R -183974f7b76b53212392b1572ae8cd7c *R/multiplot.R +decdddc63f0a8b99951d63525fdc9ea9 *R/multiplot.R cd4865b82faf10c95e2ac6441d3b77b5 *R/panelfunctions.R cd3035aad7ee190549860f64ae62517e *R/parameter.R a9ba768a5e37c3ae5d61ed0c92ebb3fc *R/s.Spatial.R @@ -53,10 +53,10 @@ c5fb3cf01f58d61a11c7f2b55dce1751 *R/utils.R cadc907d6b204acff6fd94143b178b4c *R/utilsclass.R 800f764310cebf74dbb286040c08773d *R/utilskey.R bf8d58f56fec3d532e6611ee839eb1b6 *R/utilstriangle.R -99623dc54757368ff1e66bb8dee7bffd *build/vignette.rds +c265b4c9776c8e64764b62bb2923ab01 *build/vignette.rds 04415e8f14da2aa15ba85a78303903da *inst/doc/adegraphics.R 96835067ef72b58fc1e77ababd8a7422 *inst/doc/adegraphics.Rmd -b874ea04c11baef18318a25a21d712c1 *inst/doc/adegraphics.html +da237ca4e23bac7f83585e73ee655e08 *inst/doc/adegraphics.html 5598610d87d39c76f4655ded0eb71939 *man/ADEg-class.Rd 04d2d39bbab2e82a441b1dbb4f996e29 *man/ADEg.C1-class.Rd fe42debb511ab4a929b9029778b4fdac *man/ADEg.S1-class.Rd @@ -65,7 +65,7 @@ fbdf0df2c03ed9297d5e812eef1e68a0 *man/ADEg.S2-class.Rd fefb3b817bcb32d08afb0d4d8fc9494c *man/ADEg.Tr-class.Rd 0baa08dcf2af5cb4f5907e6ddf959ac7 *man/ADEgS-class.Rd ff24343f2c2fe48dee8142b6bbd5b605 *man/ADEgS.Rd -fa08acc7a15dc7b2086a431f3c2c36e4 *man/C1.barchart-class.Rd +6e5169d571ae24a73afcfd3a7b5a3bdd *man/C1.barchart-class.Rd 1250e8ac88f1739a8cbf1274e6298467 *man/C1.curve-class.Rd 06cc64ed333d3fc5cdde3ba14f26c559 *man/C1.density-class.Rd b438e7afdb9592d106ab927d94e1e014 *man/C1.dotplot-class.Rd @@ -98,17 +98,17 @@ eebd649933116bbd0a3d157103e3893c *man/Tr.label-class.Rd 0c7b0685e07ffcc4b795eebd2cb3db38 *man/add.ADEg.Rd 1fc0b2b157d5b97948a8e93e31769f5d *man/addhist.Rd bb283a094b87babd471d66563b27a7f3 *man/addtext.Rd -58f81adbd9988c70f2cd4b147934cf6f *man/adeg.panel.Spatial.Rd -b00d3d52049c9dff5aacfe730d87ccf2 *man/adeg.panel.hist.Rd -8c7ae1f804a77a8887fa713bb9482de6 *man/adeg.panel.join.Rd -6a5e3577fd76312d52549c073c6584bc *man/adeg.panel.label.Rd -3623561abff649bb261c70026cac672a *man/adeg.panel.nb.Rd -8689bfefeeea15cd3488939e48d2250f *man/adeg.panel.values.Rd +83bc7de54cf0f219d59ec885fbc7884c *man/adeg.panel.Spatial.Rd +dedf78380758f45ca0e207941931bf5d *man/adeg.panel.hist.Rd +9332cd504eb2ceb5dedf28a26e5acc05 *man/adeg.panel.join.Rd +21da98c051653a194feb74ab787139e2 *man/adeg.panel.label.Rd +9dc0d59dcea8cfb10b0b196acd2a21e9 *man/adeg.panel.nb.Rd +9c0d74adc122976f8d165cf94525a267 *man/adeg.panel.values.Rd 616d9e555ee43859a71580ac9e9aa922 *man/adegpar.Rd b236f2fcf939e84c32c2f12947a6d646 *man/adegraphics-internal.Rd -fedc5cf01f9d563af504159774e000d5 *man/adegraphics-package.Rd +8c35327e00047b6538b22b5903e6a321 *man/adegraphics-package.Rd 4583b908e3dba3541a6aead9d4847a8d *man/cbindADEg.Rd -6c129bbd3c7d6cdb0a1250de3d60e295 *man/changelatticetheme.Rd +3ff9c210f3c3ff6f1fb07a0824bf8359 *man/changelatticetheme.Rd 3685372b4e0b9847d9cc4c002d245eb4 *man/getcall-methods.Rd 0f38ace18b1d17e3ce74086db5cecab8 *man/insert.Rd 349c1d1984cfd9297fc1cd48c1658b7a *man/layout2position.Rd @@ -116,19 +116,19 @@ fedc5cf01f9d563af504159774e000d5 *man/adegraphics-package.Rd 7179d3392bb42d312143c73f3d1fe816 *man/plot.Rd 22f22e39e74120ce0473c5bae267d26d *man/plotEig.Rd 8c1d6460e342bf764802ea0a1b4377e9 *man/prepare-methods.Rd -41cfc1dfc69a32198c38faa9ba75e224 *man/s.Spatial.Rd +b297ce96aa3a1535f151bbe5c9ad85fa *man/s.Spatial.Rd 6c34d9ac54550d66665c875b40a09010 *man/s.arrow.Rd 405755d59de8e046df922cde0ed6494c *man/s.class.Rd 62611638daec8c5448a6ce369a715107 *man/s.corcircle.Rd 0d743ad4bc59be66347c21a0a08f24e1 *man/s.density.Rd 4f4b13b10306a004ee688befecb9fe46 *man/s.distri.Rd -2e8e1ce20792aefb1308184135ffe2d2 *man/s.image.Rd +f4b7815ef4bcff9c5e014b2e2177e69f *man/s.image.Rd 3bdcb6cb1b937b09c9a5e6ec183b90a1 *man/s.label.Rd -f7b6296c463e32fe39e277d1a40429ab *man/s.logo.Rd +835971ca2fcd623bfca4cb020cd7fc4f *man/s.logo.Rd 7b61953336ea5ce084586e689eb9bce3 *man/s.match.Rd d27b943fe8bae0ce295e5fd72587dffc *man/s.traject.Rd de5a2b09ca7820b23ce4fdc372600217 *man/s.value.Rd -aa089763207bb38418192cef8e76d3df *man/s1d.barchart.Rd +8aa47a351ed23083da319be09863bcba *man/s1d.barchart.Rd 9a7a01eed3541b4f8bb4067dd94934f4 *man/s1d.boxplot.Rd b395fc2c44c262fa62e52fe3a3ec1897 *man/s1d.class.Rd 1e2078d044e58c8ae36ffedd79f751d5 *man/s1d.curve.Rd @@ -182,7 +182,7 @@ e9906442c53b7f9a7b47872344b81836 *tests/svalue.R 9f29a1e52787d2db73feed37a3e432fc *tests/tvalue.R 96835067ef72b58fc1e77ababd8a7422 *vignettes/adegraphics.Rmd fee78b9fb7f2f4c820ceba919fa3ea76 *vignettes/adegraphics.bib -1520393ca0966c7fe6a7311f3b72a27f *vignettes/classes.png +94e2c4c89709af434aea77d06cae63a7 *vignettes/classes.png 1d77c7392af1b74694a1a360391faf63 *vignettes/gargsVSclass.R b5a2e8d2b525dd92ef3d9fcac3b4fa6a *vignettes/gargsVSclass.csv f2678b6a3b44dfed82563a378d98d086 *vignettes/paramVSfunction.R diff --git a/R/ADEg.C1.R b/R/ADEg.C1.R index 1aa9617..93c3ce9 100644 --- a/R/ADEg.C1.R +++ b/R/ADEg.C1.R @@ -31,7 +31,7 @@ setMethod( else score <- eval(object@data$score, envir = sys.frame(object@data$frame)) - if(inherits(object, "C1.curve") | inherits(object, "C1.dotplot") | inherits(object, "C1.interval")) + if(inherits(object, "C1.barchart") | inherits(object, "C1.curve") | inherits(object, "C1.dotplot") | inherits(object, "C1.interval")) if(object@data$storeData) at <- object@data$at else @@ -233,7 +233,9 @@ setMethod( ## grid background and box [email protected]$panel.background$col <- [email protected]$pbackground$col if([email protected]$pbackground$box) - [email protected]$axis.line$col <- "transparent" + [email protected]$axis.line$col <- "transparent" + else + [email protected]$axis.line$col <- "black" arguments <- list( par.settings = [email protected], @@ -278,13 +280,11 @@ setMethod( score <- as.matrix(score)[, 1] ## to manage 'score' when it is a data.frame with only one column xdata <- rep(1, length(score)) - if(inherits(object, "C1.barchart")) { - xdata <- 1:length(score) - } else if(inherits(object, "C1.dotplot") | inherits(object, "C1.curve") | inherits(object, "C1.interval")) { - if(object@data$storeData) - xdata <- object@data$at - else - xdata <- eval(object@data$at, envir = sys.frame(object@data$frame)) + if(inherits(object, "C1.barchart") | inherits(object, "C1.curve") | inherits(object, "C1.dotplot") | inherits(object, "C1.interval")) { + if(object@data$storeData) + xdata <- object@data$at + else + xdata <- eval(object@data$at, envir = sys.frame(object@data$frame)) } fml <- as.formula(score ~ xdata) diff --git a/R/ADEg.S1.R b/R/ADEg.S1.R index 37ea101..89991e8 100644 --- a/R/ADEg.S1.R +++ b/R/ADEg.S1.R @@ -247,6 +247,8 @@ setMethod( [email protected]$panel.background$col <- [email protected]$pbackground$col if([email protected]$pbackground$box) [email protected]$axis.line$col <- "transparent" + else + [email protected]$axis.line$col <- "black" arguments <- list( par.settings = [email protected], diff --git a/R/ADEg.S2.R b/R/ADEg.S2.R index 1342abd..8c15715 100644 --- a/R/ADEg.S2.R +++ b/R/ADEg.S2.R @@ -205,7 +205,9 @@ setMethod( if(!inherits(object, "S2.corcircle")) [email protected]$panel.background$col <- [email protected]$pbackground$col if([email protected]$pbackground$box) - [email protected]$axis.line$col <- "transparent" + [email protected]$axis.line$col <- "transparent" + else + [email protected]$axis.line$col <- "black" arguments <- list( par.settings = [email protected], diff --git a/R/ADEg.T.R b/R/ADEg.T.R index 2467f4c..7bf05ab 100644 --- a/R/ADEg.T.R +++ b/R/ADEg.T.R @@ -192,6 +192,8 @@ setMethod( [email protected]$panel.background$col <- [email protected]$pbackground$col if([email protected]$pbackground$box) [email protected]$axis.line$col <- "transparent" + else + [email protected]$axis.line$col <- "black" arguments <- list( par.settings = [email protected], diff --git a/R/ADEg.Tr.R b/R/ADEg.Tr.R index 81c2906..792e348 100644 --- a/R/ADEg.Tr.R +++ b/R/ADEg.Tr.R @@ -144,8 +144,10 @@ setMethod( ## background and box ## [email protected]$panel.background$col <- [email protected]$pbackground$col if([email protected]$pbackground$box) - [email protected]$axis.line$col <- "transparent" - + [email protected]$axis.line$col <- "transparent" + else + [email protected]$axis.line$col <- "black" + arguments = list( par.settings = [email protected], scales = if(!is.null([email protected]$scales)) [email protected]$scales else list(draw = FALSE), diff --git a/R/C1.barchart.R b/R/C1.barchart.R index 2e98c33..97d6079 100644 --- a/R/C1.barchart.R +++ b/R/C1.barchart.R @@ -7,9 +7,11 @@ setClass( setMethod( f = "initialize", signature = "C1.barchart", - definition = function(.Object, data = list(score = NULL, labels = NULL, frame = 0, storeData = TRUE), ...) { + definition = function(.Object, data = list(score = NULL, labels = NULL, at = NULL, frame = 0, storeData = TRUE), ...) { .Object <- callNextMethod(.Object, data = data, ...) ## ADEg.C1 initialize .Object@data$labels <- data$labels + .Object@data$at <- data$at + validObject(.Object) return(.Object) }) @@ -25,11 +27,13 @@ setMethod( on.exit(adegpar(oldparamadeg)) adegtot <- adegpar([email protected]) - if(object@data$storeData) + if(object@data$storeData) { score <- object@data$score - else + at <- object@data$at + } else { score <- eval(object@data$score, envir = sys.frame(object@data$frame)) - + at <- eval(object@data$at, envir = sys.frame(object@data$frame)) + } score <- as.matrix(score)[, 1] ## to manage 'score' when it is a data.frame with only one column ## change default for some parameters @@ -46,9 +50,9 @@ setMethod( callNextMethod() ## prepare graph if([email protected]$p1d$horizontal && is.null([email protected]$ylim)) - [email protected]$ylim <- c(0, length(score) + 1) + [email protected]$ylim <- setlimits1D(min(at), max(at), 0, FALSE) if([email protected]$p1d$horizontal && is.null([email protected]$xlim)) - [email protected]$xlim <- c(0, length(score) + 1) + [email protected]$xlim <- setlimits1D(min(at), max(at), 0, FALSE) assign(nameobj, object, envir = parent.frame()) }) @@ -85,18 +89,22 @@ setMethod( ## lims <- current.panel.limits(unit = "native") + ## reorder the values + y <- y[order(x)] + x <- sort(x) + ## Starts the display ## depends on the parametres horizontal ## reverse and rug.draw are always considered as FALSE if(pscore$horizontal) { x.tmp <- y - y.tmp <- 1:length(x) + y.tmp <- x } else { - x.tmp <- 1:length(x) + x.tmp <- x y.tmp <- y } - panel.barchart(x.tmp, y.tmp, horizontal = pscore$horizontal, box.width = 0.9, origin = 0, reference = FALSE, + panel.barchart(x = x.tmp, y = y.tmp, horizontal = pscore$horizontal, box.width = 0.9, origin = 0, reference = FALSE, border = ppoly$border, col = ppoly$col, lty = ppoly$lty, lwd = ppoly$lwd, alpha = ppoly$alpha) ## panel.text(x.tmp, y.tmp, labels) if(!is.null(labels)) { @@ -126,7 +134,7 @@ setMethod( }) -s1d.barchart <- function(score, labels = NULL, facets = NULL, plot = TRUE, storeData = TRUE, add = FALSE, pos = -1, ...) { +s1d.barchart <- function(score, labels = NULL, at = 1:NROW(score), facets = NULL, plot = TRUE, storeData = TRUE, add = FALSE, pos = -1, ...) { ## evaluation of some parameters thecall <- .expand.call(match.call()) @@ -155,9 +163,9 @@ s1d.barchart <- function(score, labels = NULL, facets = NULL, plot = TRUE, store ## creation of the ADEg object if(storeData) - tmp_data <- list(score = score, labels = labels, frame = sys.nframe() + pos, storeData = storeData) + tmp_data <- list(score = score, labels = labels, at = at, frame = sys.nframe() + pos, storeData = storeData) else - tmp_data <- list(score = thecall$score, labels = thecall$labels, frame = sys.nframe() + pos, storeData = storeData) + tmp_data <- list(score = thecall$score, labels = thecall$labels, at = thecall$at, frame = sys.nframe() + pos, storeData = storeData) object <- new(Class = "C1.barchart", data = tmp_data, adeg.par = sortparameters$adepar, trellis.par = sortparameters$trellis, g.args = sortparameters$g.args, Call = match.call()) ## preparation diff --git a/R/C1.curve.R b/R/C1.curve.R index 77820e1..7d5c60d 100644 --- a/R/C1.curve.R +++ b/R/C1.curve.R @@ -26,10 +26,14 @@ setMethod( on.exit(adegpar(oldparamadeg)) adegtot <- adegpar([email protected]) - if(object@data$storeData) + if(object@data$storeData) { + score <- object@data$score at <- object@data$at - else + } else { + score <- eval(object@data$score, envir = sys.frame(object@data$frame)) at <- eval(object@data$at, envir = sys.frame(object@data$frame)) + } + score <- as.matrix(score)[, 1] ## to manage 'score' when it is a data.frame with only one column ## change some defaults adegtot$p1d$rug$draw <- FALSE diff --git a/R/C1.curves.R b/R/C1.curves.R index c01ab48..d3d6bd9 100644 --- a/R/C1.curves.R +++ b/R/C1.curves.R @@ -14,7 +14,7 @@ setMethod( ## get some parameters nr <- NROW(object@data$score) nc <- NCOL(object@data$score) - + pscore <- [email protected]$p1d ppoints <- lapply([email protected]$ppoints, FUN = function(x) {rep(rep(x, length.out = nc), each = nr)}) plines <- lapply([email protected]$plines, FUN = function(x) {rep(rep(x, length.out = nc), each = nr)}) @@ -29,19 +29,19 @@ setMethod( ## rug.draw and reverse are always considered as FALSE for(i in 1:nc){ - idx <- (i - 1)*nr + (1:nr) - if(pscore$horizontal) { + idx <- (i - 1)*nr + (1:nr) + if(pscore$horizontal) { x.tmp <- y[idx] y.tmp <- x - } else { + } else { x.tmp <- x y.tmp <- y[idx] - } - - panel.lines(x = x.tmp, y = y.tmp, lwd = plines$lwd[idx], lty = plines$lty[idx], col = plines$col[idx]) - panel.points(x = x.tmp, y = y.tmp, pch = ppoints$pch[idx], cex = ppoints$cex[idx], col = ppoints$col[idx], alpha = ppoints$alpha[idx]) + } + + panel.lines(x = x.tmp, y = y.tmp, lwd = plines$lwd[idx], lty = plines$lty[idx], col = plines$col[idx]) + panel.points(x = x.tmp, y = y.tmp, pch = ppoints$pch[idx], cex = ppoints$cex[idx], col = ppoints$col[idx], alpha = ppoints$alpha[idx]) } - }) + }) s1d.curves <- function(score, at = 1:NROW(score), facets = NULL, plot = TRUE, storeData = TRUE, add = FALSE, pos = -1, ...) { @@ -66,7 +66,7 @@ s1d.curves <- function(score, at = 1:NROW(score), facets = NULL, plot = TRUE, st ## creation of the ADEg object if(storeData) - tmp_data <- list(score = score, at = at, frame = sys.nframe() + pos, storeData = storeData) + tmp_data <- list(score = score, at = at, frame = sys.nframe() + pos, storeData = storeData) else tmp_data <- list(score = thecall$score, at = thecall$at, frame = sys.nframe() + pos, storeData = storeData) object <- new(Class = "C1.curves", data = tmp_data, adeg.par = sortparameters$adepar, trellis.par = sortparameters$trellis, g.args = sortparameters$g.args, Call = match.call()) diff --git a/R/C1.density.R b/R/C1.density.R index 2c4a6e7..44cecad 100644 --- a/R/C1.density.R +++ b/R/C1.density.R @@ -33,11 +33,11 @@ setMethod( adegtot <- adegpar([email protected]) if(object@data$storeData) { - fac <- object@data$fac score <- object@data$score + fac <- object@data$fac } else { - fac <- eval(object@data$fac, envir = sys.frame(object@data$frame)) score <- eval(object@data$score, envir = sys.frame(object@data$frame)) + fac <- eval(object@data$fac, envir = sys.frame(object@data$frame)) } score <- as.matrix(score)[, 1] ## to manage 'score' when it is a data.frame with only one column nlev <- nlevels(as.factor(fac)) diff --git a/R/C1.dotplot.R b/R/C1.dotplot.R index 34c267d..f279ff5 100644 --- a/R/C1.dotplot.R +++ b/R/C1.dotplot.R @@ -26,10 +26,14 @@ setMethod( on.exit(adegpar(oldparamadeg)) adegtot <- adegpar([email protected]) - if(object@data$storeData) + if(object@data$storeData) { + score <- object@data$score at <- object@data$at - else + } else { + score <- eval(object@data$score, envir = sys.frame(object@data$frame)) at <- eval(object@data$at, envir = sys.frame(object@data$frame)) + } + score <- as.matrix(score)[, 1] ## to manage 'score' when it is a data.frame with only one column ## change some defaults adegtot$p1d$rug$draw <- FALSE @@ -85,6 +89,8 @@ s1d.dotplot <- function(score, at = 1:NROW(score), facets = NULL, plot = TRUE, s ## evaluation of some parameters thecall <- .expand.call(match.call()) + score <- eval(thecall$score, envir = sys.frame(sys.nframe() + pos)) + ## parameters sorted sortparameters <- sortparamADEg(...) diff --git a/R/C1.gauss.R b/R/C1.gauss.R index ae90eb0..ea38af0 100644 --- a/R/C1.gauss.R +++ b/R/C1.gauss.R @@ -31,14 +31,15 @@ setMethod( adegtot <- adegpar([email protected]) if(object@data$storeData) { - fac <- object@data$fac score <- object@data$score + fac <- object@data$fac wt <- object@data$wt } else { - fac <- eval(object@data$fac, envir = sys.frame(object@data$frame)) score <- eval(object@data$score, envir = sys.frame(object@data$frame)) + fac <- eval(object@data$fac, envir = sys.frame(object@data$frame)) wt <- eval(object@data$wt, envir = sys.frame(object@data$frame)) } + score <- as.matrix(score)[, 1] ## to manage 'score' when it is a data.frame with only one column nlev <- nlevels(as.factor(fac)) ## If axes are plotted, put a label for axis diff --git a/R/C1.interval.R b/R/C1.interval.R index 793fa03..f3c3c1d 100644 --- a/R/C1.interval.R +++ b/R/C1.interval.R @@ -26,10 +26,14 @@ setMethod( on.exit(adegpar(oldparamadeg)) adegtot <- adegpar([email protected]) - if(object@data$storeData) + if(object@data$storeData) { + score <- object@data$score at <- object@data$at - else + } else { + score <- eval(object@data$score, envir = sys.frame(object@data$frame)) at <- eval(object@data$at, envir = sys.frame(object@data$frame)) + } + score <- as.matrix(score)[, 1] ## to manage 'score' when it is a data.frame with only one column ## change default for some parameters adegtot$p1d$rug$draw <- FALSE diff --git a/R/ade4-plot.R b/R/ade4-plot.R index 35d0a54..a02d2a0 100644 --- a/R/ade4-plot.R +++ b/R/ade4-plot.R @@ -257,6 +257,7 @@ appel <- as.list(x$call) fac <- eval.parent(appel$fac) + dudi <- eval.parent(appel$x) ## sort parameters for each graph graphsnames <- c("loadings", "col", "eig", "row", "Xax", "class") @@ -277,7 +278,7 @@ g1 <- do.call("s.arrow", c(list(dfxy = substitute(x$c1), xax = xax, yax = yax, plot = FALSE, storeData = storeData, pos = pos - 2), sortparameters[[1]])) g2 <- do.call("s.arrow", c(list(dfxy = substitute(x$co), xax = xax, yax = yax, plot = FALSE, storeData = storeData, pos = pos - 2), sortparameters[[2]])) g3 <- do.call("plotEig", c(list(eigvalue = substitute(x$eig), nf = 1:x$nf, xax = xax, yax = yax, plot = FALSE, storeData = storeData, pos = pos - 2), sortparameters[[3]])) - g4 <- do.call("s.class", c(list(dfxy = substitute(x$ls), fac = appel$fac, xax = xax, yax = yax, plot = FALSE, storeData = storeData, pos = pos - 2), sortparameters[[4]])) + g4 <- do.call("s.class", c(list(dfxy = substitute(x$ls), wt = substitute(dudi$lw), fac = appel$fac, xax = xax, yax = yax, plot = FALSE, storeData = storeData, pos = pos - 2), sortparameters[[4]])) g5 <- do.call("s.corcircle", c(list(dfxy = substitute(x$as), xax = xax, yax = yax, plot = FALSE, storeData = storeData, pos = pos - 2), sortparameters[[5]])) g6 <- do.call("s.label", c(list(dfxy = substitute(x$li), xax = xax, yax = yax, plot = FALSE, storeData = storeData, pos = pos - 2), sortparameters[[6]])) @@ -375,9 +376,9 @@ g1 <- do.call("s.arrow", c(list(dfxy = substitute(x$c1), xax = xax, yax = yax, plot = FALSE, storeData = storeData, pos = pos - 2), sortparameters[[1]])) g2 <- do.call("s.arrow", c(list(dfxy = substitute(x$co), xax = xax, yax = yax, plot = FALSE, storeData = storeData, pos = pos - 2), sortparameters[[2]])) g3 <- do.call("plotEig", c(list(eigvalue = substitute(x$eig), nf = 1:x$nf, xax = xax, yax = yax, plot = FALSE, storeData = storeData, pos = pos - 2), sortparameters[[3]])) - g4 <- do.call("s.class", c(list(dfxy = substitute(x$ls), fac = appel$fac, xax = xax, yax = yax, plot = FALSE, storeData = storeData, pos = pos - 2), sortparameters[[4]])) + g4 <- do.call("s.class", c(list(dfxy = substitute(x$ls), wt = substitute(x$lw), fac = appel$fac, xax = xax, yax = yax, plot = FALSE, storeData = storeData, pos = pos - 2), sortparameters[[4]])) g5 <- do.call("s.corcircle", c(list(dfxy = substitute(x$as), xax = xax, yax = yax, plot = FALSE, storeData = storeData, pos = pos - 2), sortparameters[[5]])) - g6 <- do.call("s.class", c(list(dfxy = substitute(x$li), fac = appel$fac, xax = xax, yax = yax, plot = FALSE, storeData = storeData, pos = pos - 2), sortparameters[[6]])) + g6 <- do.call("s.class", c(list(dfxy = substitute(x$li), wt = substitute(x$lw), fac = appel$fac, xax = xax, yax = yax, plot = FALSE, storeData = storeData, pos = pos - 2), sortparameters[[6]])) ## ADEgS creation lay <- matrix(c(1, 2, 3, 4, 4, 5, 4, 4, 6), 3, 3) @@ -1487,7 +1488,7 @@ origin = adegtot$porigin$origin, aspect.ratio = adegtot$paxes$aspectratio, includeOr = adegtot$porigin$include) if(type != "label") { - # if ellipses or crosses are drawn, the limits are re-calculated and the elipse size are normalized + # if ellipses or crosses are drawn, the limits are re-calculated and the ellipse size are normalized heavy_inertcolmax <- apply(heavy_inertcol, 2, max) heavy_inertcolnorm <- matrix(NA, NROW(heavy_inertcol), 2) for (i in 1:2) {heavy_inertcolnorm[, i] <- (heavy_inertcol[, i] / heavy_inertcolmax[i]) * (diff(lim.global[[i]]) / 10)} diff --git a/R/multiplot.R b/R/multiplot.R index 5510e8b..df7107e 100644 --- a/R/multiplot.R +++ b/R/multiplot.R @@ -275,28 +275,25 @@ multi.facets.C1 <- function(thecall, adepar, samelimits = TRUE) { ## creation of the plots (ADEg objects) for(i in 1:nlevels(facets)) { thenewcall$psub.text <- levels(facets)[i] + if(thecall[[1]] == "s1d.interval") { thenewcall$score1 <- call("[[", call("split", thecall$score1, thecall$facets), i) thenewcall$score2 <- call("[[", call("split", thecall$score2, thecall$facets), i) - thenewcall$at <- call("[[", call("split", thecall$at, thecall$facets), i) - } else { + } else { thenewcall$score <- call("[[", call("split", thecall$score, thecall$facets), i) } - if(thecall[[1]] == "s1d.barchart" & !is.null(thecall$labels)) thenewcall$labels <- call("[[", call("split", thecall$labels, thecall$facets), i) - if(thecall[[1]] == "s1d.dotplot" | thecall[[1]] == "s1d.curve") + if(thecall[[1]] == "s1d.barchart" | thecall[[1]] == "s1d.dotplot" | thecall[[1]] == "s1d.curve" | thecall[[1]] == "s1d.interval") thenewcall$at <- call("[[", call("split", thecall$at, thecall$facets), i) - if(thecall[[1]] == "s1d.density") + if(thecall[[1]] == "s1d.density" | thecall[[1]] == "s1d.gauss") thenewcall$fac <- call("[[", call("split", thecall$fac, thecall$facets), i) - if(thecall[[1]] == "s1d.gauss") { - thenewcall$fac <- call("[[", call("split", thecall$fac, thecall$facets), i) + if(thecall[[1]] == "s1d.gauss") thenewcall$wt <- call("[[", call("split", thecall$wt, thecall$facets), i) - } listGraph <- c(listGraph, do.call(as.character(thenewcall[[1]]), thenewcall[-1])) } @@ -305,6 +302,25 @@ multi.facets.C1 <- function(thecall, adepar, samelimits = TRUE) { names(listGraph) <- levels(facets) posmatrix <- layout2position(.n2mfrow(nlevels(facets)), ng = nlevels(facets)) object <- new(Class = "ADEgS", ADEglist = listGraph, positions = posmatrix, add = matrix(0, ncol = nlevels(facets), nrow = nlevels(facets)), Call = as.call(thecall)) + + ## same limits for all graphics when the second axis is done by intern calculations + if(inherits(object[[1]], "C1.density") | inherits(object[[1]], "C1.gauss") | inherits(object[[1]], "C1.hist")) { + if(isTRUE(samelimits) | is.null(samelimits)) { + cc <- object@Call + if(adegtot$p1d$horizontal & is.null(thecall$ylim)) { + Ylim <- range(sapply(object@ADEglist, function(x) [email protected]$ylim)) + update(object, ylim = Ylim) + object@Call <- cc # this call does not include the ylim update + } + if(!adegtot$p1d$horizontal & is.null(thecall$xlim)) { + Xlim <- range(sapply(listGraph, function(x) [email protected]$xlim)) + update(object, xlim = Xlim) + object@Call <- paste(substr(cc, 1, nchar(cc) - 1), ", xlim = c(", Xlim[1], ",", Xlim[2], ")", sep = "") + object@Call <- cc # this call does not include the xlim update + } + } + } + ## change pos et frame a posteriori ?? return(object) } diff --git a/build/vignette.rds b/build/vignette.rds index ed40d0a..ebda76c 100644 Binary files a/build/vignette.rds and b/build/vignette.rds differ diff --git a/inst/doc/adegraphics.html b/inst/doc/adegraphics.html index 069d58c..1a5b484 100644 --- a/inst/doc/adegraphics.html +++ b/inst/doc/adegraphics.html @@ -4,7 +4,7 @@ <head> -<meta charset="utf-8"> +<meta charset="utf-8" /> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> <meta name="generator" content="pandoc" /> @@ -12,7 +12,7 @@ <meta name="author" content="Alice Julien-Laferrière, Aurélie Siberchicot and Stéphane Dray" /> -<meta name="date" content="2016-12-13" /> +<meta name="date" content="2017-04-11" /> <title>The adegraphics package</title> @@ -70,7 +70,7 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf <h1 class="title toc-ignore">The <code>adegraphics</code> package</h1> <h4 class="author"><em>Alice Julien-Laferrière, Aurélie Siberchicot and Stéphane Dray</em></h4> -<h4 class="date"><em>2016-12-13</em></h4> +<h4 class="date"><em>2017-04-11</em></h4> <div id="TOC"> @@ -130,7 +130,7 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf <p>In <code>adegraphics</code>, a user-level function produces a plot that is stored (and returned) as an object. The class architecture of the objects created by <code>adegraphics</code> functions is described in <a href="#classes">Figure 1</a>.</p> <br> <div style="text-align:center"> -<p><a name="classes"></a> <span style="color:blue">Figure 1: Classes structure and user-level functions</span> <img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAACJgAAAv6CAYAAADlOjvPAAAABHNCSVQICAgIfAhkiAAAAAlwSFlzAAAN1wAADdcBQiibeAAAABl0RVh0U29mdHdhcmUAd3d3Lmlua3NjYXBlLm9yZ5vuPBoAACAASURBVHic7N13WFPn2wfwbxYjbBAQRcUBKo66965aa6vWXbtbrdpW7Z62du9lp9ZW627Vtu49cG+GAxCRLXuFEEjIfP/wZ18HOecEgqvfz3X1umq4z/M8cJJAznOf+5bFnzptAxEREREREREREREREd1abLYz1t3fPH+zl0FEREQEAPKbvQAiIiIiIiIiIiIiIiIiIiIiu [...] +<p><a name="classes"></a> <span style="color:blue">Figure 1: Classes structure and user-level functions</span> <img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAACJ0AAAv9CAYAAAAeFsAzAAAABHNCSVQICAgIfAhkiAAAAAlwSFlzAAAN1wAADdcBQiibeAAAABl0RVh0U29mdHdhcmUAd3d3Lmlua3NjYXBlLm9yZ5vuPBoAACAASURBVHic7N13QBPn/wfw9yUhgbC3IKCCLCd129Y9u7WtttY66+i0ew/Rfjvcra2z/ba1aoe22qqt1rqqdQEqQwWVvWQTCISsu/v94Vd/qCR3GRDQz+s/yXPPfeTCQe7e93mYcympPAghhBBCCCGEEEIIIYQQQkjrI5MGde3atcTRZdyq4uPjJaM9zincnJ2cZTqJs8HIO [...] </div> <p><br></p> <p>This class management highlights a hierarchy with two parent classes:</p> @@ -434,7 +434,7 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf pca1 <-<span class="st"> </span><span class="kw">dudi.pca</span>(olympic$tab, <span class="dt">scannf =</span> <span class="ot">FALSE</span>)</code></pre></div> <p>The barplot of eigenvalues is then drawn and stored in <code>g1</code>:</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">g1 <-<span class="st"> </span><span class="kw">s1d.barchart</span>(pca1$eig, <span class="dt">p1d.horizontal =</span> F, <span class="dt">ppolygons.col =</span> <span class="st">"white"</span>)</code></pre></div> -<p><img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAYAAAAGACAMAAACTGUWNAAABsFBMVEUAAAADAwMEBAQFBQUGBgYHBwcKCgoNDQ0ODg4PDw8QEBARERESEhITExMWFhYXFxcYGBgZGRkaGhobGxscHBwdHR0eHh4fHx8gICAhISEjIyMkJCQlJSUnJycoKCgpKSkqKiosLCwtLS0uLi4vLy8wMDAzMzM1NTU4ODg5OTk7Ozs8PDw+Pj4/Pz9AQEBBQUFDQ0NERERNTU1OTk5PT09VVVVWVlZaWlpiYmJjY2NkZGRlZWVmZmZnZ2dpaWlqampra2ttbW1zc3N0dHR1dXV3d3d5eXl7e3t9fX1+fn5/f3+Dg4OEhISIiIiLi4uMjIyOjo6Pj4+QkJCRkZGSkpKUlJSWlpaXl5eZmZmbm5ufn5+hoaGjo6OmpqaoqKipqamqqqqrq6usrKywsLCys [...] +<p><img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAYAAAAGACAMAAACTGUWNAAABcVBMVEUAAAAEBAQHBwcICAgKCgoLCwsNDQ0ODg4PDw8RERESEhITExMUFBQWFhYXFxcYGBgZGRkbGxscHBwdHR0eHh4fHx8gICAhISEiIiIjIyMkJCQmJiYnJycqKiorKyssLCwuLi4wMDAzMzM1NTU3Nzc5OTk7Ozs8PDxAQEBDQ0NERERHR0dQUFBTU1NVVVVWVlZYWFhiYmJjY2NkZGRlZWVmZmZnZ2dpaWlqampra2tvb29wcHBxcXFzc3N0dHR1dXV3d3d7e3t8fHx/f3+BgYGDg4OIiIiLi4uMjIyNjY2Ojo6Pj4+QkJCRkZGSkpKXl5eZmZmbm5ucnJyfn5+hoaGqqqqsrKy1tbW3t7e4uLi8vLy+vr6/v7/BwcHDw8PExMTHx8fMzMzPz8/Q0NDT0 [...] <p><br> The class of the <code>g1</code> object is <code>C1.barchart</code> which extends the <code>ADEg</code> class:</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">class</span>(g1)</code></pre></div> <pre><code>## [1] "C1.barchart" @@ -477,6 +477,9 @@ pca1 <-<span class="st"> </span><span class="kw">dudi.pca</span>(olympic$tab, ## [1] 3.4182381 2.6063931 0.9432964 0.8780212 0.5566267 0.4912275 0.4305952 ## [8] 0.3067981 0.2669494 0.1018542 ## +## $at +## [1] 1 2 3 4 5 6 7 8 9 10 +## ## $frame ## [1] 24 ## @@ -636,7 +639,7 @@ pos.mat</code></pre></div> <p>The graphs themselves can be modified, without affecting the global structure of the <code>ADEgS</code> object. Here, we replace the correlation circle by the barplot of eigenvalues:</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">g7[[<span class="dv">3</span>]] <-<span class="st"> </span>g1 g7</code></pre></div> -<p><img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAYAAAAGACAIAAAArpSLoAAAACXBIWXMAAA7DAAAOwwHHb6hkAAAgAElEQVR4nOydeXxM5/7Hv2f2JXsiCyGRREKk9q2qaotSRWntXLVcGkXVj9putW710uLq7aJUtKiQRFC1FLEGSUMQSxJEQmQhkWWSzGQyy5nz++MwxixnzuwzyfN+9XWveeac53xnzpxPnuf7PN/vFyMIAhAIBMIRMBxtAAKBaL4gAUIgEA4DCRACgXAYSIAQCITDQAKEQCAcBhIgBALhMJAAIRAIh4EECIFAOAwkQAgEwmEgAUIgEA4DCRACgXAYSIAQCITDQAKEQCAcBhIgBALhMJAAIRAIh4EECIFAOAwkQMb5/fffx4wZ42grbEVubm737t0dbYUNadu2raNNsCHdu3fPzc11tBXmgwTIONeuXbt+/bqjrbAV+fn5O [...] +<p><img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAYAAAAGACAIAAAArpSLoAAAACXBIWXMAAA7DAAAOwwHHb6hkAAAgAElEQVR4nOydeXxM5/7Hv2f2JXsim5BIIiFSbW1NVdUWpYpqi9iqykW0lP6o4t72urTconq1VSpaVEgIqpaqWIPEEsSSRERCZCGRZZLMklnOnN8fhzGZ5eTMPpM871df95pnznnOd3LmfOZ5vs/z/X4xgiAAgUAgHAHD0QYgEIi2CxIgBALhMJAAIRAIh4EECIFAOAwkQAgEwmEgAUIgEA4DCRACgXAYSIAQCITDQAKEQCAcBhIgBALhMJAAIRAIh4EECIFAOAwkQAgEwmEgAUIgEA4DCRACgXAYSIAQCITDQALUMr///vuYMWMcbYWtyMvL69mzp6OtsCGdOnVytAk2pGfPnnl5eY62wnyQALXM1atXr1275mgrbEVhY [...] <p>The <code>addhist</code> method adds univariate marginal distributions around an <code>ADEg.S2</code> and returns an <code>ADEgS</code> object:</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">addhist</span>(g3)</code></pre></div> <p><img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAYAAAAGACAMAAACTGUWNAAADAFBMVEUAAAABAQECAgIDAwMEBAQFBQUGBgYHBwcICAgJCQkKCgoLCwsMDAwNDQ0ODg4PDw8QEBARERESEhITExMUFBQVFRUWFhYXFxcYGBgZGRkaGhobGxscHBwdHR0eHh4fHx8gICAhISEiIiIjIyMkJCQlJSUmJiYnJycoKCgpKSkqKiorKyssLCwtLS0uLi4vLy8wMDAxMTEyMjIzMzM0NDQ1NTU2NjY3Nzc4ODg5OTk6Ojo7Ozs8PDw9PT0+Pj4/Pz9AQEBBQUFCQkJDQ0NERERFRUVGRkZHR0dISEhJSUlKSkpLS0tMTExNTU1OTk5PT09QUFBRUVFSUlJTU1NUVFRVVVVWVlZXV1dYWFhZWVlaWlpbW1tcXFxdXV1eXl5fX19gYGBhYWFiYmJjY2NkZ [...] @@ -780,7 +783,7 @@ g11 <-<span class="st"> </span><span class="kw">table.image</span>(d, <span c g12 <-<span class="st"> </span><span class="kw">table.image</span>(d, <span class="dt">axis.line =</span> <span class="kw">list</span>(<span class="dt">col =</span> <span class="st">"blue"</span>), <span class="dt">axis.text =</span> <span class="kw">list</span>(<span class="dt">col =</span> <span class="st">"red"</span>), <span class="dt">plot =</span> <span class="ot">FALSE</span>) <span class="kw">ADEgS</span>(<span class="kw">c</span>(g11, g12), <span class="dt">layout =</span> <span class="kw">c</span>(<span class="dv">1</span>, <span class="dv">2</span>))</code></pre></div> -<p><img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAqAAAAFQCAIAAADvJFsWAAAACXBIWXMAAA7DAAAOwwHHb6hkAAAgAElEQVR4nOzde1gU59k/8O/OwrIgHiCIICEqgvBzQWW1kChgPBSFKNiCBqxEq69Rwfe62hiT6hut2vR9Y03SKmqtMYZgGmwEUUATE40iHkFEmoAEQYuYC5STkdMue5jfH6sEWW2ZnSE7u3t/rvyB6DzcjHxzO7tzzyNhWRaEEEIIsS6MuQsghBBCiPCowRNCCCFWiBo8IYQQYoWowRNCCCFWiBo8IYQQYoWowRNCCCFWiBo8IYQQYoWowRNCCCFWiBo8IYQQYoWowRNCCCFWiBo8IYQQYoWowRNCCCFWiBo8IYQQYoWowRNCCCFWiBo8IYQQYoWowRNCCCFWiBo8IYQQYoWowRNCCCFWiBo8IYQQYoWowRNCCCFWiBo8I [...] +<p><img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAqAAAAFQCAIAAADvJFsWAAAACXBIWXMAAA7DAAAOwwHHb6hkAAAgAElEQVR4nO3de1wU97k/8M/uclW8QBRBYowIwgmgslpIFTBqimBUbEEjVo3VY1Xw9NXGmEZPtGrTc2JN2irqscYai2mw8YIKMU2iUcQLiog2ASmKFjE/UW6JCCyX3fn9sUqQJS2zM5ud3f28X/0DN86Xh9FPH2d3nvmqBEEAERER2Re1tQsgIiIi+bHBExER2SE2eCIiIjvEBk9ERGSH2OCJiIjsEBs8ERGRHWKDJyIiskNs8ERERHaIDZ6IiMgOscETERHZITZ4IiIiO8QGT0REZIfY4ImIiOwQGzwREZEdYoMnIiKyQ2zwREREdogNnoiIyA6xwRMREdkhNngiIiI7xAZPRERkh9jgiYiI7BAbPBERkR1igyciIrJDb [...] <p><a name="adegpar"></a></p> </div> <div id="parameters-in-adeg.par" class="section level2"> @@ -1015,7 +1018,7 @@ g32 <-<span class="st"> </span><span class="kw">xyplot</span>(tra1$distance ~ <span class="dt">panel =</span> function(x, y) {<span class="kw">panel.lmline</span>(x, y)}) g3 <-<span class="st"> </span><span class="kw">superpose</span>(g31, g32) G <-<span class="st"> </span><span class="kw">ADEgS</span>(<span class="kw">list</span>(g1, g2, g3))</code></pre></div> -<p><img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAqAAAADcCAIAAAAgIYQBAAAACXBIWXMAAA7DAAAOwwHHb6hkAAAgAElEQVR4nOzdeSDU2/84/ufYxi5kJxRSSCQVyZJoEy3ai0rp3hYt97anTfu+76muVFqUkmQLEdmypJKt7CJk32Z+f5z35/WbL7KOlJ6Pv8685rzO68zk3ue8zuuc56HduHHj6dOn8MsrLy9PTEw0MDDo6Y6gbsTJybl27Vp9fX3qyM2bN3+Lv882VVVV8fHx0Wi0nu5IlzQ2NgYHB5uZmfV0R7qKwWDU1tby8fF16Kzmf58I/cq4fHx85OTkfv3AGRoaGhQUZGtr29MdQd3I1dU1IiKC9X+gv8vfZ5s+fvzYv39/bm7unu5IlxQUFHh6evaC/wwrKysLCwuVlZU7dFbzv0+EfmVcADBixIhf/7/Y2traq1ev/vr9RF3x6 [...] +<p><img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAqAAAADcCAIAAAAgIYQBAAAACXBIWXMAAA7DAAAOwwHHb6hkAAAgAElEQVR4nOzdZ1gUSbQw4BqyiASVDEpQgmIgKIogQTGgoiAiKKIComuOi645oaKYcTGBsBJEMWJAwpKULCKwoKRBMkrOMOH7UffrO5ccBpDxvM/+6Kmprq5h5/FMV1edInl4eAQEBCDWVVpaWlBQoK6uPtQdAd1jZ2ffs2fPzJkziRJPT89B/n7S6fTGxkZeXt7BvGiH6uvrR44cOdS9+FW6ERISYmBgQCKRhrAP7b+fAPzKON6+fSspKamlpTXUPRkoXl5eKSkpq1atGuqOgO65u7vHxMQw/gM6+N/P1tbWnJwcRUXFQbtih6hU6rdv35SVlYe2G3Q6PT09fdKkSUPbDYTQ48ePly9fzs3NPYR9aP/9BOBXxoEQ0tTUZ [...] <p>To facilitate the graphical representation of an object of class <code>track</code>, the simplest solution is to design a function <code>plot</code> for this class. We illustrate how to define such function with a particular emphasis on the management of graphical parameters. The function is provided below and we detail the different steps.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">plot.track <-<span class="st"> </span>function(x, <span class="dt">pos =</span> -<span class="dv">1</span>, <span class="dt">storeData =</span> <span class="ot">TRUE</span>, <span class="dt">plot =</span> <span class="ot">TRUE</span>, ...) { @@ -1065,10 +1068,10 @@ In the third step, each subgraph is created. Here, we create two <code>C1.hist</ In a final step, the multiple graph is build through the creation of a new <code>ADEgS</code> object and possibly plotted.<br /> The <code>plot.track</code> function can then be used by:</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">plot</span>(tra1)</code></pre></div> -<p><img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAqAAAADcCAIAAAAgIYQBAAAACXBIWXMAAA7DAAAOwwHHb6hkAAAgAElEQVR4nOzdeSBV2/s4/ueYZQqZCYUUUpKKZMjQQDSoNKmbUjfN9zbPaZ7nmepKpaSUJCREZB5SmcssY8h8zu+P9f7s3/kixJHief21zj5rr73Oyb3P2Wuv9SzarVu3nj17Br+9ysrKxMREXV3dnu4I6kbs7Ozr16/X0dGhjty+ffuP+PvsI5qamkJCQgwNDXu6Iz2j5d8nQr8zDh8fHxkZmd8/cIaEhAQGBtrY2PR0R1A3cnFxCQ8PZ/4f6J/y99lHfP361dPTs8/+Z9jy7xOh3xkHAIwZM+b3/y+2rq7uxo0bv38/UVe8efOm5cE/4u+zj/j8+bOjo2Of/edo9e8Tod8WW093ACGEEEKshwEeIYQQ6oUwwCOEEEK9E [...] +<p><img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAqAAAADcCAIAAAAgIYQBAAAACXBIWXMAAA7DAAAOwwHHb6hkAAAgAElEQVR4nO3ddVxUy9848FlYQkRCJQUllFAMQlEECcVAReEigiIqpde4mBe9diuKjRcLBCVEMTGQkFJKQASuKLVIo3TDxu+PeX7n2YeORWT9vF/fP87Ozpkzy92vnz1zZj5D8vT0DAwMROyrtLS0oKBAXV19sDsCusfJybl9+/YZM2YQJV5eXuz9/QQ99PbtWz09PRKJNIh9aP/9BOBXRn716tWYMWO0tLQGuycDxdvbOzU1dcWKFYPdEdA9Dw+P2NhY5n9A2f77CXrowYMHy5Yt4+HhGcQ+tP9+AvArIyOENDU12Tj+JSYmJiQksPEHZCfR0dHtC9n7+wl6ztTUlI+PbxA70OH3E4BfFsdgdwAAAAAArAcBHgAAAGBDE [...] <p>Graphical parameters can be modified by:</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">plot</span>(tra1, <span class="dt">histDist.ppoly.col =</span> <span class="st">"green"</span>, <span class="dt">pbackground.col =</span> <span class="st">"grey"</span>)</code></pre></div> -<p><img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAqAAAADcCAIAAAAgIYQBAAAACXBIWXMAAA7DAAAOwwHHb6hkAAAgAElEQVR4nOzdZ0BT1xsw8CcQCCAzYW9QFBARBGQ668JRFcG66sBZravWVdyzLhzVukWo1bqqVhQRRUBBFEFky0amYCDslZD3w/m/983LEmMAgef36eTk3JNzI+2Te+85z6F5e3v7+vrCN6+8vDw2NtbBwaGzB4Lakbi4+Nq1awcPHkzV+Pj4dIm/zx6Cx+M9f/58+PDhnT2QztH07xOhbxndz8+voaHBzMyss0fyGTExMYWFhaampp09ENSO/Pz8wsPDBf8H2lX+PnsIDofz6dOnHvufYdO/T4S+ZXQAMDExGTZsWGeP5DPq6+v9/Py+/XGirxEbG9u0skv8ffYQHz9+PHHiRI/952j27xOhb5ZYZw8AIYQQQqKHAR4hh [...] +<p><img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAqAAAADcCAIAAAAgIYQBAAAACXBIWXMAAA7DAAAOwwHHb6hkAAAgAElEQVR4nO3dd1gUV7sA8HdZWNrSFliKKE1EBEHB2AuiGNEQxYhGNFhR7N1oLIlYMKiJNWJDRUDFEvKpoCBYERUpgjRFBOm99y33j3Pv3P1ooSxtfX9P/pg9O3PmDNnHd+bMOe+hXbly5d69eyC6cnNzMzIyLCwsursh6N/R6fSNGzcOHz6cKvH09BTt3ydqpcePH1taWtJotG5sQ+PfJ0I9mXhAQACPxzMxMenulnSWrKys/Pz8QYMGdXdD0L8LCAh49eqV4D+gIv/7RK108+ZNAwMDBoPRjW1o/PtEqCcTBwAjI6MJEyZ0d0s6y4cPHxITE0X4AkVJbGxs40LR/n2i1hs3bpyUlFQ3NqDJ3ydCPZZYdzcAIYQQQsKHA [...] </div> <div id="examples" class="section level1"> <h1><span class="header-section-number">6</span> Examples</h1> @@ -1079,7 +1082,7 @@ g16 <-<span class="st"> </span><span class="kw">s.label</span>(pca3$li, <span g17 <-<span class="st"> </span><span class="kw">s.label</span>(pca3$li, <span class="dt">ppoints.col=</span> <span class="st">"red"</span>, <span class="dt">plabels =</span> <span class="kw">list</span>(<span class="dt">box =</span> <span class="kw">list</span>(<span class="dt">draw =</span> <span class="ot">FALSE</span>), <span class="dt">optim =</span> <span class="ot">TRUE</span>), <span class="dt">plot =</span> <span class="ot">FALSE</span>) <span class="kw">ADEgS</span>(<span class="kw">c</span>(g16, g17), <span class="dt">layout =</span> <span class="kw">c</span>(<span class="dv">1</span>, <span class="dv">2</span>))</code></pre></div> -<p><img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAkAAAAEgCAIAAADT5FumAAAACXBIWXMAAA7DAAAOwwHHb6hkAAAgAElEQVR4nO3deVxUVf8H8O+ogCCooKAhIuKCooS5AGommgmlIuKKKG6UUlYoJooZtLiVv1xSc89HsXpyScVc0CdRCCRQIZbQBESQRWWVgWGb+f1xdRph9v3C5/16Xk8zd+499yCc+71z7vecwxEIBAQAAMA2bXRdAQAAAGUggAEAACshgAEAADulpaVxOBxd1wKA3V5//XWBOGhfAKqT1L7aPHv2zNXVVexn8uByuTdv3lT6cO2wt7dPTEzUdS2kyc7OzsnJ0XUtpKmqqkpISNB1LWS4efMml8vV/nlTUlIqKyvFNjy0L32A9qUWeti+0IUIAACshAAGAACshAAGAACshAAGAACshAAGLYerq6uJiQkRTZgw4eTJk4oef [...] +<p><img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAkAAAAEgCAIAAADT5FumAAAACXBIWXMAAA7DAAAOwwHHb6hkAAAgAElEQVR4nO3deUBUVfsH8GeURTYVFFQ2ARcWJUwUUDOXTCg3QlMRdymlXFAstwyrV9TyTTG13Hp9lbTXLRVLRX+5gCCCCrGIhqCCAiogyjCsc39/XJ0QZobZZy58P3/UzJ17zz0Izzwz9z7nHB7DMAQAAMA1rbTdAQAAAEUggQEAACchgQEAADelp6fzeDxt9wKA29566y1GHMQXgPIkxVerFy9eeHt7i31NFnw+/+rVqwofrhlOTk5JSUna7oU0OTk5ubm52u6FNOXl5YmJidruRROuXr3K5/M1f97U1NTnz5+LDTzEly5AfKmEDsYXLiECAAAnIYEBAAAnIYEBAAAnIYEBAAAnIYFB8+Ht7W1sbExEI0aMOHLkiLyHX [...] </div> <div id="ellipses-stars-and-convex-hulls" class="section level2"> <h2><span class="header-section-number">6.2</span> Ellipses, stars and convex hulls</h2> @@ -1119,7 +1122,7 @@ g28 <-<span class="st"> </span><span class="kw">s1d.density</span>(score1, fa g29 <-<span class="st"> </span><span class="kw">s1d.density</span>(score1, fac1, <span class="dt">col =</span> <span class="kw">c</span>(<span class="dv">2</span>, <span class="dv">4</span>), <span class="dt">ppolygons.alpha =</span> <span class="fl">0.2</span>, <span class="dt">p1d =</span> <span class="kw">list</span>(<span class="dt">rug =</span> <span class="kw">list</span>(<span class="dt">tck =</span> <span class="dv">1</span>, <span class="dt">line =</span> <span class="ot">FALSE</span>)), <span class="dt">plot =</span> <span class="ot">FALSE</span>) <span class="kw">ADEgS</span>(<span class="kw">c</span>(g26, g27, g28, g29), <span class="dt">layout =</span> <span class="kw">c</span>(<span class="dv">2</span>, <span class="dv">2</span>))</code></pre></div> -<p><img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAkAAAAJACAIAAADq+E5hAAAACXBIWXMAAA7DAAAOwwHHb6hkAAAgAElEQVR4nOzdeXQc13km/OfeWrt6ARo7QHBfJJIiJXmRHUcaK1ZsJz5xvnhyJjlO4ix2Esc+k/HMSU6+TDJZ9B0n8TgZW8k4thzHdmwpjiTLlmztlGhREilwE/cFC7ES+9KN3teq+/3RIASCIIilu6ur+v0dHR2y0d11SaLw9L313rdYf3//E088IYQAIWQdDMP4zGc+I8vywgcHBgbo/CJk/ZY8v9hDDz309a9//R3veEeJjiqEYIyV6M3t9dprr+VyuZ/92Z+1eyAlYVkW59zuUZREif5oTz/99IULF7Zs2bLwwX/8x3989NFHH3jggaIfrmB8fLyhoWHRWe0OTzzxRDab/Y3f+A27B1J8pmlOTEy0tbXZPZCSmJqa8 [...] +<p><img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAkAAAAJACAIAAADq+E5hAAAACXBIWXMAAA7DAAAOwwHHb6hkAAAgAElEQVR4nOzdeXRcx30v+G/VXXtFYwdIEFwlkdooyvIuR3acbfyeE+d54nlOju08L0nseYmTE48nk8kyebETO8+x5ROdPFmWLTuRHVmSbW3WRomkJFJcRFLgAhIASRAEQADE0gB6X+6tmj+ahMAFYAPo7tv39u9zfI5JortvAcLtb1fVr6rY2bNnH330USklCCEr4Pf7P//5z6uqOv8fBwYG6P4iZOWueX+xe++99zvf+c6dd95Z7stLKRlj5b5K5eXz+ccee+x3f/d3nW5IWQghOOdOt6IsSv6tPfHEE8ePH1+3bt38f/z2t7/98MMPf/CDHyzhha6Wy+VmZmZaWlrKehVHZLPZb3/721/+8pedbkhZjI2NNTU1XfGm7 [...] </div> <div id="maps-and-neighbor-graphs" class="section level2"> <h2><span class="header-section-number">6.5</span> Maps and neighbor graphs</h2> diff --git a/man/C1.barchart-class.Rd b/man/C1.barchart-class.Rd index c94a282..08fb714 100644 --- a/man/C1.barchart-class.Rd +++ b/man/C1.barchart-class.Rd @@ -23,6 +23,7 @@ \item{\code{data}}{a list containing data or data's name. \itemize{ \item{\code{score}: the displayed values in the form of a vector, a factor, a name or a matching call.} \item{\code{labels}: the labels' names drawn on the top of bars.} + \item{\code{at}: the index value.} \item{\code{frame}: a positive or null integer. It is the number of the frame containing the data (used with \code{sys.frame(..., env = data$frame)}). Only if the data are not stored (i.e. \code{data$storeData = FALSE}).} \item{\code{storeData}: a logical indicating if the data should be stored in the returned object. diff --git a/man/adeg.panel.Spatial.Rd b/man/adeg.panel.Spatial.Rd index ca3a85a..b9c10d1 100644 --- a/man/adeg.panel.Spatial.Rd +++ b/man/adeg.panel.Spatial.Rd @@ -67,7 +67,7 @@ adeg.panel.Spatial(SpObject, sp.layout = NULL, col = 1, border = 1, lwd = 1, \examples{ -if(require(maptools, quiet = TRUE) & require(lattice, quiet = TRUE)) { +if(require(maptools, quietly = TRUE) & require(lattice, quietly = TRUE)) { nc <- readShapePoly(system.file("shapes/sids.shp", package = "maptools")[1], proj4string = CRS("+proj=longlat +datum=NAD27")) diff --git a/man/adeg.panel.hist.Rd b/man/adeg.panel.hist.Rd index 8ed74a7..1e33d35 100644 --- a/man/adeg.panel.hist.Rd +++ b/man/adeg.panel.hist.Rd @@ -39,7 +39,7 @@ adeg.panel.hist(histValues, horizontal = TRUE, densi, drawLines, params = list() } \examples{ -if(require(KernSmooth, quiet = TRUE) & require(lattice, quiet = TRUE)) { +if(require(KernSmooth, quietly = TRUE) & require(lattice, quietly = TRUE)) { z <- round(rnorm(100, 30, 5)) h <- hist(z, plot = FALSE) diff --git a/man/adeg.panel.join.Rd b/man/adeg.panel.join.Rd index 4c07419..52b20c1 100644 --- a/man/adeg.panel.join.Rd +++ b/man/adeg.panel.join.Rd @@ -29,7 +29,7 @@ adeg.panel.join(drawLines, params = list()) } \examples{ -if(require(lattice, quiet = TRUE)) { +if(require(lattice, quietly = TRUE)) { xyplot(0:20 ~ 0:20, drawLines = c(5, 10, 15), params = list(plabels.cex = 2), panel = function(drawLines, params){ adeg.panel.join(drawLines = drawLines, params = params)}) diff --git a/man/adeg.panel.label.Rd b/man/adeg.panel.label.Rd index b69dd14..7749966 100644 --- a/man/adeg.panel.label.Rd +++ b/man/adeg.panel.label.Rd @@ -56,13 +56,13 @@ adeg.panel.label(x, y, labels, plabels, pos = NULL) } \examples{ -if(require(lattice, quiet = TRUE)) { +if(require(lattice, quietly = TRUE)) { param <- adegpar("plabels")[[1]] xyplot(1:10 ~ 1:10, panel = function(x, y, ...){ adeg.panel.label(x, y, LETTERS[1:10], plabels = param)}) } -if(require(lattice, quiet = TRUE)) { +if(require(lattice, quietly = TRUE)) { param$boxes$draw <- FALSE param$col <- "blue" xyplot(1:10 ~ 1:10, panel = function(x, y, ...){ diff --git a/man/adeg.panel.nb.Rd b/man/adeg.panel.nb.Rd index b0f2067..41d5d2b 100644 --- a/man/adeg.panel.nb.Rd +++ b/man/adeg.panel.nb.Rd @@ -57,8 +57,8 @@ adeg.panel.edges(edges, coords, col.edge = "black", lwd = 1, lty = 1, pch = 20, } \examples{ -if(require(maptools, quiet = TRUE) & require(lattice, quiet = TRUE) - & require(spdep, quiet = TRUE)) { +if(require(maptools, quietly = TRUE) & require(lattice, quietly = TRUE) + & require(spdep, quietly = TRUE)) { columbus <- readShapePoly(system.file("etc/shapes/columbus.shp", package = "spdep")[1]) coords <- coordinates(columbus) @@ -68,8 +68,8 @@ if(require(maptools, quiet = TRUE) & require(lattice, quiet = TRUE) panel = function(...){adeg.panel.nb(col.gal.nb, coords, col.edge = c("blue", "red"))}) } -if(require(maptools, quiet = TRUE) & require(lattice, quiet = TRUE) - & require(spdep, quiet = TRUE)) { +if(require(maptools, quietly = TRUE) & require(lattice, quietly = TRUE) + & require(spdep, quietly = TRUE)) { edges <- matrix(c(1, 2, 3, 2, 4, 1, 3, 4), byrow = TRUE, ncol = 2) coords <- matrix(c(0, 1, 1, 0, 0, -1, -1, 0), byrow = TRUE, ncol = 2) xyplot(coords[,2] ~ coords[,1], diff --git a/man/adeg.panel.values.Rd b/man/adeg.panel.values.Rd index bbc15d4..cb470d2 100644 --- a/man/adeg.panel.values.Rd +++ b/man/adeg.panel.values.Rd @@ -64,7 +64,7 @@ adeg.panel.values(x, y, z, method, symbol, ppoints, breaks, centerpar = NULL, } \examples{ -if(require(lattice, quiet = TRUE)) { +if(require(lattice, quietly = TRUE)) { param <- adegpar("ppoints")[[1]] param$col <- adegpar("ppalette")[[1L]]$quanti(2) z <- rnorm(10) @@ -73,7 +73,7 @@ xyplot(1:10 ~ 1:10, panel = function(x, y, ...){ param, breaks = pretty(z, 4))}) } -if(require(lattice, quiet = TRUE)) { +if(require(lattice, quietly = TRUE)) { param$col <- adegpar()$ppalette$quali((length(pretty(z, 2)) - 1)) xyplot(1:10 ~ 1:10, panel = function(x, y, ...){ adeg.panel.values(x, y, z, method = "color", symbol = "circle", diff --git a/man/adegraphics-package.Rd b/man/adegraphics-package.Rd index 3c0ee73..fcefe8d 100644 --- a/man/adegraphics-package.Rd +++ b/man/adegraphics-package.Rd @@ -34,10 +34,10 @@ \tabular{ll}{ Package: \tab adegraphics\cr Type: \tab Package\cr - Version: \tab 1.0-5\cr - Date: \tab 2016-03-02\cr + Version: \tab 1.0-8\cr + Date: \tab 2017-04-11\cr License: \tab GPL (>=2)\cr - Depends: \tab ade4, grDevices, grid, KernSmooth, lattice, methods, RColorBrewer, sp + Depends: \tab ade4, graphics, grid, KernSmooth, lattice, latticeExtra, methods, RColorBrewer, sp (>= 1.1-1), stats } A lot of classes were implemented. diff --git a/man/changelatticetheme.Rd b/man/changelatticetheme.Rd index 5224cfe..d9e7ce3 100644 --- a/man/changelatticetheme.Rd +++ b/man/changelatticetheme.Rd @@ -35,11 +35,11 @@ changelatticetheme(...) } \examples{ -if(require(lattice, quiet = TRUE)) { -show.settings() -changelatticetheme(list(superpose.symbol = list(pch = c(21, 22, 35), cex = 1))) -show.settings() -show.settings()[1] +if(require(lattice, quietly = TRUE)) { + show.settings() + changelatticetheme(list(superpose.symbol = list(pch = c(21, 22, 35), cex = 1))) + show.settings() + show.settings()[1] } } \keyword{iplot} diff --git a/man/s.Spatial.Rd b/man/s.Spatial.Rd index e7753a9..34516e7 100644 --- a/man/s.Spatial.Rd +++ b/man/s.Spatial.Rd @@ -60,7 +60,7 @@ data(elec88, package = "ade4") g1 <- s.Spatial(elec88$Spatial) \dontrun{ - if(require(sp, quiet = TRUE)) { + if(require(sp, quietly = TRUE)) { ## mapping whith data obj <- SpatialPolygonsDataFrame(Sr = elec88$Spatial, data = elec88$tab) g2 <- s.Spatial(obj) diff --git a/man/s.image.Rd b/man/s.image.Rd index 050a52a..b7cdf44 100644 --- a/man/s.image.Rd +++ b/man/s.image.Rd @@ -91,7 +91,7 @@ g3 <- s.image(df1, z1, gridsize = 100) ## g4 <- s.image(df1, z1, gridsize = 1000, plot = FALSE) \dontrun{ - if(require(splancs, quiet = TRUE) & require(sp, quiet = TRUE)) { + if(require(splancs, quietly = TRUE) & require(sp, quietly = TRUE)) { Sr1 <- Polygon(cbind(c(0, 1, 2, 1, 2, 0, -2, -1, -2, -1, 0), c(2.5, 1.5, 2, 0, -2, -1, -2, 0, 2, 1.5, 2.5))) Sr2 <- Polygon(cbind(c(-0.5, 0.5, 0.5, -0.5, -0.5), c(0, 0, 1 ,1, 0)), hole = TRUE) diff --git a/man/s.logo.Rd b/man/s.logo.Rd index 46ebd65..db223fb 100644 --- a/man/s.logo.Rd +++ b/man/s.logo.Rd @@ -63,12 +63,11 @@ g1 <- s.logo(ggtortoises$pop, pori.incl = FALSE, ppoints.cex = 0.5) g1 <- s.label(ggtortoises$pop, add = TRUE, plabels.boxes.alpha = 0) -g2 <- s.logo(ggtortoises$pop, - ggtortoises$ico[as.character(ggtortoises$pop$carap)], - Sp = ggtortoises$Spatial, pback.col = "lightblue", pSp.col = "white", - pgrid.draw = FALSE, ppoints.cex = 0.5) g2 <- s.label(ggtortoises$misc, pgrid.draw = FALSE, - porigin.include = FALSE, paxes.draw = FALSE, add = TRUE) + porigin.include = FALSE, paxes.draw = FALSE, + Sp = ggtortoises$Spatial, pback.col = "lightblue", pSp.col = "white") +g2 <- s.logo(ggtortoises$pop, ggtortoises$ico[as.character(ggtortoises$pop$carap)], + ppoints.cex = 0.5, add = TRUE) data(capitales, package = "ade4") g3 <- s.logo(capitales$xy[sort(rownames(capitales$xy)), ], capitales$logo, diff --git a/man/s1d.barchart.Rd b/man/s1d.barchart.Rd index 23d0c39..9f4c178 100644 --- a/man/s1d.barchart.Rd +++ b/man/s1d.barchart.Rd @@ -8,8 +8,8 @@ } \usage{ -s1d.barchart(score, labels = NULL, facets = NULL, plot = TRUE, - storeData = TRUE, add = FALSE, pos = -1, ...) +s1d.barchart(score, labels = NULL, at = 1:NROW(score), facets = NULL, + plot = TRUE, storeData = TRUE, add = FALSE, pos = -1, ...) } \arguments{ @@ -17,6 +17,8 @@ s1d.barchart(score, labels = NULL, facets = NULL, plot = TRUE, \item{labels}{the labels' names drawn on the top of bars} + \item{at}{a numeric vector used as an index} + \item{facets}{a factor splitting \code{score} so that subsets of the data are represented on different sub-graphics} diff --git a/vignettes/classes.png b/vignettes/classes.png index aff9e23..bef4638 100644 Binary files a/vignettes/classes.png and b/vignettes/classes.png differ -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-cran-adegraphics.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
