[med-svn] [r-cran-adegraphics] 10/13: New upstream version 1.0-8
Andreas Tille
tille at debian.org
Sat Sep 30 06:27:01 UTC 2017
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 <tille at debian.org>
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 <stephane.dray at univ-lyon1.fr> and Aurélie Siberchicot <aurelie.siberchicot at univ-lyon1.fr>, with contributions from Jean Thioulouse. Based on earlier work by Alice Julien-Laferrière.
Maintainer: Aurélie Siberchicot <aurelie.siberchicot at univ-lyon1.fr>
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 at data$score, envir = sys.frame(object at data$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 at data$storeData)
at <- object at data$at
else
@@ -233,7 +233,9 @@ setMethod(
## grid background and box
object at trellis.par$panel.background$col <- object at adeg.par$pbackground$col
if(!object at adeg.par$pbackground$box)
- object at trellis.par$axis.line$col <- "transparent"
+ object at trellis.par$axis.line$col <- "transparent"
+ else
+ object at trellis.par$axis.line$col <- "black"
arguments <- list(
par.settings = object at trellis.par,
@@ -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 at data$storeData)
- xdata <- object at data$at
- else
- xdata <- eval(object at data$at, envir = sys.frame(object at data$frame))
+ if(inherits(object, "C1.barchart") | inherits(object, "C1.curve") | inherits(object, "C1.dotplot") | inherits(object, "C1.interval")) {
+ if(object at data$storeData)
+ xdata <- object at data$at
+ else
+ xdata <- eval(object at data$at, envir = sys.frame(object at data$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(
object at trellis.par$panel.background$col <- object at adeg.par$pbackground$col
if(!object at adeg.par$pbackground$box)
object at trellis.par$axis.line$col <- "transparent"
+ else
+ object at trellis.par$axis.line$col <- "black"
arguments <- list(
par.settings = object at trellis.par,
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"))
object at trellis.par$panel.background$col <- object at adeg.par$pbackground$col
if(!object at adeg.par$pbackground$box)
- object at trellis.par$axis.line$col <- "transparent"
+ object at trellis.par$axis.line$col <- "transparent"
+ else
+ object at trellis.par$axis.line$col <- "black"
arguments <- list(
par.settings = object at trellis.par,
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(
object at trellis.par$panel.background$col <- object at adeg.par$pbackground$col
if(!object at adeg.par$pbackground$box)
object at trellis.par$axis.line$col <- "transparent"
+ else
+ object at trellis.par$axis.line$col <- "black"
arguments <- list(
par.settings = object at trellis.par,
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
## object at trellis.par$panel.background$col <- object at adeg.par$pbackground$col
if(!object at adeg.par$pbackground$box)
- object at trellis.par$axis.line$col <- "transparent"
-
+ object at trellis.par$axis.line$col <- "transparent"
+ else
+ object at trellis.par$axis.line$col <- "black"
+
arguments = list(
par.settings = object at trellis.par,
scales = if(!is.null(object at g.args$scales)) object at g.args$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 at data$labels <- data$labels
+ .Object at data$at <- data$at
+ validObject(.Object)
return(.Object)
})
@@ -25,11 +27,13 @@ setMethod(
on.exit(adegpar(oldparamadeg))
adegtot <- adegpar(object at adeg.par)
- if(object at data$storeData)
+ if(object at data$storeData) {
score <- object at data$score
- else
+ at <- object at data$at
+ } else {
score <- eval(object at data$score, envir = sys.frame(object at data$frame))
-
+ at <- eval(object at data$at, envir = sys.frame(object at data$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(object at adeg.par$p1d$horizontal && is.null(object at g.args$ylim))
- object at g.args$ylim <- c(0, length(score) + 1)
+ object at g.args$ylim <- setlimits1D(min(at), max(at), 0, FALSE)
if(!object at adeg.par$p1d$horizontal && is.null(object at g.args$xlim))
- object at g.args$xlim <- c(0, length(score) + 1)
+ object at g.args$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(object at adeg.par)
- if(object at data$storeData)
+ if(object at data$storeData) {
+ score <- object at data$score
at <- object at data$at
- else
+ } else {
+ score <- eval(object at data$score, envir = sys.frame(object at data$frame))
at <- eval(object at data$at, envir = sys.frame(object at data$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$draw <- FALSE
diff --git a/R/C1.curves.R b/R/C1.curves.R
index c01ab48..d3d6bd9 100644
--- a/R/C1.curves.R
+++ b/R/C1.curves.R
@@ -14,7 +14,7 @@ setMethod(
## get some parameters
nr <- NROW(object at data$score)
nc <- NCOL(object at data$score)
-
+
pscore <- object at adeg.par$p1d
ppoints <- lapply(object at adeg.par$ppoints, FUN = function(x) {rep(rep(x, length.out = nc), each = nr)})
plines <- lapply(object at adeg.par$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$g.args, Call = match.call())
diff --git a/R/C1.density.R b/R/C1.density.R
index 2c4a6e7..44cecad 100644
--- a/R/C1.density.R
+++ b/R/C1.density.R
@@ -33,11 +33,11 @@ setMethod(
adegtot <- adegpar(object at adeg.par)
if(object at data$storeData) {
- fac <- object at data$fac
score <- object at data$score
+ fac <- object at data$fac
} else {
- fac <- eval(object at data$fac, envir = sys.frame(object at data$frame))
score <- eval(object at data$score, envir = sys.frame(object at data$frame))
+ fac <- eval(object at data$fac, envir = sys.frame(object at data$frame))
}
score <- as.matrix(score)[, 1] ## to manage 'score' when it is a data.frame with only one column
nlev <- nlevels(as.factor(fac))
diff --git a/R/C1.dotplot.R b/R/C1.dotplot.R
index 34c267d..f279ff5 100644
--- a/R/C1.dotplot.R
+++ b/R/C1.dotplot.R
@@ -26,10 +26,14 @@ setMethod(
on.exit(adegpar(oldparamadeg))
adegtot <- adegpar(object at adeg.par)
- if(object at data$storeData)
+ if(object at data$storeData) {
+ score <- object at data$score
at <- object at data$at
- else
+ } else {
+ score <- eval(object at data$score, envir = sys.frame(object at data$frame))
at <- eval(object at data$at, envir = sys.frame(object at 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$score, envir = sys.frame(sys.nframe() + pos))
+
## parameters sorted
sortparameters <- sortparamADEg(...)
diff --git a/R/C1.gauss.R b/R/C1.gauss.R
index ae90eb0..ea38af0 100644
--- a/R/C1.gauss.R
+++ b/R/C1.gauss.R
@@ -31,14 +31,15 @@ setMethod(
adegtot <- adegpar(object at adeg.par)
if(object at data$storeData) {
- fac <- object at data$fac
score <- object at data$score
+ fac <- object at data$fac
wt <- object at data$wt
} else {
- fac <- eval(object at data$fac, envir = sys.frame(object at data$frame))
score <- eval(object at data$score, envir = sys.frame(object at data$frame))
+ fac <- eval(object at data$fac, envir = sys.frame(object at data$frame))
wt <- eval(object at data$wt, envir = sys.frame(object at data$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(object at adeg.par)
- if(object at data$storeData)
+ if(object at data$storeData) {
+ score <- object at data$score
at <- object at data$at
- else
+ } else {
+ score <- eval(object at data$score, envir = sys.frame(object at data$frame))
at <- eval(object at data$at, envir = sys.frame(object at data$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$facets), i)
- }
listGraph <- c(listGraph, do.call(as.character(thenewcall[[1]]), thenewcall[-1]))
}
@@ -305,6 +302,25 @@ multi.facets.C1 <- function(thecall, adepar, samelimits = TRUE) {
names(listGraph) <- levels(facets)
posmatrix <- layout2position(.n2mfrow(nlevels(facets)), ng = nlevels(facets))
object <- new(Class = "ADEgS", ADEglist = listGraph, positions = posmatrix, add = matrix(0, ncol = nlevels(facets), nrow = nlevels(facets)), Call = as.call(thecall))
+
+ ## same limits for all graphics when the second axis is done by intern calculations
+ if(inherits(object[[1]], "C1.density") | inherits(object[[1]], "C1.gauss") | inherits(object[[1]], "C1.hist")) {
+ if(isTRUE(samelimits) | is.null(samelimits)) {
+ cc <- object at Call
+ if(adegtot$p1d$horizontal & is.null(thecall$ylim)) {
+ Ylim <- range(sapply(object at ADEglist, function(x) x at g.args$ylim))
+ update(object, ylim = Ylim)
+ object at Call <- cc # this call does not include the ylim update
+ }
+ if(!adegtot$p1d$horizontal & is.null(thecall$xlim)) {
+ Xlim <- range(sapply(listGraph, function(x) x at g.args$xlim))
+ update(object, xlim = Xlim)
+ object at Call <- paste(substr(cc, 1, nchar(cc) - 1), ", xlim = c(", Xlim[1], ",", Xlim[2], ")", sep = "")
+ object at 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
More information about the debian-med-commit
mailing list