From bd96205b98ccebe5eb79b2720113b3a3b13bd212 Mon Sep 17 00:00:00 2001
From: Jason Cory Brunson session info#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz America/New_York
-#> date 2025-01-01
+#> date 2025-01-22
#> pandoc 2.16.2 @ /usr/local/bin/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
@@ -447,7 +447,7 @@
session info#> magrittr 2.0.3 2022-03-30 [2] CRAN (R 4.2.0)
#> MASS * 7.3-58.2 2023-01-23 [2] CRAN (R 4.2.3)
#> munsell 0.5.1 2024-04-01 [2] CRAN (R 4.2.3)
-#> ordr * 0.1.1.0002 2025-01-01 [1] local
+#> ordr * 0.1.1.0002 2025-01-22 [1] local
#> pillar 1.10.0 2024-12-17 [2] CRAN (R 4.2.3)
#> pkgconfig 2.0.3 2019-09-22 [2] CRAN (R 4.2.0)
#> pkgdown 2.1.1 2024-09-17 [2] CRAN (R 4.2.3)
@@ -455,7 +455,7 @@
session info#> R6 2.5.1 2021-08-19 [2] CRAN (R 4.2.0)
#> ragg 1.3.3 2024-09-11 [2] CRAN (R 4.2.3)
#> RColorBrewer 1.1-3 2022-04-03 [2] CRAN (R 4.2.0)
-#> Rcpp 1.0.13-1 2024-11-02 [2] CRAN (R 4.2.3)
+#> Rcpp 1.0.12 2024-01-09 [2] CRAN (R 4.2.3)
#> rlang 1.1.4 2024-06-04 [2] CRAN (R 4.2.3)
#> rmarkdown 2.28 2024-08-17 [2] CRAN (R 4.2.3)
#> sass 0.4.9 2024-03-15 [2] CRAN (R 4.2.3)
@@ -474,7 +474,7 @@
session info#> xfun 0.48 2024-10-03 [2] CRAN (R 4.2.3)
#> yaml 2.3.10 2024-07-26 [2] CRAN (R 4.2.3)
#>
-#> [1] /private/var/folders/k6/l4mq9ctj3219429xnvqpdbxm8tckkx/T/Rtmp2m6ADV/temp_libpath37143d897314
+#> [1] /private/var/folders/k6/l4mq9ctj3219429xnvqpdbxm8tckkx/T/Rtmpgkj8Hf/temp_libpath290134768767
#> [2] /Library/Frameworks/R.framework/Versions/4.2/Resources/library
#>
#> ──────────────────────────────────────────────────────────────────────────────
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 632ea3fc..07df5695 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -4,4 +4,4 @@ pkgdown_sha: ~
articles:
cmds-variables: cmds-variables.html
ordr: ordr.html
-last_built: 2025-01-01T15:53Z
+last_built: 2025-01-22T22:28Z
diff --git a/docs/reference/biplot-geoms.html b/docs/reference/biplot-geoms.html
index 7bd83c0d..095963bc 100644
--- a/docs/reference/biplot-geoms.html
+++ b/docs/reference/biplot-geoms.html
@@ -150,6 +150,40 @@
Convenience geoms for row and column matrix factors
inherit.aes = TRUE
)
+geom_rows_contour(
+ mapping = NULL,
+ data = NULL,
+ stat = "contour",
+ position = "identity",
+ ...,
+ bins = NULL,
+ binwidth = NULL,
+ breaks = NULL,
+ lineend = "butt",
+ linejoin = "round",
+ linemitre = 10,
+ na.rm = FALSE,
+ show.legend = NA,
+ inherit.aes = TRUE
+)
+
+geom_cols_contour(
+ mapping = NULL,
+ data = NULL,
+ stat = "contour",
+ position = "identity",
+ ...,
+ bins = NULL,
+ binwidth = NULL,
+ breaks = NULL,
+ lineend = "butt",
+ linejoin = "round",
+ linemitre = 10,
+ na.rm = FALSE,
+ show.legend = NA,
+ inherit.aes = TRUE
+)
+
geom_rows_density_2d(
mapping = NULL,
data = NULL,
@@ -404,6 +438,26 @@ Convenience geoms for row and column matrix factors
text_dodge = 0.03,
label_dodge = 0.03,
...,
+ axis.colour = NULL,
+ axis.color = NULL,
+ axis.alpha = NULL,
+ label.angle = 0,
+ label.colour = NULL,
+ label.color = NULL,
+ label.alpha = NULL,
+ tick.linewidth = 0.25,
+ tick.colour = NULL,
+ tick.color = NULL,
+ tick.alpha = NULL,
+ text.size = 2.6,
+ text.angle = 0,
+ text.hjust = 0.5,
+ text.vjust = 0.5,
+ text.family = NULL,
+ text.fontface = NULL,
+ text.colour = NULL,
+ text.color = NULL,
+ text.alpha = NULL,
parse = FALSE,
check_overlap = FALSE,
na.rm = FALSE,
@@ -425,6 +479,26 @@ Convenience geoms for row and column matrix factors
text_dodge = 0.03,
label_dodge = 0.03,
...,
+ axis.colour = NULL,
+ axis.color = NULL,
+ axis.alpha = NULL,
+ label.angle = 0,
+ label.colour = NULL,
+ label.color = NULL,
+ label.alpha = NULL,
+ tick.linewidth = 0.25,
+ tick.colour = NULL,
+ tick.color = NULL,
+ tick.alpha = NULL,
+ text.size = 2.6,
+ text.angle = 0,
+ text.hjust = 0.5,
+ text.vjust = 0.5,
+ text.family = NULL,
+ text.fontface = NULL,
+ text.colour = NULL,
+ text.color = NULL,
+ text.alpha = NULL,
parse = FALSE,
check_overlap = FALSE,
na.rm = FALSE,
@@ -432,6 +506,80 @@ Convenience geoms for row and column matrix factors
inherit.aes = TRUE
)
+geom_rows_bagplot(
+ mapping = NULL,
+ data = NULL,
+ stat = "bagplot",
+ position = "identity",
+ ...,
+ bag.linewidth = sync(),
+ bag.linetype = sync(),
+ bag.colour = "black",
+ bag.color = NULL,
+ bag.fill = sync(),
+ bag.alpha = NA,
+ median.shape = 21L,
+ median.stroke = sync(),
+ median.size = 5,
+ median.colour = sync(),
+ median.color = NULL,
+ median.fill = "white",
+ median.alpha = NA,
+ fence.linewidth = 0.25,
+ fence.linetype = 0L,
+ fence.colour = sync(),
+ fence.color = NULL,
+ fence.fill = sync(),
+ fence.alpha = 0.25,
+ outlier.shape = sync(),
+ outlier.stroke = sync(),
+ outlier.size = sync(),
+ outlier.colour = sync(),
+ outlier.color = NULL,
+ outlier.fill = NA,
+ outlier.alpha = NA,
+ na.rm = FALSE,
+ show.legend = NA,
+ inherit.aes = TRUE
+)
+
+geom_cols_bagplot(
+ mapping = NULL,
+ data = NULL,
+ stat = "bagplot",
+ position = "identity",
+ ...,
+ bag.linewidth = sync(),
+ bag.linetype = sync(),
+ bag.colour = "black",
+ bag.color = NULL,
+ bag.fill = sync(),
+ bag.alpha = NA,
+ median.shape = 21L,
+ median.stroke = sync(),
+ median.size = 5,
+ median.colour = sync(),
+ median.color = NULL,
+ median.fill = "white",
+ median.alpha = NA,
+ fence.linewidth = 0.25,
+ fence.linetype = 0L,
+ fence.colour = sync(),
+ fence.color = NULL,
+ fence.fill = sync(),
+ fence.alpha = 0.25,
+ outlier.shape = sync(),
+ outlier.stroke = sync(),
+ outlier.size = sync(),
+ outlier.colour = sync(),
+ outlier.color = NULL,
+ outlier.fill = NA,
+ outlier.alpha = NA,
+ na.rm = FALSE,
+ show.legend = NA,
+ inherit.aes = TRUE
+)
+
geom_rows_interpolation(
mapping = NULL,
data = NULL,
@@ -553,6 +701,26 @@ Convenience geoms for row and column matrix factors
text_dodge = 0.03,
label_dodge = 0.03,
...,
+ axis.colour = NULL,
+ axis.color = NULL,
+ axis.alpha = NULL,
+ label.angle = 0,
+ label.colour = NULL,
+ label.color = NULL,
+ label.alpha = NULL,
+ tick.linewidth = 0.25,
+ tick.colour = NULL,
+ tick.color = NULL,
+ tick.alpha = NULL,
+ text.size = 2.6,
+ text.angle = 0,
+ text.hjust = 0.5,
+ text.vjust = 0.5,
+ text.family = NULL,
+ text.fontface = NULL,
+ text.colour = NULL,
+ text.color = NULL,
+ text.alpha = NULL,
parse = FALSE,
check_overlap = FALSE,
na.rm = FALSE,
@@ -575,6 +743,26 @@ Convenience geoms for row and column matrix factors
text_dodge = 0.03,
label_dodge = 0.03,
...,
+ axis.colour = NULL,
+ axis.color = NULL,
+ axis.alpha = NULL,
+ label.angle = 0,
+ label.colour = NULL,
+ label.color = NULL,
+ label.alpha = NULL,
+ tick.linewidth = 0.25,
+ tick.colour = NULL,
+ tick.color = NULL,
+ tick.alpha = NULL,
+ text.size = 2.6,
+ text.angle = 0,
+ text.hjust = 0.5,
+ text.vjust = 0.5,
+ text.family = NULL,
+ text.fontface = NULL,
+ text.colour = NULL,
+ text.color = NULL,
+ text.alpha = NULL,
parse = FALSE,
check_overlap = FALSE,
na.rm = FALSE,
@@ -736,6 +924,23 @@ Arguments
an explanation.
Number of contour bins. Overridden by breaks
.
The width of the contour bins. Overridden by bins
.
One of:
Numeric vector to set the contour breaks
A function that takes the range of the data and binwidth as input +and returns breaks as output. A function can be created from a formula +(e.g. ~ fullseq(.x, .y)).
Overrides binwidth
and bins
. By default, this is a vector of length
+ten with pretty()
breaks.
Character string identifying the variable to contour
by. Can be one of "density"
, "ndensity"
, or "count"
. See the section
@@ -870,6 +1075,46 @@
Default aesthetics for axes. Set to +NULL to inherit from the data's aesthetics.
Default aesthetics +for labels. Set to NULL to inherit from the data's aesthetics.
Default aesthetics +for tick marks. Set to NULL to inherit from the data's aesthetics.
Default aesthetics for tick mark labels. Set to NULL to inherit from the +data's aesthetics.
Default aesthetics for bags. Set to sync()
to inherit from the data's
+aesthetics or to NULL
to use the data's aesthetics.
Default aesthetics for medians. Set to sync()
to inherit from the data's
+aesthetics or to NULL
to use the data's aesthetics.
Default aesthetics for fences. Set to sync()
to inherit from the data's
+aesthetics or to NULL
to use the data's aesthetics.
Default aesthetics for outliers. Set to sync()
to inherit from the data's
+aesthetics or to NULL
to use the data's aesthetics.
A list (best structured as a data.frame)
of row (geom_cols_interpolation()
) or column
diff --git a/docs/reference/biplot-stats.html b/docs/reference/biplot-stats.html
index 46933cc3..0b61e387 100644
--- a/docs/reference/biplot-stats.html
+++ b/docs/reference/biplot-stats.html
@@ -166,6 +166,36 @@
The number of segments to be used in drawing the ellipse.
Functions treated as in
-ggplot2::stat_summary()
, with fun.center
, fun.min
, and fun.max
-behaving as fun.y
, fun.ymin
, and fun.ymax
.
Fraction of the data to include in the bag.
Scale factor of the fence relative to the bag.
Logical indicators whether to include median, +fence, and outliers in the composite output.
A function that is given the complete data and should
+return a data frame with variables ymin
, y
, and ymax
.
Deprecated alias to fun
.
Alternatively, supply three individual +functions that are each passed a vector of values and should return a +single number.
Alternatively to the ggplot2::stat_summary_bin()
parameters,
+supply a summary function that takes a matrix as input and returns a named
+column summary vector. Overridden by fun.data
and fun
, cannot be used
+together with fun.min
and fun.max
.
Arguments passed to the fun.*
.
Optional additional arguments passed on to the functions.
A numeric vector of fractions (between 0
and 1
) of the
+data to contain in each hull.
Character; one of "above"
and "below"
, indicating whether each
+hull should contain at least or at most breaks
of the data,
+respectively.
FALSE
.
+Character; the name of the depth function (passed to
+ddalpha::depth.()
).
List of additional parameters passed via ...
to
+ddalpha::depth.()
.
The reference data set; see Details.
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