args4meddevn_plot  R Documentation 
Creates a list
of the values for the options of median deviations plots for smooths
Description
Creates a list
of the values for the options of median deviations plots for smooths.
Note that the arguments plots.by
, plots.group
, facet.x
and facet.y
jointly define the organization of the plots. The default settings are optimized for traitSmooth
so that,
if you want to change any of these from their default settings when using args4meddevn_plot
with a function
other than traitSmooth
, then it is recommended that you specify all of them to ensure that the complete set
has been correctly specified. Otherwise, the default settings will be those shown here and these may be different to the
default settings shown for the function with which you are using args4meddevn_plot
.
Usage
args4meddevn_plot(plots.by = NULL, plots.group = "Tuning",
facet.x = c("Method","Type"), facet.y = ".",
facet.labeller = NULL, facet.scales = "free_x",
breaks.spacing.x = 4, angle.x = 0,
colour.values = NULL, shape.values = NULL,
alpha = 0.5,
propn.note = TRUE, propn.types = NULL,
ggplotFuncs = NULL,
...)
Arguments
plots.by 
A character that give the names of the set of
factor s by which medians deviations data is to be
grouped and a separate plot produced for each group. If NULL ,
no groups are formed. If a set of factor s, such as
Type , Tuning and Method , that uniquely index the
combinations of the smoothingparameter values is specified, then
groups are formed for each combination of the levels of the these
factor s, and a separate plot is produced for each combination.

plots.group 
A character that gives the names of the set
of factor s by which the subset of medians deviations data
within a single facet in a single plot is to be grouped for plotting
as separate lines.

facet.x 
A character giving the factor s
to be used to form subsets to be plotted in separate columns of the
medians deviations plots. The default of "." results
in no split into columns.

facet.y 
A character giving the factor s
to be used to form subsets to be plotted in separate rows of the
medians deviations plots. The default of "." results
in no split into rows.

facet.labeller 
A ggplot function for labelling the
facets of a plot produced using the ggplot function.
For more information see ggplot .

facet.scales 
A character specifying whether the scales are shared
across all facets of a plot ("fixed"), or do they vary across rows (the
default, "free_x"), columns ("free_y"), or both rows and columns ("free")?

breaks.spacing.x 
A numeric whose absolute values specifies the
distance between breaks for the xaxis in a sequence beginning with the
minimum x value and continuing up to the maximum x value. If it is negative,
the breaks that do not have x values in data will be omitted.
Minor breaks will be at half this value or, if these do not correspond to
xvalues in data when breaks.spacing.x is negative, have
a spacing of one. Thus, when breaks.spacing.x is negative,
grid lines will only be included for xvalues that occur in data .
These settings can be overwritten by supplying, in ggplotFuncs ,
a scale_x_continuous function from ggplot2 .

angle.x 
A numeric between 0 and 360 that gives the angle of the
xaxis text to the xaxis. It can also be set by supplying, in
ggplotFuncs , a theme function from ggplot2 .

colour.values 
A character vector specifying the values of
the colours to use in drawing the lines for the medians deviations
within a facet. If this is a named vector, then the values will be
matched based on the names. If unnamed, values will be matched in order
(usually alphabetical) within the limits of the scale.

shape.values 
A numeric vector specifying the values of
the shapes to use in drawing the points for the medians deviations
within a facet. If this is a named vector, then the values will be
matched based on the names. If unnamed, values will be matched in
order.

alpha 
A numeric specifying the degrees of
transparency to be used in plotting a median deviations plot.
It is a ratio in which the denominator specifies the number of
points (or lines) that must be overplotted to give a solid cover.

propn.note 
A logical indicating whether a note giving the
proportion of the median value of the response for each time is
to be included in the medians.deviations plots.

propn.types 
A numeric giving, for each of the
trait.types , the proportion of the median value of the
response for each time to be used to plot envelopes in the
median deviations plots. If set to NULL , the plots of the
proprotion envelopes are omitted.

ggplotFuncs 
A list , each element of which contains the
results of evaluating a ggplot function.
It is created by calling the list function with
a ggplot function call for each element. Note that
these functions are applied to the compareian deviations plots only.

... 
allows arguments to be passed to other functions; not used at present.

Value
A named list
.
Author(s)
Chris Brien
See Also
traitSmooth
, probeSmooths
and plotSmoothsMedianDevns
.
Examples
args4meddevn_plot(plots.by = "Type", plots.group = "Tuning",
facet.x = "Method", facet.y = ".",
propn.types = c(0.02,0.1, 0.2))