Description Usage Arguments Details Value Abrem options To Do Note Author(s) See Also Examples
View source: R/options.abrem.R
This function handles the various calculation, printing and plotting options of the abrem package.
1 
... 
Options for calculating, printing and plotting with the abrem package. 
This function borrows its internal structure from
the par
function of package graphics.
It can be used in different ways:
options.abrem()
Returns the currently used options and there values.
options.abrem()$dist
options.abrem("dist")
Returns the current value of an option.
options.abrem(cl=0.95)
options.abrem(list(cl=0.95,S=5e4))
Sets the specified options.
Currently, there is no way to reset the options to the default values using this function. One might, before changing any options, store the option list in a temporary variable like
abrem.defaults < options.abrem()
for restoring it later by running options.abrem(abrem.defaults)
.
The function creates a globally accessible list named options_abrem
,
holding the options. One should always use the options.abrem
function to access the option list, do not access this list directly.
Executing options.abrem
without arguments returns a named list
containing the currently active global options of the abrem package.
When arguments were supplied, these are returned in a named list.
cex.points
A number describing the relative size of the datapoint glyphs.
Defaults to 1
.
cl
Confidence level: A single number from the interval [0,[1
specifying the confidence level for various confidence calculations.
Defaults to 0.9
.
col
An integer or character string describing the color of a
graphical entity.
See function colors
for available colors.
Defaults to "black"
.
col.grid
An integer or character string describing the color of the grid
Defaults to "gray"
.
conf.blives.sides
Either "lower"
, "upper"
or "double"
,
specifying the type of bound(s) to be calculated.
Defaults to c("double")
.
conf.what
A vector of class "character"
describing for which entities
that confidence should be calculated.
Defaults to c("blives")
.
coordinate.text.size
A number determining the relative coordinate text label size.
Defaults to 0.7
.
dist
A character string with the distribution target for fitting.
See abrem.fit
for indepth discussion of the settings.
Defaults to "weibull"
.
in.legend
Logical value controlling the inclusion of various elements in
the legend. See abrem.fit
and abrem.conf
for more details.
Defaults to TRUE
.
in.legend.blives
Logical value controlling the inclusion of Blife confidence bounds in the legend.
Defaults to TRUE
.
in.legend.gof
Logical value controlling the inclusion of goodnessoffit
indicators in the legend. Note that this does not prohibit
calculation of sometimes time consuming prr
values, it only
prevents inclusion in the legend.
Defaults to TRUE
.
is.plot.cb
Logical value controlling the plotting of various types of
confidence bounds (if any present in the abrem
object).
Defaults to TRUE
.
is.plot.fit
Logical value controlling the plotting of the fitted line.
Defaults to TRUE
.
is.plot.grid
Logical value controlling the plotting of the grid.
Defaults to TRUE
.
is.plot.legend
Logical value controlling the plotting of the legend.
Defaults to TRUE
.
is.plot.pp
Logical value controlling the plotting of the (life)time observations' probability plot positions.
Defaults to TRUE
.
label
A character string with the title of the legend box, can be used to label a dataset or fit.
Defaults to NULL
.
legend.text.size
A number determining the relative legend text size.
Defaults to 0.7
.
log
A character string describing the type of plotting canvas to use.
Possible values are "x"
(Weibull canvas), "xy"
(Lognormal canvas), ""
(Weibull Y axis, linear X axis)
and "y"
(Lognormal Y axis, linear X axis).
Defaults to "x"
, Weibull canvas.
For contour plots, log
is always ""
and cannot be set.
lty
An integer describing the line type of both the fitted
line and the confidence bounds, if any.
See function par
for available line types.
Defaults to 1
.
lwd
An integer describing the line width of both the fitted line and the confidence bounds, if any.
Defaults to 2
.
lwd.points
An integer describing the thickness of the datapoint glyphs.
Defaults to 2
.
main
, main.contour
A character string; the main title of the plot or contour plot.
Defaults to "Probability Plot"
or "Contour Plot"
.
mar
A numerical vector of the form c(bottom, left, top, right)
which gives the number of lines of margin to be specified on
the four sides of the plot.
See function par
for more info.
Defaults to c(5.1,4.1,5.1,2.1)
.
method.conf.blives
A vector of class "character"
describing the techniques used
for calculating confidence for Blives.
See abrem.conf
for indepth discussion of the settings.
Defaults to c("mcpivotals")
.
method.fit
A vector of class "character"
with fitting options.
See abrem.fit
for indepth discussion of the settings.
Defaults to c("rr","xony")
.
pch
An integer or single character describing the plotting symbol, used for
plotting the datapoints. For more info, see
points
.
Defaults to 1
.
persistent
Experimental parameter, do not use.
Defaults to TRUE
.
pivotals
Currently unused. Defaults to FALSE
.
pp
pp
is short for "probability plot positions", it is a vector of
class "character"
describing the type of plot positions to be
calculated.
Possible values are "median"
(exact median plot postions
calculated using the Incomplete Beta function) and "benard"
(a good approximation to the median plot positions). Both options
can be supplied at the same time but currently, only the first
element in the pp
vector will be used for
further fitting by abrem.fit
Currently, there are no plans to implement
"hazen"
and "mean"
plotting positions.
Defaults to c("median")
.
S
An integer describing the number of Monte Carlo simulations on
which the Monte Carlo pivotal confidence bounds and calculation
of the "prr" goodnessoffit indicator are based (See
prrVal
of package pivotals for more
details).
Defaults to 10000
.
signif
An integer describing the significant digits of various numbers that are displayed in the legend.
Defaults to 4
.
sub
, sub.contour
A character string; the subtitle of the plot or contour plot.
Defaults to ""
.
threshold
A logical value specifying whether a threshold time value should be
substracted from the graphical elements before plotting. This is
particulary useful when fitting three parameter models like
weibull3p
, where the third model parameter is a threshold value.
If TRUE
, the software will subtract the threshold value
(that is to be calculated by abrem.fit
) from its
associated graphical
elements like plot poistions, fits and confidence bounds.
If a numeric value is passed, the software will subtract this value from the appropriate graphical elements.
Note: currently, "threshold"
should only be used in combination with
Abrem
and abrem.fit
and not with
plot.abrem
. See abrem.fit
for more info.
Defaults to FALSE
unrel
An unordered numeric vector with unreliability levels for which Blife confidence will be calculated.
Defaults to c(0.1,0.05,0.01)
.
unrel.n
An integer controlling the amount of unreliability levels for
which confidence bounds are calculated and ultimately plotted.
See abrem.conf
for more details.
Defaults to 25
verbosity
An integer from c(1,2,3)
setting the level of verbosity of
all abrem functions. Use this for debugging.
Defaults to 1
.
xlab
, ylab
Character strings with the labels for the X and Y axis.
Default to "Time To Failure"
and
"Unreliability [%]"
respectively.
For contour plots, Default to "Eta"
and "Beta"
respectively.
xlim
A numeric vector with two values determining the plotting range
of the horizontal axis of the plot.
plot.abrem
calculates horizontal limits automatically
from its data argument.
Defaults to NULL
.
ylim
A numeric vector with two values determining the plotting range
of the vertical axis of the plot. Allowed values come
from the interval ]0,1[
. plot.abrem
calculates
vertical limits automatically from its data argument; if vertical
plotting positions do not exceed the standard range of
c(0.01,0.99)
, then the latter is used.
Otherwise, the standard range is expanded to include the
extreme plot positions.
The standard vertical range is currently hardcoded to c(0.01,0.99)
.
Defaults to NULL
.
Add the possibility to reset to the default values.
Implement returning of the pivotals dataframe in the
abrem
object.
Add detection of unsupported arguments.
Typical usage of abrem involves calling a sequence of functions like:
da < Abrem(c(10,11,27))
da < abrem.fit(da)
da < abrem.conf(da)
plot(da)
Do not call options.abrem
in between these functions because some
options are locked and cannot be altered further in this chain. This is an
implication of the way the abrem
object is structured.
The correct time to specify an option is when it is needed for the first
time. For example, when the color setting option col = "red"
is
passed as an argument of function Abrem
, it will be used for
datapoints, fits and confidence bounds. If supplied to abrem.conf
,
only the confidence bounds will have the specified color, hereby overriding
any previously inherited color settings from abrem.fit
or Abrem
.
Jurgen Symynck [email protected]
Abrem
,
abrem.fit
,
abrem.conf
,
plot.abrem
1 2 3 4 5 6 7 8 9 10 11 12 13  ## backup options ##
abrem.defaults < options.abrem()
## setting new options ##
options.abrem(S=5e5,cl=0.99)
## listing options ##
options.abrem()
options.abrem()$main
## restore options ##
options.abrem(abrem.defaults)

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