Uses intervalValueCalculate and the function
anom to identify anomalous individuals. The user can
elect to print the anomalous individuals, a longitudinal profile plot
without the anomalous individuals and/or a longitudinal profile plot
with only the anomalous individuals. The plots are produced using
ggplot. The plot can be facetted so that a grid of plots is
produced.
Warning: anomPlot will be deprecated in future versions, its synonym plotAnom
being preferred.
plotAnom(data, x="xDays+24.16666667", response="Area.smooth.RGR",
individuals="Snapshot.ID.Tag",
breaks=seq(12, 36, by=2), vertical.line=NULL,
groupsFactor=NULL, lower=NULL, upper=NULL,
start.time=NULL, end.time=NULL, times.factor = "Days",
suffix.interval=NULL,
columns.retained=c("Snapshot.ID.Tag", "Smarthouse", "Lane",
"Position", "Treatment.1", "Genotype.ID"),
whichPrint=c("anomalous","innerPlot","outerPlot"), na.rm=TRUE, ...)A data.frame containing the data to be tested
and plotted.
A character giving the variable to be plotted on
the x-axis.
A character specifying the response variable that
is to be tested and plotted on the y-axis.
A character giving the name(s) of the
factor(s) that define the subsets of the data for
which each subset corresponds to the response value for an
individual.
A numeric vector giving the breaks to be plotted on
the x-axis scale.
A numeric giving position on the x-axis
at which a vertical line is to be drawn. If NULL,
no line is drawn.
A factor giving the name of a
factor that defines groups of individuals between which the
test for anomalous individuals can be varied by setting values for
one or more of lower, upper, start.time and
end.time to be NULL, a single value or a set of values whose number
equals the number of levels of groupsFactor. If NULL or
only a dingle value is supplied,
the test is the same for all individuals.
A numeric such that values in response below
it are considered to be anomalous. If NULL, there is no
testing for values below the lower bound.
A numeric such that values in response above
it are considered to be anomalous. If NULL, there is no
testing for values above the upper bound.
A numeric giving the start of the time interval,
in terms of a level of times.factor,
during which testing for anomalous values is to occur.
If NULL, the interval will start with the first
observation.
A numeric giving the end of the time interval,
in terms of a level of times.factor,
during which testing for anomalous values is to occur.
If NULL, the interval will end with the last
observation.
A character giving the name of the column in
data containing the factor for times at which the data was
collected. Its levels should be numeric values stored as
characters.
A character giving the suffix to be
appended to response to form the
name of the column containing the calculated values. If it is
NULL then nothing will be appended.
A character giving the names of the
columns in data that are to be retained in the
data.frame of anomalous individuals.
A character indicating what is to be printed.
If anomalous is included, the columns.retained
are printed for the anomalous individuals.
A logical indicating whether NA values should
be stripped before the testing proceeds.
allows for arguments to be passed to plotLongitudinal.
A list with three components:
data, a data frame resulting from the merge
of data and the logical identifying whether
or not an individual is anomalous;
innerPlot, an object of class ggplot storing the
longitudinal plot of the individuals that are not anomalous;
outerPlot, an object of class ggplot storing the
longitudinal plot of only the individuals that are anomalous.
The name of the column indicating anomalous individuals will be result of
concatenating the response, anom and, if it is not
NULL, suffix.interval, each separated by a full stop.
The ggplot objects can be plotted using print and can be
modified by adding ggplot functions before printing. If there are
no observations to plot, NULL will be returned for the plot.
# NOT RUN {
data(exampleData)
anomalous <- plotAnom(longi.dat, response="Area.smooth.AGR",
lower=2.5, start.time=40,
x = "xDays+35.42857143", vertical.line=29,
breaks=seq(28, 42, by=2),
whichPrint=c("innerPlot"),
y.title="Area.smooth.AGR")
# }
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