RankPlot creates a figure with a plot of ranking data,
from among several options for showing uncertainty in the ranked estimates.
This function is meant for use within RankPlotWithTable,
which draws a ranking table aligned with this plot of the data
in one combined figure.
RankPlot(
est,
se,
names,
refName = NULL,
confLevel = 0.9,
plotType = c("individual", "difference", "comparison", "columns"),
tiers = 1,
GH = FALSE,
Bonferroni = ifelse(plotType == "individual", "none", "demi"),
tikzText = FALSE,
cex = 1,
tickWidth = NULL,
rangeFactor = 1.2,
textPad = 0,
legendX = "topleft",
legendY = NULL,
legendText = NULL,
lwdReg = 1,
lwdBold = 3,
thetaLine = 1,
xlim = NULL
)Vectors containing the point estimate and its standard error for each area.
Vector containing the name of each area. Abbreviations may be preferable to full names (e.g. "CO" instead of "Colorado") since these names will be displayed directly on the plot.
String containing the name of the reference area;
must be one of the values in names.
Required for plotType = c("difference", "comparison").
Optional for plotType = "individual" (where it only determines
the row above/below which the names are plotted to the right/left
of the intervals; if unspecified, defaults to median rank);
or for plotType = "columns" (where it selects one column
to be highlighted by vertical lines, if specified).
Number between 0 and 1: confidence level for individual
(uncorrected) hypothesis tests and/or confidence intervals. E.g. with
plotType = "individual", confLevel = 0.9 will plot
individual 90% confidence intervals. If using GH = TRUE
and/or Bonferroni != "none", the Goldstein-Healy and/or Bonferroni
corrections will be applied to the confLevel baseline.
Which type of ranking plot to use. See vignettes for examples and details.
"individual" is used for usual individual
confidence intervals, with or without Goldstein-Healy adjustment and/or
(demi or full) Bonferroni corrections.
"difference" shows confidence intervals for the differences
between the reference area refName and all other areas.
"comparison" also compares the reference area refName
to all others, but using the "comparison intervals"
of Almond et al. (2000).
"columns" plots a grid of shaded columns, where each column
uses shading to report demi-Bonferroni-corrected significance tests
for comparing the reference area (labeled at the bottom of the column)
with all other areas.
Numeric, either 1 for usual confidence intervals,
or 2 for two-tiered intervals. 2 can only be used with
plotType = "individual", when either GH = TRUE
or Bonferroni != "none" or both.
In that case, the "inner tiers" run between each interval's cross-bars,
and the "outer tiers" run past the cross-bars
all the way to the ends of each interval.
One of the tiers will show uncorrected
confLevel*100% confidence intervals,
and the other tier will show the Golstein-Healy and/or Bonferroni
adjusted intervals. A legend will show which tier is which;
usually Goldstein-Healy alone gives shorter intervals (inner tier),
but Bonferroni corrections make them into longer intervals (outer tier).
Logical, for whether or not to plot adjusted
confidence intervals at an "average" confLevel*100%
confidence level as in Goldstein and Healy (1995).
Can only be used with plotType = "individual".
Whether and how to correct for multiple comparisons by a
Bonferroni correction to the confidence level of the tests or intervals.
"none" performs no correction; "demi" corrects for
comparing one reference area to all n-1 other areas; and
"full" corrects for comparing all possible choose(n-1, 2)
pairs of areas.
If GH = TRUE, the Goldstein-Healy adjustment
is performed first, and any Bonferroni correction is applied afterwards.
Settings "none" and "full" can only be used
with plotType = "individual";
all other plot types use the setting "demi".
Logical, for whether or not to format text for tikz plotting.
Character expansion factor for the points use to plot each area's point estimate, and for the text used to plot each area's name next to its interval.
Numeric height of the cross-bars on interval endpoints
(or inner tiers, if tiers = 2). The function tries to leave
a reasonable amount of space between intervals plotted in different rows,
but sometimes it may help to adjust tickWidth manually.
Numeric multiple by which to expand the range of the data
when setting the x-axis limits. The function tries to leave sufficient room
for plotting margins of error and names next to each area,
but sometimes it may help to adjust rangeFactor manually.
Numeric amount by which to shift the text of names
past the interval endpoints when plotting. Positive values shift outwards
(towards the edges of the plot); negative values shift inwards.
The x and y co-ordinates used to position the legend;
see legend for details on specifying x by keyword.
String, or string vector, with legend text. By default,
each plot type adds informative legend text, but the user may override.
To remove legends entirely, set legendText=NA.
Positive number for the line width of regular lines.
Used for all intervals when plotType = "individual",
or for intervals not significantly different from the reference area
when plotType = c("difference", "comparison").
Positive number for the line width of bold lines.
Used for intervals significantly different from the reference area
when plotType = c("difference", "comparison").
Number for how many lines below bottom axis to display
"theta" or other default x-axis labels (which depend on plotType).
Vector of 2 numbers for x-axis limits. If NULL,
will be automatically set using range of data
expanded by rangeFactor.
Users may wish to modify this code and write
their own plot function, which can be swapped into figureFunction
within RankPlotWithTable. Be aware that
RankPlotWithTable uses layout to arrange
the table and plot side-by-side, so layout cannot be used within
a new figureFunction.
See Goldstein and Healy (1995) for details on the
"average" confidence level procedure used when GH = TRUE.
See Almond et al. (2000) for details
on the "comparison intervals" procedure.
Almond, R.G., Lewis, C., Tukey, J.W., and Yan, D. (2000). "Displays for Comparing a Given State to Many Others," The American Statistician, vol. 54, no. 2, 89-93.
Goldstein, H. and Healy, M.J.R. (1995). "The Graphical Presentation of a Collection of Means," JRSS A, vol. 158, no. 1, 175-177.
# NOT RUN {
# Plot of 90% confidence intervals for differences
# between each state and Colorado, with demi-Bonferroni correction,
# for US states' mean travel times to work, from the 2011 ACS
data(TravelTime2011)
with(TravelTime2011,
RankPlot(est = Estimate.2dec, se = SE.2dec,
names = Abbreviation, refName = "CO",
confLevel = 0.90, cex = 0.6,
plotType = "difference"))
# }
Run the code above in your browser using DataCamp Workspace