plot.loddsratio: Plotting (Log) Odds Ratios

In vcd: Visualizing Categorical Data

Plotting (Log) Odds Ratios

Description

Produces a (conditional) line plot of extended (log) odds ratios.

Usage

## S3 method for class 'loddsratio'
plot(x, baseline = TRUE, gp_baseline = gpar(lty = 2),
     lines = TRUE, lwd_lines = 3,
     confidence = TRUE, conf_level = 0.95, lwd_confidence = 2,
     whiskers = 0, transpose = FALSE,
     col = NULL, cex = 0.8, pch = NULL,
     bars = NULL, gp_bars = gpar(fill = "lightgray", alpha = 0.5),
     bar_width = unit(0.05, "npc"),
             
     legend = TRUE, legend_pos = "topright", legend_inset = c(0, 0),
     legend_vgap = unit(0.5, "lines"),
     gp_legend_frame = gpar(lwd = 1, col = "black"),
     gp_legend_title = gpar(fontface = "bold"),
     gp_legend = gpar(), legend_lwd = 1, legend_size = 1,
             
     xlab = NULL, ylab = NULL, xlim = NULL, ylim = NULL,
     main = NULL, gp_main = gpar(fontsize = 12, fontface = "bold"),
     newpage = TRUE, pop = FALSE, return_grob = FALSE,
     add = FALSE, prefix = "", ...)
## S3 method for class 'loddsratio'
lines(x, legend = FALSE, confidence = FALSE, cex = 0, ...)

Arguments

x	an object of class loddsratio.
baseline	if TRUE, a dashed line is plotted at a value of 1 (in case of odds) or 0 (in case of log-odds).
gp_baseline	object of class "gpar" used for the baseline.
lines	if TRUE, the points are connected by lines (only sensible if the variable represented by the x-axis is ordinal).
lwd_lines	Width of the connecting lines (in char units).
confidence	logical; shall confindence intervals be plotted?
conf_level	confidence level used for confidence intervals.
lwd_confidence	Line width of the confidence interval bars (in char units).
whiskers	width of the confidence interval whiskers.
transpose	if TRUE, the plot is transposed.
col	character vector specifying the colors of the fitted lines, by default chosen with rainbow_hcl.
cex	size of the plot symbols (in lines).
pch	character or numeric vector of symbols used for plotting the (possibly conditioned) observed values, recycled as needed.
bars	logical; shall bars be plotted additionally to the points? Defaults to TRUE in case of only one conditioning variable.
gp_bars	object of class "gpar" used for the bars.
bar_width	Width of the bars, if drawn.
legend	logical; if TRUE (default), a legend is drawn.
legend_pos	numeric vector of length 2, specifying x and y coordinates of the legend, or a character string (e.g., "topleft", "center" etc.). Defaults to "topleft" if the fitted curve's slope is positive, and "topright" else.
legend_inset	numeric vector or length 2 specifying the inset from the legend's x and y coordinates in npc units.
legend_vgap	vertical space between the legend's line entries.
gp_legend_frame	object of class "gpar" used for the legend frame.
gp_legend_title	object of class "gpar" used for the legend title.
gp_legend	object of class "gpar" used for the legend defaults.
legend_lwd	line width used in the legend for the different groups.
legend_size	size used for the group symbols (in char units).
xlab	label for the x-axis. Defaults to "Strata" if transpose is FALSE.
ylab	label for the y-axis. Defaults to "Strata" if transpose is TRUE.
xlim	x-axis limits. Ignored if transpose is FALSE.
ylim	y-axis limits. Ignored if transpose is TRUE.
main	user-specified main title.
gp_main	object of class "gpar" used for the main title.
newpage	logical; if TRUE, the plot is drawn on a new page.
pop	logical; if TRUE, all newly generated viewports are popped after plotting.
return_grob	logical. Should a snapshot of the display be returned as a grid grob?
add	logical; should the plot added to an existing log odds ratio plot?
prefix	character string used as prefix for the viewport name.
...	other graphics parameters (see par).

Details

The function basically produces conditioned line plots of the (log) odds ratios structure provided in x.

The lines method can be used to overlay different plots (for example, observed and expected values).

cotabplot can be used for stratified analyses (see examples).

Value

if return_grob is TRUE, a grob object corresponding to the plot. NULL (invisibly) else.

Author(s)

David Meyer [e-mail]

References

M. Friendly (2000), Visualizing Categorical Data. SAS Institute, Cary, NC.

See Also

loddsratio

Examples

## 2 x 2 x k cases
data(CoalMiners, package = "vcd")
lor_CM <- loddsratio(CoalMiners)
plot(lor_CM)
lor_CM_df <- as.data.frame(lor_CM)

# fit linear models using WLS
age <- seq(20, 60, by = 5)
lmod <- lm(LOR ~ age, weights = 1 / ASE^2, data = lor_CM_df)
grid.lines(seq_along(age), fitted(lmod), gp = gpar(col = "blue", lwd = 2), default.units = "native")
qmod <- lm(LOR ~ poly(age, 2), weights = 1 / ASE^2, data = lor_CM_df)
grid.lines(seq_along(age), fitted(qmod), gp = gpar(col = "red", lwd = 2), default.units = "native")

## 2 x k x 2
lor_Emp <-loddsratio(Employment)
plot(lor_Emp)

## 4 way tables 
data(Punishment, package = "vcd")
mosaic(attitude ~ age + education + memory, data = Punishment,
highlighting_direction="left", rep = c(attitude = FALSE))

# visualize the log odds ratios, by education
plot(loddsratio(~ attitude + memory | education, data = Punishment))

# visualize the log odds ratios, by age
plot(loddsratio(~ attitude + memory | age, data = Punishment))

# visualize the log odds ratios, by age and education
plot(loddsratio(~ attitude + memory | age + education, data = Punishment))

# same, transposed
plot(loddsratio(~ attitude + memory | age + education, data = Punishment), transpose = TRUE)

# alternative visualization methods
image(loddsratio(Freq ~ ., data = Punishment))
tile(loddsratio(Freq ~ ., data = Punishment))

## cotabplots for more complex tables
cotabplot(Titanic, cond = c("Age","Sex"), panel = cotab_loddsratio)

cotabplot(Freq ~ opinion + grade + year | gender, data = JointSports, panel = cotab_loddsratio)
cotabplot(Freq ~ opinion + grade | year + gender, data = JointSports, panel = cotab_loddsratio)

vcd documentation built on Sept. 17, 2024, 1:08 a.m.