coefplot: Plot model coefficients

In MuMIn: Multi-Model Inference

Plot model coefficients

Description

Produce dot-and-whisker plot of the model(-averaged) coefficients, with confidence intervals

Usage

coefplot(
  x, lci, uci,
  labels = NULL, width = 0.15,
  shift = 0, horizontal = TRUE,
  main = NULL, xlab = NULL, ylab = NULL,
  xlim = NULL, ylim = NULL,
  labAsExpr = TRUE, mar.adj = TRUE, lab.line = 0.5, 
  lty = par("lty"), lwd = par("lwd"), pch = 21,
  col = par("col"), bg = par("bg"),
  dotcex = par("cex"), dotcol = col,
  staplelty = lty, staplelwd = lwd, staplecol = col,
  zerolty = "dotted", zerolwd = lwd, zerocol = "gray",
  las = 2, ann = TRUE, axes = TRUE, add = FALSE,
  type = "p",
  ...
)

## S3 method for class 'averaging'
plot(
  x,
  full = TRUE, level = 0.95, intercept = TRUE,
  parm = NULL, labels = NULL, width = 0.1,
  shift = max(0.2, width * 2.1 + 0.05),
  horizontal = TRUE, 
  xlim = NULL, ylim = NULL,
  main = "Model-averaged coefficients",
  xlab = NULL, ylab = NULL, 
  add = FALSE,
  ...
)

Arguments

x	either a (possibly named) vector of coefficients (for coefplot), or an "averaging" object.
lci, uci	vectors of lower and upper confidence intervals. Alternatively a two-column matrix with columns containing confidence intervals, in which case uci is ignored.
labels	optional vector of coefficient names. By default, names of x are used for labels.
width	width of the staples (= end of whisker).
shift	the amount of perpendicular shift for the dots and whiskers. Useful when adding to an existing plot.
horizontal	logical indicating if the plots should be horizontal; defaults to TRUE.
main	an overall title for the plot: see title.
xlab, ylab	x- and y-axis annotation. Can be suppressed by ann=FALSE.
xlim, ylim	optional, the x and y limits of the plot.
labAsExpr	logical indicating whether the coefficient names should be transformed to expressions to create prettier labels (see plotmath)
mar.adj	logical indicating whether the (left or lower) margin should be expanded to fit the labels
lab.line	margin line for the labels
lty, lwd, pch, col, bg	default line type, line width, point character, foreground colour for all elements, and background colour for open symbols.
dotcex, dotcol	dots point size expansion and colour.
staplelty, staplelwd, staplecol	staple line type, width, and colour.
zerolty, zerolwd, zerocol	zero-line type, line width, colour. Setting zerolty to NA suppresses the line.
las	the style of labels for coefficient names. See par.
ann	logical indicating if axes should be annotated (by xlab and ylab).
axes	a logical value indicating whether both axes should be drawn on the plot.
add	logical, if true add to current plot.
type	if "n", the plot region is left empty, any other value causes the plot being drawn.
...	additional arguments passed to coefplot or more graphical parameters.
full	a logical value specifying whether the “full” model-averaged coefficients are plotted. If FALSE, the “subset”-averaged coefficients are plotted, and both types if NA. See model.avg.
level	the confidence level required.
intercept	logical indicating if intercept should be included in the plot
parm	a specification of which parameters are to be plotted, either a vector of numbers or a vector of names. If missing, all parameters are considered.

Details

Plot model(-averaged) coefficients with confidence intervals.

Value

An invisible matrix containing coordinates of points and whiskers, or, a two-element list of such, one for each coefficient type in plot.averaging when full is NA.

Author(s)

Kamil Bartoń

Examples

fm <- glm(Prop ~ dose + I(dose^2) + log(dose) + I(log(dose)^2),
  data = Beetle, family = binomial, na.action = na.fail)
ma <- model.avg(dredge(fm))

# default coefficient plot:
plot(ma, full = NA, intercept = FALSE)

# Add colours per coefficient type
# Replicate each colour n(=number of coefficients) times
clr <- c("black", "red2")
i <- rep(1:2, each = length(coef(ma)) - 1)
plot(ma, full = NA, intercept = FALSE,
   pch = 22, dotcex = 1.5,
   col = clr[i], bg = clr[i],
   lwd = 6, lend = 1, width = 0, horizontal = 0)

# Use `type = "n"` and `add` argument to e.g. add grid beneath the figure
plot(ma, full = NA, intercept = FALSE,
   width = 0, horizontal = FALSE, zerolty = NA, type = "n")
grid()
plot(ma, full = NA, intercept = FALSE,
   pch = 22, dotcex = 1.5,
   col = clr[i], bg = clr[i],
   lwd = 6, lend = 1, width = 0, horizontal = FALSE, add = TRUE)

MuMIn documentation built on June 22, 2024, 6:44 p.m.