plotEst: Plot estimates with confidence limits (forest plot)

In Epi: Statistical Analysis in Epidemiology

Plot estimates with confidence limits (forest plot)

Description

Plots parameter estimates with confidence intervals, annotated with parameter names. A dot is plotted at the estimate and a horizontal line extending from the lower to the upper limit is superimposed.

Usage

plotEst( ests,
            y = dim(ests)[1]:1,
          txt = rownames(ests),
       txtpos = y,
         ylim = range(y)-c(0.5,0),
         xlab = "",
         xtic = nice(ests[!is.na(ests)], log = xlog),
         xlim = range( xtic ),
         xlog = FALSE,
          pch = 16,
          cex = 1,
          lwd = 2,
          col = "black",
      col.txt = "black",
     font.txt = 1,
    col.lines = col,
   col.points = col,
         vref = NULL,
         grid = FALSE,
     col.grid = gray(0.9),
  restore.par = TRUE,
          ... )

linesEst( ests, y = dim(ests)[1]:1, pch = 16, cex = 1, lwd = 2,
          col="black", col.lines=col, col.points=col, ... )

pointsEst( ests, y = dim(ests)[1]:1, pch = 16, cex = 1, lwd = 2,
          col="black", col.lines=col, col.points=col, ... )

Arguments

ests	Matrix with three columns: Estimate, lower limit, upper limit. If a model object is supplied, ci.lin is invoked for this object first.
y	Vertical position of the lines.
txt	Annotation of the estimates. Either a character vector or an expression vector.
txtpos	Vertical position of the text. Defaults to y.
ylim	Extent of the vertical axis.
xlab	Annotation of the horizontal axis.
xtic	Location of tickmarks on the x-axis.
xlim	Extent of the x-axis.
xlog	Should the x-axis be logarithmic?
pch	What symbol should be used?
cex	Expansion of the symbol.
col	Colour of the points and lines.
col.txt	Colour of the text annotating the estimates.
font.txt	Font for the text annotating the estimates.
col.lines	Colour of the lines.
col.points	Colour of the symbol.
lwd	Thickness of the lines.
vref	Where should vertical reference line(s) be drawn?
grid	If TRUE, vertical gridlines are drawn at the tickmarks. If a numerical vector is given vertical lines are drawn at grid.
col.grid	Colour of the vertical gridlines
restore.par	Should the graphics parameters be restored? If set to FALSE the coordinate system will still be available for additional plotting, and par("mai") will still have the very large value set in order to make room for the labelling of the estimates.
...	Arguments passed on to ci.lin when a model object is supplied as ests.

Details

plotEst makes a news plot, whereas linesEst and pointsEst (identical functions) adds to an existing plot.

If a model object of class "glm", "coxph", "clogistic" or "gnlm" is supplied the argument xlog defaults to TRUE, and exponentiated estimates are extracted by default.

Value

NULL

Author(s)

Bendix Carstensen, [e-mail], http://bendixcarstensen.com

See Also

ci.lin

Examples

# Bogus data and a linear model
f <- factor( sample( letters[1:5], 100, replace=TRUE ) )
x <- rnorm( 100 )
y <- 5 + 2 * as.integer( f ) + 0.8 * x + rnorm(100) * 2
m1 <- lm( y ~ f )

# Produce some confidence intervals for contrast to first level
( cf <- ci.lin( m1, subset=-1 )[,-(2:4)] )

# Plots with increasing amounts of bells and whistles
par( mfcol=c(3,2), mar=c(3,3,2,1) )
plotEst( cf )
plotEst( cf, grid=TRUE, cex=2, lwd=3 )
plotEst( cf, grid=TRUE, cex=2, col.points="red", col.lines="green" )
plotEst( cf, grid=TRUE, cex=2, col.points="red", col.lines="green",
             xlog=TRUE, xtic=c(1:8), xlim=c(0.8,6) )
rownames( cf )[1] <- "Contrast to fa:\n fb"
plotEst( cf, grid=TRUE, cex=2, col.points=rainbow(4),
                                col.lines=rainbow(4), vref=1 )
#
etxt <- expression("Plain text, qouted",
                   "combined with maths:"*sqrt(a)*phi[c],
                   f^d*"  Hb"*A[1][c],
                   eff^e*"  kg/"*m^2)
plotEst( cf, txt=etxt, grid=TRUE, cex=2, col.points=rainbow(4),
                                         col.lines =rainbow(4), vref=1 )
  

Epi documentation built on Oct. 1, 2024, 5:07 p.m.