Epi: plotEst – R documentation

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plotEst

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, b@bxc.dk, http://bendixcarstensen.com

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

Statistical Analysis in Epidemiology

v2.44

GPL-2

Authors

Bendix Carstensen [aut, cre], Martyn Plummer [aut], Esa Laara [ctb], Michael Hills [ctb]

Initial release

2021-02-28