bmeta (version 0.1.2)

forest.plot: Function to create forest plot

Description

A function to call package forestplot from R library and produce forest plot using results from bmeta. The posterior estimate and credible interval for each study are given by a square and a horizontal line, respectively. The summary estimate is drawn as a diamond.

Usage

forest.plot(x,title=NULL,xlab=NULL,log=FALSE,study.label=NULL,clip=c(-3,3),
lines="black",box="blue",summary="orange",box.symb="box",label.cex=.8,
xlab.cex=1,ticks.cex=.8,...)

Arguments

x

a bmeta object with results of the model

title

title of the plot

xlab

title of the x-axis label

log

estimates on natural scale is displayed by default. If TRUE, log scale is used (i.e. log odds ratio, log incidence rate ratio). For continuous data, estimates are always presented on natural scale and users do not need to specify this argument.

study.label

label for each study and the summary estimate. See details.

clip

lower and upper limits for clipping credible intervals to arrows

lines

selects the colour for the lines of the intervals. If the extra option add.null is set to TRUE, then lines should be specified as a two-element vector. If the user fails to do so, bmeta will overwrite this setting and select suitable values.

box

selects the colour for mean study-specific estimates. If the extra option add.null is set to TRUE, then box should be specified as a two-element vector. If the user fails to do so, bmeta will overwrite this setting and select suitable values.

summary

selects the colour for the pooled estimate

box.symb

selects the symbol used to plot the mean. Options are "box" (default) or "circle"

label.cex

defines the size of the text for the label. Defaults at .8 of normal size

xlab.cex

defines the size of the text for the x-label. Defaults at 1 of the normal size

ticks.cex

defines the size of the text for the x-axis ticks. Defaults at .8 of the normal size

...

Additional arguments. Includes

- add.null = TRUE/FALSE. If set to true, adds a plot of the null (no-pooling model) - line.margin = the distance between lines in case multiple graphs are shown on the same plot - box.size = the size of the summary box - new.page = TRUE/FALSE. If set to true, then a new graph overwrite the existing one - zero (x-axis coordinate for zero line. If you provide a vector of length 2 it will print a rectangle instead of just a line. Default at 0 or 1 depending on log scale) - legend = a legend for the multi-graph plot (including the null/no-pooling model)

Examples

### Read and format the data (binary)
data = read.csv(url("http://www.statistica.it/gianluca/bmeta/Data-bin.csv"))

### List data for binary outcome 
data.list <- list(y0=data$y0,y1=data$y1,n0=data$n0,n1=data$n1) 

### Select fixed-effects meta-analysis with normal prior for binary data 
x <- bmeta(data.list, outcome="bin", model="std.norm", type="fix")

### Plot forest plot 
forest.plot(x)

### Plot forest plot on log scale 
forest.plot(x,log=TRUE)

### Select random-effects meta-analysis with t-distribution prior for binary
### data
x <- bmeta(data.list, outcome="bin", model="std.dt", type="ran")

### Plot 'two-line' forest plot showing estimates from both randome-effects 
### model and no-pooling effects model for comparison
forest.plot(x,add.null=TRUE,title="Two-line forestplot for comparison")


### Read and format the data (continuous)
data = read.csv(url("http://www.statistica.it/gianluca/bmeta/Data-ctns.csv"))

### List data for continuous outcome
data.list <- list(y0=data$y0,y1=data$y1,se0=data$se0,se1=data$se1)  

### Select fix-effects meta-analysis for studies reporting two arms separately
x <- bmeta(data=data.list,outcome="ctns",model="std.ta",type="fix")

### Define for individual studies
study.label <- c(paste0(data$study,", ",data$year),"Summary estimate")

### Produce forest plot with label for each study and control the lower and upper 
### limits for clipping credible intervals to arrows   
forest.plot(x,study.label=study.label,clip=c(-7,4))