Package 'forplot'

Demonstration data set

Description

Simulated summary data from 10 outcomes to be presented in a forst plot. Each row represents the summary of one outcome variable for two treatment groups with columns for the variable name (vlabel), number of observations and mean (sd) for each group (n1, n2, n3 and n4), the difference between groups (beta), with 95% CI (beta_lci and beta_uci), and a p-value (p1)

Usage

forplotdata

Format

A data frame with 9 columns: vlabel, n1, n2, n3, n4, beta, beta_lci, beta_uci and p1.

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forest

Description

produces forest plots

Usage

fplot(
  dat,
  nrows = 1,
  ncols = NA,
  nns = NA,
  lheights = c(0.1, 1, 0.05),
  lwidths = NA,
  y.at = NA,
  font = NA,
  arrow = TRUE,
  arrow_length = 0.05,
  arrow_angle = 30,
  cap_length = 0,
  shift_label_col = 0,
  center_label_col = NA,
  shift_textbeta_col = 0,
  shift_ymax = 0,
  shift_ymin = 0,
  xlab = NA,
  xlab_text = NA,
  xlim = NA,
  xlab_cex = 0.6,
  xlab_line = 0,
  tck = -0.04,
  shift_xaxis = 0,
  xtitle = NA,
  lwd = 1,
  pcol = rgb(0.1, 0.1, 0.1, 0.2),
  lscale = FALSE,
  ps = NA,
  header = NA,
  ref = list(x = NA, extend = 0, lty = 2, col = "grey50", lwd = lwd),
  bottomline = NA,
  headline = NA,
  headline_pos = c(0, 1),
  beta2 = NULL,
  xlab2 = NA,
  xlab_text2 = NA,
  xlim2 = NA,
  xtitle2 = NA,
  ...
)

Arguments

dat	data frame with variables called vlabel (labels), nx with x=1,2,... (num or chr columns with strings, e.g. number of observations or descriptives), beta, beta_lci, beta_uci (num columns with point estimates and confidence interval) optionally beta_format (num or chr column with formatted text to be printed along forest, generated from beta if not given) px with x=1,2,.. (num or chr columns with p-value(s))
nrows	number of rows, setting for layout, default is 1
ncols	number of columns, setting for layout, typically derived from the data
nns	number of n columns, derived from data if not given
lheights	lheights: relative height of rows, length is typically 3 (header, data ,footer)
lwidths	lwidths: relative width of columns, length correpsonds to columns in forest plus 2 (left and right margin)
y.at	position of lines, 1:nrow(dat) by default
font	font for variable vlabel, length has to correspond to rows of dat, default is rep(1,nrow(dat))
arrow	logical, whether to use arrows if xlim does not include confidence interval limits
arrow_length	length of the edges of the arrow head (in inches)
arrow_angle	angle from the shaft of the arrow to the edge of the arrow head
cap_length	length of the confidence interval cap, 0 if none
shift_label_col	inset of labels in the first column, default is 0
center_label_col	centering of label in first column
shift_textbeta_col	inset of formatted effects (beta_format)
shift_ymax	down-shift of maximal y-value, smaller space to top
shift_ymin	up-shift of minimal y-value, smaller space to bottom
xlab	position of labels for x-axis, derived from beta by default
xlab_text	text at the labels, derived from beta by default
xlim	limits for x-axis in forest plots, derived from beta by default
xlab_cex	size of x-axis labels (not title)
xlab_line	position of x-axis label (not title)
tck	x-axis tick length
shift_xaxis	shift position of x-axis
xtitle	x axis title and format, list with x (xpos), y (ypos), textr and textl (text at the right/left side), cex (text size)
lwd	line widths
pcol	color if symbols are used, not active
lscale	logicial, beta given on log scale, use exp to format beta, default is FALSE
ps	points for plot, list with pch, cex, and col
header	for table, either a character vector or a list with any of x (vector with xpos), y (single y-position), text (character vector with labels), cex (text size), the list can be >1 to define more than one header line
ref	reference line, list with x (xposition), extend (extension on top), lty (line type), col (line color), lwd (line width)
bottomline	line at the bottom if not NA
headline	line for header if not NA, 1 for one line at the bottom, 2 for a line at the bottom and top
headline_pos	vector with position of lower and upper headline (if applicable), default c(0,1)
beta2	if not NULL a second forest is generated, needs variables beta2, beta_lci2 and beta_uci2 in dat
xlab2	see xlab for 2nd forest
xlab_text2	see xlab_text for 2nd forest
xlim2	see xlim for 2nd forest
xtitle2	see xtitle for 2nd forest
...	options passed to ff_ci for formatting the effects (if beta_format not given)

Details

required input is a data frame with a column called vlabel, beta, beta_lci and beta_uci.

Value

forest plot

Examples

data(forplotdata)
# Minimal example
 fplot(dat=forplotdata[,c("vlabel","beta","beta_lci","beta_uci")])

# Standard example
fplot(dat=forplotdata)

# Set widths and heights
lwidths<-c(0.05,0.5,0.2,0.8,0.2,0.8,1.2,1.2,0.5,0.05)
lheights<-c(0.14,1,0.08)
fplot(dat=forplotdata,lwidths=lwidths,lheights=lheights)


# Include header:
header<-c("","Group1\nN","Group0\nmean (sd)","Group2\nN","Group2\nmean (sd)",
"Mean difference\n95% CI","","P-value")
fplot(dat=forplotdata,lwidths=lwidths,lheights=lheights,header=header)

header<-list(list(y=0.7,
	text=c("Group1","Group2","Mean difference (95% CI)","P-value"),
	x=c(0.10,0.32,0.7,0.98)),
	list(y=0.3,text=c("N","mean (sd)","N","mean (sd)"),
	x=c(0.07,0.18,0.28,0.38)))
fplot(dat=forplotdata,header=header,lwidths=lwidths,lheights=lheights)

# Reference line and xlim
xtitle<-list(x=0.86,y=0.2,textl="Group 1 better  ",textr="  Group 2 better")
fplot(dat=forplotdata,header=header,lwidths=lwidths,lheights=lheights,
xtitle=xtitle,ref=list(x=0),xlim=c(-1,0.5))

# Shift x-axis, labels and title
xtitle<-list(x=0.86,y=0.6,textl="Group 1 better  ",textr="  Group 2 better")
fplot(dat=forplotdata,header=header,lwidths=lwidths,lheights=lheights,
ref=list(x=0,col=2,extend=2),
xtitle=xtitle,xlim=c(-1,0.5),shift_xaxis=0.3,xlab_line=-0.8)

# Lines at header and bottom
fplot(dat=forplotdata,header=header,lwidths=lwidths,lheights=lheights,
 	ref=list(x=0,col=2,extend=2),
	xtitle=xtitle,xlim=c(-1,0.5),shift_xaxis=0.3,xlab_line=-0.8,
	headline=2,bottomline=1)

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