fpDrawCI: Draw standard confidence intervals

In forestplot: Advanced Forest Plot Using 'grid' Graphics

Draw standard confidence intervals

Description

A function that is used to draw the different confidence intervals for the non-summary lines. Use the fpDrawNormalCI function as a template if you want to make your own funky line + marker.

Usage

fpDrawNormalCI(
  lower_limit,
  estimate,
  upper_limit,
  size,
  y.offset = 0.5,
  clr.line,
  clr.marker,
  lwd,
  lty = 1,
  vertices,
  vertices.height = 0.1,
  shapes_gp = fpShapesGp(),
  shape_coordinates = structure(c(1, 1), max.coords = c(1, 1)),
  ...
)

fpDrawDiamondCI(
  lower_limit,
  estimate,
  upper_limit,
  size,
  y.offset = 0.5,
  clr.line,
  clr.marker,
  lwd,
  lty = 1,
  vertices,
  vertices.height = 0.1,
  shapes_gp = fpShapesGp(),
  shape_coordinates = structure(c(1, 1), max.coords = c(1, 1)),
  ...
)

fpDrawCircleCI(
  lower_limit,
  estimate,
  upper_limit,
  size,
  y.offset = 0.5,
  clr.line,
  clr.marker,
  lwd,
  lty = 1,
  vertices,
  vertices.height = 0.1,
  shapes_gp = fpShapesGp(),
  shape_coordinates = structure(c(1, 1), max.coords = c(1, 1)),
  ...
)

fpDrawPointCI(
  lower_limit,
  estimate,
  upper_limit,
  size,
  y.offset = 0.5,
  clr.line,
  clr.marker,
  lwd,
  lty = 1,
  vertices,
  vertices.height = 0.1,
  pch = 1,
  shapes_gp = fpShapesGp(),
  shape_coordinates = structure(c(1, 1), max.coords = c(1, 1)),
  ...
)

fpDrawSummaryCI(
  lower_limit,
  estimate,
  upper_limit,
  size,
  col,
  y.offset = 0.5,
  shapes_gp = fpShapesGp(),
  shape_coordinates = structure(c(1, 1), max.coords = c(1, 1)),
  ...
)

fpDrawBarCI(
  lower_limit,
  estimate,
  upper_limit,
  size,
  col,
  y.offset = 0.5,
  shapes_gp = fpShapesGp(),
  shape_coordinates = structure(c(1, 1), max.coords = c(1, 1)),
  ...
)

Arguments

lower_limit	The lower limit of the confidence line. A native numeric variable that can actually be outside the boundaries. If you want to see if it is outside then convert it to 'npc' and see if the value ends up more than 1 or less than 0. Here's how you do the conversion: convertX(unit(upper_limit, "native"), "npc", valueOnly = TRUE) and the convertX together with unit is needed to get the right values while you need to provide the valueOnly as you cannot compare a unit object.
estimate	The estimate indicating the placement of the actual box. Note, this can also be outside bounds and is provided in a numeric format the same way as the lower_limit.
upper_limit	The upper limit of the confidence line. See lower_limit for details.
size	The actual size of the box/diamond/marker. This provided in the 'snpc' format to generate a perfect marker. Although you can provide it alternative units as well, this is useful for the legends to work nicely.
y.offset	If you have multiple lines they need an offset in the y-direction.
clr.line	The color of the line.
clr.marker	The color of the estimate marker
lwd	Line width, see gpar
lty	Line type, see gpar
vertices	Set this to TRUE if you want the ends of the confidence intervals to be shaped as a T. This is set default to TRUE if you have any other line type than 1 since there is a risk of a dash occurring at the very end, i.e. showing incorrectly narrow confidence interval.
vertices.height	The height hoft the vertices. Defaults to npc units corresponding to 10% of the row height.
shapes_gp	A set of graphical parameters of class fpShapesGp
shape_coordinates	A vector of length 2 the label (first item of the vector) and the band (second item of the vector) of the confidence interval. This is used together with shapes_gp to retrieve graphical parameters for that item.
...	Allows additional parameters for sibling functions
pch	Type of point see grid.points for details
col	The color of the summary object

Value

void The function outputs the line using grid compatible functions and does not return anything.

Author(s)

Max Gordon, Thomas Lumley

See Also

Other forestplot functions: forestplot(), fpColors(), fpLegend(), fpShapesGp(), fp_add_lines(), fp_decorate_graph(), fp_insert_row(), fp_set_style(), fp_set_zebra_style()

Examples

ask <- par(ask = TRUE)

test_data <- data.frame(
  coef1 = c(1, 1.59, 1.3, 1.24),
  coef2 = c(1, 1.7, 1.4, 1.04)
)

test_data$low1 <- test_data$coef1 - 1.96 * c(0, .2, .1, .15)
test_data$high1 <- test_data$coef1 + 1.96 * c(0, .2, .1, .15)

test_data$low2 <- test_data$coef2 - 1.96 * c(0, .1, .15, .2)
test_data$high2 <- test_data$coef2 + 1.96 * c(0, .1, .15, .2)

col_no <- grep("coef", colnames(test_data))
row_names <- list(
  list("Category 1", "Category 2", "Category 3", expression(Category >= 4)),
  list(
    "ref",
    substitute(
      expression(bar(x) == val),
      list(val = round(rowMeans(test_data[2, col_no]), 2))
    ),
    substitute(
      expression(bar(x) == val),
      list(val = round(rowMeans(test_data[3, col_no]), 2))
    ),
    substitute(
      expression(bar(x) == val),
      list(val = round(rowMeans(test_data[4, col_no]), 2))
    )
  )
)

coef <- with(test_data, cbind(coef1, coef2))
low <- with(test_data, cbind(low1, low2))
high <- with(test_data, cbind(high1, high2))

# Change all to diamonds
forestplot(row_names, coef, low, high,
  fn.ci_norm = fpDrawDiamondCI,
  title = "Cool study",
  zero = 1, boxsize = 0.25,
  col = fpColors(
    box = c("royalblue", "gold"),
    line = c("darkblue", "orange"),
    summary = c("darkblue", "red")
  ),
  xlab = "The estimates",
  new_page = TRUE,
  legend = c("Treatment", "Placebo"),
  legend_args = fpLegend(
    title = "Group",
    pos = list("topright", inset = .1),
    r = unit(.1, "snpc"),
    gp = gpar(col = "#CCCCCC", lwd = 1.5)
  )
)

# Change first to diamonds
forestplot(row_names, coef, low, high,
  fn.ci_norm = c(
    "fpDrawDiamondCI",
    rep("fpDrawNormalCI",
      times = nrow(coef) - 1
    )
  ),
  title = "Cool study",
  zero = 1, boxsize = 0.25,
  col = fpColors(
    box = c("royalblue", "gold"),
    line = c("darkblue", "orange"),
    summary = c("darkblue", "red")
  ),
  xlab = "The estimates",
  new_page = TRUE,
  legend = c("Treatment", "Placebo"),
  legend_args = fpLegend(
    title = "Group",
    pos = list("topright", inset = .1),
    r = unit(.1, "snpc"),
    gp = gpar(col = "#CCCCCC", lwd = 1.5)
  )
)

# You can also use a list with the actual functions
# as long as it is formatted [[row]][[column]]
# Note: if you have a non-square input then
# the software will reformat [[col]][[row]]
# to [[row]][[col]]
forestplot(row_names, coef, low, high,
  fn.ci_norm = list(
    list(fpDrawDiamondCI, fpDrawCircleCI),
    list(fpDrawNormalCI, fpDrawNormalCI),
    list(fpDrawNormalCI, fpDrawCircleCI),
    list(fpDrawNormalCI, fpDrawNormalCI)
  ),
  title = "Cool study",
  zero = 1, boxsize = 0.25,
  col = fpColors(
    box = c("royalblue", "gold"),
    line = c("darkblue", "orange"),
    summary = c("darkblue", "red")
  ),
  xlab = "The estimates",
  new_page = TRUE,
  legend = c("Treatment", "Placebo"),
  legend_args = fpLegend(
    title = "Group",
    pos = list("topright", inset = .1),
    r = unit(.1, "snpc"),
    gp = gpar(col = "#CCCCCC", lwd = 1.5)
  )
)

par(ask = ask)

forestplot documentation built on Oct. 11, 2024, 5:07 p.m.