coat (version 0.2.0)

print.coat: Methods for Conditional Method Agreement Trees (COAT)

Description

Extracting information from or visualization of conditional method agreement trees. Visualizations use trees with Bland-Altman plots in terminal nodes, drawn either via grid graphics directly or via ggplot2.

Usage

# S3 method for coat
print(
  x,
  digits = 2L,
  header = TRUE,
  footer = TRUE,
  title = "Conditional method agreement tree (COAT)",
  ...
)
# S3 method for coat
coef(object, node = NULL, drop = TRUE, ...)
# S3 method for coat
plot(x, terminal_panel = node_baplot, tnex = 2, drop_terminal = TRUE, ...)
node_baplot(
  obj,
  level = 0.95,
  digits = 2,
  pch = 1,
  cex = 0.5,
  col = 1,
  linecol = 4,
  lty = c(1, 2),
  bg = "white",
  confint = FALSE,
  B = 500,
  cilevel = 0.95,
  cicol = "lightgray",
  xscale = NULL,
  yscale = NULL,
  ylines = 3,
  id = TRUE,
  mainlab = NULL,
  gp = gpar()
)
# S3 method for coat
autoplot(
  object,
  digits = 2,
  xlim.max = NULL,
  level = 0.95,
  label.align = 0.95,
  ...
)

Value

The print() method returns the printed object invisibly. The coef() method returns the vector (for a single node) or matrix (for multiple nodes) of estimated parameters (bias and standard deviation). The plot() method returns NULL. The node_baplot() panel-generating function returns a function that can be plugged into the plot() method. The autoplot() method returns a ggplot object.

Arguments

x, object, obj

a coat object as returned by coat.

digits

numeric. Number of digits used for rounding the displayed coefficients or limits of agreement.

header, footer

logical. Should a header/footer be printed for the tree?

title

character with the title for the tree.

...

further arguments passed to methods.

node

integer. ID of the node for which the Bland-Altman parameters (coefficients) should be extracted.

drop

logical. Should the matrix attribute be dropped if the parameters from only a single node are extracted?

terminal_panel

a panel function or panel-generating function passed to plot.party. By default, node_baplot is used to generate a suitable panel function for drawing Bland-Altman plots based on the the provided coat object. It can be customized using the tp_args argument (passed through ...).

tnex

numeric specification of the terminal node extension relative to the inner nodes (default is twice the size).

drop_terminal

logical. Should all terminal nodes be "dropped" to the bottom row?

level

numeric level for the limits of agreement.

pch, cex, col, linecol, lty, bg

graphical parameters for the scatter plot and limits of agreement in the Bland-Altman plot (scatter plot character, character extension, plot color, line color, line types, and background color).

confint

logical. Should nonparametric bootstrap percentile confidence intervals be plotted?

B

numeric. Number of bootstrap samples to be used if confint = TRUE.

cilevel

numeric. Level of the confidence intervals if confint = TRUE.

cicol

color specification for the confidence intervals if confint = TRUE.

xscale, yscale

numeric specification of scale of x-axis and y-axis, respectively. By default the range of all scatter plots and limits of agreement across all nodes are used.

ylines

numeric. Number of lines for spaces in y-direction.

id

logical. Should node IDs be plotted?

mainlab

character or function. An optional title for the plots. Either a character or a function(id, nobs).

gp

grid graphical parameters.

xlim.max

numeric. Optional value to define the upper limit of the x-axis.

label.align

numeric. Specification between 0 and 1 for the alignment of labels relative to the plot width or xlim.max.

Details

Various methods are provided for trees fitted by coat, in particular print, plot (via grid/partykit), autoplot (via ggplot2/ggparty), coef. The plot method draws Bland-Altman plots in the terminal panels by default, using the function node_baplot. The autoplot draws very similar plots by customizing the geom_node_plot "from scratch".

In addition to these dedicated coat methods, further methods are inherited from ctree or mob, respectively, depending on which type of coat was fitted.

Examples

 if(!requireNamespace("MethComp")) {
  if(interactive() || is.na(Sys.getenv("_R_CHECK_PACKAGE_NAME_", NA))) {
    stop("the MethComp package is required for this example but is not installed")
  } else q() }

## package and data (reshaped to wide format)
library("coat")
data("scint", package = "MethComp")
scint_wide <- reshape(scint, v.names = "y", timevar = "meth", idvar = "item", direction = "wide")

## conditional method agreement tree
tr <- coat(y.DTPA + y.DMSA ~ age + sex, data = scint_wide)

## illustration of methods (including some customization)

## printing
print(tr)
print(tr, header = FALSE, footer = FALSE)

## extracting Bland-Altman parameters
coef(tr)
coef(tr, node = 1)

## visualization (via grid with node_baplot)
plot(tr)
plot(tr, ip_args = list(id = FALSE),
  tp_args = list(col = "slategray", id = FALSE, digits = 3, pch = 19))

## visualization (via ggplot2 with ggparty)
library("ggplot2")
autoplot(tr)
autoplot(tr, digits = 3) + ggtitle("Conditional method agreement tree") +
  theme(plot.title = element_text(hjust = 0.5))