grab: Summarises a Node of the Tree

In pkuhnert/diet: Performs an analysis of diet data using univariate trees

Summarises a Node of the Tree

Description

The grab functions allow you to select nodes of the tree for further investigation and summary. Once a node is selected, a map of the points is shown with highlighted points of the selection along with a barplot of the prey distribution found at that node. When applied to an object of class bag, bagged distributions of prey are shown. The grabmulti function produces multiple summaries on successive nodes selected by the user.

Usage

grab(object, LatID, LonID, setID = NULL, node.cols = NULL, cex = 0.8,
  mapxlim = NULL, mapylim = NULL, database = "world",
  display.object = NULL, oob = FALSE, n = NULL, ylimit)

## S3 method for class 'dpart'
grab(object, LatID, LonID, setID = NULL,
  node.cols = NULL, cex = 0.8, mapxlim = NULL, mapylim = NULL,
  database = "world", display.object = NULL, oob = FALSE, n = NULL,
  ylimit = NULL)

## S3 method for class 'bag'
grab(object, LatID, LonID, setID = NULL,
  node.cols = NULL, cex = 0.8, mapxlim = NULL, mapylim = NULL,
  database = "world", display.object, oob = FALSE, n = NULL, ylimit)

## S3 method for class 'dpart'
grabmulti(object, LatID, LonID, setID = NULL,
  node.cols = NULL, cex = 0.8, mapxlim = NULL, mapylim = NULL,
  n = nrow(object$frame), database = "world")

grabmulti(object, LatID, LonID, setID = NULL, node.cols = NULL,
  cex = 0.8, mapxlim = NULL, mapylim = NULL,
  n = nrow(object$frame), database = "world")

Arguments

object	tree object either of class dpart or bag
LatID	string. Column name of latitude.
LonID	string. Column name of longitude.
setID	optional set identification number.
node.cols	vector of node colours assigned to each prey. Use output from apc function. If node colours are not provided, the trees will not be produced in colour.
cex	numeric. Size of plotting symbols and labels (default: 0.8)
mapxlim	optional map x-limits. If none are specified then the range of the data are used.
mapylim	optional map y-limits. If none are specified then the range of the data are used.
database	either 'world' or 'world2' are available for plotting. Defaults to 'world' if not specified.
display.object	tree object to display. This may be different to object when bagging is used.
oob	logical. Option when a bagged tree is passed to the grab.bag function to use out of bag estimates.
n	numeric. Maximum number of nodes to investigate in the tree. Defaults to the number in the tree.
ylimit	y-axis limit for barcharts that are produced by the explore function

Details

The grab.dpart function can be used on any tree object of class dpart. The grab.bag function can be used on any tree object of class bag. The grabmulti.dpart function can only be used on tree objects of class dpart. These functions can be invoked explicitly or just by calling the grab and grabmulti functions.

Value

Summary output from the node/s selected in the tree consisting of the node number, number of observations, number of sets (if the setID was provided), number of predators, number of prey, deviance, expected loss and predicted class.

References

Kuhnert, P.M., Duffy, L. M and Olson, R.J. (2012) The Analysis of Predator Diet and Stable Isotope Data, Journal of Statistical Software, In Prep.

See Also

plot.dpart; bagging

Examples

# Assigning prey colours for default palette
  val <- apc(x = yftdiet, preyfile = PreyTaxonSort, check = TRUE)
  node.colsY <- val$cols
  dietPP <- val$x   # updated diet matrix with Group assigned prey taxa codes
  
# Fitting the classification tree
  yft.dp <- dpart(Group ~ Lat + Lon + Year + Quarter + SST  + Length, 
                      data = dietPP, weights = W, minsplit = 10,
                                        cp = 0.001)
                                       
# Pruning the tree
yft.pr <- prune(yft.dp, se = 1)                   

# Exploring Nodes: This suite of graphics is interactive and therefore has
# been commented out. When run, the code will ask you to select a node for
# viewing.
## Not run: 
  # Exploring nodes of the tree - single page
  val <- grab(object = yft.pr, LatID = "Lat", LonID = "Lon", setID = "TripSetNo", 
              node.cols = node.colsY, cex = 1, mapxlim = c(-125, -75), mapylim = c(0, 30))
                          
 # Exploring nodes of the tree - multiple pages
 val <- grab(object = yft.pr, LatID = "Lat", LonID = "Lon", setID = "TripSetNo", 
             node.cols = node.colsY, cex = 1, mapxlim = c(-125, -75), mapylim = c(0, 30))
                         
 # Exploring multiple nodes
 grabmulti(object = yft.pr, LatID = "Lat", LonID = "Lon", setID = "TripSetNo", 
           node.cols = node.colsY, cex = 0.8, mapxlim = c(-125, -75), mapylim = c(0, 30))

## End(Not run)

pkuhnert/diet documentation built on June 10, 2025, 2:59 a.m.