resids: Residual Analysis

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

Residual Analysis

Description

Examines the residuals from the fit of the model to determine whether spatial dependence exists. Operates on objects of class dpart.

Usage

## S3 method for class 'dpart'
resids(object, LonID, LatID, predID, plot = TRUE)
## S3 method for class 'bag'
resids(object, LonID, LatID, predID, plot = TRUE)

## S3 method for class 'dpart'
resids(object, LonID, LatID, predID, plot = TRUE)

## S3 method for class 'bag'
resids(object, LonID, LatID, predID, plot = TRUE)

Arguments

object	object of class dpart.
LonID	column name for longitude.
LatID	column name for latitude.
predID	predator ID
plot	logical. Whether plotting should be performed

Details

Produces a variogram of the residuals to check for spatial dependence.

Value

Outputs the residuals and a variogram plot of the residuals for checking.

See Also

objects to See Also as variog

Examples

# Load data
#data(yftdiet)  

# Load the prey taxa data
#data(PreyTaxonSort)

# 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)                   

# Checking residuals
#yft.resid <- resids(yft.pr, LonID = "Lon", LatID = "Lat", 
#     predID = "TripSetPredNo", plot = TRUE) # need to compute resids from bootstrapping
    
# Bagging
# Bagging with NO spatial bootstrapping (nBaggs set to something small)
#yft.bag <- bagging(Group ~ Lat + Lon + Year + Quarter + SST  + Length,
#                     data = dietPP, weights = W, minsplit = 50,
#                     cp = 0.001, nBaggs = 10, predID = "TripSetPredNo")
                    
# Checking for spatial dependence
#yft.bag.resid <- resids(yft.bag, LonID = "Lon", LatID = "Lat", 
#predID = "TripSetPredNo", plot = TRUE) # need to compute resids from bootstrapping
          
                    

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