diversity: Diversity Plots

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

Diversity Plots

Description

This function produces maps of diversity based on a fitted tree object of class dpart.

Usage

diversity(object, newdata = NULL, too.far = 0.1, LatID, LonID,
  projection = "+proj=longlat +datum=WGS84", maxpixels = 1e+05,
  col = "lightgrey", fill = "lightgrey", zlim = c(0, 1))

## S3 method for class 'dpart'
diversity(object, newdata = NULL, too.far = 0.1, LatID,
  LonID, projection = "+proj=longlat +datum=WGS84", maxpixels = 1e+05,
  col = "lightgrey", fill = "lightgrey", zlim = c(0, 1))

Arguments

object	fitted tree object of class dpart.
newdata	optional new dataset to base the diversity estimates on. By default, the dataset used to create the tree is used.
too.far	too.far
LatID	column labelling the latitude co-ordinate
LonID	column labelling the longitude co-ordinate
projection	projection
maxpixels	maxpixels
col	col
fill	fill
zlim	zlim

Details

Depending on the extent of the data collected and co-ordinate system required, "world2" may produce a better map than "world".

Value

Two maps showing the diversity of predators diet spanning the sampled locations. The first map shows the diversity for each sampled point represented by a colour matched to a 0-1 scale. The second plot shows the interpolated diversity from fitting a GAM (see mgcv) to the diversity score with smooth terms for latitude and longitude. A data frame listing the latitude, longitude, diversity, diversity bin and associated colours.

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

mgcv, mappoints.data, map

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)
 yft.pr <- prune(yft.dp, se = 1)
 diversity(object = yft.pr, LatID = "Lat", LonID = "Lon", too.far = 0.05,
          projection = "+proj=longlat +datum=WGS84", maxpixels = 1e5,
          col = "black", fill = "lightgrey")
                                                         

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