plot.diet: Exploratory Plots of the Diet Data
In pkuhnert/diet: Performs an analysis of diet data using univariate trees

plot.diet

R Documentation

Exploratory Plots of the Diet Data

Description

Produces a number of exploratory plots of the diet data

Usage

## S3 method for class 'diet'
plot(x, y = NULL, Xvar, LonID, LatID, mapxlim, mapylim,
  PredSpID = NULL, SmXvar = NULL, leg.loc = "topleft",
  col = "black", Factor, database = "world", PredIDno = NULL,
  prey.cols = NULL, filenm = NULL, ...)

Arguments

`x`	object of class `diet`. The result of reading in the data using either the `read.dm` and `link{read.pp}` functions.
`y`	NULL (not used)
`Xvar`	vector listing the names of x-variables to explore.
`LonID`	column name listing the longitude.
`LatID`	column name listing the latitude
`mapxlim`	optional map x-axis ranges in the form of c(lower, upper).
`mapylim`	optional map y-axis ranges in the form of c(lower, upper).
`PredSpID`	optional column name listing the predator species label
`SmXvar`	optional vector listing the column names of variables to be explored on a smooth surface. Latitude and Longitude column names need to be specified for GAMs to be fitted. Note, choice of variables for smoothing needs some careful thought and exploration as the GAM fit to each variable assumes Gaussian errors.
`leg.loc`	legend location for some plots where legends are required. Defaults to "top left"
`col`	colour for map outline (default: black)
`Factor`	categorical variable used to condition the compositional maps. For example, if "Predator" was used, compositional plots of prey would be produced for each predator listed in the predator variable.
`database`	either 'world' or 'world2' depending on the area being plotted. Defaults to 'world'.
`PredIDno`	optional column name specifying the predator label. Used in determining the number of predators in the database. If this is left NULL then the number of predators in the summary table defaults to NA.
`prey.cols`	colours for prey. If NULL, default colours are used.
`filenm`	Name of pdf file (with .pdf extension) where plots are produced. Defaults to exploratory_plots.pdf
`...`	additional arguments passed to the function.

Details

This function produces a number of exploratory plots. Here is a summary. (1) Maps: If latitude and longitude column headings are provided, maps of the data are produced. (2) Distributional summaries of the x-variables (Xvar): These consist of pairwise plots, histograms, barcharts. (3) Smooth plots of the x-variables (SmXvar): These consist of plots of each variable in space (require latitude and longitude variables) as fitted by a GAM using the mgcv package. Note, these are predictions. (4) Distributional summaries of the prey composition (by predator if predator ID is provided). (5) Summary statistics of the x-variables provided.

Value

A list consisting of:

SmGAMOutputGAM fits for each variable specified in SmXvar has been specified. This is stored as a list.
dataS1Data summary providing the minimum, maximum, mean, median, 1st and 3rd quartiles of each variable in x
dataS2vector specifying the number of observations, number of predators and number of species in x

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.

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
explore.diet <- plot(x = dietPP, LonID = "Lon", LatID = "Lat", 
                        Xvar = c("Quarter", "Year", "SST", "Length", "Lat", "Lon"),  
                         PredSpID = "PredSpp", mapxlim = c(-125, -75), mapylim = c(0, 30),
                         SmXvar = c("SST", "Length"), PredIDno = "TripSetPredNo", col = "gold3",
                         Factor = "PredSpp", prey.cols = node.colsY)
  names(explore.diet)
 explore.diet$dataS2

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