siteplot: Summary plot of site-specific captures

In btorobrob/cesr: Trend analysis of Constant Effort Site ringing data

Summary plot of site-specific captures

Description

Generate boxplot of captures for all sites, by year or species, with those from one site highlighted.

Usage

siteplot(data, site=0, year=0, visit=FALSE, splist=NULL, nspecies=20, nyears=NA, age=0, subset=NULL, effort=FALSE, ylab=NULL, margin=8, pch=21, pt.cex=2, pt.col='red', plot=TRUE, ...)

Arguments

data	either a dataframe generated by readces or a boxplot summary created by previously running siteplot, see details
site	character, the site to highlight
year	integer, specify a year to create a summary by species or visit
visit	logical, summarise catches within a year by visit number? If visit=FALSE (the default), catches will be summarised by species
splist	character, if a year is specified, optionally either a vector of Euring codes, or 'all' (not generally advised)
nspecies	numeric, if a year is specified and splist not, then plot the commonest 'n' species on the site
nyears	numeric, limit the number of years plotted to the number that the site operated, with this as a minimum. For example, if nyears=10 and the site has operated for 15 years, 15 bars (and dots) will be shown, but if the site has only operated for 5 years, then 10 bars will be plotted.
age	numeric, either 3 or 4 to select only juvenile or adult captures
subset	a logical expression to subset the data
effort	logical, should the number of captures be divided by netlength on the site?
ylab	character, a label for the number axis
margin	if year is specified, either a single number for the width of the left margin, or a vector of length 4 specifying each margin width, see details
pch	the symbol with which the site counts are plotted
pt.cex	size of the symbol with which the site counts are plotted
pt.col	colour of the symbol with which the site counts are plotted
plot	logical, should a plot be produced. For larger datasets, creating the summary data first without plotting may be helpful, see details
...	additional arguments passed to bxp for drawing the boxplot, such as 'main' (for a title) or 'whisklty' (change the whisker line type)

Details

Generates a boxplot of captures per site, with those from 'site' highlighted using an overlain point. Data may be summarised either annually (if year=0), or by species (if a year is specified). In the former case the boxes will be vertical, in the latter horizontal. The width of the margin(s) can be changed (by using margin=) if there is not enough room for the species names.

For larger datasets, creating the boxplot summaries may take some time. In this case it is advised to run the function with plot=FALSE to create the data for the boxplot. This can then be supplied to data=, meaning that only the individual site counts need to be extracted and plotted each time.

Value

A list with three components:

ds	the (subsetted) dataset
ds.bxp	data for the boxplot in summary form
ds.attr	some useful attributes

Note

It is assumed that this function will be used for current sites, so the nyears argument only counts backwards from the current year.

Author(s)

Rob Robinson

Examples

data(ukdata)
uk.bxp <- siteplot(ukdata, site='656')
siteplot(uk.bxp, site='420')

btorobrob/cesr documentation built on June 9, 2025, 5:39 a.m.