Graphs: Classical, useful plots from CONOP output.

In plannapus/CONOP9companion: Tools for integrating biostratigraphic software CONOP9 in a statistical workflow

Description

draw.ranges plots a range-chart. culling shows the full range of positions where an event may be placed in the optimal sequence. fence plots a fence diagram. collection.quality plots the events and ranges observed in each given samples vs the events or ranges that should be observed in each given samples according to the solution of the optimization. Section_vs_Composite create a plot of the composite section with the range occupied by the queried section highlighted. sect_range create a plot of taxa ranges on a section, comparing observed range and predicted range.

Usage

draw.ranges(CONOP, order = "FAD", method = "depth", ...)
culling(CONOP, cpcht, FO.col = "blue", LO.col = "red")
fence(CONOP, events = "observed", tag = 1)
collection.quality(CONOP, section)
Section.vs.Composite(CONOP, section, col, cex=1, axes=TRUE)
sect.range(CONOP, section, cex=0.8)

Arguments

CONOP	An object of class CONOP, typically the output of function read.CONOP.
order	The rangechart can be ordered by "FAD" or by "LAD".
method	If "depth", then the rangechart is plotted according to the composite sequence 'depth'. If "age" it is plotted according to the age of the events.
cpcht	The output of function read.cpchrt.
FO.col	Color for FO.
LO.col	Color for LO.
col	Color of the highlighted area.
events	A character string. Can be observed, in which case the events are plotted at the depth (or height) they have been observed, or placed, in which case they are plotted at their optimal depth (or height).
tag	Two possible values: if 1 then each sites will be named after its abridged name, if 2 after its complete name (respectively columns 2 and 4 of the input file SECTFILE).
section	Section name. Should correspond to the complete name of the section as entered in the SECTFILE.
cex	Size factor for the annotations. To be decreased when plotting several sections on the same plot.
axes	Logical. TRUE if axes desired, FALSE otherwise. Two x-axes are to be plotted: one corresponding to the composite section, the other labels the extremes of the queried section. If only the composite section depth is desired, use axes=FALSE and then axis(1,...) or axis(3,...) after the call to Section.vs.Composite.
...	Any argument that could be passed to segments.

Author(s)

Johan Renaudie, based on the CONOP9 functionalities created by Peter Sadler.

Examples

	data(riley)
	par(mfcol=c(2,1))
	par(mar=c(0,5,1,1))
	fence(riley,"placed")
	par(mar=c(1,5,0,1))
	fence(riley, "observed")
	
	collection.quality(riley, "Wht")
	
	par(mfrow=c(nrow(riley@Sectfile),1))
	for(i in riley@Sectfile[,4]){
		par(mar=c(1,3,1,1))
		Section.vs.Composite(riley,i,col="lightblue",cex=0.8,axes=FALSE)
		}
	
	sect.range(riley,"Morgan")

plannapus/CONOP9companion documentation built on March 18, 2021, 9:39 a.m.