rangechart: Plots a range chart

In stratigraph: Toolkit for the plotting and analysis of stratigraphic and palaeontological data

Description

Plots a range chart of stratigraphic data.

Usage

rangechart(x = NULL,
            counts = NULL,
            depths = NULL,
            sample.labels = NULL,
            taxa = NULL,
            short.names = NULL,
            higher.grp = NULL,
            tax.cat = NULL,
            reorder = NULL,
            plot.points = FALSE,
            plot.depths.increasing.down = TRUE,
            llwd = 2,
            cex.xaxis = 0.5,
            cex.yaxis = 1,
            ...)

Arguments

x	an object of class strat.column to be plotted.
counts	a data frame or matrix of counts or a string giving the path to a comma separated flat text file in the proper form to be read in by read.csv() to a data frame and plotted.
depths	a vector of depths the same length as the number of rows in counts.
sample.labels	a character vector of labels, the same length as the number of rows in counts, with which to label the samples.
taxa	taxon names.
short.names	abbreviated taxon names.
higher.grp	a higher taxonomic group for each taxon, empty by default (Factor taking levels: ???).
tax.cat	a category or label for each taxon, empty by default (Factor taking levels: ??? ).
reorder	a vector to reorder the taxa. Ignored if NULL(default). If a string of length 1, invokes special options 'fad.by.category', 'lad.by.category', and 'by.count'
plot.points	FALSE (default) plots actual occurrences as points when TRUE.
plot.depths.increasing.down	TRUE (default) plots depths increasing from the top to the bottom of the plot.
llwd	line width of the range bars, defaulting to 2. Compare par(lwd = 2); passed to segments().
cex.xaxis	character expansion applied to x-axis labels, defaulting to 0.5. Compare par(cex.axis = 0.5); passed to axis(1, ...).
cex.yaxis	character expansion applied to y-axis labels, defaulting to 1. Compare par(cex.axis = 1); passed to axis(2, ...).
...	arguments passed through to lower level plotting functions.

Value

Returns invisibly.

Author(s)

Walton Green

See Also

strat.column

Examples

## Examples

#data(cerrejon)
#cerrejon.counts <- t(cerrejon[-(1:2),])
#cerrejon.counts <- apply(cerrejon.counts, 2, as.numeric)
#row.names(cerrejon.counts) <- names(cerrejon)
#cerrejon.depths <- names(cerrejon)
#cerrejon.depths <- as.numeric(gsub('X', '', cerrejon.depths, perl = TRUE))
#cerrejon.samp.names <- cerrejon[1,]
#cerrejon.lith <- as.factor(as.character(cerrejon[2,]))
#rangechart(counts = cerrejon.counts, depths = cerrejon.depths)

data(corneta)
corneta.counts <- corneta[-1,-(1:2)]
corneta.counts <- corneta.counts[,-(ncol(corneta.counts))]
corneta.counts <- apply(corneta.counts, 2, as.numeric)
corneta.depths <- row.names(corneta)[-1]
corneta.samp.names <- corneta$label[-1]
corneta.tax.cat <- as.factor(as.character(corneta[1,-(1:2)]))
corneta.tax.cat <- corneta.tax.cat[1:(length(corneta.tax.cat)-1)]
rangechart(counts = corneta.counts, depths = corneta.depths,
          tax.cat = corneta.tax.cat,
          reorder = 'lad.by.category')

data(plain)
rangechart(counts = plain[,2:4], depths = plain[,1],
          tax.cat = as.factor(c(1,2,1)),
          reorder = 'lad.by.category')

data(rogerslk)
rangechart(as.strat.column(rogerslk), reorder = 'fad', pch = 20)

## Coloring the different categories....
data(mohawk)
rangechart(counts = mohawk$counts, depths = mohawk$depths,
          tax.cat = mohawk$tax.cat, reorder = 'lad.by.category')

stratigraph documentation built on May 30, 2017, 12:31 a.m.