stratigraph (version 0.66)

rangechart: Plots a range chart

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

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')