strat.column: Creates a strat.column object

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

Description

Creates and manipulates S3 objects of class strat.column

Usage

  ## S3 method for class 'strat.column'
summary(object, ...)
  strat.column(counts, ...)
  is.strat.column(x, ...)
  as.strat.column(x)

Arguments

counts	a count matrix to be converted to a strat.column object.
x	an object to be checked for class attribute or coerced to a strat.column.
object	a strat.column object.
...	other components of a strat.column object to be included; see below for argument names that can be assigned values.

Details

An object of class strat.column is a list x with attr(x, 'class') == 'strat.column'. is.strat.column() only checks that it has the correct class attribute and a non-empty counts, which is the minimum needed for plotting. summary.strat.column provides a longer summary of what data are available, and str provdes a full description of the data structure.

The following names are defined elements of a strat.column; more can be defined by the user simply by assigning a value to x\$new.name.

REQUIRED: counts

OPTIONAL: taxa, short.names, higher.grp, tax.cat, reorder, depths, sample.names, absolute.ages, envir.facies, sample.labels, sample.label.title, CaCO3, TOC, TIC, N, S, caliper, gamma.ray, density, fe.resist, mag.sus, resistivity, lithology, porosity, taxa.clust, sample.clust, lat.ddmmss, lat.dd, long.dddmmss, long.dd, loc.descript, site.name, country, state, county, elevation, elev.units, rc.ages, contact, refs, metadata

THE BASIC COUNT MATRIX with m taxa as columns and n depths as rows

$counts : num [1:n, 1:m]

ATTRIBUTES OF THE TAXA

$taxa : chr [1:m]

$short.names : chr [1:m]

$higher.grp : Factor [1:m] w/ levels: Angiosperm, Conifer, Fern, Pteridophyte, Moss, Indet. (levels not on this list can also be used.)

$tax.cat : Factor [1:m] w/ levels: Arborescent, Herbaceous, Wetland, Xerophyte, Phytolith, Indet., Marker (levels not on this list can also be used.)

$reorder : num [1:m]

ATTRIBUTES OF THE SAMPLES

$depths : num [1:n] by default, depths are measured down from a datum.

$sample.names : chr [1:n] text for labels in addition to the depths.

$absolute.ages: num [1:n]

$envir.facies : factor [1:n] w/ levels: ??? (a factor giving an environmental interpretation of the sample.)

$sample.labels: chr [1:n] other labels for each sample (e.g. numbers)

$sample.label.title: chr [1] title for the extra sample label, e.g. 'Sample Number'.

GEOCHEMICAL DATA $CaCO3 : num [1:n] (wt

$TOC : num [1:n] (wt

$TIC : num [1:n] (wt

$N : num [1:n] (wt

$S : num [1:n] (wt

CORE LOG DATA

$caliper : num [1:p]

$gamma.ray : num [1:p]

$density : num [1:p]

$fe.resist : num [1:p]

$mag.sus : num [1:p]

$resistivity : num [1:p]

$lithology : num [1:p]

$porosity : num [1:p]

where p can be any integer; the complete vector fits into the same distance in the stratigraphic column as the n samples. If alignment of log and sample data is required, it is up to the user to down-sample appropriately.

CLUSTERING

$taxa.clust : cluster object for columns

$sample.clust : cluster object for rows

SITE INFORMATION

$lat.ddmmss : chr [1]

$lat.dd : chr [1]

$long.dddmmss : chr [1]

$long.dd : chr [1]

$loc.descript : chr [1]

$site.name : chr [1]

$country : chr [1]

$state : chr [1]

$county : chr [1]

$elevation : num [1]

$elev.units : chr [1]

DATING METADATA

$rc.ages : data.frame [,]

METADATA

$contact : chr [1:x] \# a person to contact

$refs : chr [1:y] \# citations

$metadata : chr [1:z] \# random other notes

Value

Returns an object of type strat.column

Author(s)

Walton Green

See Also

readGPDascii, plot.strat.column

Examples

  # PUT EXAMPLES HERE

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