strat.column
"summary"(object, ...) strat.column(counts, ...) is.strat.column(x, ...) as.strat.column(x)
strat.column
object.strat.column
.strat.column
object.strat.column
object to be included; see below for argument names that can be assigned values.strat.column
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
readGPDascii
, plot.strat.column