A virtual S4 class to represent archaeological data.
samplesA character vector.
groupsA character vector.
totalsA numeric vector giving the absolute row sums.
datesAn integer vector specifying the date point estimate of each
row.
tpqAn integer vector specifying the TPQ of each row.
taqAn integer vector specifying the TAQ of each row.
In the code snippets below, x is an AbundanceMatrix object.
get_samples(x) and get_samples(x) <- valueGet or set
the sample names of x.
get_groups(x) and set_groups(x) <- valueGet or set
the groups of x.
get_dates(x) and set_dates(x) <- valueGet or set
the dates of x. value can be a list with components tpq (TPQ -
terminus post quem) and taq (TAQ - terminus ante quem) or a
numeric vector (point estimate). The elements of value are coerced to
integer with as.integer() (hence truncated towards zero).
The CountMatrix, CompositionMatrix and IncidenceMatrix classes have
special slots:
samples for replicated measurements/observation,
groups to group data by site/area,
dates to specify the date point estimate of an assemblage,
tqp and taq to specify the chronology of an assemblage.
When coercing a data.frame to a *Matrix object, an attempt is made to
automatically assign values to these slots by mapping column names (case
insensitive, plural insensitive). This behavior can be disabled by setting
options(arkhe.autodetect = FALSE) or overrided by explicitly specifying
the columns to be used in as_*().
The way chronological information is handled is somewhat opinionated.
Sub-annual precision is overkill/meaningless in most situations: dates are
assumed to be expressed in years CE and are stored as integers (values are
coerced with as.integer() and hence truncated towards zero).
N. Frerebeau