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Getters and setters to retrieve or set parts of an object.

Usage

has_groups(x)

get_groups(x)

set_groups(x) <- value

get_samples(x)

set_samples(x) <- value

has_dates(x)

get_dates(x)

set_dates(x) <- value

has_terminus(x)

get_terminus(x)

set_terminus(x) <- value

get_tpq(x)

set_tpq(x) <- value

get_taq(x)

set_taq(x) <- value

get_totals(x)

set_totals(x) <- value

# S4 method for AbundanceMatrix
has_groups(x)

# S4 method for AbundanceMatrix
get_groups(x)

# S4 method for AbundanceMatrix
get_samples(x)

# S4 method for AbundanceMatrix
has_dates(x)

# S4 method for AbundanceMatrix
get_dates(x)

# S4 method for AbundanceMatrix
has_terminus(x)

# S4 method for AbundanceMatrix
get_terminus(x)

# S4 method for AbundanceMatrix
get_tpq(x)

# S4 method for AbundanceMatrix
get_taq(x)

# S4 method for AbundanceMatrix
get_totals(x)

# S4 method for OccurrenceMatrix
get_totals(x)

# S4 method for AbundanceMatrix
set_groups(x) <- value

# S4 method for AbundanceMatrix
set_samples(x) <- value

# S4 method for AbundanceMatrix,`NULL`
set_dates(x) <- value

# S4 method for AbundanceMatrix,numeric
set_dates(x) <- value

# S4 method for AbundanceMatrix,`NULL`
set_terminus(x) <- value

# S4 method for AbundanceMatrix,list
set_terminus(x) <- value

# S4 method for AbundanceMatrix,`NULL`
set_tpq(x) <- value

# S4 method for AbundanceMatrix,numeric
set_tpq(x) <- value

# S4 method for AbundanceMatrix,`NULL`
set_taq(x) <- value

# S4 method for AbundanceMatrix,numeric
set_taq(x) <- value

# S4 method for AbundanceMatrix
set_totals(x) <- value

Arguments

x

An object from which to get or set element(s) (typically an AbundanceMatrix object).

value

A possible value for the element(s) of x.

Value

  • set_*() returns an object of the same sort as x with the new values assigned.

  • get_*() returns the part of x.

  • has_*() returns a logical scalar.

Details

get_samples(x) and get_samples(x) <- value

Get or set the sample names of x.

get_groups(x) and set_groups(x) <- value

Get or set the groups of x.

get_dates(x) and set_dates(x) <- value

Get or set the dates of x.

get_terminus(x) and set_terminus(x) <- value

Get or set the chronology of x. value must be a list with components tpq (TPQ - terminus post quem) and taq (TAQ - terminus ante quem).

get_tpq(x) and set_tpq(x) <- value, get_taq(x) and set_taq(x) <- value

Get or set the TPQ/TAQ of x.

Chronology

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).

See also

Other mutators: subset(), summary()

Author

N. Frerebeau

Examples

## Create a data.frame
X <- matrix(data = sample(0:10, 50, TRUE), nrow = 10, ncol = 5)
Y <- as.data.frame(X)

## Coerce to a count matrix
Z <- as_count(Y)

## Set/get groups
set_samples(Z) <- rep(c("a", "b", "c", "d", "e"), each = 2)
get_samples(Z)
#>  [1] "a" "a" "b" "b" "c" "c" "d" "d" "e" "e"

## Set/get groups
set_groups(Z) <- rep(c("A", "B"), each = 5)
get_groups(Z)
#>  [1] "A" "A" "A" "A" "A" "B" "B" "B" "B" "B"

## Get/get TPQ/TAQ
chrono <- list(
  tpq = sample(1301:1400, 10, replace = TRUE),
  taq = sample(1451:1500, 10, replace = TRUE)
)
set_terminus(Z) <- chrono
get_terminus(Z)
#>        tpq  taq
#> row1  1398 1472
#> row2  1346 1494
#> row3  1397 1482
#> row4  1301 1498
#> row5  1333 1490
#> row6  1324 1453
#> row7  1331 1492
#> row8  1343 1483
#> row9  1370 1473
#> row10 1392 1460

## Collection of features
as_features(Z)
#>       V1 V2 V3 V4 V5 samples group dates  tpq  taq
#> row1   1  7  7  7  4       a     A    NA 1398 1472
#> row2   7  5  6  7  5       a     A    NA 1346 1494
#> row3   9  4  9  8  6       b     A    NA 1397 1482
#> row4  10  6  7  6  8       b     A    NA 1301 1498
#> row5   8  9  9  9  1       c     A    NA 1333 1490
#> row6  10 10  6  0  6       c     B    NA 1324 1453
#> row7   4  5  9  6  7       d     B    NA 1331 1492
#> row8   3  9  7  7  2       d     B    NA 1343 1483
#> row9   8  1 10  4  8       e     B    NA 1370 1473
#> row10  9 10  2 10  6       e     B    NA 1392 1460

## Summarize data
summary(Z)
#> <AbundanceSummary: 10 x 5>
#> A ------------------------------------------------------------------------------
#> * Observations: 5
#> * Variables: 5
#> * Replicated measurements: TRUE
#> * Chronology: 1301 - 1498 (year CE)
#> B ------------------------------------------------------------------------------
#> * Observations: 5
#> * Variables: 5
#> * Replicated measurements: TRUE
#> * Chronology: 1324 - 1492 (year CE)
#> --------------------------------------------------------------------------------