Function reference

Classes

CompositionMatrix()

Relative Frequency Matrix

CountMatrix()

Absolute Frequency Matrix

IncidenceMatrix()

Incidence Matrix

OccurrenceMatrix-class .OccurrenceMatrix

Co-Occurrence Matrix

StratigraphicMatrix-class .StratigraphicMatrix

Stratigraphic Matrix

as_long() as_count() as_composition() as_incidence() as_occurrence() as_features() as_stratigraphy()

Coerce

Getters and Setters

mutators get set has_groups has_groups-method get_groups get_groups-method set_groups set_groups-method get_samples get_samples-method set_samples set_samples-method has_dates has_dates-method get_dates get_dates-method set_dates set_dates-method has_terminus has_terminus-method get_terminus get_terminus-method set_terminus set_terminus-method get_tpq get_tpq-method set_tpq set_tpq-method get_taq get_taq-method set_taq set_taq-method get_totals get_totals-method set_totals set_totals-method has_groups,AbundanceMatrix-method get_groups,AbundanceMatrix-method get_samples,AbundanceMatrix-method has_dates,AbundanceMatrix-method get_dates,AbundanceMatrix-method has_terminus,AbundanceMatrix-method get_terminus,AbundanceMatrix-method get_tpq,AbundanceMatrix-method get_taq,AbundanceMatrix-method get_totals,AbundanceMatrix-method get_totals,OccurrenceMatrix-method set_groups set_groups,AbundanceMatrix-method set_samples set_samples,AbundanceMatrix-method set_dates set_dates,AbundanceMatrix,NULL-method set_dates set_dates,AbundanceMatrix,numeric-method set_terminus set_terminus,AbundanceMatrix,NULL-method set_terminus set_terminus,AbundanceMatrix,list-method set_tpq set_tpq,AbundanceMatrix,NULL-method set_tpq set_tpq,AbundanceMatrix,numeric-method set_taq set_taq,AbundanceMatrix,NULL-method set_taq set_taq,AbundanceMatrix,numeric-method set_totals set_totals,AbundanceMatrix-method

Get or Set Parts of an Object

`[`(<AbundanceMatrix>) `[<-`(<AbundanceMatrix>) `[[<-`(<AbundanceMatrix>)

Extract or Replace Parts of an Object

summary(<AbundanceMatrix>)

Object Summaries

Statistics

confidence()

Confidence Interval for a Mean

jackknife()

Jackknife Estimation

Data cleaning

assign_colnames() assign_rownames()

Assign a specific row/column to the column/row names

count count-method count,matrix,function-method count,data.frame,function-method

Count values according to a given predicate

detect detect-method detect,ANY,function-method

Find values according to a given predicate

remove compact compact-method remove_NA remove_NA-method remove_Inf remove_Inf-method remove_zero remove_zero-method remove_empty remove_empty-method compact,ANY,function-method remove_NA,ANY-method remove_Inf,ANY-method remove_zero,ANY-method remove_empty,ANY-method

Remove values according to a given predicate

replace_NA() replace_Inf() replace_zero()

Data Replacement

Predicates

is_square() is_symmetric()

Matrix Predicates

is_zero() is_odd() is_even() is_positive() is_negative() is_whole()

Numeric Predicates

is_scalar_list() is_scalar_atomic() is_scalar_vector() is_scalar_numeric() is_scalar_integer() is_scalar_double() is_scalar_character() is_scalar_logical()

Scalar Type Predicates

is_constant() is_increasing() is_decreasing() is_greater() is_lower()

Numeric Trend Predicates

is_list() is_atomic() is_vector() is_numeric() is_integer() is_double() is_character() is_logical() is_error() is_warning() is_message()

Type Predicates

has_length() has_names() has_duplicates() has_missing() has_infinite() is_empty()

Utility Predicates

Validation

assert_empty() assert_filled() assert_length() assert_lengths() assert_dimensions() assert_names() assert_dimnames()

Check Object Attributes

assert_missing() assert_infinite() assert_unique()

Check Data

assert_matrix()

Check Matrix

assert_count() assert_numeric() assert_trend() assert_relation()

Check Numeric Values

assert_type() assert_scalar()

Check Data Types

validate()

Validate a Condition