Changelog

Source: NEWS.md

arkhe 1.0.0.9000

arkhe 1.0.0

CRAN release: 2022-10-28

New classes and methods

• Add append_rownames() to convert row names to an explicit column.
• Add assert_positive(), assert_negative(), assert_odd(), assert_even(), assert_constant(), assert_decreasing(), assert_increasing(), assert_lower() and assert_greater() to check numeric vectors.
• Add bootstrap() for bootstrap estimation.
• Add compact() to remove empty columns/rows in an array-like object.
• Add discard() and keep() remove/keep rows/columns in an array-like object using a predicate function.
• Add to_long() to transform a matrix to a long data.frame.

Bugfixes & changes

• Export all predicate functions.
• Deprecate as_long(), assert_numeric(), assert_trend(), assert_relation(), assert_matrix() and remove_empty().

Breaking changes

• Remove all *Matrix classes and methods.
• Rename compact() to discard().

arkhe 0.5.0

CRAN release: 2022-06-15

New classes and methods

• Add assign_rownames() and assign_colnames() to make a specific row/column the column/row names of a data.frame.
• Add assert_count() to validate count data (absolute frequencies/integer).
• Add count() to count values by rows/columns according to a given predicate.
• Add detect() to find rows/columns in an array-like object according to a given predicate.
• Add compact() to remove rows/columns in an array-like object according to a given predicate.
• Add jackknife() for jackknife estimation.
• Add confidence() to compute confidence interval for the mean.

arkhe 0.4.0

CRAN release: 2021-09-18

New classes and methods

• Add replace_Inf() to replace infinite values in a matrix-like object.
• Add replace_zero() to replace zero in a matrix-like object.
• Add remove_Inf() to remove infinite values in a matrix-like object.
• Add assert_*() and validate() to validate objects.
• Add get_dates(), set_dates()<- to extract/replace dates slot.
• Add get_terminus(), set_terminus()<-, get_tpq(), set_tpq()<-, get_taq(), set_taq()<- to extract/replace tpq and taq slots.
• Add summary() for AbundanceMatrix objects.

Internals

• AbundanceMatrix class gained a new slot to store the sample sizes (totals).
• AbundanceMatrix class gained two new slots to store chronological information (dates, tpq, taq).
• Add AbundanceSummary class to store summary of an AbundanceMatrix object.

arkhe 0.3.1

CRAN release: 2021-05-14

Bugfixes & changes

• Fix warning “data length differs from size of matrix” in examples (R-devel).

arkhe 0.3.0

CRAN release: 2021-04-09

New classes and methods

• Add replace_NA() to replace missing values.
• Add remove_NA(), remove_zero() and remove_empty() to remove missing values, zeros and empty rows/columns in a matrix.
• Add get_samples(), set_samples()<-, get_groups() and set_groups()<- to extract/replace samples and groups slots.

Bugfixes & changes

• Change OccurrenceMatrix inheritance (from NumericMatrix to IntegerMatrix).
• Rename AbundanceMatrix (ambiguous) to CompositionMatrix.
• Deprecate as_abundance().
• Remove SimilarityMatrix class.
• as_long() gained a new reverse argument.

arkhe 0.2.2

CRAN release: 2020-03-23

Bugfixes & changes

• CRAN package check error has been fixed (random error with testthat).
• CRAN package check warnings have been fixed (remove nomnoml from suggested packages).

arkhe 0.2.1

CRAN release: 2020-02-15

Bugfixes & changes

• CRAN package check warnings have been fixed (“documented arguments not in ” in the r-devel checks).

arkhe 0.2.0

CRAN release: 2019-12-18

• Initial version on CRAN.

arkhe 0.1.0

• Beta release.