NEWS

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arkhe 1.7.0 (2024-07-29)

New classes and methods

• Add scale_midpoint to rescale a continuous vector to have specified minimum, midpoint and maximum.

Internals

• Reexport %||% from base on newer versions of R to avoid conflict messages.

Breaking changes

• Move palette_*() functions to khroma.

arkhe 1.6.0 (2024-02-22)

New classes and methods

• Add describe() to quickly describe a matrix-like object.
• Add sparsity() to computes data sparsity (proportion of zeros).

arkhe 1.5.0 (2024-01-19)

New classes and methods

• Add palette_color_continuous() and palette_color_discrete() for color mapping.
• Add palette_shape() and palette_size() for symbol shape and size mapping.
• Add clean_whitespace() to remove leading/trailing Whitespace.
• Add seek_*() and get_*() to find and get rows/columns by names in a data.frame.

Enhancements

• compact() and remove_*() gained a new verbose argument to report extra information on progress.

Bugfixes & changes

• Rename needs() to assert_package().

arkhe 1.4.0 (2023-11-17)

New classes and methods

• Add %||% to replace NULL with a default value.
• Add %+% to concatenate character vectors.
• Add scale_range to rescale a continuous vector to have specified minimum and maximum.

Bugfixes & changes

• Remove deprecated methods.
• Remove na.rm argument of numeric predicates (so that the length of the output equals the length of the input).

arkhe 1.3.0 (2023-09-01)

New classes and methods

• Add remove_constant() to remove constant columns.
• Add remove_empty() to remove empty strings in a matrix-like object.
• Add replace_empty() to replace empty strings in a matrix-like object.

Bugfixes & changes

• Remove deprecated methods.
• Deprecate to_long() and wide_to_long().

Internals

• Use tinytest instead of testthat.

arkhe 1.2.0 (2023-05-11)

New classes and methods

• Add math_lcm() and math_gcd() to compute the lowest common multiple and the greatest common divisor.
• Add interval_hdr() and interval_credible() to compute the credible intervals.

Bugfixes & changes

• jackknife() gained a new argument to apply a function on the leave-one-out values (f).

Internals

• Add with_seed() to evaluate an expression with a temporarily seed.

arkhe 1.1.0 (2023-01-18)

New classes and methods

• Add needs() to check for the availability of a package.

Bugfixes & changes

• Remove deprecated methods.
• Remove unused argument in assert_unique().

arkhe 1.0.0 (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 (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 (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 (2021-05-14)

Bugfixes & changes

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

arkhe 0.3.0 (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 (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 (2020-02-15)

Bugfixes & changes

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

arkhe 0.2.0 (2019-12-18)

• Initial version on CRAN.

arkhe 0.1.0

• Beta release.