arkhe 1.1.0

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.

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

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.

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.

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.

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.

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.

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

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