Changelog

Source: NEWS.md

matsbyname 0.6.10 (2024-02-12)

CRAN release: 2024-02-12

• Now skipping speed tests on CRAN. These tests are appropriate only for certain machines whose timings from previous runs are hard-wired into the tests. Put another way, these are not actually unit tests that verify correctness of code. They are timing tests. So no need to run these tests on CRAN (or in continuous integration tests, for that matter).
• No new tests.
  • Still at 2113 tests, all passing.
  • Test coverage remains at 100%.

matsbyname 0.6.9 (2024-01-30)

CRAN release: 2024-01-31

• Now running tests in parallel.
• Added performance tests.
• Fixed a bug in replaceNaN_byname() where a Matrix::sparseMatrix would error when nothing needed to be replaced.
• select_rows_byname() and select_cols_byname() now both
  1. have grep() arguments ignore.case, perl, fixed, and useBytes, and
  2. pass those arguments to grep(), enabling more flexible matching of row and column names.
• New tests for fixed bugs and performance.
  • Now up to 2113 tests, all passing.
  • Test coverage remains at 100%.

matsbyname 0.6.8 (2023-12-20)

CRAN release: 2023-12-21

• Added a statement of need.
• Updated the GitHub pages approach to use the gh-pages branch.
• No new tests.
  • Still at 2095 tests, all passing.
  • Test coverage remains at 100%.

matsbyname 0.6.7 (2023-12-01)

CRAN release: 2023-12-01

• Added code of conduct and contributing pages to documentation.
• No new tests.
  • Still at 2095 tests, all passing.
  • Test coverage remains at 100%.

matsbyname 0.6.6 (2023-10-18)

CRAN release: 2023-10-19

• Fixed a bug in matricize_byname(). If the incoming matrix had NULL rowtype, the coltype of the outgoing matrix was set to list(). The coltype of the outgoing matrix is now set to NULL, as expected.
• Added new tests to verify rowtype() and coltype() behavior in matrixproduct_byname().
• New tests for new features.
  • Now at 2095 tests, all passing.
  • Test coverage remains at 100%.

matsbyname 0.6.5 (2023-09-16)

CRAN release: 2023-09-17

• Remove deprecated column argument on vec_from_store_byname().
• Remove deprecated argument matrix.class in many places.
• Fixed tests to work with updated version of the Matrix package (1.6-2).
• Removed a few tests dealing with deprecated arguments.
  • Now at 2089 tests, all passing.
  • Test coverage is back up to 100%, due only to deprecation code.

matsbyname 0.6.4 (2023-08-17)

CRAN release: 2023-08-18

• matsbyname::Matrix now vectorized for lists of matrix objects in the data argument.
• Policy change: vec_from_store_byname() now always returns a column vector.
• Deprecate the column argument of vec_from_store_byname() in favor of a new margin argument, which is standard throughout R.
• Added a few new tests for vec_from_store_byname() to verify operation when multiple rows in a match v.
• Added a new test for ncol_byname() to verify operation.
• New tests for new features.
  • Up to 2092 tests, all passing.
  • Test coverage is at 99.41%, due only to deprecation code.

matsbyname 0.6.3 (2023-05-22)

CRAN release: 2023-05-22

• Deprecated matrix.class argument. It will be removed soon.
• Renamed matrix.class argument to matrix_class.
• New tests for matrix.class –> matrix_class transition.
  • Still at 2085 tests, all passing.
  • Test coverage remains at 100%.

matsbyname 0.6.2 (2023-05-04)

• Move to latest version of GitHub test coverage workflow.
• This version not released to CRAN.
• No new tests.
  • Still at 2082 tests, all passing.
  • Test coverage remains at 100%.

matsbyname 0.6.1 (2023-04-25)

CRAN release: 2023-04-25

• equal_byname() gains tol argument to control the precision with which equality is decided.
• Fixed a bug where equal_byname() wasn’t using equal_matrix_or_Matrix(). As a result, it was difficult to tell whether a matrix and a Matrix were equal.
• New tests for new features.
  • Now at 2082 tests, all passing.
  • Test coverage remains at 100%.

matsbyname 0.6.0 (2023-03-04)

CRAN release: 2023-03-04

• Fixed a bug in aggregate_pieces_byname() where failure occurred if there were repeated row (or column) names not included in the aggregation_map.
• All functions now work with Matrix objects, thereby enabling use of sparse matrices. Use matsbyname::Matrix() to create sparse matrices if desired.
• create_matrix_byname() gains matrix.class argument that tells whether the created object is of class matrix or Matrix. Default is “matrix”.
• New function is.Matrix() assists with determining whether an object is a Matrix. The base functionis.matrix() assists with determining whether an object is a matrix.
• First function (sum_byname()) now works with Matrix objects, paving the way for sparse matrix representation throughout matsbyname.
• In tests, cleaned up many warnings emanating from the change to testthat v3.
• Reacted to a change in grouping policy in dplyr that caused one test to issue a deprecation warning.
• Update to latest GitHub actions continuous integration workflow.
• Many new tests for new features.
  • Now at 2078 tests, all passing.
  • Test coverage remains at 100%.

matsbyname 0.5.1 (2023-01-16)

CRAN release: 2023-01-16

• Responded to deprecation warnings from purrr::cross2().
• Responded to deprecation warnings from tidyselect.
• transpose_byname() no longer converts a constant into a 1x1 matrix without row or column names.
• New function select_rowcol_piece_byname() enables selecting rows and columns using the RCLabels notation and label pieces.
• New function svd_byname() calculates singular value decomposition of a matrix.
• New argument method on invert_byname() allows callers to select the method for inverting a matrix.
• New functions eigenvalues_byname() and eigenvectors_byname() calculate eigenvalues and eigenvectors of matrices or lists of matrices.
• Added tol argument added to invert_byname(). The value of the tol argument is passed to base::solve().
• invert_byname() now reports names of zero rows and columns when attempting to invert a singular matrix. The new error message will be a huge help for debugging.
• New functions select_zero_rows_byname() and select_zero_cols_byname() assist with detecting problem areas for singular matrices.
• rowsums_byname(), colsums_byname(), and sumall_byname() now correctly return only a single number when a single number is the input.
• aggregate_byname() now returns its argument (a_mat) if a string margin resolves to NA (isn’t a row of column type).
• Aggregation vignette now demonstrates that
  • margins for renaming and aggregating can be determined from row and column types and
  • inference on row and column label notation.
• Renaming and aggregation functions now (by default) infer row and column notations.
• Many new tests for new features.
  • Now at 1165 tests, all passing.
  • Test coverage remains at 100%.

matsbyname 0.5.0 (2022-04-01)

CRAN release: 2022-04-01

• New format for documentation pages, including a search function!
• New vignette “Using summarise in matsbyname” clarifies issues around ambiguities in functions that use a ... argument.
• aggregation-vignette now includes details on using sum_byname(.summarise = TRUE) with dplyr::summarise().
• sum_byname(), matrixproduct_byname(), hadamardproduct_byname(), mean_byname(), geometricmean_byname(), equal_byname(), identical_byname(), samestructure_byname(), and and_byname() all gain argument .summarise to signal intention to operate down a column (.summarise = TRUE) or along a list (.summarise = FALSE). The default value is .summarise = FALSE, thereby maintaining previous behavior.
• New functions agg_table_to_agg_map() and agg_map_to_agg_table() assist with manipulating aggregation maps.
• New vignette aggregation-vignette demonstrates the new aggregation functions.
• Functions rename_to_pref_suff_byname() and aggregate_to_pref_suff_byname() now route to new functions rename_to_piece_byname() and aggregate_pieces_byname(), thereby avoiding code duplication. This change may break some code. These functions now return an empty string (““) when a suffix is requested and one is not found. Previously, these functions returned the entire string when a suffix was not found.
• New function aggregate_pieces_byname() brings the flexibility of the RCLabels to matsbyname.
• Remove (comment for now) notation functions in notation.R that have been moved to RCLabels.
• New function rename_to_piece_byname() will assist with renaming and aggregating according to pieces of row and column names.
• New function vec_from_store_byname() creates vectors from a matrix (from which row of column names are taken) and a vector (which acts as a store of values) based on matching of pieces of the labels. This new function is made possible by the new RCLabels package.
• Notation code moved to new package, RCLabels.
• RCLabels::make_or_pattern() gains new pattern_type, “literal”, which returns the row_col_names argument unmodified.
• trim_rows_cols() gains a warn_if_a_incomplete argument. When TRUE, a warning is issued if argument a is missing entries on margin that are present in mat.
• Many new tests for new features. But some functions have been moved to RCLabels, so the total number of tests has gone down slightly.
  • Now at 1072 tests, all passing.
  • Test coverage remains at 100%.

matsbyname 0.4.25 (2021-10-12)

CRAN release: 2021-10-12

• New notation functions preposition_notation(), from_notation(), and of_notation().
• Many new tests for new features.
  • Now at 1077 tests, all passing.
  • Test coverage remains at 100%.

matsbyname 0.4.24 (2021-10-01)

CRAN release: 2021-10-02

• Added a test to trigger errors when dimnames are NULL.
• Fixed a bug where a 0x0 matrix was not being completed by another matrix.
• New function trim_rows_cols() eliminates rows and/or columns in one matrix based on another.
• Many new tests for new features.
  • Now at 1057 tests, all passing.
  • Test coverage remains at 100%.

matsbyname 0.4.23 (2021-09-01)

CRAN release: 2021-09-02

• hatize_byname() now allows a missing keep argument, eliminating a regression in reverse dependency with the matsindf package.
• This release is for CRAN.
• One test could be deleted, because the hatize_byname() function is now simpler.
  • Now at 1039 tests, all passing.
  • Test coverage remains at 100%.

matsbyname 0.4.22 (2021-07-26)

• Now issuing a helpful warning when hatize_byname() is called with a keep argument that is different from the structure of the vector. This will be a safe way to encourage callers to specify their expectations in the function call.
• Note this version was not released to CRAN, due to frequent revisions.
• New tests for new features.
  • Now up to 1040 tests, all passing.
  • Test coverage remains at 100%.

matsbyname 0.4.21 (2021-07-23)

• hatize_byname() and hatinv_byname() gain a new argument keep that tells whether to keep row names or column names when a 1x1 matrix is supplied. This feature assists with code that may occasionally encounter 1x1 vectors as input.
• Note this version was not released to CRAN, due to frequent revisions.
• New tests for new feature.
  • Now up to 1030 tests, all passing.
  • Test coverage remains at 100%.

matsbyname 0.4.20 (2021-07-19)

CRAN release: 2021-07-21

• New function keep_pref_suff() keeps prefixes or suffixes of individual strings or lists of strings, based on the notation provided.
• New tests for new functions.
  • Now up to 1025 tests, all passing.
  • Test coverage remains at 100%.

matsbyname 0.4.19 (2021-07-17)

CRAN release: 2021-07-18

• Breaking change: New logic for situations where prefix or suffix is not found in split_pref_suff(). Previously, NULL was returned for a missing prefix or suffix. Now, an empty string ("") is returned.
• New tests for whether split_pref_suff() works in a data frame.
• New tests for new logic.
  • Now up to 1009 tests, all passing.
  • Test coverage remains at 100%.

matsbyname 0.4.18 (2021-06-02)

CRAN release: 2021-06-03

• New function kvec_from_template_byname() that creates a row or column vector from a template matrix.
• New function create_colvec_byname() builds on create_matrix_byname().
• New function create_rowvec_byname() builds on create_matrix_byname().
• New function create_matrix_byname() that behaves much like matrix() with “byname” characteristics.
• New tests for new functions.
  • Now up to 1000 tests, all passing.
  • Test coverage remains at 100%.

matsbyname 0.4.17 (2021-04-10)

• Transition to GitHub actions for continuous integration.
• No new tests.
  • Still at 906 tests, all passing.
  • Test coverage remains at 100%.

matsbyname 0.4.16 (2020-11-25)

CRAN release: 2020-11-26

• Moved URLs to https:// where appropriate.
• Fixed a bug in rename_to_pref_suff_byname() where a column vector would fail with “subscript out of bounds” error. The fix was to wrap the return list containing “pref” and “suff” in a list, as the rest of the function expected, when a single row was present.
• Fixed a bug in colsums_byname() and rowsums_byname() where setting the rowname or colname argument to NULL did not result in an empty row name or column name.
• Fixed a bug in hatize_byname() where a 1x1 vector gave error: length of 'dimnames' [1] not equal to array extent. The solution is to check for 1x1 vectors and act accordingly.
• Fixed a warning emitted from stringi.
• New tests for bug fixes.
  Now up to 906 tests, all passing.
• Test coverage remains at 100%.

matsbyname 0.4.15 (2020-05-29)

CRAN release: 2020-05-29

• Added additional tests for new features.
  • Now up to 900 tests, all passing.
  • Test coverage remains at 100%.
• Added tol argument to clean_byname(), allowing for machine precision issues to be addressed.
• Ensured that all old functions, such as rename_to_pref_suff_byname(), aggregate_byname(), and aggregate_to_pref_suff_byname() respect notation when using notation to renaming rows and columns.
• New functions for manipulating names of rows and columns: notation_vec(), arrow_notation(), paren_notation(), bracket_notation(), split_pref_suff(), join_pref_suff(), flip_pref_suff(), switch_notation(), and switch_notation_byname().
• Eliminated a warning in GitHub actions about README.md requiring a nonempty <title> element.

matsbyname 0.4.14 (2020-05-01)

CRAN release: 2020-05-01

• Added additional tests for bug fixes and new features.
  • Now up to 829 tests, all passing.
  • Test coverage remains at 100%.
• Enhanced prep_vector_arg() to duplicate matrices when present as the vector_arg.
• Better error messages for sort_rows_cols(). Now telling which row or column names are duplicates.
• Added function aggregate_pref_suff_byname() that combines rename_to_pref_suff_byname() and aggregate_byname().
• Fixed a crashing bug that appeared when aggregate_byname() collapsed all rows or columns into a single row or single column or both.
• Added new function aggregate_byname() which aggregates rows, columns, or both, according to an aggregation_map. I wanted to add this function for a long time, and I finally found a reason, namely the need to aggregate by prefixes or suffixes in the IEATools package. Furthermore, the aggregation_map idea seems to be solid. Note that aggregation_map = NULL (the default) aggregates rows with same names and columns with same names.
• Added function rename_rowcol_to_pref_suff_byname() which renames rows or columns to prefixes or suffixes in row and column names.
• Fixed a bug in clean_byname() which caused a NULL response when unnamed rows or columns were present.
• Now using new prepare_.FUNdots() function in all *apply_byname() functions.
• Refactored new code for unaryapply_byname() into function prepare_.FUNdots(), so it can be used in other *apply_byname() functions.

matsbyname 0.4.13 (2020-04-17)

CRAN release: 2020-04-18

• Added additional tests for bug fixes.
  • Now up to 766 tests, all passing.
  • Code coverage remains at 100%.
• Fixed a bug in unaryapply_byname(), which was not correctly handling a rectangular two-dimensional list of arguments to FUN supplied in .FUNdots. A rectangular two-dimensional list of arguments in .FUNdots is now interpreted as follows:
  • First dimension contains named arguments to FUN.
  • Second dimension contains unique values of the named arguments to be applied along the main argument a.
  The length of the first dimension of .FUNdots is the number of arguments supplied to FUN. The length of the second dimension of .FUNdots must be equal to the length of a.

matsbyname 0.4.12 (2020-03-21)

CRAN release: 2020-03-22

• Maintenance to prepare for dplyr 1.0.0. Several tests and examples in matsbyname needed a column of a data frame constructed with I(). dplyr::group_by() now requires all groups to have same type, but that wasn’t true in some tests, as some entries were I<list> (items in groups with more than one member) and others were list (items in single-item groups). The solution was to modify two test to
  1. move from data.frame to tibble when creating the data frames for testing and
  2. eliminate the use of I(), as tibble is friendly to list columns.
• Added new function matricize_byname() that converts a column (or row) vector into a matrix. matricize_byname() is the inverse of vectorize_byname().
• Added new function vectorize_byname that converts a matrix into a column vector.
• Added section to vignette about matsindf. This section could be re-added now that matsindf is now on CRAN.

matsbyname 0.4.11 (2019-12-04)

CRAN release: 2019-12-05

• Maintenance release to get ready for R4.0.0. matrix objects now inherit from both matrix and array. Thus, code should no longer assume that class(A) returns an object of length 1 when A is a matrix. So, I eliminated all instances of class(A) == "matrix" in if statements in favor of inherits(A, "matrix"). See https://developer.r-project.org/Blog/public/2019/11/09/when-you-think-class.-think-again/index.html for more details.

matsbyname 0.4.10 (2019-02-16)

CRAN release: 2019-02-16

• Added CRAN installation instructions to README.Rmd, now that the package is on CRAN.
• Added CITATION file. citation("matsbyname") now gives useful information.
• Fixed a bug in matrixproduct_byname in which row and column types were not set correctly when one operand was a matrix and the other operand was NA.

matsbyname 0.4.9 (2019-01-17)

CRAN release: 2019-01-25

• Improved LICENSE file for submission to CRAN.
• First version to appear on CRAN.
• Added CRAN and lifecycle badges.

matsbyname 0.4.8 (2019-01-16)

• Improved cran-comments.md for submission to CRAN.

matsbyname 0.4.7 (2019-01-07)

• Cleaned up dependencies for testing.

matsbyname 0.4.6 (2019-01-07)

• Now all external function calls are fully qualified.

matsbyname 0.4.5 (2019-01-07)

• New function elementapply_byname() applies a function to an element of a matrix specified by row and col arguments.
• Breaking changes:
  • elementproduct_byname() changed to hadamardproduct_byname() to avoid name collision with elementapply_byname().
  • elementquotient_byname() changed to quotient_byname().
  • elementpow_byname() changed to pow_byname().
  • elementexp_byname() changed to exp_byname().

matsbyname 0.4.4 (2019-01-02)

• Added tests to achieve 100% code coverage.

matsbyname 0.4.3 (2019-01-02)

• complete_rows_cols() is now agnostic about the order of columns in fillrow and the order of rows in fillcol.

matsbyname 0.4.2 (2019-01-02)

• sort_rows_cols() now allows entries in roworder and colorder that are not presently names of rows or columns. Extraneous names are silently ignored.

matsbyname 0.4.1 (2019-01-01)

• Adding code coverage badge.

matsbyname 0.4.0 (2018-12-27)

• Attempted first release to CRAN. (Failed.)

matsbyname 0.3.8 (2018-12-21)

• fractionize_byname() now correctly handles non-square matrices.

matsbyname 0.3.7 (2018-12-02)

• hatinv_byname() now handles 0 values in input vectors gracefully. By default, 0 values become .Machine$double.xmax.
  To choose a different value, set new argument inf_becomes to a numerical value. To suppress default behavior, set inf_becomes = NULL.

matsbyname 0.3.6 (2018-11-25)

• iszero_byname() now checks if values of abs(a) are <= tol. (Previously, iszero_byname() tested with < tol.) This change allows the zero matrix to pass the test when tol = 0, as we would want.
• Reverted equal_byname() to use isTRUE(all.equal()) when checking for equality.
• New function identical_byname() checks for exact equality using identical.
• Now up to 672 tests.

matsbyname 0.3.5 (2018-11-18)

• Now using identical() instead of isTRUE(all.equal()) for equal_byname() function.

matsbyname 0.3.4 (2018-11-18)

• Added new function hatinv_byname().
• Documented defaults for arguments to count_* functions.
• Now importing pipe operator from magrittr package at global level

matsbyname 0.3.3 (2018-10-29)

• Fix version number on pkgdown website.
• Updated many details of pkgdown website for better user navigation.

matsbyname 0.3.2 (2018-10-29)

• First release to CRAN didn’t work.
• Added online documentation at github with pkgdown.

matsbyname 0.3.1 (2018-08-25)

• Updated to new version of Roxygen which changed line breaks in some .Rd files.
• First release to CRAN.

matsbyname 0.3.0 (2018-06-20)

• Removed parallelism features introduced in v0.2.6. Detailed timings revealed that the parallel code was slower than single-thread code. This topic may be revisited in the future. But for now, it is best to remove the multicore code. So there are no longer any mc.cores arguments to matsbyname functions.

matsbyname 0.2.9 (2018-05-24)

• Beginnings of S3 class matbyname. Not sure if I want to keep it.
• Fixed an argument name error exposed by check.

matsbyname 0.2.8 (2018-05-17)

• New functions all_byname() and any_byname() make logical tests easy.
• New function replaceNaN_byname() replaces NaN entries with a value (default is 0).

matsbyname 0.2.7 (2018-04-15)

• Refactored most *col*_byname functions to call their respective *row*_byname functions with a transposed argument, thereby simplifying code.
• Fixed a bug caused by the above refactoring. In select_cols_byname, a NULL result terminated the executing thread.
• Added new function replaceNaNWith0.
• Added new functions count_vals_byname, count_vals_inrows_byname, and count_vals_incols_byname that return the number of matrix entries that meet a criterion for the entire matrix, in each row, and in each column, respectively.
• Improvements to documentation.
• Now up to 646 passing tests.

matsbyname 0.2.6 (2018-03-16)

• New multicore functionality available in most *_byname functions.
  • New functions set_mc_cores and get_mc_cores to set and get package-wide mc.cores variable. Default is 1, so all functions work as previously unless mc.cores is more than 1.
  • Alternatively, specify the mc.cores argument of any function to specify the number of cores to be used for an individual calculation. Default is get_mc_cores(). A useful approach is to set_mc_cores(detectCores(logical = FALSE)).
• Suggested usage
  • sum_byname(list(1,2,3,4), list(1,2,3,4), mc.cores = 4) to send each sum to a different core.
  • set_mc_cores(4L); sum_byname(list(1,2,3,4), list(1,2,3,4), mc.cores = 4); set_mc_cores(1L) to do the same thing and set the package-wide value back to 1.

matsbyname 0.2.5 (2018-03-13)

• New *apply_byname functions enable API improvements
  • These are API changes, but they shouldn’t affect any existing code, because calls to binary functions will “just work.”
  • naryapply_byname: enables ... arguments
  • naryapplylogical_byname: enables logical functions
  • Add ... arguments for functions that deserve them.
• New functions with ... arguments including
  • sum_byname
  • matrixproduct_byname
  • elementproduct_byname
  • mean_byname
  • geometricmean_byname
  • equal_byname
  • samestructure_byname
• New and_byname(...) function that provides logical and “by name.”
  • The infrastructure is in place to add other logical functions in the future: or_byname, xor_byname, and not_byname.

matsbyname 0.2.4 (2018-03-08)

• Preparing for submission to CRAN. Changed many variable names in the APIs to standardize on “a” and “b” as names for matrix or list of matrices arguments.

matsbyname 0.2.3 (2018-03-08)

• Eliminate dependence (temporarily) on matsindf. Doing so allows matsbyname to be submitted first to CRAN. Also, Travis builds are now successful, having eliminated the circular dependence between matsbyname and matsindf.

matsbyname 0.2.2 (2018-03-02)

• New function elementpow_byname raises all elements of a matrix to a power.

matsbyname 0.2.1 (2018-02-28)

• complete_rows_cols now accepts fillrow and fillcol arguments. These arguments can be used (instead of the fill argument) to specify the values of filled rows and columns when completing a matrix. When conflicts arise, precedence among the fill* arguments is fillrow then fillcol then fill.

matsbyname 0.2.0 (2018-02-23)

• Name change to matsbyname.