NEWS.md

In scrutiny: Error Detection in Science

scrutiny 0.5.0

The package is now released under the MIT license.

Breaking changes

• The ratio column in the output of grim_map() and grim_map_seq() was replaced by a probability column. This means:

  • Numerically, the only difference is that probability is zero whenever ratio was negative.

  • Conceptually, it is much easier to interpret: it is the probability that a reported mean or percentage of integer data that has a specific number of decimal places but is otherwise random is GRIM-inconsistent with the reported sample size.

    For example, probability is 0.6 for a mean of 1.23 and a sample size of 40. The same is true for any other mean with two decimal places. Thus, a randomly chosen mean with two decimal places, ostensibly derived from integer data, has a 0.6 probability of being GRIM-inconsistent with the reported sample size.

• In the functions around grim_ratio(), the x argument must now be a string. This is consistent with grim_map(), unround(), etc.; and it prevents erroneous results that could previously occur by omitting trailing zeros.

• The GRIMMER implementation was debugged, so that grimmer_map() etc. may now yield different results in a few cases. In particular, the items argument now works correctly, thanks to Aurélien Allard and Lukas Wallrich (#58).

• is_seq_dispersed() now correctly returns FALSE if different numbers of missing values at the start and end of x mean that x cannot be dispersed around from.

New features

• The probability column (see above) is created by a new function, grim_probability().

Lifecycle updates

Deprecated

• As a consequence of the above, the show_prob argument of grim_map() is now deprecated and will be removed in a future version. It no longer has any effect.

• grim_ratio_upper() is deprecated and will be removed in a future version. It no longer seems very interesting (and likely never was), especially now that the GRIM ratio in general has taken a backseat.

• All 15 (!) functions around is_subset_of() are deprecated and will be removed in a future version. In truth, they were always poorly written and widely out of scope for scrutiny.

Removed

All of these had been deprecated since scrutiny 0.3.0:

• audit_list() was removed.

• The sep argument in restore_zeros() and restore_zeros_df() was removed.

• The numeric_only argument in duplicate_count() and duplicate_detect() was removed.

• The na.rm argument in duplicate_count_colpair() was removed.

scrutiny 0.4.0

This version brings major performance improvements. Furthermore:

Bugfixes

• Fixed a bug in audit_seq(): If the dispersion argument in the preceding call to a function like grim_map_seq() was specified as something other than a linearly increasing sequence, the "diff_*" columns in the data frames returned by audit_seq() may have contained incorrect values.
• Similarly, audit_seq() and reverse_map_seq() used to reconstruct the reported values incorrectly if the dispersion default was overridden as described above. At least for now, the issue is handled by throwing an error if these functions operate on data frames that are the result of specifying dispersion as something other than a linearly increasing sequence.
• Fixed a bug that incorrectly threw an error in grim_map_seq(), other functions made by function_map_seq(), as well as seq_disperse() and seq_disperse_df() if an input value was so close to out_min or out_max that the output sequence would be shorter than implied by dispersion / .dispersion , and if track_var_change / .track_var_change (see below) was TRUE. Again, note that the bug only occurred if an error was thrown.

New features

• A new vignette lists the options for specifying the rounding argument that many scrutiny functions have: vignette("rounding-options").
• Another new vignette shows the minimal steps to implement a consistency test using scrutiny: vignette("consistency-tests-simple").
• The output of grim_map_seq(), grimmer_map_seq(), debit_map_seq() and any other function made by function_map_seq() now has a diff_var column that tracks the difference between the dispersed variable (see the var column) and the reported value. Following the diff_* columns in the output of audit_seq(), this is the number of dispersion steps, not the actual numeric difference.
• The same diff_* columns are now integer, not double.
• function_map(), function_map_seq(), and function_map_total_n() have a new .name_key_result argument that controls the name of the key result column in the output of the factory-made function. This is "consistency" by default, but other names will fit better for other kinds of tests. (The results of these tests must still be logical values.)

Minor changes

• In duplicate_count(), the count column in the output tibble was renamed to frequency. This makes for a more streamlined frequency table and removes an ambiguity with duplicate_count_colpair(), where the count output column means something different.
• In seq_disperse() and seq_disperse_df(), the track_var_change / .track_var_change argument was renamed to track_diff_var / .track_diff_var. The arguments with the old names are still present for now but will be removed in a future version. Also, the unit of these values is now dispersion steps, for consistency with grim_map_seq() etc. as well as audit_seq().
• grim_total(), grim_ratio(), and grim_ratio_upper() now require x to have length 1.
• The docs now link to functions when opened in RStudio, not just on the website.
• Accordingly, the output of write_doc_factory_map_conventions() now renders links. The function also has a new scrutiny_prefix argument for use in another package.
• The "Infrastructure" article was renamed to "Developer tools"; vignette("devtools").
• Some dependencies that used to be suggested are now imported.

scrutiny 0.3.0

Duplicate analysis overhaul

The duplicate_*() functions now present their output better and have overall been streamlined. Read more at vignette("duplicates").

• A new function, duplicate_tally(), marks each observation with its overall frequency. It is similar to duplicate_detect() but more informative.

• In duplicate_count():

  • All values are now treated like character strings, so all can be checked. The numeric_only argument is deprecated and should no longer be used.

  • The output tibble has two new columns, locations and locations_n. These hold the names of all input columns in which a value appears and the number of these columns. Details are controlled by the new locations_type argument.

  • New ignore argument for specifying one or more values that will not be checked for duplicates.

• In duplicate_count_colpair():

  • New total_x and total_y columns in the output show how many non-missing values were checked for duplicates.

  • New ignore argument as in duplicate_count().

  • The na.rm argument is deprecated. It wasn't very useful because missing values are never checked for duplicates.

• duplicate_detect() is superseded. It is less informative than duplicate_count() and, in particular, duplicate_tally(). Still, it shares in the overhaul:

  • As in duplicate_count(), all values are now treated like character strings, so all can be checked. The numeric_only argument is deprecated and should no longer be used.
  • The duplicate status of missing values is now shown as NA.
  • New ignore argument as in duplicate_count().

Bugfixes

• Fixed a numeric precision bug in round_up_from() and round_down_from() that occurred when rounding numbers greater than circa 2100 with a part to be truncated that was equal to 5 on that decimal level (thanks to \@kaz462, #43). These functions are called within round_up() and round_down(), and indirectly by all consistency-testing functions.

• Fixed a bug in audit_seq() that displayed one "hit" found by varying a given reported value if there were no such hits. The other columns were not affected.

• Fixed a bug in function_map() that displayed the wrong calling function's name in case of an error.

Minor improvements

• Documentation for grim_map_seq() and all other functions made by function_map(), function_map_seq(), or function_map_total_n() now displays meaningful defaults. Printing the factory-made functions is more meaningful, as well. Internally, they now work with rlang::new_function(), which allows for flexible metaprogramming.

• The experimental function audit_list() is deprecated. Just use audit() instead. audit_seq() and audit_total_n() are now documented separately from audit() and audit_list().

• The lifecycle package is now imported and used in formal deprecations such as that of sep in the restore_*() functions. The janitor package is no longer suggested.

• Adjusted to new CRAN requirements for packageVersion() usage.

• Some performance improvements.

scrutiny 0.2.4

• New decimal_places_df() function that takes a data frame and counts the decimal places in all numeric-like columns.
• Four new predicate functions centered around is_map_df() test whether an object is the output of a scrutiny-style mapper function for consistency tests.
• Newly exported is_numeric_like() function to test whether an object (e.g., a string vector) can be coerced to numeric.
• New grim_ratio_upper() function gives an upper bound for grim_ratio().

• Changes in split_by_parens():

  • The function now uses a cols argument instead of the dots (...). This follows tidyselect development guidelines. The default, cols = everything(), is to select all columns that contain the sep elements (by default, parentheses). Set the new check_sep argument to FALSE to select all columns regardless.

  • All other arguments were renamed: they no longer start on a dot. Furthermore, .col1 and .col2 have been renamed to end1 and end2.

  • A warning is now issued if one or more columns can't be split (or is de-selected from splitting). This occurs if a column doesn't contain the sep elements.

  • Internal changes for compatibility with dplyr 1.1.0.

  • In restore_zeros_df() as well, the dots (...) were replaced by a cols argument, and each other argument no longer has a prefix dot. This follows the changes in split_by_parens(), but note the default selection restrictions by the new check_numeric_like argument. The optional check_decimals argument goes even further.
  • Prevent false-positive warnings when printing ggplot objects (they had occurred since ggplot2 3.4.0).

scrutiny 0.2.3

Some new features and bugfixes:

• New audit() methods for the output of audit_seq() and audit_total_n().

• New duplicate_count_colpair() function that checks each combination of columns in a data frame for duplicates.

• New restore_zeros_df() function to easily restore trailing zeros in all numeric-like columns in a data frame.

• New seq_length() function to extend or shorten linear sequences.

• Bugfixes in the is_seq_*() functions.

• Argument evaluation is now forced in the function factories: function_map(), function_map_seq(), and function_map_total_n().

• Some possible corner case issues in split_by_parens() are now prevented.

• Internal changes for compatibility with purrr 1.0.0 and tidyselect 1.2.0.

scrutiny 0.2.2

This is a patch for CRAN compliance.

• The package now requires R version >= 3.4.0 and rlang version >= 1.0.2.

• Subtle changes to split_by_parens() that users generally won't notice.

• Minor shifts in the documentation (e.g., vignette("consistency-tests") now has instructions on exporting factory-made functions.).

scrutiny 0.2.1

This is a patch.

• It reduces the scope of some examples for CRAN compliance.

• Minor vignette changes.

scrutiny 0.2.0

This is a massive release, with many new features and improvements all over scrutiny. Most notably, the package now includes an entirely new system for implementing consistency tests.

• A new vignette lays out how to implement consistency tests using scrutiny's infrastructure. It describes many of the features mentioned below.
• GRIMMER support was added, as explained in another new vignette. All GRIM and DEBIT functions mentioned below have GRIMMER analogues. For example, grimmer_map_seq() is analogous to grim_map_seq().
• Because of the new, stricter rules for consistency tests, the output of grim_map() no longer includes an items column by default. Instead, the numbers of items (1 by default) are factored into the output's n column. This focuses the presentation on the essence of GRIM.
• GRIM and DEBIT functions are now somewhat less likely to flag value sets as inconsistent. That is because measures were taken to reduce spurious, computer-induced differences when comparing floating-point numbers. The same applies to the new GRIMMER functions.
• function_map() enables users to quickly create consistency test functions for data frames much like grim_map() or debit_map().
• grim_map_seq() checks if GRIM inconsistencies might be due to small errors, and the true values might be close to the reported ones. It varies the inputs up and down in a specified range, holding the respective other ones constant, and tests all those combinations. For summaries, call audit_seq() on the results.
• debit_map_seq() does the same for DEBIT.
• The above two are powered by function_map_seq(), which allows users to easily create functions just like these for any consistency test. All that's needed is a data-frame-level consistency testing function like grim_map() or debit_map().
• grim_map_total_n() applies GRIM in cases where no group sizes are reported, only total sample sizes. It systematically matches possible group sizes (around half the total) with reported mean or proportion values, GRIM-tests them, and counts the scenarios in which both matches are consistent. For summaries, call audit_total_n() on the results.
• debit_map_total_n() does the same for DEBIT.
• The above two are powered by function_map_total_n(), which allows users to easily create new functions like grim_map_total_n() or debit_map_total_n(), provided a data-frame-level consistency testing function like grim_map() or debit_map().
• On a lower level still, disperse_total() takes a total sample size (comprised of the two unknown group sizes on interest) and calls the appropriate group-level function: disperse() for even totals, disperse2() for odd ones.
• seq_disperse() and seq_disperse_df() extend scrutiny's support for string decimal sequences with trailing zeros. They construct sequences centered around the input; a use case not directly covered by base::seq().
• Predicate functions around is_seq_linear() test whether a vector represents a certain kind of numeric sequence.
• In debit_map(), the x column is now to the left of the sd column if show_rec is FALSE, in accordance with the show_rec = TRUE default.
• debit() is now vectorized.
• The functions around is_subset_of() and is_superset_of() functions now have stricter variants grouped around is_proper_subset_of() and is_proper_superset_of().
• split_by_parens() now accepts any pair of separators passed to .sep as a length-2 vector.

scrutiny 0.1.1

This is a patch, mainly fixing a bug that used to affect the presentation of input data in grim_map()'s results. It needs to be emphasized that this bug only affected a convenience feature, namely the presentation of certain input data in the output, not the GRIM test itself.

• Previously, if percent was set to TRUE, the x values were converted to percentages. Because they need to be presented as strings, percentage conversion involves restoring the correct number of trailing zeros. The bug, then, was that all the x values appearing in the output (not in the internal computations!) were restored to the same "length" as the single longest one. This was now remedied, and x values are restored to their individually appropriate number of trailing zeros.

• Another bugfix concerns versioning. Previously, the package had an incorrect version number. It was now corrected.

• The last change was to remove an outdated and potentially misleading paragraph in the documentation of reround_to_fraction().

scrutiny 0.1.0

• This version includes an overhaul of grim_plot():

  • It extends the function to cover cases of decimals values greater than 2, using a gradient instead of a raster.

  • It enables data-free calls to grim_plot() with the new show_data argument. Resulting plots only display the background raster. This mirrors Figure 1 in Brown and Heathers' GRIM paper. (Although grim_plot() as a whole is modeled after this figure, the default addition of empirical summary data is specific to scrutiny.) Like Brown and Heathers, users may wish to create such raster-only plots in order to demonstrate some principled points. The key parameters decimals and rounding can be controlled directly to make up for the lack of information from data.

  • The function now checks if all input means or proportions (x) have the same number of decimal places. If they don't, it throws an error. This strict criterion can be circumvented by specifying the decimals argument. However, since each raster is specific to one number of decimal places (and hence cannot be interpreted regarding x values with a different number), the recommended solution is to plot x values separately --- once for each number of decimal places.

  • The show_full_range argument was removed because I now think it is superfluous.

  • Previously, there was some space between the raster and the y-axis. It has now been removed.

  • Test result data points, shown in blue and/or red by default, are now built on top of the raster, which makes for a more distinct appearance.

• Two new functions, reround_to_fraction(), and reround_to_fraction_level(), enable fractional rounding, inspired by janitor::round_to_fraction(). For example, they might round 0.4 to 0.5 for fractions of 2. What tells the new functions apart is that they come with all the flexibility of reround(). Furthermore, reround_to_fraction_level() is closer to a conventional rounding function than the other two.

• The new version also fixes a bug in row_to_colnames(), rewriting the function's core.

• Another bug was fixed in grim() and grim_map(), concerning show_rec: For rounding strings that lead to four reconstructed numbers per x value rather than just two, it used to be the case that only the two values corresponding to the first of the two rounding procedures were displayed in the output tibble. Now, all four are displayed, bearing appropriate names.

• Another bugfix is for the threshold argument in reround(), which didn't work properly before. This used to affect higher-level functions such as grim(), grim_map(), debit(), and debit_map(), as well. The default for threshold is now 5 in all such functions. Note that rounding up and down from 5 has been fully functional independently of it.

• Also in reround(), the rec argument has been renamed to x in accordance with general naming conventions. The decimals argument has been renamed to digits in accordance with naming conventions among rounding functions.

• In split_by_parens(), ellipsis support was added to protect the user from silent, unexpected results following named arguments in tidy evaluation. The ellipsis package has been added to the Suggests field in DESCRIPTION.

• In some high-level functions, internal checks now determine if the lengths of multiple arguments that are factored into the same internal function call are mutually congruent. That is, if two such arguments are length > 1, they need to have the same length (which will throw a warning). Otherwise, there will be an explicit and very specific error message.

• Finally, some minor refactoring and other small changes that users generally won't notice.

scrutiny 0.0.1

• Added vignette about other packages for error detection, called Related software.
• Exported grim_plot().
• Minor refactoring.

scrutiny 0.0.0.9000

• Added a NEWS.md file to track changes to the package.

scrutiny documentation built on Sept. 22, 2024, 9:06 a.m.