revdep/library/diyar/new/diyar/NEWS.md

In OlisaNsonwu/diyar: Record Linkage and Epidemiological Case Definitions in 'R'

Version 0.2.0.9000

New features

• New function - links_wf_probabilistic(). Probabilistic record linkage.
• New function - partitions(). Spilt events into sections in time.
• New function - schema(). Plot schema diagrams for pid, epid, pane and number_line objects.
• New functions - encode() and decode(). Encoding and decoding slots values to minimise memory usage.
• New argument - case_sub_criteria and recurrence_sub_criteria in episodes(). Additional matching conditions for temporal links.
• New argument - case_length_total and recurrence_length_total in episodes(). Number of temporal links required for a window/episode.
• New argument - recursive in links(). Control if matches can spawn new matches.
• New argument - check_duplicates in links(). Control the checking of logical tests on duplicate values. If FALSE, results are recycled for the duplicates.
• as.data.frame and as.list for the pid, number_line, epid, pane objects.
• A new type of episode - “recursive” episodes.
• recurrence_from_last renamed to reference_event and given two new options.
• Optimised episodes() and links(). Speed improvements.

Changes

• Default time zone for an epid_interval or pane_interval with POSIXct objects is now “GMT”.
• number_line_sequence() - splits number_line objects. Also available as a seq method.
• epid_total, pid_total and pane_total slots are populated by default. No need to used group_stats to get these.
• to_df() - Removed. Use as.data.frame() instead.
• to_s4() - Now an internal function. It’s no longer exported.
• compress_number_line() - Now an internal function. It’s no longer exported. Use episodes() instead.
• sub_criteria() - produces a sub_criteria object. Nested “AND” and “OR” conditions are now possible.
• case_overlap_methods, recurrence_overlap_methods and overlap_methods now take integer codes for different combinations of overlap methods. See overlap_methods$options for the full list. character inputs are still supported.

Bug fixes

• "Single-record" was wrong in links summary output. Resolved.

Version 0.2.0

New features

• Better support for Inf in number_line objects.
• Can now use multiple case_lengths or recurrence_lengths for the same event.
  • Can now use multiple overlap_methods for the corresponding case_lengths and recurrence_lengths.
• New function links() to replace record_group().
• New function sub_criteria(). The new way of supplying a sub_criteria in links().
• New functions exact_match(), range_match() and range_match_legacy(). Predefined logical tests for use with sub_criteria(). User-defined tests can also be used. See ?sub_criteria.
• New function custom_sort() for nested sorting.
• New function epid_lengths() to show the required case_length or recurrence_length for an analyses. Useful in confirming the required case_length or recurrence_length for episode tracking.
• New function epid_windows(). Shows the period a date will overlap with given particular case_lengths or recurrence_lengths. Useful in confirming the required case_length or recurrence_length for episode tracking.
• New argument - strata in links(). Useful for stratified data linkage. As in stratified episode tracking, a record with a missing strata (NA_character_) is skipped from data linkage.
• New argument - data_links in links(). Unlink record groups that do not include records from certain data sources
• New convenience functions
  • listr(). Format atomic vectors as a written list.
  • combns(). An extension of combn to generate permutations not ordinarily captured by combn.
• New iteration slot for pid and epid objects
• New overlap_method - reverse()

Changes

• number_line() - l and r must have the same length or be 1.
• episodes() - case_nm differentiates between duplicates of "Case" ("Duplicate_C") and "Recurrent" events ("Duplicate_R").
• Strata and episode-level options for most arguments. This gives greater flexibility within the same instance of episodes().
  • Episode-level - The behaviour for each episode is determined by the corresponding option for its index event ("Case").
    • episode_type - simultaneously track both "fixed" and "rolling" episodes.
    • skip_if_b4_lengths - simultaneously track episodes where events before a cut-off range are both skipped and not skipped.
    • episode_unit - simultaneously track episodes by different units of time.
    • case_for_recurrence - simultaneously track "rolling" episodes with and without an additional case window for recurrent events.
    • recurrence_from_last - simultaneously track "rolling" episodes with reference windows calculated from the first and last event of the previous window.
  • Strata-level - The behaviour for each episode is determined by the corresponding option for its strata. Options must be the same in each strata.
    • from_last - simultaneously track episodes in both directions of time - past to present and present to past.
    • episodes_max - simultaneously track different number of episodes within the dataset.
• include_overlap_method - "overlap" and "none" will not be combined with other methods.
  • "overlap" - mutually inclusive with the other methods, so their inclusion is not necessary.
  • "none" - mutually exclusive and prioritised over the other methods (including "none"), so their inclusion is not necessary.
• Events can now have missing cut-off points (NA_real_) or periods (number_line(NA_real_, NA_real_)) case_length and recurrence_length. This ensures that the event does not become an index case however, it can still be part of different episode. For reference, an event with a missing strata (NA_character_) ensures that the event does not become an index case nor part of any episode.

Bug fixes

• fixed_episodes, rolling_episodes and episode_group - include_index_period didn’t work in certain situations. Corrected.
• fixed_episodes, rolling_episodes and episode_group - dist_from_wind was wrong in certain situations. Corrected.

Version 0.1.0

New features

• record_group() - strata argument. Perform record grouping separately within subsets of a dataset.
• overlap(), compress_number_line(), fixed_sepisodes(), rolling_episodes() and episode_group() - overlap_methods and methods arguments replaces overlap_method and method respectively. Use different sets of methods within the same dataset when grouping episodes or collapsing number_line objects. overlap_method and method only permits 1 method per per dataset.
• epid objects - win_nm slot. Shows the type of window each event belongs to i.e. case or recurrence window
• epid objects - win_id slot. Unique ID for each window. The ID is the sn of the reference event for each window
  • Format of epid objects updated to reflect this
• epid objects - dist_from_wind slot. Shows the duration of each event from its window’s reference event
• epid objects - dist_from_epid slot. Shows the duration of each event from its episode’s reference event
• episode_group() and rolling_episodes() - recurrence_from_last argument. Determine if reference events should be the first or last event from the previous window.
• episode_group() and rolling_episodes() - case_for_recurrence argument. Determine if recurrent events should have their own case windows or not.
• episode_group(), fixed_episodes() and rolling_episodes() - data_links argument. Ungroup episodes that do not include records from certain data_source(s).
• episode_group(), fixed_episodes() and rolling_episodes() - case_length and recurrence_length arguments. You can now use a range (number_line object).
• episode_group(), fixed_episodes() and rolling_episodes() - case_length and recurrence_length arguments. You can now use a range (number_line object).
• episode_group(), fixed_episodes() and rolling_episodes() - include_index_period argument. If TRUE, overlaps with the index event or period are grouped together even if they are outside the cut-off range (case_length or recurrence_length).
• pid objects - link_id slot. Shows the record (sn slot) to which every record in the dataset has matched to.
• invert_number_line() - Invert the left and/or right points to the opposite end of the number line
• left_point(x)<-, right_point(x)<-, start_point(x)<- and end_point(x)<- accessor functions

Changes

• overlap() renamed to overlaps(). overlap() is now a convenience overlap_method for ANY kind of overlap
• "none" is another convenience overlap_method for NO kind of overlap
• expand_number_line() - new options for point; "left" and "right"
• compress_number_line() - compressed number_line object inherits the direction of the widest number_line among overlapping group of number_line objects
• overlap_methods - have been changed such that each pair of number_line objects can only overlap in one way. E.g.
  • "chain" and "aligns_end" used to be possible but this is now considered a "chain" overlap only
  • "aligns_start" and "aligns_end" use to be possible but this is now considered an "exact" overlap
• number_line_sequence() - Output is now a list.
• number_line_sequence() - now works across multiple number_line objects.
• to_df() - can now change number_line objects to data.frames.
  • to_s4() can do the reverse.
• epid objects are the default outputs for fixed_episodes(), rolling_episodes() and episode_group()
• pid objects are the default outputs for record_group()
• In episode grouping, the case_nm for events that were skipped due to rolls_max or episodes_max is now "Skipped".
• In episode_group() and record_group(), sn can be negative numbers but must still be unique
• Optimised episode_group() and record_group(). Runs just a little bit faster …
• Relaxed the requirement for x and y to have the same lengths in overlap functions.
  • The behaviour of overlap functions will now be the same as that of standard R logical tests
• episode_group - case_length and recurrence_length arguments. Now accepts negative numbers.
  • negative “lengths” will collapse two periods into one, if the second one is within some days before the end_point() of the first period.
    • if the “lengths” are larger than the number_line_width(), both will be collapsed if the second one is within some days (or any other episode_unit) before the start_point() of the first period.
• cheat sheet updated

Bug fixes

• Recurrence was not checked if the initial case event had no duplicates. Resolved
• case_nm wasn’t right for rolling episodes. Resolved

Version 0.0.3

Changes

• #7 episode_group(), fixed_episodes() and rolling_episodes() - optimized to take less time when working with large datasets
• episode_group(), fixed_episodes() and rolling_episodes() - date argument now supports numeric values
• compress_number_line() - the output (gid slot) is now a group identifier just like in epid objects (epid_interval)

Version 0.0.2

New feature

• pid S4 object class for results of record_group(). This will replace the current default (data.frame) in the next major release
• epid S4 object class for results of episode_group(), fixed_episodes() and rolling_episodes(). This will replace the current default (data.frame) in the next release
• to_s4() and to_s4 argument in record_group(), episode_group(), fixed_episodes() and rolling_episodes(). Changes their output from a data.frame (current default) to epid or pid objects
• to_df() changes epid or pid objects to a data.frame
• deduplicate argument from fixed_episodes() and rolling_episodes() added to episode_group()

Changes

• fixed_episodes() and rolling_episodes() are now wrapper functions of episode_group(). Functionality remains the same but now includes all arguments available to episode_group()
• Changed the output of fixed_episodes() and rolling_episodes() from number_line to data.frame, pending the change to epid objects
• pid_cri column returned in record_group is now numeric. 0 indicates no match.
• columns can now be used as criteria multiple times record_group()
• #6 number_line objects can now be used as a criteria in record_group()

Bug fixes

• #3 - Resolved a bug with episode_unit in episode_group()
• #4 - Resolved a bug with bi_direction in episode_group()

Version 0.0.1

Features

• fixed_episodes() and rolling_episodes() - Group records into fixed or rolling episodes of events or period of events.
• episode_group() - A more comprehensive implementation of fixed_episodes() and rolling_episodes(), with additional features such as user defined case assignment.
• record_group() - Multistage deterministic linkage that addresses missing data.
• number_line S4 object.
  • Used to represent a range of numeric values to match using record_group()
  • Used to represent a period in time to be grouped using fixed_episodes(), rolling_episodes() and episode_group()
  • Used as the returned output of fixed_episodes() and rolling_episodes()

OlisaNsonwu/diyar documentation built on April 22, 2024, 6:27 p.m.