NEWS

diyar 0.5.1.9000

New features

Changes

Bug fixes

diyar 0.5.1 (2023-11-12)

New features

Changes

Bug fixes

links() - Incorrect results in some situations. Resolved.
links_af_probabilistic() - Failed in some situations. Resolved.

diyar 0.5.0 (2023-11-05)

New features

New option ("semi") for the batched argument in links(). All matches are compared against the record-set in the next iteration. Therefore, the number of record-pairs increase exponentially as new matches are found. This means fewer record-pairs (memory usage) but a longer run time compared to the "no" option. Conversely, it leads to more record-pairs (memory usage) but a shorter run time compared to the "yes" option.
New argument (batched) in episodes()
New argument (split) in episodes(). Split the analysis in N-splits of strata. This leads to fewer record-pairs (and memory usage) but a longer run time.
New argument (decode) in as.data.frame.pid(), as.data.frame.epid() and as.data.frame.pane()
New function - episodes_af_shift(). A more vectorised approach to episodes() based on epidm::group_time().
New function - links_wf_episodes(). Implantation of episodes() using links().

Changes

Optimised episodes() and links(). Each iteration now uses less time and memory.
link_id slot in pid objects is now a list.
links() - records with missing values in a sub_criteria are now skipped at the corresponding iteration.
Updated argument in links()- recursive. This now takes any of three options [c("linked", "unlinked", "none")] . [c("linked", "unlinked")] collectively were previously [TRUE], while ["none"] was previously [FALSE].
as.epids() now calls make_episodes().
The default value for the window argument in partitions() is now NULL
as.data.frame() and as.data.list() now only creates elements/fields from non-empty fields
id and gid slots in number_line objects are now integer(0) by default.
episode_group(), record_group() and range_match_legacy() have been removed.
["recurisve"] episodes from episodes() are now presented as ["rolling"] episodes with reference_event = "all_records" i.e
- Old syntax ~ episodes(..., episode_type == "recursive")
- New syntax ~ episodes(..., episode_type == "rolling", reference_event = "all_records")

Bug fixes

When recursive was TRUE, links() ended prematurely and therefore missed some matches. Resolved.
recurrence_sub_criteria in episodes() was not implemented correctly and lead to incorrect linkage result in some instances. Resolved.
overlap_method() - logical tests recycled incorrectly. Resolved.
check_links argument - Option "g" implemented as option "l". Resolved.
make_pairs_wf_source(). Created incorrect pairs. Resolved.
case_sub_criteria and recurrence_sub_criteria in episodes() led to incorrect results. Resolved.

diyar 0.4.2 (2022-12-20)

New features

New argument in merge_ids() - shrink and expand.
New S3 method for class ‘d_report’ - plot.
New S3 method for class ‘sub_criteria’ - format.
New function - true(). Predefined logical test for use with sub_criteria().
New function - false(). Predefined logical test for use with sub_criteria().
New argument in links()- batched. Specify if all record pairs are created or compared at once ("no") or in batches ("yes").
New argument in links()- repeats_allowed. Specify if record-pairs with duplicate elements should be created.
New argument in links()- permutations_allowed. Specify if permutations of the same record-pair should be created.
New argument in links()- ignore_same_source. Specify if record-pairs from different datasets should be created.
New argument in eval_sub_criteria()- depth. First order of recursion.
New function - sets() and make_sets(). Create permutations of record-sets.

Changes

links() - When shrink is TRUE, records in a record-group must meet every listed match criteria and sub_criteria. For example, if pid_cri is 3, then the record must have meet matched another on the the first three match criteria.
links() - pid@iteration now tracks when a record was dealt with instead of when it was assigned to a record-group. For example, a record can be closed (matched or not matched) at iteration 1 but assigned to a record-group at iteration 5.
make_pairs() - x.* and y.* values in the output are now swapped.
sub_criteria can now export any data created by match_func. To do this, match_func must export a list, where the first element is a logical object. See an example below.

library(diyar)
val <- rep(month.abb[1:5], 2); val
#>  [1] "Jan" "Feb" "Mar" "Apr" "May" "Jan" "Feb" "Mar" "Apr" "May"
match_and_export <- function(x, y){
  output <- list(x == y, 
                 data.frame(x_val = x, y_val = y, is_match = x == y))
  return(output)
}
sub.cri.1 <- sub_criteria(
  val, match_funcs = list(match.export = match_and_export)
)

format(sub.cri.1, show_levels = TRUE)
#> logical_test-{
#> Lv.0.1-match.export(Jan,Feb,Mar ...)
#> }
eval_sub_criteria(sub.cri.1)
#> $logical_test
#>  [1] 1 0 0 0 0 1 0 0 0 0
#> 
#> $mf.0.1
#>    x_val y_val is_match
#> 1    Jan   Jan     TRUE
#> 2    Feb   Jan    FALSE
#> 3    Mar   Jan    FALSE
#> 4    Apr   Jan    FALSE
#> 5    May   Jan    FALSE
#> 6    Jan   Jan     TRUE
#> 7    Feb   Jan    FALSE
#> 8    Mar   Jan    FALSE
#> 9    Apr   Jan    FALSE
#> 10   May   Jan    FALSE

links can now export any data created within a sub_criteria. To do this, the sub_criteria must be created as described above. See an example below

val <- 1:5
diff_one_and_export <- function(x, y){
  diff <- x - y
  is_match <- diff <= 1
  output <- list(is_match, 
                 data.frame(x_val = x, y_val = y, diff = diff,  is_match = is_match))
  return(output)
}
sub.cri.2 <- sub_criteria(
  val, match_funcs = list(diff.export = diff_one_and_export)
)
links(
  criteria = "place_holder", 
  sub_criteria = list("cr1" = sub.cri.2))
#> $pid
#> [1] "P.1 (CRI 001)" "P.1 (CRI 001)" "P.3 (CRI 001)" "P.3 (CRI 001)"
#> [5] "P.5 (No hits)"
#> 
#> $export
#> $export$cri.1
#> $export$cri.1$iteration.1
#> $export$cri.1$iteration.1$mf.0.1
#>   x_val y_val diff is_match
#> 1     1     1    0     TRUE
#> 2     2     1    1     TRUE
#> 3     3     1    2    FALSE
#> 4     4     1    3    FALSE
#> 5     5     1    4    FALSE
#> 
#> 
#> $export$cri.1$iteration.2
#> $export$cri.1$iteration.2$mf.0.1
#>   x_val y_val diff is_match
#> 1     3     3    0     TRUE
#> 2     4     3    1     TRUE
#> 3     5     3    2    FALSE

Bug fixes

summary.epid() - Incorrect count for ‘by episode type’. Resolved.
episodes() - Incorrect results in some instances with skip_order. Resolved.
make_ids() - Did not capture all records in that should be in a record-group when matches are recursive. Resolved.
make_pairs() - Incorrect record-pairs in some instances. Resolved.
eval_sub_criteria() - When output of match_func is length one, it’s not recycled. Resolved.
reverse_number_line() - Incorrect results in some instances. Resolved.
links()- Incorrect iteration (pids slot) for non-matches. Resolved.
links() and episodes() - Timing for each iteration was incorrect. Resolved.

diyar 0.4.1 (2021-12-05)

New features

New function - overlap_method_names(). Overlap methods for a corresponding overlap method codes.
Memory usage added to *with_report options for display.

Changes

"chain" overlap method split into "x_chain_y" and "y_chain_x". "chain" will continue to be supported as a keyword for "x_chain_y" OR "y_chain_x" method
"across" overlap method split into "x_across_y" and "y_across_x". "across" will continue to be supported as a keyword for "x_across_y" OR "y_across_x" methods
"inbetween" overlap method split into "x_inbetween_y" and "y_inbetween_x". "inbetween" will continue to be supported as a keyword for "x_inbetween_y" OR "y_inbetween_x" methods
Optimised overlaps().
Some overlap method codes have changed. Please review any previously specified codes with overlap_method_names().

Bug fixes

make_batch_pairs() (internal) created invalid record pairs. Resolved.

diyar 0.4.0 (2021-11-30)

New features

New function - reframe(). Modify the attributes of a sub_criteria object.
New function - link_records(). Record linkage by creating all record pairs as opposed to batches as with link().
New function - make_pairs(). Create every combination of records-pairs for a given dataset.
New function - make_pairs_wf_source(). Create records-pairs from different sources only.
New function - make_ids(). Convert an edge list to a group identifier.
New function - merge_ids(). Merge two group identifiers.
New function - attrs(). Pass a set of attributes to one instance of match_funcs or equal_funcs.

Changes

Optimised episodes_wf_splits()
Optimised episodes() and links(). Reduced processing times.
Three new options for the display argument. "progress_with_report", "stats_with_report" and "none_with_report". Creates a d_report; a status of the analysis over its run time.
eval_sub_criteria(). Record-pairs are no longer created in the function. Therefore, index_record and sn arguments have been replaced with x_pos and y_pos.
link_records() and links_wf_probabilistic(). The cmp_threshold argument has been renamed to attr_threshold.
show_labels argument in schema(). Two new options - "wind_nm" and "length" to replace "length_label".

Bug fixes

Incorrect wind_id list in episodes(..., data_link = "XX") in . Resolved.
Incorrect link_id in links(..., recursive = TRUE). Resolved.
iteration not recorded in some situations with episodes(). Resolved.
skip_order ends an open episode. Resolved.
NA in dist_wind_index and dist_epid_index when sn is supplied. Resolved.
overlap_method_codes() - overlap method codes not recycled properly. Resolved.

diyar 0.3.1 (2021-08-09)

New features

New function - delink(). Unlink identifiers.
New function - episodes_wf_splits(). Wrapper function of episodes(). Better optimised for handling datasets with many duplicate records.
New function - combi(). Numeric codes for unique combination of vectors.
New function - attr_eval(). Recursive evaluation of a function on each attribute of a sub_criteria.

Changes

Two new case_nm values - Case_CR and Recurrence_CR which are Case and Recurrence without a sub-criteria match.

Bug fixes

Corrected length arrows in schema.epid.
Corrected outcome of eval_sub_criteria with 1 result.

diyar 0.3.0 (2021-04-25)

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(). Encode and decode slots values to minimise memory usage.
New argument in episodes() - case_sub_criteria and recurrence_sub_criteria. Additional matching conditions for temporal links.
New argument in episodes()- case_length_total and recurrence_length_total. Number of temporal links required for a window/episode.
New argument in links() - recursive. Control if matches can spawn new matches.
New argument in links() - check_duplicates. Control the checking of logical tests on duplicate values. If FALSE, results are recycled for the duplicates.
as.data.frame and as.list S3 methods for the pid, number_line, epid, pane objects.
New option for episode_type in episodes() - “recursive”. For recursive episodes where every linked events can be used as a subsequent index event.
recurrence_from_last renamed to reference_event and given two new options.

Changes

episodes() and links(). Speed improvements.
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.

diyar 0.2.0 (2020-09-17)

New features

Better support for Inf in number_line objects.
Can now use multiple case_length or recurrence_length for the same event.
- Can now use multiple overlap_methods for the corresponding case_length and recurrence_length.
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 a particular case_length or recurrence_length. 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.

diyar 0.1.0 (2020-06-13)

New features

New argument in record_group() - strata. Perform record linkage separately within subsets of a dataset.
New argument in overlap(), compress_number_line(), fixed_sepisodes(), rolling_episodes() and episode_group() - overlap_methods and methods. 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.
New slot in epid objects - win_nm. Shows the type of window each event belongs to i.e. case or recurrence window
New slot in epid objects - win_id. 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
New slot in epid objects - dist_from_wind. Shows the duration of each event from its window’s reference event
New slot in epid objects - dist_from_epid. Shows the duration of each event from its episode’s reference event
New argument in episode_group() and rolling_episodes() - recurrence_from_last. Determine if reference events should be the first or last event from the previous window.
New argument in episode_group() and rolling_episodes() - case_for_recurrence. Determine if recurrent events should have their own case windows or not.
New argument in episode_group(), fixed_episodes() and rolling_episodes() - data_links. Unlink 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).
New argument in episode_group(), fixed_episodes() and rolling_episodes() - include_index_period. 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).
New slot in pid objects - link_id. Shows the record (sn slot) to which every record in the dataset has matched to.
New function - invert_number_line(). Invert the left and/or right points to the opposite end of the number line
New accessor functions -left_point(x)<-, right_point(x)<-, start_point(x)<- and end_point(x)<-

Changes

overlap() renamed to overlaps(). overlap() is now a convenience overlap_method to capture 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

diyar 0.0.3 (2019-12-08)

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)

diyar 0.0.2 (2019-11-11)

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()

diyar 0.0.1 (2019-10-06)

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()