Package: diyar 0.5.1.9001

diyar: Record Linkage and Epidemiological Case Definitions in 'R'

An R package for iterative and batched record linkage, and applying epidemiological case definitions. 'diyar' can be used for deterministic and probabilistic record linkage, or multistage record linkage combining both approaches. It features the implementation of nested match criteria, and mechanisms to address missing data and conflicting matches during stepwise record linkage. Case definitions are implemented by assigning records to groups based on match criteria such as person or place, and overlapping time or duration of events e.g. sample collection dates or periods of hospital stays. Matching records are assigned a unique group ID. Index and duplicate records are removed or further analyses as required.

Authors:Olisaeloka Nsonwu

diyar_0.5.1.9001.tar.gz
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diyar.pdf |diyar.html
diyar/json (API)
NEWS

# Install 'diyar' in R:
install.packages('diyar', repos = c('https://olisansonwu.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/olisansonwu/diyar/issues

Datasets:

On CRAN:

6.30 score 6 stars 33 scripts 432 downloads 102 exports 28 dependencies

Last updated 30 days agofrom:317dfb5fab. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 23 2024
R-4.5-winWARNINGNov 23 2024
R-4.5-linuxWARNINGNov 23 2024
R-4.4-winWARNINGNov 23 2024
R-4.4-macWARNINGNov 23 2024
R-4.3-winWARNINGNov 23 2024
R-4.3-macWARNINGNov 23 2024

Exports:acrossaligns_endaligns_startas.epidas.number_lineas.paneas.pidattr_evalattrsbys_countbys_cummaxbys_cumminbys_cumprodbys_cumsumbys_lagbys_leadbys_maxbys_minbys_nvalbys_positionbys_prodbys_rankbys_sumbys_valchaincombicustom_sortdecodedelinkencodeend_pointend_point<-epid_lengthsepid_windowsepisodesepisodes_af_shiftepisodes_wf_repeatsepisodes_wf_splitseval_sub_criteriaexactexact_matchexclude_overlap_methodexpand_number_linefalseinbetweeninclude_overlap_methodindex_windowintersect_number_linesinvert_number_lineis.epidis.number_lineis.paneis.pidleft_pointleft_point<-linkslinks_af_probabilisticlinks_wf_episodeslinks_wf_probabilisticlistrmake_episodesmake_idsmake_pairsmake_pairs_wf_sourcemake_setsmerge_idsnonenumber_linenumber_line_sequencenumber_line_widthoverlapoverlap_methodoverlap_method_codesoverlap_method_namesoverlapspartitionsprob_linkprob_score_rangerange_matchreframereverse_number_lineright_pointright_point<-schemasetsshift_number_linestart_pointstart_point<-sub_criteriasubtract_number_linestrueunion_number_linesx_across_yx_aligns_end_yx_aligns_start_yx_chain_yx_inbetween_yy_across_xy_aligns_end_xy_aligns_start_xy_chain_xy_inbetween_x

Dependencies:clicolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithr

Divvy up events with partitions

Rendered frompanes.Rmdusingknitr::rmarkdownon Nov 23 2024.

Last update: 2023-10-30
Started: 2021-10-27

Introduction to epidemiological case definitions with diyar

Rendered fromepisodes.Rmdusingknitr::rmarkdownon Nov 23 2024.

Last update: 2023-10-30
Started: 2020-08-15

Introduction to record linkage with diyar

Rendered fromlinks.Rmdusingknitr::rmarkdownon Nov 23 2024.

Last update: 2023-11-12
Started: 2020-08-15

number_line and overlaps

Rendered fromnumber_line.Rmdusingknitr::rmarkdownon Nov 23 2024.

Last update: 2022-12-16
Started: 2020-04-07

Readme and manuals

Help Manual

Help pageTopics
Sub-criteria attributes.attr_eval
Vectorised approach to group operations.bys_count bys_cummax bys_cummin bys_cumprod bys_cumsum bys_funcs bys_lag bys_lead bys_max bys_min bys_nval bys_position bys_prod bys_rank bys_sum bys_val
Vector combinationscombi
Nested sortingcustom_sort
d_reportas.data.frame.d_report as.list.d_report d_report plot.d_report
Unlink group identifiersdelink delink.epid delink.pane delink.pid
Labelling in 'diyar'decode decode.default decode.d_label encode encode.default encode.d_label rep.d_label [.d_label [[.d_label
'epid' objectas.data.frame.epid as.epid as.list.epid c,epid-method epid-class format.epid is.epid print.epid_summary rep,epid-method show,epid-method summary.epid unique.epid [,epid-method [[,epid-method
Group dated events into episodes.episodes episodes_af_shift links_wf_episodes
Link events to chronological episodes.episodes_wf_repeats
Record linkagelinks_af_probabilistic links_wf links_wf_probabilistic link_wf prob_score_range
Multistage record linkagelinks
Grammatical lists.listr
Convert an edge list to record identifiers.make_ids
Combinations and permutations of record-sets.make_pairs make_pairs_wf_source make_sets sets
Create 'epid' and 'pid' objects with index of matching recordsmake_episodes make_pids make_s4_ids
Merge group identifiersmerge_identifiers merge_ids merge_ids.default merge_ids.epid merge_ids.pane merge_ids.pid
'number_line'as.number_line end_point end_point<- expand_number_line invert_number_line is.number_line left_point left_point<- number_line number_line_sequence number_line_width reverse_number_line right_point right_point<- shift_number_line start_point start_point<-
'number_line' object$,number_line-method $<-,number_line-method as.data.frame.number_line as.list.number_line c,number_line-method format.number_line number_line-class rep,number_line-method seq.number_line show,number_line-method sort.number_line unique.number_line [,number_line-method [<-,number_line-method [[,number_line-method [[<-,number_line-method
Overlapping number line objectsacross aligns_end aligns_start chain exact exclude_overlap_method inbetween include_overlap_method none overlap overlaps overlap_method overlap_method_codes overlap_method_names x_across_y x_aligns_end_y x_aligns_start_y x_chain_y x_inbetween_y y_across_x y_aligns_end_x y_aligns_start_x y_chain_x y_inbetween_x
'pane' objectas.data.frame.pane as.list.pane as.pane c,pane-method format.pane is.pane pane-class print.pane_summary rep,pane-method show,pane-method summary.pane unique.pane [,pane-method [[,pane-method
Distribute events into specified intervals.partitions
'pid' objectsas.data.frame.pid as.list.pid as.pid c,pid-method format.pid is.pid pid-class print.pid_summary rep,pid-method show,pid-method summary.pid unique.pid [,pid-method [[,pid-method
Predefined logical tests in *'diyar'*exact_match false predefined_tests prob_link range_match true
Modify 'sub_criteria' objectsreframe reframe.sub_criteria
Schema diagram for group identifiersschema schema.epid schema.number_line schema.pane schema.pid
Set operations on number line objectsintersect_number_lines set_operations subtract_number_lines union_number_lines
Datasets in 'diyar' packageepisode_unit hospital_admissions hourly_data infections infections_2 infections_3 infections_4 missing_staff_id Opes overlap_methods patient_list patient_list_2 patient_records staff_records
Match criteriaattrs eval_sub_criteria eval_sub_criteria.sub_criteria format.sub_criteria print.sub_criteria sub_criteria
Windows and lengthsepid_lengths epid_windows index_window windows