Package: diyar 0.5.1.9001
Olisaeloka Nsonwu
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:
diyar_0.5.1.9001.tar.gz
diyar_0.5.1.9001.zip(r-4.5)diyar_0.5.1.9001.zip(r-4.4)diyar_0.5.1.9001.zip(r-4.3)
diyar_0.5.1.9001.tgz(r-4.4-any)diyar_0.5.1.9001.tgz(r-4.3-any)
diyar_0.5.1.9001.tar.gz(r-4.5-noble)diyar_0.5.1.9001.tar.gz(r-4.4-noble)
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diyar.pdf |diyar.html✨
diyar/json (API)
NEWS
| # Install 'diyar' in R: |
| install.packages('diyar', repos = c('https://epiverse-connect.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/olisansonwu/diyar/issues
- Opes - Datasets in 'diyar' package
- episode_unit - Datasets in 'diyar' package
- hospital_admissions - Datasets in 'diyar' package
- hourly_data - Datasets in 'diyar' package
- infections - Datasets in 'diyar' package
- infections_2 - Datasets in 'diyar' package
- infections_3 - Datasets in 'diyar' package
- infections_4 - Datasets in 'diyar' package
- missing_staff_id - Datasets in 'diyar' package
- overlap_methods - Datasets in 'diyar' package
- patient_list - Datasets in 'diyar' package
- patient_list_2 - Datasets in 'diyar' package
- patient_records - Datasets in 'diyar' package
- staff_records - Datasets in 'diyar' package
Last updated 1 months agofrom:317dfb5fab. Checks:OK: 1 WARNING: 6. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 23 2024 |
| R-4.5-win | WARNING | Nov 23 2024 |
| R-4.5-linux | WARNING | Nov 23 2024 |
| R-4.4-win | WARNING | Nov 23 2024 |
| R-4.4-mac | WARNING | Nov 23 2024 |
| R-4.3-win | WARNING | Nov 23 2024 |
| R-4.3-mac | WARNING | Nov 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 page | Topics |
|---|---|
| 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 combinations | combi |
| Nested sorting | custom_sort |
| d_report | as.data.frame.d_report as.list.d_report d_report plot.d_report |
| Unlink group identifiers | delink 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' object | as.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 linkage | links_af_probabilistic links_wf links_wf_probabilistic link_wf prob_score_range |
| Multistage record linkage | links |
| 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 records | make_episodes make_pids make_s4_ids |
| Merge group identifiers | merge_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 objects | across 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' object | as.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' objects | as.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' objects | reframe reframe.sub_criteria |
| Schema diagram for group identifiers | schema schema.epid schema.number_line schema.pane schema.pid |
| Set operations on number line objects | intersect_number_lines set_operations subtract_number_lines union_number_lines |
| Datasets in 'diyar' package | episode_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 criteria | attrs eval_sub_criteria eval_sub_criteria.sub_criteria format.sub_criteria print.sub_criteria sub_criteria |
| Windows and lengths | epid_lengths epid_windows index_window windows |
