├── .Rbuildignore ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── LICENSE ├── Makefile ├── NAMESPACE ├── R ├── RcppExports.R ├── ccRecord.R ├── ccTable.R ├── cchic_xml.R ├── data.R ├── data.quality.report.R ├── deltaTime.R ├── demographics.R ├── filter.categorical.R ├── filter.missingness.R ├── filter.range.R ├── imputation.R ├── stdid.R ├── utilities.R └── zzz.R ├── README-not.md ├── README.md ├── appveyor.yml ├── data ├── ITEM_REFTABLE.RData ├── icnarc_table.csv └── sample_ccd.RData ├── inst ├── conf │ ├── ANALYSIS_REF.yaml │ ├── ITEM_REF.yaml │ ├── accept_completeness.yaml │ └── icnarc_codes.csv └── report │ ├── bar.png │ ├── ccd_color.png │ ├── ccd_gray.png │ ├── data_quality_report.Rmd │ ├── listings-setup.tex │ └── report.latex ├── man ├── ITEM_REF.Rd ├── StdId.Rd ├── as.number.Rd ├── ccEpisode-class.Rd ├── ccRecord-class.Rd ├── ccTable-class.Rd ├── ccTable_apply_filters.Rd ├── ccTable_clean.Rd ├── ccTable_create_cctable.Rd ├── ccTable_export_csv.Rd ├── ccTable_filter_categories.Rd ├── ccTable_filter_missingness.Rd ├── ccTable_filter_nodata.Rd ├── ccTable_filter_range.Rd ├── ccTable_reload_conf.Rd ├── ccTable_reset.Rd ├── ccd.Rd ├── ccd_demographic_spell.Rd ├── ccd_demographic_table.Rd ├── ccd_select_table.Rd ├── ccd_unique_spell.Rd ├── code2stname.Rd ├── create2dclean.Rd ├── create_cctable.Rd ├── data.checklist.Rd ├── data.quality.report.Rd ├── data.quality.report.brc.Rd ├── deltaTime.Rd ├── demg.distribution.Rd ├── demographic.data.completeness.Rd ├── extract_file_origin.Rd ├── extract_info.Rd ├── file.summary.Rd ├── for_each_episode.Rd ├── getEpisodePeriod.Rd ├── getXmlepisode.Rd ├── icnarc2diagnosis.Rd ├── icnarc_table.Rd ├── inrange.Rd ├── is.demographic.Rd ├── is.drugs.Rd ├── is.laboratory.Rd ├── is.physiology.Rd ├── lenstay.Rd ├── long2stname.Rd ├── lookup.items.Rd ├── new.episode.Rd ├── physio.distribution.Rd ├── plot_episode-ccEpisode-character-method.Rd ├── plot_episode-ccEpisode-missing-method.Rd ├── plot_episode.Rd ├── plus-ccRecord-NULL-method.Rd ├── plus-ccRecord-ccEpisode-method.Rd ├── plus-ccRecord-ccRecord-method.Rd ├── plus-ccRecord-list-method.Rd ├── reallocateTimeRecord.Rd ├── samplerate2d.Rd ├── site.info.Rd ├── stname2code.Rd ├── stname2longname.Rd ├── sub-ccRecord-ANY-method.Rd ├── sub-ccRecord-character-method.Rd ├── sub-sub-ccRecord-method.Rd ├── table1.Rd ├── total.data.point.Rd ├── which.classification.Rd ├── whichIsCode.Rd ├── xml.file.duration.plot.Rd ├── xml.site.duration.plot.Rd ├── xml2Data.Rd ├── xmlLoad.Rd └── xmlTime2POSIX.Rd ├── paper ├── graph │ ├── episode_graph.pdf │ ├── item_ref_time.png │ └── range_filter.png ├── paper.bib └── paper.md ├── src ├── Makevars ├── RcppExports.cpp └── collapseTime.cpp ├── tests ├── data │ ├── ANALYSIS_REF.yaml │ ├── break_into.sh │ ├── check_config.yaml │ ├── sample_ccd.RData │ ├── test_2yml.yml │ ├── test_aggregate_patients.xml │ ├── test_analysis_ref.yaml │ ├── test_data_anonym.xml │ ├── test_sofa.yml │ └── test_spec.yml ├── testthat.R └── 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