Package: ricu 0.6.1
Nicolas Bennett
ricu: Intensive Care Unit Data with R
Focused on (but not exclusive to) data sets hosted on PhysioNet (<https://physionet.org>), 'ricu' provides utilities for download, setup and access of intensive care unit (ICU) data sets. In addition to functions for running arbitrary queries against available data sets, a system for defining clinical concepts and encoding their representations in tabular ICU data is presented.
Authors:
ricu_0.6.1.tar.gz
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ricu.pdf |ricu.html✨
ricu/json (API)
NEWS
| # Install 'ricu' in R: |
| install.packages('ricu', repos = c('https://eth-mds.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/eth-mds/ricu/issues
Last updated 6 months agofrom:c1206dabed. Checks:ERROR: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Nov 12 2024 |
| R-4.5-win | WARNING | Nov 12 2024 |
| R-4.5-linux | WARNING | Nov 12 2024 |
| R-4.4-win | WARNING | Nov 12 2024 |
| R-4.4-mac | WARNING | Nov 12 2024 |
| R-4.3-win | WARNING | Nov 12 2024 |
| R-4.3-mac | WARNING | Nov 12 2024 |
Exports:add_conceptadd_weightapply_mapas_col_cfgas_conceptas_id_cfgas_id_tblas_itemas_ptypeas_src_cfgas_src_envas_src_tblas_tbl_cfgas_ts_tblas_win_tblattach_srcattached_srcsaumcauto_attach_srcsavpubinary_opbmicalc_durcbind_id_tblchange_dur_unitchange_idchange_intervalcol_renamercollapsecombine_callbackscomp_naconceptconcept_availabilityconfig_pathsconvert_unitdatadata_coldata_dirdata_vardata_varsdaysdefault_varsdelta_cummindelta_mindelta_startdetach_srcdo_callbackdo_itm_loaddowngrade_iddownload_srcdt_gforcedur_coldur_unitdur_vareicueicu_demoexpandexplain_dictionaryfill_gapsfirst_elemfmt_msggcsget_configget_itm_varget_targethas_gapshas_no_gapshiridhophoursid_colid_mapid_map_helperid_orig_helperid_originid_tblid_varid_var_optsid_varsid_win_helperid_windowsimport_srcimport_tblindex_colindex_varinit_cncptinit_itmintervalis_cncptis_conceptis_data_availis_falseis_id_tblis_itemis_itmis_regularis_sortedis_src_envis_src_tblis_tbl_availis_trueis_ts_tblis_uniqueis_valis_win_tblitemlast_elemload_conceptsload_dictionaryload_difftimeload_idload_srcload_src_cfgload_tsload_winmax_or_namerge_lstmeta_varsmews_scoremiivmimicmimic_demomin_or_naminsmsg_progressn_ticknew_cncptnew_conceptnew_itemnew_itmnew_src_envnew_src_tblnews_scorenorepi_equivnot_valpafiprepare_queryqsofa_scorerbind_id_tblrbind_lstread_psvreclass_tblremove_gapsrename_colsreplace_narm_colsrm_nasafisecssep3set_callbackset_configset_targetset_valsetup_src_datasetup_src_envsicsirs_scoreslideslide_indexsofa_cardiosofa_cnssofa_coagsofa_liversofa_renalsofa_respsofa_scoresrc_data_availsrc_data_dirsrc_extra_cfgsrc_namesrc_prefixsrc_tbl_availstay_windowssubset_srcsupp_o2susp_inftbl_nametime_steptime_unittime_varstransform_funtry_add_varsts_tblunclass_tblunmergeupgrade_idurine24validate_tblvaso_indvaso60vent_indweekswin_tblwrite_psv
Dependencies:askpassassertthatbackportsbitbit64clicliprcpp11crayoncurldata.tablefansifstfstcoregluehmsjsonlitelifecyclemagrittropensslpillarpkgconfigprettyunitsprogressprtR6Rcppreadrrlangsystibbletidyselecttzdbutf8vctrsvroomwithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Data attach utilities | attach_src attach_src.character attach_src.src_cfg detach_src setup_src_env setup_src_env.src_cfg |
| Switch between id types | change_id downgrade_id downgrade_id.id_tbl downgrade_id.ts_tbl upgrade_id upgrade_id.id_tbl upgrade_id.ts_tbl |
| ICU datasets | aumc data eicu eicu_demo hirid miiv mimic mimic_demo sic |
| File system utilities | auto_attach_srcs config_paths data_dir get_config set_config src_data_dir |
| Data download utilities | download_src download_src.aumc_cfg download_src.character download_src.src_cfg |
| Time series utility functions | collapse expand fill_gaps has_gaps has_no_gaps hop is_regular remove_gaps slide slide_index |
| Tabular ICU data classes | as.data.frame.id_tbl as.data.table.id_tbl as_id_tbl as_ts_tbl as_win_tbl id_tbl is_id_tbl is_ts_tbl is_win_tbl ts_tbl validate_tbl win_tbl |
| ICU class meta data utilities | data_col data_var data_vars dur_col dur_unit dur_var id_col id_var id_vars index_col index_var interval meta_vars time_step time_unit time_vars |
| Data import utilities | import_src import_src.aumc_cfg import_src.character import_src.src_cfg import_tbl import_tbl.tbl_cfg |
| Load concept data | load_concepts load_concepts.character load_concepts.cncpt load_concepts.concept load_concepts.fct_cncpt load_concepts.integer load_concepts.item load_concepts.itm load_concepts.lgl_cncpt load_concepts.numeric load_concepts.num_cncpt load_concepts.rec_cncpt load_concepts.unt_cncpt |
| Load concept dictionaries | concept_availability explain_dictionary load_dictionary |
| Load data as 'id_tbl' or 'ts_tbl' objects | load_id load_id.character load_id.default load_id.fun_itm load_id.itm load_id.src_tbl load_ts load_ts.character load_ts.default load_ts.fun_itm load_ts.itm load_ts.src_tbl load_win load_win.character load_win.default load_win.fun_itm load_win.itm load_win.src_tbl |
| Low level functions for loading data | load_difftime load_difftime.aumc_tbl load_difftime.character load_difftime.eicu_tbl load_difftime.hirid_tbl load_difftime.miiv_tbl load_difftime.mimic_tbl load_difftime.sic_tbl load_src load_src.character load_src.src_tbl |
| Load configuration for a data source | load_src_cfg |
| Utility functions | first_elem is_false is_true is_val last_elem max_or_na min_or_na not_val |
| Message signaling nested with progress reporting | fmt_msg msg_progress |
| Data Concepts | as_concept concept init_cncpt init_cncpt.cncpt init_cncpt.fct_cncpt init_cncpt.num_cncpt init_cncpt.rec_cncpt init_cncpt.unt_cncpt is_cncpt is_concept new_cncpt new_concept |
| Data items | as_item init_itm init_itm.col_itm init_itm.fun_itm init_itm.hrd_itm init_itm.itm init_itm.rgx_itm init_itm.sel_itm is_item is_itm item new_item new_itm |
| Concept callback functions | avpu bmi gcs norepi_equiv pafi safi supp_o2 urine24 vaso60 vaso_ind vent_ind |
| ICU class data utilities | aggregate.id_tbl anyDuplicated.id_tbl change_dur_unit change_interval dt_gforce duplicated.id_tbl is_sorted is_unique rename_cols replace_na rm_cols rm_na sort.id_tbl unique.id_tbl |
| Utilities for 'difftime' | days hours mins secs weeks |
| Sepsis 3 label | delta_cummin delta_min delta_start sep3 |
| Data setup | setup_src_data |
| SIRS score label | mews_score news_score qsofa_score sirs_score |
| SOFA score label | sofa_cardio sofa_cns sofa_coag sofa_liver sofa_renal sofa_resp sofa_score |
| Stays | stay_windows stay_windows.character stay_windows.default stay_windows.list stay_windows.src_env |
| Suspicion of infection label | susp_inf |
| Item callback utilities | apply_map binary_op comp_na convert_unit set_val transform_fun |
| Read and write utilities | read_psv write_psv |
