diff --git a/searchindex.js b/searchindex.js index 2b8486b..d29b553 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"API Reference": [[0, "api-reference"]], "Coding guidelines": [[1, "coding-guidelines"]], "Contents:": [[2, null]], "Contributing": [[3, "contributing"]], "Contributing to cycquery": [[1, "contributing-to-cycquery"]], "Example 1. Get all female patients discharged in 2014 (limit to 100 rows).": [[64, "Example-1.-Get-all-female-patients-discharged-in-2014-(limit-to-100-rows)."]], "Example 1. Get all male patients with a mortality outcome.": [[66, "Example-1.-Get-all-male-patients-with-a-mortality-outcome."]], "Example 1. Get all patient admissions from 2021 or later (approx year of admission)": [[67, "Example-1.-Get-all-patient-admissions-from-2021-or-later-(approx-year-of-admission)"]], "Example 1. Get all patient visits in or after 2010.": [[68, "Example-1.-Get-all-patient-visits-in-or-after-2010."]], "Example 1. Get all patient visits that ended in a mortality outcome in or after 2010.": [[68, "Example-1.-Get-all-patient-visits-that-ended-in-a-mortality-outcome-in-or-after-2010."]], "Example 1a. Create a table with only one hospitalization per patient, keeping the most recent encounter for each patient. Sort the dataset by patient_id_hashed and discharge_date_time, and then keep the recent record.": [[65, "Example-1a.-Create-a-table-with-only-one-hospitalization-per-patient,-keeping-the-most-recent-encounter-for-each-patient.-Sort-the-dataset-by-patient_id_hashed-and-discharge_date_time,-and-then-keep-the-recent-record."]], "Example 1b. From the above set of encounters, take a subset of patients who were discharged between April 1, 2015 and March 31, 2016.": [[65, "Example-1b.-From-the-above-set-of-encounters,-take-a-subset-of-patients-who-were-discharged-between-April-1,-2015-and-March-31,-2016."]], "Example 1c. From the above set of encounters, get the total number of admissions for each hospital.": [[65, "Example-1c.-From-the-above-set-of-encounters,-get-the-total-number-of-admissions-for-each-hospital."]], "Example 2. Get all female patient encounters with diagnoses (gastroenteritis in ICD-9 long title).": [[66, "Example-2.-Get-all-female-patient-encounters-with-diagnoses-(gastroenteritis-in-ICD-9-long-title)."]], "Example 2. Get all measurements for female patient visits with sepsis diagnoses, that ended in a mortality outcome.": [[68, "Example-2.-Get-all-measurements-for-female-patient-visits-with-sepsis-diagnoses,-that-ended-in-a-mortality-outcome."]], "Example 2. Get all patient encounters with diagnoses (schizophrenia in ICD-10 long title), in the year 2015.": [[67, "Example-2.-Get-all-patient-encounters-with-diagnoses-(schizophrenia-in-ICD-10-long-title),-in-the-year-2015."]], "Example 2. Get all patient encounters with diagnoses (schizophrenia in diagnosisstring), discharged in the year 2015.": [[64, "Example-2.-Get-all-patient-encounters-with-diagnoses-(schizophrenia-in-diagnosisstring),-discharged-in-the-year-2015."]], "Example 2. Get measurements for all visits in or after 2020.": [[68, "Example-2.-Get-measurements-for-all-visits-in-or-after-2020."]], "Example 2a. How many sodium tests were placed between Apr 1, 2015 and May 31, 2015 at hospital 101?": [[65, "Example-2a.-How-many-sodium-tests-were-placed-between-Apr-1,-2015-and-May-31,-2015-at-hospital-101?"]], "Example 3. Advanced - uses ConditionRegexMatch from cycquery.ops. Get all patient encounters with diagnoses (ICD-9 long title contains schizophrenia and chronic ), in the year 2015.": [[67, "Example-3.-Advanced---uses-ConditionRegexMatch-from-cycquery.ops.-Get-all-patient-encounters-with-diagnoses-(ICD-9-long-title-contains-schizophrenia-and-chronic-),-in-the-year-2015."]], "Example 3. Get potassium lab tests for female patients.": [[66, "Example-3.-Get-potassium-lab-tests-for-female-patients."]], "Example 3. Get potassium lab tests for patients discharged in the year 2014, for all teaching hospitals.": [[64, "Example-3.-Get-potassium-lab-tests-for-patients-discharged-in-the-year-2014,-for-all-teaching-hospitals."]], "Example 4. Get AaDO2 carevue chart events for male patients that have a valuenum of less than 20.": [[66, "Example-4.-Get-AaDO2-carevue-chart-events-for-male-patients-that-have-a-valuenum-of-less-than-20."]], "Example 4. Get glucose medications (substring search) for female patients discharged in 2014.": [[64, "Example-4.-Get-glucose-medications-(substring-search)-for-female-patients-discharged-in-2014."]], "Example 4. Get routine vital signs for patients from year 2015.": [[67, "Example-4.-Get-routine-vital-signs-for-patients-from-year-2015."]], "Example 5. Get hemoglobin lab tests for patients from year 2009.": [[67, "Example-5.-Get-hemoglobin-lab-tests-for-patients-from-year-2009."]], "Example 6. Get radiology reports and filter on keywords lymphadenopathy and infectious occurring together from year 2009.": [[67, "Example-6.-Get-radiology-reports-and-filter-on-keywords-lymphadenopathy-and-infectious-occurring-together-from-year-2009."]], "Example 7. Get all female patient encounters from year 2015, and return batches partitioned and indexed on subject_id.": [[67, "Example-7.-Get-all-female-patient-encounters-from-year-2015,-and-return-batches-partitioned-and-indexed-on-subject_id."]], "Example 8. Running a raw SQL string.": [[67, "Example-8.-Running-a-raw-SQL-string."]], "GEMINI tutorial": [[65, "GEMINI-tutorial"]], "Imports and instantiate EICUQuerier": [[64, "Imports-and-instantiate-EICUQuerier"]], "Imports and instantiate GEMINIQuerier.": [[65, "Imports-and-instantiate-GEMINIQuerier."]], "Imports and instantiate MIMICIIIQuerier": [[66, "Imports-and-instantiate-MIMICIIIQuerier"]], "Imports and instantiate MIMICIVQuerier": [[67, "Imports-and-instantiate-MIMICIVQuerier"]], "Imports and instantiate OMOPQuerier.": [[68, "Imports-and-instantiate-OMOPQuerier."], [68, "id1"]], "Installing cycquery using pip": [[3, "installing-cycquery-using-pip"]], "MIMIC-III tutorial": [[66, "MIMIC-III-tutorial"]], "MIMIC-IV tutorial": [[67, "MIMIC-IV-tutorial"]], "OMOP tutorial": [[68, "OMOP-tutorial"]], "Pre-commit hooks": [[1, "pre-commit-hooks"]], "Query postgresql database": [[3, "query-postgresql-database"]], "Tutorials": [[63, "tutorials"]], "Using poetry": [[3, "using-poetry"]], "Welcome to cycquery\u2019s documentation!": [[2, "welcome-to-cycquery-s-documentation"]], "cycquery": [[3, "cycquery"], [62, "module-cycquery"]], "cycquery.base": [[4, "module-cycquery.base"]], "cycquery.base.DatasetQuerier": [[5, "cycquery-base-datasetquerier"]], "cycquery.eicu": [[6, "module-cycquery.eicu"]], "cycquery.eicu.EICUQuerier": [[7, "cycquery-eicu-eicuquerier"]], "cycquery.gemini": [[8, "module-cycquery.gemini"]], "cycquery.gemini.GEMINIQuerier": [[9, "cycquery-gemini-geminiquerier"]], "cycquery.interface": [[10, "module-cycquery.interface"]], "cycquery.interface.QueryInterface": [[11, "cycquery-interface-queryinterface"]], "cycquery.mimiciii": [[12, "module-cycquery.mimiciii"]], "cycquery.mimiciii.MIMICIIIQuerier": [[13, "cycquery-mimiciii-mimiciiiquerier"]], "cycquery.mimiciv": [[14, "module-cycquery.mimiciv"]], "cycquery.mimiciv.MIMICIVQuerier": [[15, "cycquery-mimiciv-mimicivquerier"]], "cycquery.omop": [[16, "module-cycquery.omop"]], "cycquery.omop.OMOPQuerier": [[17, "cycquery-omop-omopquerier"]], "cycquery.ops": [[18, "module-cycquery.ops"]], "cycquery.ops.AddColumn": [[19, "cycquery-ops-addcolumn"]], "cycquery.ops.AddDeltaColumn": [[20, "cycquery-ops-adddeltacolumn"]], "cycquery.ops.AddDeltaConstant": [[21, "cycquery-ops-adddeltaconstant"]], "cycquery.ops.AddNumeric": [[22, "cycquery-ops-addnumeric"]], "cycquery.ops.And": [[23, "cycquery-ops-and"]], "cycquery.ops.Apply": [[24, "cycquery-ops-apply"]], "cycquery.ops.Cast": [[25, "cycquery-ops-cast"]], "cycquery.ops.ConditionAfterDate": [[26, "cycquery-ops-conditionafterdate"]], "cycquery.ops.ConditionBeforeDate": [[27, "cycquery-ops-conditionbeforedate"]], "cycquery.ops.ConditionEndsWith": [[28, "cycquery-ops-conditionendswith"]], "cycquery.ops.ConditionEquals": [[29, "cycquery-ops-conditionequals"]], "cycquery.ops.ConditionGreaterThan": [[30, "cycquery-ops-conditiongreaterthan"]], "cycquery.ops.ConditionIn": [[31, "cycquery-ops-conditionin"]], "cycquery.ops.ConditionInMonths": [[32, "cycquery-ops-conditioninmonths"]], "cycquery.ops.ConditionInYears": [[33, "cycquery-ops-conditioninyears"]], "cycquery.ops.ConditionLessThan": [[34, "cycquery-ops-conditionlessthan"]], "cycquery.ops.ConditionLike": [[35, "cycquery-ops-conditionlike"]], "cycquery.ops.ConditionRegexMatch": [[36, "cycquery-ops-conditionregexmatch"]], "cycquery.ops.ConditionStartsWith": [[37, "cycquery-ops-conditionstartswith"]], "cycquery.ops.ConditionSubstring": [[38, "cycquery-ops-conditionsubstring"]], "cycquery.ops.Count": [[39, "cycquery-ops-count"]], "cycquery.ops.Distinct": [[40, "cycquery-ops-distinct"]], "cycquery.ops.Drop": [[41, "cycquery-ops-drop"]], "cycquery.ops.DropEmpty": [[42, "cycquery-ops-dropempty"]], "cycquery.ops.DropNulls": [[43, "cycquery-ops-dropnulls"]], "cycquery.ops.ExtractTimestampComponent": [[44, "cycquery-ops-extracttimestampcomponent"]], "cycquery.ops.FillNull": [[45, "cycquery-ops-fillnull"]], "cycquery.ops.GroupByAggregate": [[46, "cycquery-ops-groupbyaggregate"]], "cycquery.ops.Join": [[47, "cycquery-ops-join"]], "cycquery.ops.Keep": [[48, "cycquery-ops-keep"]], "cycquery.ops.Limit": [[49, "cycquery-ops-limit"]], "cycquery.ops.Literal": [[50, "cycquery-ops-literal"]], "cycquery.ops.Or": [[51, "cycquery-ops-or"]], "cycquery.ops.OrderBy": [[52, "cycquery-ops-orderby"]], "cycquery.ops.QueryOp": [[53, "cycquery-ops-queryop"]], "cycquery.ops.RandomizeOrder": [[54, "cycquery-ops-randomizeorder"]], "cycquery.ops.Rename": [[55, "cycquery-ops-rename"]], "cycquery.ops.Reorder": [[56, "cycquery-ops-reorder"]], "cycquery.ops.ReorderAfter": [[57, "cycquery-ops-reorderafter"]], "cycquery.ops.Sequential": [[58, "cycquery-ops-sequential"]], "cycquery.ops.Substring": [[59, "cycquery-ops-substring"]], "cycquery.ops.Trim": [[60, "cycquery-ops-trim"]], "cycquery.ops.Union": [[61, "cycquery-ops-union"]], "dataset APIs": [[62, "dataset-apis"]], "eICU-CRD tutorial": [[64, "eICU-CRD-tutorial"]], "\ud83d\udc23 Getting Started": [[3, "getting-started"]], "\ud83d\udcda Documentation": [[3, "documentation"]], "\ud83e\uddd1\ud83c\udfff\u200d\ud83d\udcbb Developing": [[3, "developing"]]}, "docnames": ["api", "contributing", "index", "intro", "reference/api/_autosummary/cycquery.base", "reference/api/_autosummary/cycquery.base.DatasetQuerier", "reference/api/_autosummary/cycquery.eicu", "reference/api/_autosummary/cycquery.eicu.EICUQuerier", "reference/api/_autosummary/cycquery.gemini", "reference/api/_autosummary/cycquery.gemini.GEMINIQuerier", "reference/api/_autosummary/cycquery.interface", "reference/api/_autosummary/cycquery.interface.QueryInterface", "reference/api/_autosummary/cycquery.mimiciii", "reference/api/_autosummary/cycquery.mimiciii.MIMICIIIQuerier", "reference/api/_autosummary/cycquery.mimiciv", "reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier", "reference/api/_autosummary/cycquery.omop", "reference/api/_autosummary/cycquery.omop.OMOPQuerier", "reference/api/_autosummary/cycquery.ops", "reference/api/_autosummary/cycquery.ops.AddColumn", "reference/api/_autosummary/cycquery.ops.AddDeltaColumn", "reference/api/_autosummary/cycquery.ops.AddDeltaConstant", "reference/api/_autosummary/cycquery.ops.AddNumeric", "reference/api/_autosummary/cycquery.ops.And", "reference/api/_autosummary/cycquery.ops.Apply", "reference/api/_autosummary/cycquery.ops.Cast", "reference/api/_autosummary/cycquery.ops.ConditionAfterDate", "reference/api/_autosummary/cycquery.ops.ConditionBeforeDate", "reference/api/_autosummary/cycquery.ops.ConditionEndsWith", "reference/api/_autosummary/cycquery.ops.ConditionEquals", "reference/api/_autosummary/cycquery.ops.ConditionGreaterThan", "reference/api/_autosummary/cycquery.ops.ConditionIn", "reference/api/_autosummary/cycquery.ops.ConditionInMonths", "reference/api/_autosummary/cycquery.ops.ConditionInYears", "reference/api/_autosummary/cycquery.ops.ConditionLessThan", "reference/api/_autosummary/cycquery.ops.ConditionLike", "reference/api/_autosummary/cycquery.ops.ConditionRegexMatch", "reference/api/_autosummary/cycquery.ops.ConditionStartsWith", "reference/api/_autosummary/cycquery.ops.ConditionSubstring", "reference/api/_autosummary/cycquery.ops.Count", "reference/api/_autosummary/cycquery.ops.Distinct", "reference/api/_autosummary/cycquery.ops.Drop", "reference/api/_autosummary/cycquery.ops.DropEmpty", "reference/api/_autosummary/cycquery.ops.DropNulls", "reference/api/_autosummary/cycquery.ops.ExtractTimestampComponent", "reference/api/_autosummary/cycquery.ops.FillNull", "reference/api/_autosummary/cycquery.ops.GroupByAggregate", "reference/api/_autosummary/cycquery.ops.Join", "reference/api/_autosummary/cycquery.ops.Keep", "reference/api/_autosummary/cycquery.ops.Limit", "reference/api/_autosummary/cycquery.ops.Literal", "reference/api/_autosummary/cycquery.ops.Or", "reference/api/_autosummary/cycquery.ops.OrderBy", "reference/api/_autosummary/cycquery.ops.QueryOp", "reference/api/_autosummary/cycquery.ops.RandomizeOrder", "reference/api/_autosummary/cycquery.ops.Rename", "reference/api/_autosummary/cycquery.ops.Reorder", "reference/api/_autosummary/cycquery.ops.ReorderAfter", "reference/api/_autosummary/cycquery.ops.Sequential", "reference/api/_autosummary/cycquery.ops.Substring", "reference/api/_autosummary/cycquery.ops.Trim", "reference/api/_autosummary/cycquery.ops.Union", "reference/api/cycquery", "tutorials", "tutorials/eicu", "tutorials/gemini", "tutorials/mimiciii", "tutorials/mimiciv", "tutorials/omop"], "envversion": {"nbsphinx": 4, "sphinx": 61, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1}, "filenames": ["api.rst", "contributing.rst", "index.rst", "intro.rst", "reference/api/_autosummary/cycquery.base.rst", "reference/api/_autosummary/cycquery.base.DatasetQuerier.rst", "reference/api/_autosummary/cycquery.eicu.rst", "reference/api/_autosummary/cycquery.eicu.EICUQuerier.rst", "reference/api/_autosummary/cycquery.gemini.rst", "reference/api/_autosummary/cycquery.gemini.GEMINIQuerier.rst", "reference/api/_autosummary/cycquery.interface.rst", "reference/api/_autosummary/cycquery.interface.QueryInterface.rst", "reference/api/_autosummary/cycquery.mimiciii.rst", "reference/api/_autosummary/cycquery.mimiciii.MIMICIIIQuerier.rst", "reference/api/_autosummary/cycquery.mimiciv.rst", "reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.rst", "reference/api/_autosummary/cycquery.omop.rst", "reference/api/_autosummary/cycquery.omop.OMOPQuerier.rst", "reference/api/_autosummary/cycquery.ops.rst", "reference/api/_autosummary/cycquery.ops.AddColumn.rst", "reference/api/_autosummary/cycquery.ops.AddDeltaColumn.rst", "reference/api/_autosummary/cycquery.ops.AddDeltaConstant.rst", "reference/api/_autosummary/cycquery.ops.AddNumeric.rst", "reference/api/_autosummary/cycquery.ops.And.rst", "reference/api/_autosummary/cycquery.ops.Apply.rst", "reference/api/_autosummary/cycquery.ops.Cast.rst", "reference/api/_autosummary/cycquery.ops.ConditionAfterDate.rst", "reference/api/_autosummary/cycquery.ops.ConditionBeforeDate.rst", "reference/api/_autosummary/cycquery.ops.ConditionEndsWith.rst", "reference/api/_autosummary/cycquery.ops.ConditionEquals.rst", "reference/api/_autosummary/cycquery.ops.ConditionGreaterThan.rst", "reference/api/_autosummary/cycquery.ops.ConditionIn.rst", "reference/api/_autosummary/cycquery.ops.ConditionInMonths.rst", "reference/api/_autosummary/cycquery.ops.ConditionInYears.rst", "reference/api/_autosummary/cycquery.ops.ConditionLessThan.rst", "reference/api/_autosummary/cycquery.ops.ConditionLike.rst", "reference/api/_autosummary/cycquery.ops.ConditionRegexMatch.rst", "reference/api/_autosummary/cycquery.ops.ConditionStartsWith.rst", "reference/api/_autosummary/cycquery.ops.ConditionSubstring.rst", "reference/api/_autosummary/cycquery.ops.Count.rst", "reference/api/_autosummary/cycquery.ops.Distinct.rst", "reference/api/_autosummary/cycquery.ops.Drop.rst", "reference/api/_autosummary/cycquery.ops.DropEmpty.rst", "reference/api/_autosummary/cycquery.ops.DropNulls.rst", "reference/api/_autosummary/cycquery.ops.ExtractTimestampComponent.rst", "reference/api/_autosummary/cycquery.ops.FillNull.rst", "reference/api/_autosummary/cycquery.ops.GroupByAggregate.rst", "reference/api/_autosummary/cycquery.ops.Join.rst", "reference/api/_autosummary/cycquery.ops.Keep.rst", "reference/api/_autosummary/cycquery.ops.Limit.rst", "reference/api/_autosummary/cycquery.ops.Literal.rst", "reference/api/_autosummary/cycquery.ops.Or.rst", "reference/api/_autosummary/cycquery.ops.OrderBy.rst", "reference/api/_autosummary/cycquery.ops.QueryOp.rst", "reference/api/_autosummary/cycquery.ops.RandomizeOrder.rst", "reference/api/_autosummary/cycquery.ops.Rename.rst", "reference/api/_autosummary/cycquery.ops.Reorder.rst", "reference/api/_autosummary/cycquery.ops.ReorderAfter.rst", "reference/api/_autosummary/cycquery.ops.Sequential.rst", "reference/api/_autosummary/cycquery.ops.Substring.rst", "reference/api/_autosummary/cycquery.ops.Trim.rst", "reference/api/_autosummary/cycquery.ops.Union.rst", "reference/api/cycquery.rst", "tutorials.rst", "tutorials/eicu.ipynb", "tutorials/gemini.ipynb", "tutorials/mimiciii.ipynb", "tutorials/mimiciv.ipynb", "tutorials/omop.ipynb"], "indexentries": {"__add__() (sequential method)": [[58, "cycquery.ops.Sequential.__add__", false]], "__call__() (addcolumn method)": [[19, "cycquery.ops.AddColumn.__call__", false]], "__call__() (adddeltacolumn method)": [[20, "cycquery.ops.AddDeltaColumn.__call__", false]], "__call__() (adddeltaconstant method)": [[21, "cycquery.ops.AddDeltaConstant.__call__", false]], "__call__() (addnumeric method)": [[22, "cycquery.ops.AddNumeric.__call__", false]], "__call__() (and method)": [[23, "cycquery.ops.And.__call__", false]], "__call__() (apply method)": [[24, "cycquery.ops.Apply.__call__", false]], "__call__() (cast method)": [[25, "cycquery.ops.Cast.__call__", false]], "__call__() (conditionafterdate method)": [[26, "cycquery.ops.ConditionAfterDate.__call__", false]], "__call__() (conditionbeforedate method)": [[27, "cycquery.ops.ConditionBeforeDate.__call__", false]], "__call__() (conditionendswith method)": [[28, "cycquery.ops.ConditionEndsWith.__call__", false]], "__call__() (conditionequals method)": [[29, "cycquery.ops.ConditionEquals.__call__", false]], "__call__() (conditiongreaterthan method)": [[30, "cycquery.ops.ConditionGreaterThan.__call__", false]], "__call__() (conditionin method)": [[31, "cycquery.ops.ConditionIn.__call__", false]], "__call__() (conditioninmonths method)": [[32, "cycquery.ops.ConditionInMonths.__call__", false]], "__call__() (conditioninyears method)": [[33, "cycquery.ops.ConditionInYears.__call__", false]], "__call__() (conditionlessthan method)": [[34, "cycquery.ops.ConditionLessThan.__call__", false]], "__call__() (conditionlike method)": [[35, "cycquery.ops.ConditionLike.__call__", false]], "__call__() (conditionregexmatch method)": [[36, "cycquery.ops.ConditionRegexMatch.__call__", false]], "__call__() (conditionstartswith method)": [[37, "cycquery.ops.ConditionStartsWith.__call__", false]], "__call__() (conditionsubstring method)": [[38, "cycquery.ops.ConditionSubstring.__call__", false]], "__call__() (count method)": [[39, "cycquery.ops.Count.__call__", false]], "__call__() (distinct method)": [[40, "cycquery.ops.Distinct.__call__", false]], "__call__() (drop method)": [[41, "cycquery.ops.Drop.__call__", false]], "__call__() (dropempty method)": [[42, "cycquery.ops.DropEmpty.__call__", false]], "__call__() (dropnulls method)": [[43, "cycquery.ops.DropNulls.__call__", false]], "__call__() (extracttimestampcomponent method)": [[44, "cycquery.ops.ExtractTimestampComponent.__call__", false]], "__call__() (fillnull method)": [[45, "cycquery.ops.FillNull.__call__", false]], "__call__() (groupbyaggregate method)": [[46, "cycquery.ops.GroupByAggregate.__call__", false]], "__call__() (join method)": [[47, "cycquery.ops.Join.__call__", false]], "__call__() (keep method)": [[48, "cycquery.ops.Keep.__call__", false]], "__call__() (limit method)": [[49, "cycquery.ops.Limit.__call__", false]], "__call__() (literal method)": [[50, "cycquery.ops.Literal.__call__", false]], "__call__() (or method)": [[51, "cycquery.ops.Or.__call__", false]], "__call__() (orderby method)": [[52, "cycquery.ops.OrderBy.__call__", false]], "__call__() (queryop method)": [[53, "cycquery.ops.QueryOp.__call__", false]], "__call__() (randomizeorder method)": [[54, "cycquery.ops.RandomizeOrder.__call__", false]], "__call__() (rename method)": [[55, "cycquery.ops.Rename.__call__", false]], "__call__() (reorder method)": [[56, "cycquery.ops.Reorder.__call__", false]], "__call__() (reorderafter method)": [[57, "cycquery.ops.ReorderAfter.__call__", false]], "__call__() (sequential method)": [[58, "cycquery.ops.Sequential.__call__", false]], "__call__() (substring method)": [[59, "cycquery.ops.Substring.__call__", false]], "__call__() (trim method)": [[60, "cycquery.ops.Trim.__call__", false]], "__call__() (union method)": [[61, "cycquery.ops.Union.__call__", false]], "__init__() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.__init__", false]], "__init__() (sequential method)": [[58, "cycquery.ops.Sequential.__init__", false]], "addcolumn (class in cycquery.ops)": [[19, "cycquery.ops.AddColumn", false]], "adddeltacolumn (class in cycquery.ops)": [[20, "cycquery.ops.AddDeltaColumn", false]], "adddeltaconstant (class in cycquery.ops)": [[21, "cycquery.ops.AddDeltaConstant", false]], "addnumeric (class in cycquery.ops)": [[22, "cycquery.ops.AddNumeric", false]], "and (class in cycquery.ops)": [[23, "cycquery.ops.And", false]], "append() (sequential method)": [[58, "cycquery.ops.Sequential.append", false]], "apply (class in cycquery.ops)": [[24, "cycquery.ops.Apply", false]], "care_units() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.care_units", false]], "cast (class in cycquery.ops)": [[25, "cycquery.ops.Cast", false]], "chartevents() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.chartevents", false]], "chartevents() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.chartevents", false]], "clear_data() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.clear_data", false]], "conditionafterdate (class in cycquery.ops)": [[26, "cycquery.ops.ConditionAfterDate", false]], "conditionbeforedate (class in cycquery.ops)": [[27, "cycquery.ops.ConditionBeforeDate", false]], "conditionendswith (class in cycquery.ops)": [[28, "cycquery.ops.ConditionEndsWith", false]], "conditionequals (class in cycquery.ops)": [[29, "cycquery.ops.ConditionEquals", false]], "conditiongreaterthan (class in cycquery.ops)": [[30, "cycquery.ops.ConditionGreaterThan", false]], "conditionin (class in cycquery.ops)": [[31, "cycquery.ops.ConditionIn", false]], "conditioninmonths (class in cycquery.ops)": [[32, "cycquery.ops.ConditionInMonths", false]], "conditioninyears (class in cycquery.ops)": [[33, "cycquery.ops.ConditionInYears", false]], "conditionlessthan (class in cycquery.ops)": [[34, "cycquery.ops.ConditionLessThan", false]], "conditionlike (class in cycquery.ops)": [[35, "cycquery.ops.ConditionLike", false]], "conditionregexmatch (class in cycquery.ops)": [[36, "cycquery.ops.ConditionRegexMatch", false]], "conditionstartswith (class in cycquery.ops)": [[37, "cycquery.ops.ConditionStartsWith", false]], "conditionsubstring (class in cycquery.ops)": [[38, "cycquery.ops.ConditionSubstring", false]], "count (class in cycquery.ops)": [[39, "cycquery.ops.Count", false]], "cycquery": [[62, "module-cycquery", false]], "cycquery.base": [[4, "module-cycquery.base", false]], "cycquery.eicu": [[6, "module-cycquery.eicu", false]], "cycquery.gemini": [[8, "module-cycquery.gemini", false]], "cycquery.interface": [[10, "module-cycquery.interface", false]], "cycquery.mimiciii": [[12, "module-cycquery.mimiciii", false]], "cycquery.mimiciv": [[14, "module-cycquery.mimiciv", false]], "cycquery.omop": [[16, "module-cycquery.omop", false]], "cycquery.ops": [[18, "module-cycquery.ops", false]], "data (queryinterface property)": [[11, "cycquery.interface.QueryInterface.data", false]], "datasetquerier (class in cycquery.base)": [[5, "cycquery.base.DatasetQuerier", false]], "db (datasetquerier attribute)": [[5, "cycquery.base.DatasetQuerier.db", false]], "diagnoses() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.diagnoses", false]], "diagnoses() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.diagnoses", false]], "diagnoses_icd() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.diagnoses_icd", false]], "distinct (class in cycquery.ops)": [[40, "cycquery.ops.Distinct", false]], "drop (class in cycquery.ops)": [[41, "cycquery.ops.Drop", false]], "dropempty (class in cycquery.ops)": [[42, "cycquery.ops.DropEmpty", false]], "dropnulls (class in cycquery.ops)": [[43, "cycquery.ops.DropNulls", false]], "eicuquerier (class in cycquery.eicu)": [[7, "cycquery.eicu.EICUQuerier", false]], "extend() (sequential method)": [[58, "cycquery.ops.Sequential.extend", false]], "extracttimestampcomponent (class in cycquery.ops)": [[44, "cycquery.ops.ExtractTimestampComponent", false]], "fillnull (class in cycquery.ops)": [[45, "cycquery.ops.FillNull", false]], "geminiquerier (class in cycquery.gemini)": [[9, "cycquery.gemini.GEMINIQuerier", false]], "get_table() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.get_table", false]], "get_table() (eicuquerier method)": [[7, "cycquery.eicu.EICUQuerier.get_table", false]], "get_table() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.get_table", false]], "get_table() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.get_table", false]], "get_table() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.get_table", false]], "get_table() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.get_table", false]], "groupbyaggregate (class in cycquery.ops)": [[46, "cycquery.ops.GroupByAggregate", false]], "imaging() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.imaging", false]], "insert() (sequential method)": [[58, "cycquery.ops.Sequential.insert", false]], "ip_admin() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.ip_admin", false]], "join (class in cycquery.ops)": [[47, "cycquery.ops.Join", false]], "join() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.join", false]], "keep (class in cycquery.ops)": [[48, "cycquery.ops.Keep", false]], "labevents() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.labevents", false]], "labevents() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.labevents", false]], "limit (class in cycquery.ops)": [[49, "cycquery.ops.Limit", false]], "list_columns() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.list_columns", false]], "list_columns() (eicuquerier method)": [[7, "cycquery.eicu.EICUQuerier.list_columns", false]], "list_columns() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.list_columns", false]], "list_columns() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.list_columns", false]], "list_columns() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.list_columns", false]], "list_columns() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.list_columns", false]], "list_custom_tables() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.list_custom_tables", false]], "list_custom_tables() (eicuquerier method)": [[7, "cycquery.eicu.EICUQuerier.list_custom_tables", false]], "list_custom_tables() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.list_custom_tables", false]], "list_custom_tables() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.list_custom_tables", false]], "list_custom_tables() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.list_custom_tables", false]], "list_custom_tables() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.list_custom_tables", false]], "list_schemas() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.list_schemas", false]], "list_schemas() (eicuquerier method)": [[7, "cycquery.eicu.EICUQuerier.list_schemas", false]], "list_schemas() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.list_schemas", false]], "list_schemas() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.list_schemas", false]], "list_schemas() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.list_schemas", false]], "list_schemas() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.list_schemas", false]], "list_tables() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.list_tables", false]], "list_tables() (eicuquerier method)": [[7, "cycquery.eicu.EICUQuerier.list_tables", false]], "list_tables() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.list_tables", false]], "list_tables() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.list_tables", false]], "list_tables() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.list_tables", false]], "list_tables() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.list_tables", false]], "literal (class in cycquery.ops)": [[50, "cycquery.ops.Literal", false]], "map_concept_ids_to_name() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.map_concept_ids_to_name", false]], "measurement() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.measurement", false]], "mimiciiiquerier (class in cycquery.mimiciii)": [[13, "cycquery.mimiciii.MIMICIIIQuerier", false]], "mimicivquerier (class in cycquery.mimiciv)": [[15, "cycquery.mimiciv.MIMICIVQuerier", false]], "module": [[4, "module-cycquery.base", false], [6, "module-cycquery.eicu", false], [8, "module-cycquery.gemini", false], [10, "module-cycquery.interface", false], [12, "module-cycquery.mimiciii", false], [14, "module-cycquery.mimiciv", false], [16, "module-cycquery.omop", false], [18, "module-cycquery.ops", false], [62, "module-cycquery", false]], "observation() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.observation", false]], "omopquerier (class in cycquery.omop)": [[17, "cycquery.omop.OMOPQuerier", false]], "ops() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.ops", false]], "or (class in cycquery.ops)": [[51, "cycquery.ops.Or", false]], "orderby (class in cycquery.ops)": [[52, "cycquery.ops.OrderBy", false]], "patients() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.patients", false]], "person() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.person", false]], "pop() (sequential method)": [[58, "cycquery.ops.Sequential.pop", false]], "procedures_icd() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.procedures_icd", false]], "queryinterface (class in cycquery.interface)": [[11, "cycquery.interface.QueryInterface", false]], "queryop (class in cycquery.ops)": [[53, "cycquery.ops.QueryOp", false]], "randomizeorder (class in cycquery.ops)": [[54, "cycquery.ops.RandomizeOrder", false]], "rename (class in cycquery.ops)": [[55, "cycquery.ops.Rename", false]], "reorder (class in cycquery.ops)": [[56, "cycquery.ops.Reorder", false]], "reorderafter (class in cycquery.ops)": [[57, "cycquery.ops.ReorderAfter", false]], "room_transfer() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.room_transfer", false]], "run() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.run", false]], "save() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.save", false]], "sequential (class in cycquery.ops)": [[58, "cycquery.ops.Sequential", false]], "substring (class in cycquery.ops)": [[59, "cycquery.ops.Substring", false]], "trim (class in cycquery.ops)": [[60, "cycquery.ops.Trim", false]], "union (class in cycquery.ops)": [[61, "cycquery.ops.Union", false]], "union() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.union", false]], "union_all() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.union_all", false]], "visit_detail() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.visit_detail", false]], "visit_occurrence() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.visit_occurrence", false]]}, "objects": {"": [[62, 0, 0, "-", "cycquery"]], "cycquery": [[4, 0, 0, "-", "base"], [6, 0, 0, "-", "eicu"], [8, 0, 0, "-", "gemini"], [10, 0, 0, "-", "interface"], [12, 0, 0, "-", "mimiciii"], [14, 0, 0, "-", "mimiciv"], [16, 0, 0, "-", "omop"], [18, 0, 0, "-", "ops"]], "cycquery.base": [[5, 1, 1, "", "DatasetQuerier"]], "cycquery.base.DatasetQuerier": [[5, 2, 1, "", "db"], [5, 3, 1, "", "get_table"], [5, 3, 1, "", "list_columns"], [5, 3, 1, "", "list_custom_tables"], [5, 3, 1, "", "list_schemas"], [5, 3, 1, "", "list_tables"]], "cycquery.eicu": [[7, 1, 1, "", "EICUQuerier"]], "cycquery.eicu.EICUQuerier": [[7, 3, 1, "", "get_table"], [7, 3, 1, "", "list_columns"], [7, 3, 1, "", "list_custom_tables"], [7, 3, 1, "", "list_schemas"], [7, 3, 1, "", "list_tables"]], "cycquery.gemini": [[9, 1, 1, "", "GEMINIQuerier"]], "cycquery.gemini.GEMINIQuerier": [[9, 3, 1, "", "care_units"], [9, 3, 1, "", "diagnoses"], [9, 3, 1, "", "get_table"], [9, 3, 1, "", "imaging"], [9, 3, 1, "", "ip_admin"], [9, 3, 1, "", "list_columns"], [9, 3, 1, "", "list_custom_tables"], [9, 3, 1, "", "list_schemas"], [9, 3, 1, "", "list_tables"], [9, 3, 1, "", "room_transfer"]], "cycquery.interface": [[11, 1, 1, "", "QueryInterface"]], "cycquery.interface.QueryInterface": [[11, 3, 1, "", "__init__"], [11, 3, 1, "", "clear_data"], [11, 4, 1, "", "data"], [11, 3, 1, "", "join"], [11, 3, 1, "", "ops"], [11, 3, 1, "", "run"], [11, 3, 1, "", "save"], [11, 3, 1, "", "union"], [11, 3, 1, "", "union_all"]], "cycquery.mimiciii": [[13, 1, 1, "", "MIMICIIIQuerier"]], "cycquery.mimiciii.MIMICIIIQuerier": [[13, 3, 1, "", "chartevents"], [13, 3, 1, "", "diagnoses"], [13, 3, 1, "", "get_table"], [13, 3, 1, "", "labevents"], [13, 3, 1, "", "list_columns"], [13, 3, 1, "", "list_custom_tables"], [13, 3, 1, "", "list_schemas"], [13, 3, 1, "", "list_tables"]], "cycquery.mimiciv": [[15, 1, 1, "", "MIMICIVQuerier"]], "cycquery.mimiciv.MIMICIVQuerier": [[15, 3, 1, "", "chartevents"], [15, 3, 1, "", "diagnoses_icd"], [15, 3, 1, "", "get_table"], [15, 3, 1, "", "labevents"], [15, 3, 1, "", "list_columns"], [15, 3, 1, "", "list_custom_tables"], [15, 3, 1, "", "list_schemas"], [15, 3, 1, "", "list_tables"], [15, 3, 1, "", "patients"], [15, 3, 1, "", "procedures_icd"]], "cycquery.omop": [[17, 1, 1, "", "OMOPQuerier"]], "cycquery.omop.OMOPQuerier": [[17, 3, 1, "", "get_table"], [17, 3, 1, "", "list_columns"], [17, 3, 1, "", "list_custom_tables"], [17, 3, 1, "", "list_schemas"], [17, 3, 1, "", "list_tables"], [17, 3, 1, "", "map_concept_ids_to_name"], [17, 3, 1, "", "measurement"], [17, 3, 1, "", "observation"], [17, 3, 1, "", "person"], [17, 3, 1, "", "visit_detail"], [17, 3, 1, "", "visit_occurrence"]], "cycquery.ops": [[19, 1, 1, "", "AddColumn"], [20, 1, 1, "", "AddDeltaColumn"], [21, 1, 1, "", "AddDeltaConstant"], [22, 1, 1, "", "AddNumeric"], [23, 1, 1, "", "And"], [24, 1, 1, "", "Apply"], [25, 1, 1, "", "Cast"], [26, 1, 1, "", "ConditionAfterDate"], [27, 1, 1, "", "ConditionBeforeDate"], [28, 1, 1, "", "ConditionEndsWith"], [29, 1, 1, "", "ConditionEquals"], [30, 1, 1, "", "ConditionGreaterThan"], [31, 1, 1, "", "ConditionIn"], [32, 1, 1, "", "ConditionInMonths"], [33, 1, 1, "", "ConditionInYears"], [34, 1, 1, "", "ConditionLessThan"], [35, 1, 1, "", "ConditionLike"], [36, 1, 1, "", "ConditionRegexMatch"], [37, 1, 1, "", "ConditionStartsWith"], [38, 1, 1, "", "ConditionSubstring"], [39, 1, 1, "", "Count"], [40, 1, 1, "", "Distinct"], [41, 1, 1, "", "Drop"], [42, 1, 1, "", "DropEmpty"], [43, 1, 1, "", "DropNulls"], [44, 1, 1, "", "ExtractTimestampComponent"], [45, 1, 1, "", "FillNull"], [46, 1, 1, "", "GroupByAggregate"], [47, 1, 1, "", "Join"], [48, 1, 1, "", "Keep"], [49, 1, 1, "", "Limit"], [50, 1, 1, "", "Literal"], [51, 1, 1, "", "Or"], [52, 1, 1, "", "OrderBy"], [53, 1, 1, "", "QueryOp"], [54, 1, 1, "", "RandomizeOrder"], [55, 1, 1, "", "Rename"], [56, 1, 1, "", "Reorder"], [57, 1, 1, "", "ReorderAfter"], [58, 1, 1, "", "Sequential"], [59, 1, 1, "", "Substring"], [60, 1, 1, "", "Trim"], [61, 1, 1, "", "Union"]], "cycquery.ops.AddColumn": [[19, 3, 1, "", "__call__"]], "cycquery.ops.AddDeltaColumn": [[20, 3, 1, "", "__call__"]], "cycquery.ops.AddDeltaConstant": [[21, 3, 1, "", "__call__"]], "cycquery.ops.AddNumeric": [[22, 3, 1, "", "__call__"]], "cycquery.ops.And": [[23, 3, 1, "", "__call__"]], "cycquery.ops.Apply": [[24, 3, 1, "", "__call__"]], "cycquery.ops.Cast": [[25, 3, 1, "", "__call__"]], "cycquery.ops.ConditionAfterDate": [[26, 3, 1, "", "__call__"]], "cycquery.ops.ConditionBeforeDate": [[27, 3, 1, "", "__call__"]], "cycquery.ops.ConditionEndsWith": [[28, 3, 1, "", "__call__"]], "cycquery.ops.ConditionEquals": [[29, 3, 1, "", "__call__"]], "cycquery.ops.ConditionGreaterThan": [[30, 3, 1, "", "__call__"]], "cycquery.ops.ConditionIn": [[31, 3, 1, "", "__call__"]], "cycquery.ops.ConditionInMonths": [[32, 3, 1, "", "__call__"]], "cycquery.ops.ConditionInYears": [[33, 3, 1, "", "__call__"]], "cycquery.ops.ConditionLessThan": [[34, 3, 1, "", "__call__"]], "cycquery.ops.ConditionLike": [[35, 3, 1, "", "__call__"]], "cycquery.ops.ConditionRegexMatch": [[36, 3, 1, "", "__call__"]], "cycquery.ops.ConditionStartsWith": [[37, 3, 1, "", "__call__"]], "cycquery.ops.ConditionSubstring": [[38, 3, 1, "", "__call__"]], "cycquery.ops.Count": [[39, 3, 1, "", "__call__"]], "cycquery.ops.Distinct": [[40, 3, 1, "", "__call__"]], "cycquery.ops.Drop": [[41, 3, 1, "", "__call__"]], "cycquery.ops.DropEmpty": [[42, 3, 1, "", "__call__"]], "cycquery.ops.DropNulls": [[43, 3, 1, "", "__call__"]], "cycquery.ops.ExtractTimestampComponent": [[44, 3, 1, "", "__call__"]], "cycquery.ops.FillNull": [[45, 3, 1, "", "__call__"]], "cycquery.ops.GroupByAggregate": [[46, 3, 1, "", "__call__"]], "cycquery.ops.Join": [[47, 3, 1, "", "__call__"]], "cycquery.ops.Keep": [[48, 3, 1, "", "__call__"]], "cycquery.ops.Limit": [[49, 3, 1, "", "__call__"]], "cycquery.ops.Literal": [[50, 3, 1, "", "__call__"]], "cycquery.ops.Or": [[51, 3, 1, "", "__call__"]], "cycquery.ops.OrderBy": [[52, 3, 1, "", "__call__"]], "cycquery.ops.QueryOp": [[53, 3, 1, "", "__call__"]], "cycquery.ops.RandomizeOrder": [[54, 3, 1, "", "__call__"]], "cycquery.ops.Rename": [[55, 3, 1, "", "__call__"]], "cycquery.ops.Reorder": [[56, 3, 1, "", "__call__"]], "cycquery.ops.ReorderAfter": [[57, 3, 1, "", "__call__"]], "cycquery.ops.Sequential": [[58, 3, 1, "", "__add__"], [58, 3, 1, "", "__call__"], [58, 3, 1, "", "__init__"], [58, 3, 1, "", "append"], [58, 3, 1, "", "extend"], [58, 3, 1, "", "insert"], [58, 3, 1, "", "pop"]], "cycquery.ops.Substring": [[59, 3, 1, "", "__call__"]], "cycquery.ops.Trim": [[60, 3, 1, "", "__call__"]], "cycquery.ops.Union": [[61, 3, 1, "", "__call__"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "class", "Python class"], "2": ["py", "attribute", "Python attribute"], "3": ["py", "method", "Python method"], "4": ["py", "property", "Python property"]}, "objtypes": {"0": "py:module", "1": "py:class", "2": "py:attribute", "3": "py:method", "4": "py:property"}, "terms": {"": [5, 11, 17, 24, 45, 64, 65, 66, 67, 68], "0": [14, 45, 59, 64, 65, 66, 67, 68], "01": [26, 27, 65, 67, 68], "010": 67, "012": 67, "013542": 67, "018": 67, "020": 67, "03": [65, 67], "030955": 67, "04": [64, 65, 66, 67, 68], "043617": 67, "05": [65, 67], "060": 64, "062": 64, "09": [65, 67], "093352": 65, "1": [3, 11, 21, 22, 24, 26, 27, 29, 30, 31, 32, 34, 45, 50, 63], "10": [49, 63, 66, 68], "100": [63, 66, 67, 68], "1000": 67, "1000000": 11, "101": [63, 64], "103": 64, "103100": 68, "11": [64, 66, 67, 68], "118": 66, "120": 66, "13": 67, "144103": 66, "145693": 65, "15": 68, "17": [65, 66, 67], "18": [64, 66, 67, 68], "180": 67, "182": 67, "189734": 65, "19": [65, 66, 68], "1a": 63, "1b": 63, "1c": 63, "2": [3, 14, 22, 24, 31, 32, 59, 63, 65], "20": 63, "2009": 63, "2010": 63, "2011": 68, "2012": 68, "2013": 68, "2014": [63, 68], "2015": [63, 68], "2016": [63, 68], "2017": 68, "2018": 68, "2019": [33, 68], "2020": [26, 27, 33, 63], "2021": [63, 68], "2022": 68, "2023": [65, 68], "2024": [64, 66, 67, 68], "203": 68, "21": [65, 67], "215": 68, "216": 68, "217": 68, "239": 64, "245811": 66, "249": 64, "250": 64, "26": 65, "267212": 64, "27": 64, "270279": 64, "28": 66, "282214": 67, "2a": 63, "3": [63, 65, 68], "31": 63, "314": 67, "317": 67, "322607": 67, "32567": 65, "33": 67, "34": 67, "343278": 68, "355687": 66, "39": [64, 65, 66, 67, 68], "4": [63, 65, 68], "40": [67, 68], "41": 68, "416": [64, 66], "418": 64, "419": 66, "42": 68, "43": 68, "44": 68, "449": 65, "45": 65, "49": 68, "490": 67, "5": [63, 64, 65, 66, 68], "506": 65, "51": [65, 68], "52": 65, "525": 68, "527": 68, "53": 66, "5432": [3, 17, 64, 66, 67, 68], "55": 64, "56": [64, 68], "561": 68, "563": 68, "57": 64, "58": 64, "5815": 68, "583": 68, "585587": 68, "587958": 67, "591": 65, "592": 65, "6": [63, 65, 66, 68], "605530": 64, "668646": 68, "675141": 65, "679": 67, "681": 67, "690": 67, "692": 67, "693": 66, "7": [63, 65, 68], "732": 66, "734": 66, "751": 68, "753": 68, "795": 67, "797": 67, "8": [63, 68], "814": 65, "815": 65, "82": 67, "820": 66, "820597": 64, "821": 66, "847932": 66, "856": 65, "857": 65, "9": 63, "902": 65, "903": 65, "924": 66, "9305": 65, "936798": 67, "939296": 65, "946522": 67, "988": 67, "989": 67, "999": 67, "A": [10, 11, 21, 26, 27, 47], "And": [0, 67], "For": [1, 17], "If": [1, 17, 19, 20, 21, 22, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 52, 60], "In": 3, "It": [3, 24, 63], "No": [11, 68], "Not": 5, "OR": 51, "Or": 0, "The": [1, 3, 5, 11, 15, 20, 24, 48, 62, 63, 64, 66, 67, 68], "To": 1, "__add__": [0, 58], "__call__": [0, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61], "__init__": [0, 11, 58], "aado2": 63, "abov": 63, "abstract": 53, "accord": [17, 64, 66, 67, 68], "accordingli": [64, 66, 67, 68], "activ": 3, "ad": [11, 19, 20, 21, 22, 58], "add": [19, 20, 21, 22, 50, 58], "add_to": [19, 20, 21, 22], "addcolumn": 0, "adddeltacolumn": [0, 67], "adddeltaconst": 0, "addnumer": 0, "address": 5, "adjust": 15, "admdad": 65, "admiss": [63, 66], "admissiondrug": 64, "admissiondx": 64, "admittim": 67, "admitting_concept_id": 68, "advanc": 63, "after": [5, 15, 24, 26, 57, 58, 63], "aggfunc": 46, "aggreg": [3, 46], "aggsep": 46, "all": [1, 3, 11, 38, 52, 55, 61, 63, 65], "all_visit": 68, "allergi": 64, "allow": [5, 7, 9, 13, 15, 17, 63], "along": 1, "also": 24, "an": [1, 9, 11, 13, 15, 17, 20, 23, 47, 51, 55], "analysi": 1, "analyz": 54, "anchor_year": 15, "anchor_year_differ": 67, "anchor_year_group": 15, "ani": [11, 20, 28, 29, 30, 31, 34, 37, 38, 45, 50], "anoth": [11, 47, 55, 58], "any_": 38, "apacheapsvar": 64, "apachepatientresult": 64, "apachepredvar": 64, "api": [2, 3, 5, 7, 9, 13, 15, 16, 17, 63], "append": [0, 58], "appli": [0, 1, 15, 19, 20, 21, 22, 60], "approx": 63, "approxim": 15, "apr": 63, "april": 63, "ar": [5, 15, 24, 47], "arg": [53, 54, 58], "argument": [20, 28, 29, 30, 31, 34, 37, 38], "around": [3, 63], "ascend": [52, 65], "assign": 17, "assign_all_visit_id": 68, "assum": [24, 64, 66, 67, 68], "attent": 19, "attribut": 11, "automat": 5, "b": 38, "backend": 11, "base": [0, 3, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61], "batch": [11, 63], "batch_mod": [11, 67], "batch_siz": [11, 67], "becom": [11, 54], "befor": [1, 27, 47], "being": [19, 20, 21, 22, 26, 27, 29, 32, 33], "between": 63, "bin": 3, "binarize_col": [26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38], "binaryexpress": [11, 47], "black": 1, "bodi": 68, "bool": [5, 7, 9, 11, 13, 15, 17, 19, 20, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 51, 52, 55, 61], "boolean": [26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38], "both": 47, "build": [5, 63], "built": 3, "ca": 65, "call": 53, "callabl": 24, "can": [1, 3, 5, 7, 9, 13, 15, 17, 24, 38], "cannot": 54, "care": [9, 15], "care_sit": 68, "care_unit": [0, 9], "careplancareprovid": 64, "careplaneol": 64, "careplangener": 64, "careplango": 64, "careplaninfectiousdiseas": 64, "carevu": 63, "cartesian": 47, "cast": [0, 5, 7, 9, 11, 13, 15, 17, 65, 67], "cast_timestamp_col": [5, 7, 9, 13, 15, 17], "categori": 67, "cd": 3, "cdm_sourc": 68, "cdm_synthea10": 68, "certain": 54, "chain": [11, 58], "chart": [15, 63], "chart_ev": [66, 67], "chartev": [0, 13, 15, 66, 67], "chartevents_op": 66, "check": [1, 55], "check_exist": 55, "chronic": 63, "class": [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62], "clear": 11, "clear_data": [0, 11], "code": [2, 64, 66, 67, 68], "codestyl": 3, "cohort": 68, "cohort_definit": 68, "col": [19, 24, 25, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 48, 50, 52, 56, 57, 59, 60], "col1": [3, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 41, 42, 43, 44, 45, 47, 48, 50, 52, 55, 56, 57, 58, 59, 60], "col1_bool": [26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38], "col1_new": [24, 45, 55], "col1_plus_1": [21, 22], "col1_plus_col2": [19, 20], "col1_plus_col3": 19, "col1_substr": 59, "col1_trim": 60, "col2": [3, 19, 20, 21, 22, 24, 25, 41, 42, 43, 45, 47, 48, 52, 56, 57, 58, 60], "col2_new": [24, 45], "col2_plus_1": 22, "col2_plus_col3": 19, "col2_trim": 60, "col3": [3, 19, 20, 47, 57], "collection_date_tim": 65, "column": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 52, 55, 56, 57, 59, 60], "combin": [19, 23, 51], "come": 57, "commit": 2, "common": 68, "commun": 63, "complet": 56, "compon": 44, "comput": 11, "concept": [17, 68], "concept_ancestor": 68, "concept_class": 68, "concept_relationship": 68, "concept_synonym": 68, "cond": [11, 47], "cond_kwarg": [28, 29, 30, 31, 34, 37, 38], "cond_op": [23, 51], "condit": [3, 11, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 51, 68], "condition_concept_id": 68, "condition_concept_nam": 68, "condition_era": 68, "condition_occurr": 68, "conditionafterd": [0, 65, 67, 68], "conditionbefored": [0, 65], "conditionendswith": 0, "conditionequ": [0, 64, 65, 66, 67], "conditiongreaterthan": 0, "conditionin": [0, 3, 23, 51], "conditioninmonth": 0, "conditioninyear": [0, 67], "conditionlessthan": [0, 66], "conditionlik": [0, 23, 51, 67], "conditionregexmatch": [0, 63], "conditionstartswith": 0, "conditionsubstr": [0, 3, 64, 65, 66, 67, 68], "config": [64, 66, 67, 68], "consid": 17, "construct": [9, 13, 15, 17, 20, 21], "contain": [11, 63], "contribut": 2, "convers": 25, "convert": [25, 47], "correspond": [17, 42, 43], "cost": 68, "count": [0, 46, 65, 68], "crd": [2, 6, 63], "creat": [3, 5, 11, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 60, 63], "csv": [11, 68], "current": 25, "custom": [5, 7, 9, 13, 15, 17, 66], "customlab": 64, "cycqueri": [0, 63, 64, 65, 66, 68], "d": 3, "dai": 21, "dask": 11, "data": [0, 3, 9, 11, 13, 15, 54, 67, 68], "databas": [2, 5, 7, 9, 10, 11, 13, 15, 17, 62, 63, 64, 65, 66, 67, 68], "dataclass": 11, "datafram": [3, 11], "dataset": [0, 5, 7, 9, 11, 13, 15, 17, 63], "datasetqueri": [0, 3, 7, 9, 13, 15, 17], "date": [25, 26, 27], "datetim": [5, 7, 9, 13, 15, 17, 21, 26, 27], "db": [0, 5, 65, 67], "dbm": [3, 5, 7, 9, 13, 15, 17, 64, 66, 67, 68], "dbname": 3, "dbsourc": 66, "dbtabl": [11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 58, 59, 60, 61], "dd": [26, 27], "death": 68, "default": [5, 11, 37], "defin": 11, "delirium_v4_0_1": 65, "delta": 21, "delta_kwarg": 20, "depend": 3, "derived_vari": 65, "descend": 52, "develop": 2, "device_exposur": 68, "df": 3, "di": 68, "diagnos": [0, 9, 13, 63], "diagnoses_icd": [0, 15, 67], "diagnoses_op": 67, "diagnosi": [9, 13, 15, 64], "diagnosisstr": 63, "dict": [46, 55], "dictionari": 46, "differ": [38, 47], "disabl": 24, "discharg": 63, "discharge_date_tim": 63, "discharge_to_concept_id": 68, "discharge_to_concept_nam": 68, "dischtim": 67, "distinct": [0, 3, 65], "doc": 3, "docstr": 1, "dod": 15, "domain": 68, "don": 1, "dose_era": 68, "downstream": [5, 7, 9, 13, 15, 17], "drop": [0, 58], "dropempti": [0, 65], "dropnul": [0, 3], "drug_era": 68, "drug_exposur": 68, "drug_strength": 68, "drugnam": 64, "dst_col": 17, "dt": 68, "dtype": 68, "dtype_backend": 11, "e": [3, 5, 44, 47, 50], "e501": 24, "each": [17, 24, 52, 63, 64, 66, 67, 68], "ehr": [3, 5, 62, 63, 68], "eicu": [0, 2, 63], "eicu_crd": 64, "eicuqueri": [0, 63], "electron": 3, "empti": [5, 42], "encount": [9, 63], "encounters_lab": 65, "encounters_per_sit": 65, "encounters_queri": 65, "end": [28, 58, 63], "env": 3, "environ": [1, 3], "episod": 68, "episode_ev": 68, "equal": [29, 30, 34], "er": 65, "erdiagnosi": 65, "erintervent": 65, "error": 1, "etl": 68, "event": [15, 63], "exampl": [19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 58, 59, 60, 61, 63], "execut": [58, 64, 65, 66, 67, 68], "exist": [19, 20, 21, 22, 55, 60], "expens": 47, "expire_flag": 66, "express": 36, "extend": [0, 58], "extract": [44, 59, 64, 65, 66, 67, 68], "extract_str": 44, "extracttimestampcompon": 0, "f": [64, 65, 66, 67, 68], "fact_relationship": 68, "fals": [11, 19, 20, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 51, 52, 61, 65], "femal": 63, "fetch": [9, 11], "fhir_etl": 67, "fhir_trm": 67, "file": [1, 5, 11], "file_format": 11, "fill": [1, 45], "fill_valu": 45, "fillnul": 0, "filter": [3, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 51, 63], "final": 58, "final_visit_id": 68, "finish": [64, 65, 66, 67, 68], "first": [61, 64, 66, 67, 68], "fix": 1, "flag": 47, "float": [22, 25], "follow": [57, 68], "forget": 1, "format": [1, 11, 26, 27, 47, 68], "framework": 11, "from": [3, 9, 11, 15, 17, 44, 47, 55, 60, 63, 64, 66, 68], "func": 24, "function": [15, 19, 20, 21, 22, 24, 46, 53, 60, 63, 64, 65, 66, 67, 68], "further": 1, "g": [3, 5, 44, 47, 50], "gastroenter": 63, "gemini": [0, 2, 63], "geminiqueri": [0, 63], "genc_id": 65, "gender": [64, 66, 67], "gender_concept_nam": 68, "gener": [11, 68], "get": [2, 5, 7, 9, 11, 13, 15, 17, 40, 59, 63], "get_tabl": [0, 5, 7, 9, 13, 15, 17], "given": [45, 58], "glucos": 63, "googl": 1, "greater": [30, 34], "group": 46, "groupbi": 3, "groupby_col": 46, "groupbyaggreg": [0, 65], "guid": 1, "guidelin": [2, 3], "ha": 59, "hadm_id": [66, 67], "have": [5, 7, 9, 13, 15, 17, 31, 38, 47, 63], "hba1c": [23, 35, 51], "health": 3, "hemoglobin": 63, "henc": 3, "hint": 1, "hook": 2, "hospit": [15, 63], "hospital_num": 65, "hospitaldischargeyear": 64, "hospitalid": 64, "host": [3, 5, 7, 9, 13, 15, 17, 64, 65, 66, 67, 68], "hous": 68, "how": [63, 64, 66, 67, 68], "hpc": 65, "html": 3, "i": [1, 3, 5, 11, 15, 17, 19, 20, 21, 22, 24, 38, 42, 43, 47, 54, 63, 64, 66, 67, 68], "icd": 63, "icd_vers": 67, "icu": 15, "id": 17, "iii": [2, 12, 13, 63, 68], "imag": [0, 9], "implement": 53, "import": [3, 63], "includ": [3, 30, 34], "index": [11, 58, 59, 63], "index_col": [11, 67], "infecti": 63, "infer": 15, "info": [3, 9, 64, 65, 66, 67, 68], "inform": 44, "information_schema": [67, 68], "infusiondrug": 64, "initi": [11, 58], "input": 24, "insert": [0, 58], "instal": 2, "instanti": [5, 63], "instead": [23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 51], "instruct": [64, 66, 67, 68], "int": [5, 11, 22, 25, 32, 33, 47, 49, 58, 59], "int64": 68, "intakeoutput": 64, "integ": 50, "integr": 3, "intend": 5, "interest": 1, "interfac": [0, 9, 13, 15, 17], "interv": 20, "ip_admin": [0, 9], "ipdiagnosi": 65, "ipintervent": 65, "ipscu": 65, "isout": [11, 47, 68], "issu": 1, "iv": [2, 14, 63], "jane": [23, 51], "john": [23, 51], "join": [0, 3, 11, 15, 64, 65, 66, 67, 68], "join_tabl": [11, 47, 64, 66, 67, 68], "join_table_col": [11, 47], "just": 38, "keep": [0, 47, 63], "kei": [46, 55, 58], "keyword": [28, 29, 30, 31, 34, 37, 38, 61, 63], "kwarg": [53, 54], "lab": [15, 63, 65], "lab_nam": [23, 35, 46, 51], "lab_name_agg": 46, "lab_name_bool": 35, "lab_op": 65, "label": [19, 20, 21, 22, 44, 46, 50, 60, 66, 67], "labev": [0, 13, 15, 66], "labnam": 64, "lambda": 24, "larg": 54, "last": 1, "later": 63, "least": 1, "left": 47, "len": [64, 65, 66, 67, 68], "less": [34, 63], "like": [3, 17, 35], "limit": [0, 11, 54, 63, 66, 67, 68], "line": 24, "link": 1, "list": [3, 5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 24, 25, 31, 32, 33, 38, 40, 41, 42, 43, 45, 46, 47, 48, 51, 52, 56, 57, 58, 60, 64, 65, 66, 67, 68], "list_column": [0, 5, 7, 9, 13, 15, 17], "list_custom_t": [0, 5, 7, 9, 13, 15, 17, 66], "list_schema": [0, 5, 7, 9, 13, 15, 17, 67, 68], "list_tabl": [0, 3, 5, 7, 9, 13, 15, 17, 64, 65, 68], "liter": [0, 11], "load": 68, "local": 3, "localhost": [3, 17, 64, 66, 67, 68], "locality_vari": 65, "locat": 68, "long": [24, 63], "long_titl": [66, 67], "lookup_cci": 65, "lookup_ccsr": 65, "lookup_diagnosi": 65, "lookup_er_administr": 65, "lookup_hospital_num": 65, "lookup_icd10_ca_descript": 65, "lookup_icd10_ca_to_ccsr": 65, "lookup_imag": 65, "lookup_ip_administr": 65, "lookup_ip_scu": 65, "lookup_lab_concept": 65, "lookup_pharmacy_concept": 65, "lookup_pharmacy_rout": 65, "lookup_phy_characterist": 65, "lookup_room_transf": 65, "lookup_statcan": 65, "lookup_transf": 65, "lookup_transfusion_concept": 65, "lookup_vitals_concept": 65, "lymphadenopathi": 63, "m": [3, 66], "mai": 63, "make": [3, 38], "male": 63, "manag": 5, "mani": [3, 63], "map": [5, 7, 9, 13, 15, 17, 55], "map_concept_ids_to_nam": [0, 17, 68], "march": 63, "match": [3, 36, 68], "measur": [0, 17, 63], "measurement_concept_nam": 68, "medic": 63, "metadata": 68, "method": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 66], "microlab": 64, "million": 11, "mimic": [2, 12, 13, 14, 15, 63, 68], "mimic_fhir": 67, "mimiciii": [0, 66, 68], "mimiciiiqueri": [0, 63, 68], "mimiciv": [0, 67], "mimiciv_": 67, "mimiciv_deriv": 67, "mimiciv_hosp": 67, "mimiciv_icu": 67, "mimiciv_not": 67, "mimicivqueri": [0, 63], "mm": [26, 27], "mode": 11, "model": 68, "modul": [6, 8, 12, 14, 15], "month": [32, 44], "more": 3, "mortal": 63, "most": 63, "multipl": [9, 23, 24, 46, 51], "must": [25, 31, 32, 33, 38, 46], "mypi": 1, "mysql": 5, "name": [5, 7, 9, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 51, 55, 56, 57, 59, 68], "nbsphinx_allow_error": 3, "need": [1, 59], "neg": [19, 20], "negat": [26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38], "neither": 47, "new": [19, 20, 21, 22, 24, 45, 46, 50, 56, 59, 60], "new_col": 24, "new_col_label": [19, 20, 21, 22, 59, 60], "new_col_nam": [45, 59], "next": 67, "none": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 52, 59, 60], "noqa": 24, "nor": 47, "not_": [26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38], "note": [5, 15, 64, 68], "note_nlp": 68, "notebook": [64, 65, 66, 67, 68], "null": [43, 45], "number": [5, 39, 49, 57, 63], "numer": 22, "numpi": 1, "nurseassess": 64, "nursecar": 64, "nursechart": 64, "object": [5, 9, 10, 11, 13, 15, 17, 20, 21, 24, 26, 27, 46, 53, 58, 63], "observ": [0, 17, 68], "observation_period": 68, "occur": 63, "omop": [0, 2, 63], "omopqueri": [0, 63], "on_to_typ": [11, 47], "onc": 1, "one": [38, 63], "onli": [38, 47, 48, 63], "op": [0, 3, 11, 15, 63, 64, 65, 66, 68], "op_": 58, "oper": [3, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61], "oppos": 47, "option": [5, 7, 9, 11, 13, 15, 17, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 61], "order": [3, 11, 52, 54, 56, 57], "orderbi": [0, 65], "ordereddict": 58, "origin": 11, "orm": [5, 11, 63, 64, 65, 66, 67, 68], "other": [11, 19, 57, 58], "otherwis": [19, 20, 21, 22, 60], "our": 1, "out": 1, "outcom": 63, "outer": [11, 47], "over": 46, "pai": 19, "pair": 46, "panda": [3, 11, 68], "paramet": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 58, 59, 60, 61, 64, 66, 67, 68], "parquet": 11, "partit": [11, 63], "pass": [64, 66, 67, 68], "password": [3, 5, 7, 9, 13, 15, 17, 64, 65, 66, 67, 68], "pasthistori": 64, "path": [3, 5, 11], "patient": [0, 9, 15, 63], "patient_admiss": [66, 67], "patient_admissions_df": 67, "patient_admissions_diagnos": [66, 67], "patient_admissions_lab": 67, "patient_admissions_radiology_not": 67, "patient_admissions_vit": 67, "patient_chart_ev": 66, "patient_diagnos": 64, "patient_id_hash": 63, "patient_lab": [64, 66], "patient_med": 64, "patientunitstayid": 64, "pattern": 35, "payer_plan_period": 68, "pd": 68, "per": 63, "perform": [3, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 59, 60, 61, 68], "person": [0, 17, 68], "person_id": [39, 40, 46, 68], "person_visit": 68, "person_visits_condit": 68, "person_visits_conditions_measur": 68, "pharmaci": 65, "physicalexam": 64, "pip": 2, "place": 63, "pleas": 1, "poetri": 2, "pop": [0, 58], "port": [3, 5, 7, 9, 13, 15, 17, 64, 66, 67, 68], "possibli": [5, 7, 9, 13, 15, 17], "postgr": [64, 66, 67, 68], "postgresql": [2, 5, 17, 63, 64, 66, 67, 68], "potassium": 63, "pr": 1, "pre": 2, "prevent": 46, "print": [64, 65, 66, 67, 68], "procedur": 15, "procedure_occurr": 68, "procedures_icd": [0, 15], "process": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 59, 60, 61], "product": 47, "profil": [64, 65, 66, 67, 68], "properti": 11, "provid": [5, 7, 9, 13, 15, 17, 24, 38, 45, 46, 52, 62, 68], "public": [65, 67, 68], "pwd": [5, 64, 66, 67, 68], "pyarrow": [11, 68], "pylint": 24, "python": [1, 3, 63], "python3": 3, "qo": [3, 64, 65, 66, 67, 68], "queri": [2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 49, 51, 53, 58, 62, 63, 64, 65, 66, 67, 68], "querier": [3, 4, 7, 9, 13, 15, 17, 64, 65, 66, 67, 68], "queryinterfac": [0, 9, 13, 15, 17], "queryop": [0, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 58, 59, 60, 61], "quick": [64, 66, 67, 68], "quit": 54, "r": 67, "radiologi": [63, 65], "radiology_not": 67, "radiology_notes_op": 67, "random": 54, "randomizeord": 0, "rather": [19, 20], "raw": 63, "readi": [64, 65, 66, 67, 68], "receiv": 15, "recent": 63, "recogn": [5, 7, 9, 13, 15, 17], "recommend": 1, "record": [3, 63], "refer": 2, "regex": 36, "regular": 36, "relat": 3, "relationship": 68, "releas": 68, "remov": [42, 43], "renam": 0, "rename_map": 55, "reorder": [0, 57], "reorderaft": 0, "repo": 68, "report": [9, 63], "repres": 47, "respiratorycar": 64, "respiratorychart": 64, "result": [11, 58, 64, 66, 67, 68], "return": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 65, 66, 68], "return_cond": [23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 51], "room": 9, "room_transf": [0, 9], "roomtransf": 65, "routin": 63, "row": [11, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 49, 52, 54, 63, 65, 66, 67, 68], "ruff": 1, "run": [0, 1, 3, 5, 11, 63, 64, 65, 66, 68], "run_queri": [64, 65, 66, 67, 68], "sai": 47, "same": [46, 47], "save": [0, 11], "schema": [3, 5, 7, 9, 13, 15, 17, 67, 68], "schema_nam": [5, 7, 9, 13, 15, 17, 68], "schizophrenia": 63, "search": 63, "see": 3, "seen": 54, "select": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 58, 59, 60, 61, 67], "self": 5, "separ": 46, "sepsi": 63, "sequenc": [46, 58], "sequenti": [0, 3, 11, 64, 65, 66, 67, 68], "server": 11, "set": [3, 11, 63], "setup": [1, 64, 65, 66, 67, 68], "should": 11, "show": [1, 64, 65, 66, 67, 68], "showcas": 68, "sign": 63, "simpl": 3, "singl": 24, "size": 11, "slice": 58, "slow": 54, "so": 54, "sodium": 63, "sodium_test": 65, "some": [3, 19, 20, 21, 22, 26, 27, 28, 29, 30, 34, 37, 41, 42, 43, 52, 55, 60], "somecol_concept_id": 17, "somecol_concept_nam": 17, "somet": 3, "sort": [52, 63], "sort_index": 68, "sourc": [3, 5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61], "source_to_concept_map": 68, "source_to_source_vocab_map": 68, "source_to_standard_vocab_map": 68, "specif": 3, "specifi": [17, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 46, 47, 48, 57, 60], "specimen": 68, "sphinx": 3, "sphinxopt": 3, "sql": [3, 5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 59, 60, 61, 63], "sqlalchemi": [3, 5, 7, 9, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 59, 60, 61, 63], "sqlite": 5, "src_col": 17, "src_tabl": 17, "standard": [5, 7, 9, 13, 15, 17], "start": [2, 37, 59], "start_index": 59, "static": 1, "stop": 59, "stop_index": 59, "str": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 52, 55, 56, 57, 58, 59, 60, 67], "string": [28, 37, 46, 47, 50, 59, 60, 63], "string_agg": 46, "string_aggfunc": 46, "style": [1, 47], "subclass": 5, "subject_id": [63, 66], "submit": 1, "subqueri": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61], "subset": 63, "substr": [0, 3, 38, 63], "subtract": [19, 20], "successfulli": [64, 65, 66, 67, 68], "suggest": 47, "suppli": 15, "support": [6, 12, 14, 25], "sure": 3, "synthea": 68, "synthea_integration_test": 68, "system": 5, "t": 1, "tabl": [3, 5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 66, 68], "table1": [47, 61], "table2": [47, 61], "table_col": [11, 47], "table_nam": [5, 7, 9, 13, 15, 17], "take": [24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 63], "teach": 63, "teachingstatu": 64, "templat": 1, "test": [3, 63], "test_type_map": 65, "text": 67, "than": [19, 20, 30, 34, 63], "thank": 1, "them": 11, "thi": [5, 22, 38, 46, 47, 64, 65, 66, 67, 68], "thu": 11, "time": 44, "timedelta": 21, "timestamp": [5, 7, 9, 13, 15, 17, 25, 26, 27, 32, 33, 44, 65], "timestamp_col": [26, 27, 32, 33, 44], "titl": 63, "to_datetim": 68, "togeth": 63, "too": 24, "tool": [1, 3, 63, 64, 65, 66, 67, 68], "total": 63, "transfer": 9, "transfus": 65, "treatment": 64, "trim": 0, "true": [3, 5, 7, 9, 11, 13, 15, 17, 19, 20, 35, 38, 52, 55, 61, 64, 65, 67, 68], "tupl": [11, 47], "tutori": 2, "two": [47, 58, 61], "type": [1, 5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61], "type_": 25, "union": [0, 5, 11, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 58, 59, 60], "union_al": [0, 11, 61], "union_t": 61, "unit": [3, 9], "up": 3, "updat": [64, 66, 67, 68], "upstream": 11, "us": [1, 2, 5, 7, 9, 11, 13, 15, 17, 20, 23, 40, 46, 47, 51, 54, 61, 63, 64, 65, 66, 68], "usenam": 3, "user": [3, 5, 7, 9, 13, 15, 17, 64, 65, 66, 67, 68], "usernam": [5, 64, 65, 66, 67, 68], "util": [64, 65, 66, 67, 68], "v1": [66, 68], "v2": [67, 68], "valu": [22, 29, 30, 31, 34, 42, 43, 45, 46, 47, 50], "value_count": 68, "valuenum": 63, "virtual": 1, "visit": 63, "visit_count": 46, "visit_detail": [0, 17, 68], "visit_id": 40, "visit_occurr": [0, 17, 68], "visit_occurrence_id": 68, "visit_start_d": 68, "visits_concept_map": 68, "visits_concept_mapped_di": 68, "visits_measur": 68, "vital": [63, 65], "vitalaperiod": 64, "vitalperiod": 64, "vocabulari": 68, "we": [1, 68], "weight": 68, "welcom": 3, "were": 63, "when": [5, 38, 47, 54], "where": [11, 59], "wherea": 19, "whether": [5, 7, 9, 11, 13, 15, 17, 38, 52, 55, 61], "which": [1, 5, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 59, 60, 61, 68], "whitespac": 60, "who": 63, "work": 19, "wrap": [9, 10, 11, 13, 15, 17], "wrapper": [3, 63], "write": 3, "x": 24, "y": 24, "year": [15, 32, 33, 44, 63, 68], "you": [1, 63], "your": 1, "yyyi": [26, 27]}, "titles": ["API Reference", "Contributing to cycquery", "Welcome to cycquery\u2019s documentation!", "cycquery", "cycquery.base", "cycquery.base.DatasetQuerier", "cycquery.eicu", "cycquery.eicu.EICUQuerier", "cycquery.gemini", "cycquery.gemini.GEMINIQuerier", "cycquery.interface", "cycquery.interface.QueryInterface", "cycquery.mimiciii", "cycquery.mimiciii.MIMICIIIQuerier", "cycquery.mimiciv", "cycquery.mimiciv.MIMICIVQuerier", "cycquery.omop", "cycquery.omop.OMOPQuerier", "cycquery.ops", "cycquery.ops.AddColumn", "cycquery.ops.AddDeltaColumn", "cycquery.ops.AddDeltaConstant", "cycquery.ops.AddNumeric", "cycquery.ops.And", "cycquery.ops.Apply", "cycquery.ops.Cast", "cycquery.ops.ConditionAfterDate", "cycquery.ops.ConditionBeforeDate", "cycquery.ops.ConditionEndsWith", "cycquery.ops.ConditionEquals", "cycquery.ops.ConditionGreaterThan", "cycquery.ops.ConditionIn", "cycquery.ops.ConditionInMonths", "cycquery.ops.ConditionInYears", "cycquery.ops.ConditionLessThan", "cycquery.ops.ConditionLike", "cycquery.ops.ConditionRegexMatch", "cycquery.ops.ConditionStartsWith", "cycquery.ops.ConditionSubstring", "cycquery.ops.Count", "cycquery.ops.Distinct", "cycquery.ops.Drop", "cycquery.ops.DropEmpty", "cycquery.ops.DropNulls", "cycquery.ops.ExtractTimestampComponent", "cycquery.ops.FillNull", "cycquery.ops.GroupByAggregate", "cycquery.ops.Join", "cycquery.ops.Keep", "cycquery.ops.Limit", "cycquery.ops.Literal", "cycquery.ops.Or", "cycquery.ops.OrderBy", "cycquery.ops.QueryOp", "cycquery.ops.RandomizeOrder", "cycquery.ops.Rename", "cycquery.ops.Reorder", "cycquery.ops.ReorderAfter", "cycquery.ops.Sequential", "cycquery.ops.Substring", "cycquery.ops.Trim", "cycquery.ops.Union", "cycquery", "Tutorials", "eICU-CRD tutorial", "GEMINI tutorial", "MIMIC-III tutorial", "MIMIC-IV tutorial", "OMOP tutorial"], "titleterms": {"": 2, "1": [64, 65, 66, 67, 68], "10": 67, "100": 64, "101": 65, "1a": 65, "1b": 65, "1c": 65, "2": [64, 66, 67, 68], "20": 66, "2009": 67, "2010": 68, "2014": 64, "2015": [64, 65, 67], "2016": 65, "2020": 68, "2021": 67, "2a": 65, "3": [64, 66, 67], "31": 65, "4": [64, 66, 67], "5": 67, "6": 67, "7": 67, "8": 67, "9": [66, 67], "And": 23, "Or": 51, "aado2": 66, "abov": 65, "addcolumn": 19, "adddeltacolumn": 20, "adddeltaconst": 21, "addnumer": 22, "admiss": [65, 67], "advanc": 67, "after": 68, "all": [64, 66, 67, 68], "api": [0, 62], "appli": 24, "approx": 67, "apr": 65, "april": 65, "base": [4, 5], "batch": 67, "between": 65, "carevu": 66, "cast": 25, "chart": 66, "chronic": 67, "code": 1, "commit": 1, "conditionafterd": 26, "conditionbefored": 27, "conditionendswith": 28, "conditionequ": 29, "conditiongreaterthan": 30, "conditionin": 31, "conditioninmonth": 32, "conditioninyear": 33, "conditionlessthan": 34, "conditionlik": 35, "conditionregexmatch": [36, 67], "conditionstartswith": 37, "conditionsubstr": 38, "contain": 67, "content": 2, "contribut": [1, 3], "count": 39, "crd": 64, "creat": 65, "cycqueri": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 67], "databas": 3, "dataset": [62, 65], "datasetqueri": 5, "develop": 3, "diagnos": [64, 66, 67, 68], "diagnosisstr": 64, "discharg": [64, 65], "discharge_date_tim": 65, "distinct": 40, "document": [2, 3], "drop": 41, "dropempti": 42, "dropnul": 43, "each": 65, "eicu": [6, 7, 64], "eicuqueri": [7, 64], "encount": [64, 65, 66, 67], "end": 68, "event": 66, "exampl": [64, 65, 66, 67, 68], "extracttimestampcompon": 44, "femal": [64, 66, 67, 68], "fillnul": 45, "filter": 67, "from": [65, 67], "gastroenter": 66, "gemini": [8, 9, 65], "geminiqueri": [9, 65], "get": [3, 64, 65, 66, 67, 68], "glucos": 64, "groupbyaggreg": 46, "guidelin": 1, "have": 66, "hemoglobin": 67, "hook": 1, "hospit": [64, 65], "how": 65, "icd": [66, 67], "iii": 66, "import": [64, 65, 66, 67, 68], "index": 67, "infecti": 67, "instal": 3, "instanti": [64, 65, 66, 67, 68], "interfac": [10, 11], "iv": 67, "join": 47, "keep": [48, 65], "keyword": 67, "lab": [64, 66, 67], "later": 67, "less": 66, "limit": [49, 64], "liter": 50, "long": [66, 67], "lymphadenopathi": 67, "mai": 65, "male": 66, "mani": 65, "march": 65, "measur": 68, "medic": 64, "mimic": [66, 67], "mimiciii": [12, 13], "mimiciiiqueri": [13, 66], "mimiciv": [14, 15], "mimicivqueri": [15, 67], "mortal": [66, 68], "most": 65, "number": 65, "occur": 67, "omop": [16, 17, 68], "omopqueri": [17, 68], "one": 65, "onli": 65, "op": [18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 67], "orderbi": 52, "outcom": [66, 68], "partit": 67, "patient": [64, 65, 66, 67, 68], "patient_id_hash": 65, "per": 65, "pip": 3, "place": 65, "poetri": 3, "postgresql": 3, "potassium": [64, 66], "pre": 1, "queri": 3, "queryinterfac": 11, "queryop": 53, "radiologi": 67, "randomizeord": 54, "raw": 67, "recent": 65, "record": 65, "refer": 0, "renam": 55, "reorder": 56, "reorderaft": 57, "report": 67, "return": 67, "routin": 67, "row": 64, "run": 67, "schizophrenia": [64, 67], "search": 64, "sepsi": 68, "sequenti": 58, "set": 65, "sign": 67, "sodium": 65, "sort": 65, "sql": 67, "start": 3, "string": 67, "subject_id": 67, "subset": 65, "substr": [59, 64], "tabl": 65, "take": 65, "teach": 64, "test": [64, 65, 66, 67], "than": 66, "titl": [66, 67], "togeth": 67, "total": 65, "trim": 60, "tutori": [63, 64, 65, 66, 67, 68], "union": 61, "us": [3, 67], "valuenum": 66, "visit": 68, "vital": 67, "welcom": 2, "were": 65, "who": 65, "year": [64, 67]}}) \ No newline at end of file +Search.setIndex({"alltitles": {"API Reference": [[0, "api-reference"]], "Coding guidelines": [[1, "coding-guidelines"]], "Contents:": [[2, null]], "Contributing": [[3, "contributing"]], "Contributing to cycquery": [[1, "contributing-to-cycquery"]], "Example 1. Get all female patients discharged in 2014 (limit to 100 rows).": [[64, "Example-1.-Get-all-female-patients-discharged-in-2014-(limit-to-100-rows)."]], "Example 1. Get all male patients with a mortality outcome.": [[66, "Example-1.-Get-all-male-patients-with-a-mortality-outcome."]], "Example 1. Get all patient admissions from 2021 or later (approx year of admission)": [[67, "Example-1.-Get-all-patient-admissions-from-2021-or-later-(approx-year-of-admission)"]], "Example 1. Get all patient visits in or after 2010.": [[68, "Example-1.-Get-all-patient-visits-in-or-after-2010."]], "Example 1. Get all patient visits that ended in a mortality outcome in or after 2010.": [[68, "Example-1.-Get-all-patient-visits-that-ended-in-a-mortality-outcome-in-or-after-2010."]], "Example 1a. Create a table with only one hospitalization per patient, keeping the most recent encounter for each patient. Sort the dataset by patient_id_hashed and discharge_date_time, and then keep the recent record.": [[65, "Example-1a.-Create-a-table-with-only-one-hospitalization-per-patient,-keeping-the-most-recent-encounter-for-each-patient.-Sort-the-dataset-by-patient_id_hashed-and-discharge_date_time,-and-then-keep-the-recent-record."]], "Example 1b. From the above set of encounters, take a subset of patients who were discharged between April 1, 2015 and March 31, 2016.": [[65, "Example-1b.-From-the-above-set-of-encounters,-take-a-subset-of-patients-who-were-discharged-between-April-1,-2015-and-March-31,-2016."]], "Example 1c. From the above set of encounters, get the total number of admissions for each hospital.": [[65, "Example-1c.-From-the-above-set-of-encounters,-get-the-total-number-of-admissions-for-each-hospital."]], "Example 2. Get all female patient encounters with diagnoses (gastroenteritis in ICD-9 long title).": [[66, "Example-2.-Get-all-female-patient-encounters-with-diagnoses-(gastroenteritis-in-ICD-9-long-title)."]], "Example 2. Get all measurements for female patient visits with sepsis diagnoses, that ended in a mortality outcome.": [[68, "Example-2.-Get-all-measurements-for-female-patient-visits-with-sepsis-diagnoses,-that-ended-in-a-mortality-outcome."]], "Example 2. Get all patient encounters with diagnoses (schizophrenia in ICD-10 long title), in the year 2015.": [[67, "Example-2.-Get-all-patient-encounters-with-diagnoses-(schizophrenia-in-ICD-10-long-title),-in-the-year-2015."]], "Example 2. Get all patient encounters with diagnoses (schizophrenia in diagnosisstring), discharged in the year 2015.": [[64, "Example-2.-Get-all-patient-encounters-with-diagnoses-(schizophrenia-in-diagnosisstring),-discharged-in-the-year-2015."]], "Example 2. Get measurements for all visits in or after 2020.": [[68, "Example-2.-Get-measurements-for-all-visits-in-or-after-2020."]], "Example 2a. How many sodium tests were placed between Apr 1, 2015 and May 31, 2015 at hospital 101?": [[65, "Example-2a.-How-many-sodium-tests-were-placed-between-Apr-1,-2015-and-May-31,-2015-at-hospital-101?"]], "Example 3. Advanced - uses ConditionRegexMatch from cycquery.ops. Get all patient encounters with diagnoses (ICD-9 long title contains schizophrenia and chronic ), in the year 2015.": [[67, "Example-3.-Advanced---uses-ConditionRegexMatch-from-cycquery.ops.-Get-all-patient-encounters-with-diagnoses-(ICD-9-long-title-contains-schizophrenia-and-chronic-),-in-the-year-2015."]], "Example 3. Get potassium lab tests for female patients.": [[66, "Example-3.-Get-potassium-lab-tests-for-female-patients."]], "Example 3. Get potassium lab tests for patients discharged in the year 2014, for all teaching hospitals.": [[64, "Example-3.-Get-potassium-lab-tests-for-patients-discharged-in-the-year-2014,-for-all-teaching-hospitals."]], "Example 4. Get AaDO2 carevue chart events for male patients that have a valuenum of less than 20.": [[66, "Example-4.-Get-AaDO2-carevue-chart-events-for-male-patients-that-have-a-valuenum-of-less-than-20."]], "Example 4. Get glucose medications (substring search) for female patients discharged in 2014.": [[64, "Example-4.-Get-glucose-medications-(substring-search)-for-female-patients-discharged-in-2014."]], "Example 4. Get routine vital signs for patients from year 2015.": [[67, "Example-4.-Get-routine-vital-signs-for-patients-from-year-2015."]], "Example 5. Get hemoglobin lab tests for patients from year 2009.": [[67, "Example-5.-Get-hemoglobin-lab-tests-for-patients-from-year-2009."]], "Example 6. Get radiology reports and filter on keywords lymphadenopathy and infectious occurring together from year 2009.": [[67, "Example-6.-Get-radiology-reports-and-filter-on-keywords-lymphadenopathy-and-infectious-occurring-together-from-year-2009."]], "Example 7. Get all female patient encounters from year 2015, and return batches partitioned and indexed on subject_id.": [[67, "Example-7.-Get-all-female-patient-encounters-from-year-2015,-and-return-batches-partitioned-and-indexed-on-subject_id."]], "Example 8. Running a raw SQL string.": [[67, "Example-8.-Running-a-raw-SQL-string."]], "GEMINI tutorial": [[65, "GEMINI-tutorial"]], "Imports and instantiate EICUQuerier": [[64, "Imports-and-instantiate-EICUQuerier"]], "Imports and instantiate GEMINIQuerier.": [[65, "Imports-and-instantiate-GEMINIQuerier."]], "Imports and instantiate MIMICIIIQuerier": [[66, "Imports-and-instantiate-MIMICIIIQuerier"]], "Imports and instantiate MIMICIVQuerier": [[67, "Imports-and-instantiate-MIMICIVQuerier"]], "Imports and instantiate OMOPQuerier.": [[68, "Imports-and-instantiate-OMOPQuerier."], [68, "id1"]], "Installing cycquery using pip": [[3, "installing-cycquery-using-pip"]], "MIMIC-III tutorial": [[66, "MIMIC-III-tutorial"]], "MIMIC-IV tutorial": [[67, "MIMIC-IV-tutorial"]], "OMOP tutorial": [[68, "OMOP-tutorial"]], "Pre-commit hooks": [[1, "pre-commit-hooks"]], "Query postgresql database": [[3, "query-postgresql-database"]], "Tutorials": [[63, "tutorials"]], "Using poetry": [[3, "using-poetry"]], "Welcome to cycquery\u2019s documentation!": [[2, "welcome-to-cycquery-s-documentation"]], "cycquery": [[3, "cycquery"], [62, "module-cycquery"]], "cycquery.base": [[4, "module-cycquery.base"]], "cycquery.base.DatasetQuerier": [[5, "cycquery-base-datasetquerier"]], "cycquery.eicu": [[6, "module-cycquery.eicu"]], "cycquery.eicu.EICUQuerier": [[7, "cycquery-eicu-eicuquerier"]], "cycquery.gemini": [[8, "module-cycquery.gemini"]], "cycquery.gemini.GEMINIQuerier": [[9, "cycquery-gemini-geminiquerier"]], "cycquery.interface": [[10, "module-cycquery.interface"]], "cycquery.interface.QueryInterface": [[11, "cycquery-interface-queryinterface"]], "cycquery.mimiciii": [[12, "module-cycquery.mimiciii"]], "cycquery.mimiciii.MIMICIIIQuerier": [[13, "cycquery-mimiciii-mimiciiiquerier"]], "cycquery.mimiciv": [[14, "module-cycquery.mimiciv"]], "cycquery.mimiciv.MIMICIVQuerier": [[15, "cycquery-mimiciv-mimicivquerier"]], "cycquery.omop": [[16, "module-cycquery.omop"]], "cycquery.omop.OMOPQuerier": [[17, "cycquery-omop-omopquerier"]], "cycquery.ops": [[18, "module-cycquery.ops"]], "cycquery.ops.AddColumn": [[19, "cycquery-ops-addcolumn"]], "cycquery.ops.AddDeltaColumn": [[20, "cycquery-ops-adddeltacolumn"]], "cycquery.ops.AddDeltaConstant": [[21, "cycquery-ops-adddeltaconstant"]], "cycquery.ops.AddNumeric": [[22, "cycquery-ops-addnumeric"]], "cycquery.ops.And": [[23, "cycquery-ops-and"]], "cycquery.ops.Apply": [[24, "cycquery-ops-apply"]], "cycquery.ops.Cast": [[25, "cycquery-ops-cast"]], "cycquery.ops.ConditionAfterDate": [[26, "cycquery-ops-conditionafterdate"]], "cycquery.ops.ConditionBeforeDate": [[27, "cycquery-ops-conditionbeforedate"]], "cycquery.ops.ConditionEndsWith": [[28, "cycquery-ops-conditionendswith"]], "cycquery.ops.ConditionEquals": [[29, "cycquery-ops-conditionequals"]], "cycquery.ops.ConditionGreaterThan": [[30, "cycquery-ops-conditiongreaterthan"]], "cycquery.ops.ConditionIn": [[31, "cycquery-ops-conditionin"]], "cycquery.ops.ConditionInMonths": [[32, "cycquery-ops-conditioninmonths"]], "cycquery.ops.ConditionInYears": [[33, "cycquery-ops-conditioninyears"]], "cycquery.ops.ConditionLessThan": [[34, "cycquery-ops-conditionlessthan"]], "cycquery.ops.ConditionLike": [[35, "cycquery-ops-conditionlike"]], "cycquery.ops.ConditionRegexMatch": [[36, "cycquery-ops-conditionregexmatch"]], "cycquery.ops.ConditionStartsWith": [[37, "cycquery-ops-conditionstartswith"]], "cycquery.ops.ConditionSubstring": [[38, "cycquery-ops-conditionsubstring"]], "cycquery.ops.Count": [[39, "cycquery-ops-count"]], "cycquery.ops.Distinct": [[40, "cycquery-ops-distinct"]], "cycquery.ops.Drop": [[41, "cycquery-ops-drop"]], "cycquery.ops.DropEmpty": [[42, "cycquery-ops-dropempty"]], "cycquery.ops.DropNulls": [[43, "cycquery-ops-dropnulls"]], "cycquery.ops.ExtractTimestampComponent": [[44, "cycquery-ops-extracttimestampcomponent"]], "cycquery.ops.FillNull": [[45, "cycquery-ops-fillnull"]], "cycquery.ops.GroupByAggregate": [[46, "cycquery-ops-groupbyaggregate"]], "cycquery.ops.Join": [[47, "cycquery-ops-join"]], "cycquery.ops.Keep": [[48, "cycquery-ops-keep"]], "cycquery.ops.Limit": [[49, "cycquery-ops-limit"]], "cycquery.ops.Literal": [[50, "cycquery-ops-literal"]], "cycquery.ops.Or": [[51, "cycquery-ops-or"]], "cycquery.ops.OrderBy": [[52, "cycquery-ops-orderby"]], "cycquery.ops.QueryOp": [[53, "cycquery-ops-queryop"]], "cycquery.ops.RandomizeOrder": [[54, "cycquery-ops-randomizeorder"]], "cycquery.ops.Rename": [[55, "cycquery-ops-rename"]], "cycquery.ops.Reorder": [[56, "cycquery-ops-reorder"]], "cycquery.ops.ReorderAfter": [[57, "cycquery-ops-reorderafter"]], "cycquery.ops.Sequential": [[58, "cycquery-ops-sequential"]], "cycquery.ops.Substring": [[59, "cycquery-ops-substring"]], "cycquery.ops.Trim": [[60, "cycquery-ops-trim"]], "cycquery.ops.Union": [[61, "cycquery-ops-union"]], "dataset APIs": [[62, "dataset-apis"]], "eICU-CRD tutorial": [[64, "eICU-CRD-tutorial"]], "\ud83d\udc23 Getting Started": [[3, "getting-started"]], "\ud83d\udcda Documentation": [[3, "documentation"]], "\ud83e\uddd1\ud83c\udfff\u200d\ud83d\udcbb Developing": [[3, "developing"]]}, "docnames": ["api", "contributing", "index", "intro", "reference/api/_autosummary/cycquery.base", "reference/api/_autosummary/cycquery.base.DatasetQuerier", "reference/api/_autosummary/cycquery.eicu", "reference/api/_autosummary/cycquery.eicu.EICUQuerier", "reference/api/_autosummary/cycquery.gemini", "reference/api/_autosummary/cycquery.gemini.GEMINIQuerier", "reference/api/_autosummary/cycquery.interface", "reference/api/_autosummary/cycquery.interface.QueryInterface", "reference/api/_autosummary/cycquery.mimiciii", "reference/api/_autosummary/cycquery.mimiciii.MIMICIIIQuerier", "reference/api/_autosummary/cycquery.mimiciv", "reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier", "reference/api/_autosummary/cycquery.omop", "reference/api/_autosummary/cycquery.omop.OMOPQuerier", "reference/api/_autosummary/cycquery.ops", "reference/api/_autosummary/cycquery.ops.AddColumn", "reference/api/_autosummary/cycquery.ops.AddDeltaColumn", "reference/api/_autosummary/cycquery.ops.AddDeltaConstant", "reference/api/_autosummary/cycquery.ops.AddNumeric", "reference/api/_autosummary/cycquery.ops.And", "reference/api/_autosummary/cycquery.ops.Apply", "reference/api/_autosummary/cycquery.ops.Cast", "reference/api/_autosummary/cycquery.ops.ConditionAfterDate", "reference/api/_autosummary/cycquery.ops.ConditionBeforeDate", "reference/api/_autosummary/cycquery.ops.ConditionEndsWith", "reference/api/_autosummary/cycquery.ops.ConditionEquals", "reference/api/_autosummary/cycquery.ops.ConditionGreaterThan", "reference/api/_autosummary/cycquery.ops.ConditionIn", "reference/api/_autosummary/cycquery.ops.ConditionInMonths", "reference/api/_autosummary/cycquery.ops.ConditionInYears", "reference/api/_autosummary/cycquery.ops.ConditionLessThan", "reference/api/_autosummary/cycquery.ops.ConditionLike", "reference/api/_autosummary/cycquery.ops.ConditionRegexMatch", "reference/api/_autosummary/cycquery.ops.ConditionStartsWith", "reference/api/_autosummary/cycquery.ops.ConditionSubstring", "reference/api/_autosummary/cycquery.ops.Count", "reference/api/_autosummary/cycquery.ops.Distinct", "reference/api/_autosummary/cycquery.ops.Drop", "reference/api/_autosummary/cycquery.ops.DropEmpty", "reference/api/_autosummary/cycquery.ops.DropNulls", "reference/api/_autosummary/cycquery.ops.ExtractTimestampComponent", "reference/api/_autosummary/cycquery.ops.FillNull", "reference/api/_autosummary/cycquery.ops.GroupByAggregate", "reference/api/_autosummary/cycquery.ops.Join", "reference/api/_autosummary/cycquery.ops.Keep", "reference/api/_autosummary/cycquery.ops.Limit", "reference/api/_autosummary/cycquery.ops.Literal", "reference/api/_autosummary/cycquery.ops.Or", "reference/api/_autosummary/cycquery.ops.OrderBy", "reference/api/_autosummary/cycquery.ops.QueryOp", "reference/api/_autosummary/cycquery.ops.RandomizeOrder", "reference/api/_autosummary/cycquery.ops.Rename", "reference/api/_autosummary/cycquery.ops.Reorder", "reference/api/_autosummary/cycquery.ops.ReorderAfter", "reference/api/_autosummary/cycquery.ops.Sequential", "reference/api/_autosummary/cycquery.ops.Substring", "reference/api/_autosummary/cycquery.ops.Trim", "reference/api/_autosummary/cycquery.ops.Union", "reference/api/cycquery", "tutorials", "tutorials/eicu", "tutorials/gemini", "tutorials/mimiciii", "tutorials/mimiciv", "tutorials/omop"], "envversion": {"nbsphinx": 4, "sphinx": 61, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1}, "filenames": ["api.rst", "contributing.rst", "index.rst", "intro.rst", "reference/api/_autosummary/cycquery.base.rst", "reference/api/_autosummary/cycquery.base.DatasetQuerier.rst", "reference/api/_autosummary/cycquery.eicu.rst", "reference/api/_autosummary/cycquery.eicu.EICUQuerier.rst", "reference/api/_autosummary/cycquery.gemini.rst", "reference/api/_autosummary/cycquery.gemini.GEMINIQuerier.rst", "reference/api/_autosummary/cycquery.interface.rst", "reference/api/_autosummary/cycquery.interface.QueryInterface.rst", "reference/api/_autosummary/cycquery.mimiciii.rst", "reference/api/_autosummary/cycquery.mimiciii.MIMICIIIQuerier.rst", "reference/api/_autosummary/cycquery.mimiciv.rst", "reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.rst", "reference/api/_autosummary/cycquery.omop.rst", "reference/api/_autosummary/cycquery.omop.OMOPQuerier.rst", "reference/api/_autosummary/cycquery.ops.rst", "reference/api/_autosummary/cycquery.ops.AddColumn.rst", "reference/api/_autosummary/cycquery.ops.AddDeltaColumn.rst", "reference/api/_autosummary/cycquery.ops.AddDeltaConstant.rst", "reference/api/_autosummary/cycquery.ops.AddNumeric.rst", "reference/api/_autosummary/cycquery.ops.And.rst", "reference/api/_autosummary/cycquery.ops.Apply.rst", "reference/api/_autosummary/cycquery.ops.Cast.rst", "reference/api/_autosummary/cycquery.ops.ConditionAfterDate.rst", "reference/api/_autosummary/cycquery.ops.ConditionBeforeDate.rst", "reference/api/_autosummary/cycquery.ops.ConditionEndsWith.rst", "reference/api/_autosummary/cycquery.ops.ConditionEquals.rst", "reference/api/_autosummary/cycquery.ops.ConditionGreaterThan.rst", "reference/api/_autosummary/cycquery.ops.ConditionIn.rst", "reference/api/_autosummary/cycquery.ops.ConditionInMonths.rst", "reference/api/_autosummary/cycquery.ops.ConditionInYears.rst", "reference/api/_autosummary/cycquery.ops.ConditionLessThan.rst", "reference/api/_autosummary/cycquery.ops.ConditionLike.rst", "reference/api/_autosummary/cycquery.ops.ConditionRegexMatch.rst", "reference/api/_autosummary/cycquery.ops.ConditionStartsWith.rst", "reference/api/_autosummary/cycquery.ops.ConditionSubstring.rst", "reference/api/_autosummary/cycquery.ops.Count.rst", "reference/api/_autosummary/cycquery.ops.Distinct.rst", "reference/api/_autosummary/cycquery.ops.Drop.rst", "reference/api/_autosummary/cycquery.ops.DropEmpty.rst", "reference/api/_autosummary/cycquery.ops.DropNulls.rst", "reference/api/_autosummary/cycquery.ops.ExtractTimestampComponent.rst", "reference/api/_autosummary/cycquery.ops.FillNull.rst", "reference/api/_autosummary/cycquery.ops.GroupByAggregate.rst", "reference/api/_autosummary/cycquery.ops.Join.rst", "reference/api/_autosummary/cycquery.ops.Keep.rst", "reference/api/_autosummary/cycquery.ops.Limit.rst", "reference/api/_autosummary/cycquery.ops.Literal.rst", "reference/api/_autosummary/cycquery.ops.Or.rst", "reference/api/_autosummary/cycquery.ops.OrderBy.rst", "reference/api/_autosummary/cycquery.ops.QueryOp.rst", "reference/api/_autosummary/cycquery.ops.RandomizeOrder.rst", "reference/api/_autosummary/cycquery.ops.Rename.rst", "reference/api/_autosummary/cycquery.ops.Reorder.rst", "reference/api/_autosummary/cycquery.ops.ReorderAfter.rst", "reference/api/_autosummary/cycquery.ops.Sequential.rst", "reference/api/_autosummary/cycquery.ops.Substring.rst", "reference/api/_autosummary/cycquery.ops.Trim.rst", "reference/api/_autosummary/cycquery.ops.Union.rst", "reference/api/cycquery.rst", "tutorials.rst", "tutorials/eicu.ipynb", "tutorials/gemini.ipynb", "tutorials/mimiciii.ipynb", "tutorials/mimiciv.ipynb", "tutorials/omop.ipynb"], "indexentries": {"__add__() (sequential method)": [[58, "cycquery.ops.Sequential.__add__", false]], "__call__() (addcolumn method)": [[19, "cycquery.ops.AddColumn.__call__", false]], "__call__() (adddeltacolumn method)": [[20, "cycquery.ops.AddDeltaColumn.__call__", false]], "__call__() (adddeltaconstant method)": [[21, "cycquery.ops.AddDeltaConstant.__call__", false]], "__call__() (addnumeric method)": [[22, "cycquery.ops.AddNumeric.__call__", false]], "__call__() (and method)": [[23, "cycquery.ops.And.__call__", false]], "__call__() (apply method)": [[24, "cycquery.ops.Apply.__call__", false]], "__call__() (cast method)": [[25, "cycquery.ops.Cast.__call__", false]], "__call__() (conditionafterdate method)": [[26, "cycquery.ops.ConditionAfterDate.__call__", false]], "__call__() (conditionbeforedate method)": [[27, "cycquery.ops.ConditionBeforeDate.__call__", false]], "__call__() (conditionendswith method)": [[28, "cycquery.ops.ConditionEndsWith.__call__", false]], "__call__() (conditionequals method)": [[29, "cycquery.ops.ConditionEquals.__call__", false]], "__call__() (conditiongreaterthan method)": [[30, "cycquery.ops.ConditionGreaterThan.__call__", false]], "__call__() (conditionin method)": [[31, "cycquery.ops.ConditionIn.__call__", false]], "__call__() (conditioninmonths method)": [[32, "cycquery.ops.ConditionInMonths.__call__", false]], "__call__() (conditioninyears method)": [[33, "cycquery.ops.ConditionInYears.__call__", false]], "__call__() (conditionlessthan method)": [[34, "cycquery.ops.ConditionLessThan.__call__", false]], "__call__() (conditionlike method)": [[35, "cycquery.ops.ConditionLike.__call__", false]], "__call__() (conditionregexmatch method)": [[36, "cycquery.ops.ConditionRegexMatch.__call__", false]], "__call__() (conditionstartswith method)": [[37, "cycquery.ops.ConditionStartsWith.__call__", false]], "__call__() (conditionsubstring method)": [[38, "cycquery.ops.ConditionSubstring.__call__", false]], "__call__() (count method)": [[39, "cycquery.ops.Count.__call__", false]], "__call__() (distinct method)": [[40, "cycquery.ops.Distinct.__call__", false]], "__call__() (drop method)": [[41, "cycquery.ops.Drop.__call__", false]], "__call__() (dropempty method)": [[42, "cycquery.ops.DropEmpty.__call__", false]], "__call__() (dropnulls method)": [[43, "cycquery.ops.DropNulls.__call__", false]], "__call__() (extracttimestampcomponent method)": [[44, "cycquery.ops.ExtractTimestampComponent.__call__", false]], "__call__() (fillnull method)": [[45, "cycquery.ops.FillNull.__call__", false]], "__call__() (groupbyaggregate method)": [[46, "cycquery.ops.GroupByAggregate.__call__", false]], "__call__() (join method)": [[47, "cycquery.ops.Join.__call__", false]], "__call__() (keep method)": [[48, "cycquery.ops.Keep.__call__", false]], "__call__() (limit method)": [[49, "cycquery.ops.Limit.__call__", false]], "__call__() (literal method)": [[50, "cycquery.ops.Literal.__call__", false]], "__call__() (or method)": [[51, "cycquery.ops.Or.__call__", false]], "__call__() (orderby method)": [[52, "cycquery.ops.OrderBy.__call__", false]], "__call__() (queryop method)": [[53, "cycquery.ops.QueryOp.__call__", false]], "__call__() (randomizeorder method)": [[54, "cycquery.ops.RandomizeOrder.__call__", false]], "__call__() (rename method)": [[55, "cycquery.ops.Rename.__call__", false]], "__call__() (reorder method)": [[56, "cycquery.ops.Reorder.__call__", false]], "__call__() (reorderafter method)": [[57, "cycquery.ops.ReorderAfter.__call__", false]], "__call__() (sequential method)": [[58, "cycquery.ops.Sequential.__call__", false]], "__call__() (substring method)": [[59, "cycquery.ops.Substring.__call__", false]], "__call__() (trim method)": [[60, "cycquery.ops.Trim.__call__", false]], "__call__() (union method)": [[61, "cycquery.ops.Union.__call__", false]], "__init__() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.__init__", false]], "__init__() (sequential method)": [[58, "cycquery.ops.Sequential.__init__", false]], "addcolumn (class in cycquery.ops)": [[19, "cycquery.ops.AddColumn", false]], "adddeltacolumn (class in cycquery.ops)": [[20, "cycquery.ops.AddDeltaColumn", false]], "adddeltaconstant (class in cycquery.ops)": [[21, "cycquery.ops.AddDeltaConstant", false]], "addnumeric (class in cycquery.ops)": [[22, "cycquery.ops.AddNumeric", false]], "and (class in cycquery.ops)": [[23, "cycquery.ops.And", false]], "append() (sequential method)": [[58, "cycquery.ops.Sequential.append", false]], "apply (class in cycquery.ops)": [[24, "cycquery.ops.Apply", false]], "care_units() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.care_units", false]], "cast (class in cycquery.ops)": [[25, "cycquery.ops.Cast", false]], "chartevents() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.chartevents", false]], "chartevents() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.chartevents", false]], "clear_data() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.clear_data", false]], "conditionafterdate (class in cycquery.ops)": [[26, "cycquery.ops.ConditionAfterDate", false]], "conditionbeforedate (class in cycquery.ops)": [[27, "cycquery.ops.ConditionBeforeDate", false]], "conditionendswith (class in cycquery.ops)": [[28, "cycquery.ops.ConditionEndsWith", false]], "conditionequals (class in cycquery.ops)": [[29, "cycquery.ops.ConditionEquals", false]], "conditiongreaterthan (class in cycquery.ops)": [[30, "cycquery.ops.ConditionGreaterThan", false]], "conditionin (class in cycquery.ops)": [[31, "cycquery.ops.ConditionIn", false]], "conditioninmonths (class in cycquery.ops)": [[32, "cycquery.ops.ConditionInMonths", false]], "conditioninyears (class in cycquery.ops)": [[33, "cycquery.ops.ConditionInYears", false]], "conditionlessthan (class in cycquery.ops)": [[34, "cycquery.ops.ConditionLessThan", false]], "conditionlike (class in cycquery.ops)": [[35, "cycquery.ops.ConditionLike", false]], "conditionregexmatch (class in cycquery.ops)": [[36, "cycquery.ops.ConditionRegexMatch", false]], "conditionstartswith (class in cycquery.ops)": [[37, "cycquery.ops.ConditionStartsWith", false]], "conditionsubstring (class in cycquery.ops)": [[38, "cycquery.ops.ConditionSubstring", false]], "count (class in cycquery.ops)": [[39, "cycquery.ops.Count", false]], "cycquery": [[62, "module-cycquery", false]], "cycquery.base": [[4, "module-cycquery.base", false]], "cycquery.eicu": [[6, "module-cycquery.eicu", false]], "cycquery.gemini": [[8, "module-cycquery.gemini", false]], "cycquery.interface": [[10, "module-cycquery.interface", false]], "cycquery.mimiciii": [[12, "module-cycquery.mimiciii", false]], "cycquery.mimiciv": [[14, "module-cycquery.mimiciv", false]], "cycquery.omop": [[16, "module-cycquery.omop", false]], "cycquery.ops": [[18, "module-cycquery.ops", false]], "data (queryinterface property)": [[11, "cycquery.interface.QueryInterface.data", false]], "datasetquerier (class in cycquery.base)": [[5, "cycquery.base.DatasetQuerier", false]], "db (datasetquerier attribute)": [[5, "cycquery.base.DatasetQuerier.db", false]], "diagnoses() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.diagnoses", false]], "diagnoses() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.diagnoses", false]], "diagnoses_icd() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.diagnoses_icd", false]], "distinct (class in cycquery.ops)": [[40, "cycquery.ops.Distinct", false]], "drop (class in cycquery.ops)": [[41, "cycquery.ops.Drop", false]], "dropempty (class in cycquery.ops)": [[42, "cycquery.ops.DropEmpty", false]], "dropnulls (class in cycquery.ops)": [[43, "cycquery.ops.DropNulls", false]], "eicuquerier (class in cycquery.eicu)": [[7, "cycquery.eicu.EICUQuerier", false]], "extend() (sequential method)": [[58, "cycquery.ops.Sequential.extend", false]], "extracttimestampcomponent (class in cycquery.ops)": [[44, "cycquery.ops.ExtractTimestampComponent", false]], "fillnull (class in cycquery.ops)": [[45, "cycquery.ops.FillNull", false]], "geminiquerier (class in cycquery.gemini)": [[9, "cycquery.gemini.GEMINIQuerier", false]], "get_table() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.get_table", false]], "get_table() (eicuquerier method)": [[7, "cycquery.eicu.EICUQuerier.get_table", false]], "get_table() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.get_table", false]], "get_table() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.get_table", false]], "get_table() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.get_table", false]], "get_table() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.get_table", false]], "groupbyaggregate (class in cycquery.ops)": [[46, "cycquery.ops.GroupByAggregate", false]], "imaging() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.imaging", false]], "insert() (sequential method)": [[58, "cycquery.ops.Sequential.insert", false]], "ip_admin() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.ip_admin", false]], "join (class in cycquery.ops)": [[47, "cycquery.ops.Join", false]], "join() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.join", false]], "keep (class in cycquery.ops)": [[48, "cycquery.ops.Keep", false]], "labevents() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.labevents", false]], "labevents() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.labevents", false]], "limit (class in cycquery.ops)": [[49, "cycquery.ops.Limit", false]], "list_columns() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.list_columns", false]], "list_columns() (eicuquerier method)": [[7, "cycquery.eicu.EICUQuerier.list_columns", false]], "list_columns() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.list_columns", false]], "list_columns() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.list_columns", false]], "list_columns() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.list_columns", false]], "list_columns() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.list_columns", false]], "list_custom_tables() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.list_custom_tables", false]], "list_custom_tables() (eicuquerier method)": [[7, "cycquery.eicu.EICUQuerier.list_custom_tables", false]], "list_custom_tables() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.list_custom_tables", false]], "list_custom_tables() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.list_custom_tables", false]], "list_custom_tables() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.list_custom_tables", false]], "list_custom_tables() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.list_custom_tables", false]], "list_schemas() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.list_schemas", false]], "list_schemas() (eicuquerier method)": [[7, "cycquery.eicu.EICUQuerier.list_schemas", false]], "list_schemas() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.list_schemas", false]], "list_schemas() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.list_schemas", false]], "list_schemas() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.list_schemas", false]], "list_schemas() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.list_schemas", false]], "list_tables() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.list_tables", false]], "list_tables() (eicuquerier method)": [[7, "cycquery.eicu.EICUQuerier.list_tables", false]], "list_tables() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.list_tables", false]], "list_tables() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.list_tables", false]], "list_tables() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.list_tables", false]], "list_tables() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.list_tables", false]], "literal (class in cycquery.ops)": [[50, "cycquery.ops.Literal", false]], "map_concept_ids_to_name() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.map_concept_ids_to_name", false]], "measurement() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.measurement", false]], "mimiciiiquerier (class in cycquery.mimiciii)": [[13, "cycquery.mimiciii.MIMICIIIQuerier", false]], "mimicivquerier (class in cycquery.mimiciv)": [[15, "cycquery.mimiciv.MIMICIVQuerier", false]], "module": [[4, "module-cycquery.base", false], [6, "module-cycquery.eicu", false], [8, "module-cycquery.gemini", false], [10, "module-cycquery.interface", false], [12, "module-cycquery.mimiciii", false], [14, "module-cycquery.mimiciv", false], [16, "module-cycquery.omop", false], [18, "module-cycquery.ops", false], [62, "module-cycquery", false]], "observation() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.observation", false]], "omopquerier (class in cycquery.omop)": [[17, "cycquery.omop.OMOPQuerier", false]], "ops() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.ops", false]], "or (class in cycquery.ops)": [[51, "cycquery.ops.Or", false]], "orderby (class in cycquery.ops)": [[52, "cycquery.ops.OrderBy", false]], "patients() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.patients", false]], "person() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.person", false]], "pop() (sequential method)": [[58, "cycquery.ops.Sequential.pop", false]], "procedures_icd() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.procedures_icd", false]], "queryinterface (class in cycquery.interface)": [[11, "cycquery.interface.QueryInterface", false]], "queryop (class in cycquery.ops)": [[53, "cycquery.ops.QueryOp", false]], "randomizeorder (class in cycquery.ops)": [[54, "cycquery.ops.RandomizeOrder", false]], "rename (class in cycquery.ops)": [[55, "cycquery.ops.Rename", false]], "reorder (class in cycquery.ops)": [[56, "cycquery.ops.Reorder", false]], "reorderafter (class in cycquery.ops)": [[57, "cycquery.ops.ReorderAfter", false]], "room_transfer() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.room_transfer", false]], "run() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.run", false]], "save() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.save", false]], "sequential (class in cycquery.ops)": [[58, "cycquery.ops.Sequential", false]], "substring (class in cycquery.ops)": [[59, "cycquery.ops.Substring", false]], "trim (class in cycquery.ops)": [[60, "cycquery.ops.Trim", false]], "union (class in cycquery.ops)": [[61, "cycquery.ops.Union", false]], "union() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.union", false]], "union_all() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.union_all", false]], "visit_detail() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.visit_detail", false]], "visit_occurrence() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.visit_occurrence", false]]}, "objects": {"": [[62, 0, 0, "-", "cycquery"]], "cycquery": [[4, 0, 0, "-", "base"], [6, 0, 0, "-", "eicu"], [8, 0, 0, "-", "gemini"], [10, 0, 0, "-", "interface"], [12, 0, 0, "-", "mimiciii"], [14, 0, 0, "-", "mimiciv"], [16, 0, 0, "-", "omop"], [18, 0, 0, "-", "ops"]], "cycquery.base": [[5, 1, 1, "", "DatasetQuerier"]], "cycquery.base.DatasetQuerier": [[5, 2, 1, "", "db"], [5, 3, 1, "", "get_table"], [5, 3, 1, "", "list_columns"], [5, 3, 1, "", "list_custom_tables"], [5, 3, 1, "", "list_schemas"], [5, 3, 1, "", "list_tables"]], "cycquery.eicu": [[7, 1, 1, "", "EICUQuerier"]], "cycquery.eicu.EICUQuerier": [[7, 3, 1, "", "get_table"], [7, 3, 1, "", "list_columns"], [7, 3, 1, "", "list_custom_tables"], [7, 3, 1, "", "list_schemas"], [7, 3, 1, "", "list_tables"]], "cycquery.gemini": [[9, 1, 1, "", "GEMINIQuerier"]], "cycquery.gemini.GEMINIQuerier": [[9, 3, 1, "", "care_units"], [9, 3, 1, "", "diagnoses"], [9, 3, 1, "", "get_table"], [9, 3, 1, "", "imaging"], [9, 3, 1, "", "ip_admin"], [9, 3, 1, "", "list_columns"], [9, 3, 1, "", "list_custom_tables"], [9, 3, 1, "", "list_schemas"], [9, 3, 1, "", "list_tables"], [9, 3, 1, "", "room_transfer"]], "cycquery.interface": [[11, 1, 1, "", "QueryInterface"]], "cycquery.interface.QueryInterface": [[11, 3, 1, "", "__init__"], [11, 3, 1, "", "clear_data"], [11, 4, 1, "", "data"], [11, 3, 1, "", "join"], [11, 3, 1, "", "ops"], [11, 3, 1, "", "run"], [11, 3, 1, "", "save"], [11, 3, 1, "", "union"], [11, 3, 1, "", "union_all"]], "cycquery.mimiciii": [[13, 1, 1, "", "MIMICIIIQuerier"]], "cycquery.mimiciii.MIMICIIIQuerier": [[13, 3, 1, "", "chartevents"], [13, 3, 1, "", "diagnoses"], [13, 3, 1, "", "get_table"], [13, 3, 1, "", "labevents"], [13, 3, 1, "", "list_columns"], [13, 3, 1, "", "list_custom_tables"], [13, 3, 1, "", "list_schemas"], [13, 3, 1, "", "list_tables"]], "cycquery.mimiciv": [[15, 1, 1, "", "MIMICIVQuerier"]], "cycquery.mimiciv.MIMICIVQuerier": [[15, 3, 1, "", "chartevents"], [15, 3, 1, "", "diagnoses_icd"], [15, 3, 1, "", "get_table"], [15, 3, 1, "", "labevents"], [15, 3, 1, "", "list_columns"], [15, 3, 1, "", "list_custom_tables"], [15, 3, 1, "", "list_schemas"], [15, 3, 1, "", "list_tables"], [15, 3, 1, "", "patients"], [15, 3, 1, "", "procedures_icd"]], "cycquery.omop": [[17, 1, 1, "", "OMOPQuerier"]], "cycquery.omop.OMOPQuerier": [[17, 3, 1, "", "get_table"], [17, 3, 1, "", "list_columns"], [17, 3, 1, "", "list_custom_tables"], [17, 3, 1, "", "list_schemas"], [17, 3, 1, "", "list_tables"], [17, 3, 1, "", "map_concept_ids_to_name"], [17, 3, 1, "", "measurement"], [17, 3, 1, "", "observation"], [17, 3, 1, "", "person"], [17, 3, 1, "", "visit_detail"], [17, 3, 1, "", "visit_occurrence"]], "cycquery.ops": [[19, 1, 1, "", "AddColumn"], [20, 1, 1, "", "AddDeltaColumn"], [21, 1, 1, "", "AddDeltaConstant"], [22, 1, 1, "", "AddNumeric"], [23, 1, 1, "", "And"], [24, 1, 1, "", "Apply"], [25, 1, 1, "", "Cast"], [26, 1, 1, "", "ConditionAfterDate"], [27, 1, 1, "", "ConditionBeforeDate"], [28, 1, 1, "", "ConditionEndsWith"], [29, 1, 1, "", "ConditionEquals"], [30, 1, 1, "", "ConditionGreaterThan"], [31, 1, 1, "", "ConditionIn"], [32, 1, 1, "", "ConditionInMonths"], [33, 1, 1, "", "ConditionInYears"], [34, 1, 1, "", "ConditionLessThan"], [35, 1, 1, "", "ConditionLike"], [36, 1, 1, "", "ConditionRegexMatch"], [37, 1, 1, "", "ConditionStartsWith"], [38, 1, 1, "", "ConditionSubstring"], [39, 1, 1, "", "Count"], [40, 1, 1, "", "Distinct"], [41, 1, 1, "", "Drop"], [42, 1, 1, "", "DropEmpty"], [43, 1, 1, "", "DropNulls"], [44, 1, 1, "", "ExtractTimestampComponent"], [45, 1, 1, "", "FillNull"], [46, 1, 1, "", "GroupByAggregate"], [47, 1, 1, "", "Join"], [48, 1, 1, "", "Keep"], [49, 1, 1, "", "Limit"], [50, 1, 1, "", "Literal"], [51, 1, 1, "", "Or"], [52, 1, 1, "", "OrderBy"], [53, 1, 1, "", "QueryOp"], [54, 1, 1, "", "RandomizeOrder"], [55, 1, 1, "", "Rename"], [56, 1, 1, "", "Reorder"], [57, 1, 1, "", "ReorderAfter"], [58, 1, 1, "", "Sequential"], [59, 1, 1, "", "Substring"], [60, 1, 1, "", "Trim"], [61, 1, 1, "", "Union"]], "cycquery.ops.AddColumn": [[19, 3, 1, "", "__call__"]], "cycquery.ops.AddDeltaColumn": [[20, 3, 1, "", "__call__"]], "cycquery.ops.AddDeltaConstant": [[21, 3, 1, "", "__call__"]], "cycquery.ops.AddNumeric": [[22, 3, 1, "", "__call__"]], "cycquery.ops.And": [[23, 3, 1, "", "__call__"]], "cycquery.ops.Apply": [[24, 3, 1, "", "__call__"]], "cycquery.ops.Cast": [[25, 3, 1, "", "__call__"]], "cycquery.ops.ConditionAfterDate": [[26, 3, 1, "", "__call__"]], "cycquery.ops.ConditionBeforeDate": [[27, 3, 1, "", "__call__"]], "cycquery.ops.ConditionEndsWith": [[28, 3, 1, "", "__call__"]], "cycquery.ops.ConditionEquals": [[29, 3, 1, "", "__call__"]], "cycquery.ops.ConditionGreaterThan": [[30, 3, 1, "", "__call__"]], "cycquery.ops.ConditionIn": [[31, 3, 1, "", "__call__"]], "cycquery.ops.ConditionInMonths": [[32, 3, 1, "", "__call__"]], "cycquery.ops.ConditionInYears": [[33, 3, 1, "", "__call__"]], "cycquery.ops.ConditionLessThan": [[34, 3, 1, "", "__call__"]], "cycquery.ops.ConditionLike": [[35, 3, 1, "", "__call__"]], "cycquery.ops.ConditionRegexMatch": [[36, 3, 1, "", "__call__"]], "cycquery.ops.ConditionStartsWith": [[37, 3, 1, "", "__call__"]], "cycquery.ops.ConditionSubstring": [[38, 3, 1, "", "__call__"]], "cycquery.ops.Count": [[39, 3, 1, "", "__call__"]], "cycquery.ops.Distinct": [[40, 3, 1, "", "__call__"]], "cycquery.ops.Drop": [[41, 3, 1, "", "__call__"]], "cycquery.ops.DropEmpty": [[42, 3, 1, "", "__call__"]], "cycquery.ops.DropNulls": [[43, 3, 1, "", "__call__"]], "cycquery.ops.ExtractTimestampComponent": [[44, 3, 1, "", "__call__"]], "cycquery.ops.FillNull": [[45, 3, 1, "", "__call__"]], "cycquery.ops.GroupByAggregate": [[46, 3, 1, "", "__call__"]], "cycquery.ops.Join": [[47, 3, 1, "", "__call__"]], "cycquery.ops.Keep": [[48, 3, 1, "", "__call__"]], "cycquery.ops.Limit": [[49, 3, 1, "", "__call__"]], "cycquery.ops.Literal": [[50, 3, 1, "", "__call__"]], "cycquery.ops.Or": [[51, 3, 1, "", "__call__"]], "cycquery.ops.OrderBy": [[52, 3, 1, "", "__call__"]], "cycquery.ops.QueryOp": [[53, 3, 1, "", "__call__"]], "cycquery.ops.RandomizeOrder": [[54, 3, 1, "", "__call__"]], "cycquery.ops.Rename": [[55, 3, 1, "", "__call__"]], "cycquery.ops.Reorder": [[56, 3, 1, "", "__call__"]], "cycquery.ops.ReorderAfter": [[57, 3, 1, "", "__call__"]], "cycquery.ops.Sequential": [[58, 3, 1, "", "__add__"], [58, 3, 1, "", "__call__"], [58, 3, 1, "", "__init__"], [58, 3, 1, "", "append"], [58, 3, 1, "", "extend"], [58, 3, 1, "", "insert"], [58, 3, 1, "", "pop"]], "cycquery.ops.Substring": [[59, 3, 1, "", "__call__"]], "cycquery.ops.Trim": [[60, 3, 1, "", "__call__"]], "cycquery.ops.Union": [[61, 3, 1, "", "__call__"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "class", "Python class"], "2": ["py", "attribute", "Python attribute"], "3": ["py", "method", "Python method"], "4": ["py", "property", "Python property"]}, "objtypes": {"0": "py:module", "1": "py:class", "2": "py:attribute", "3": "py:method", "4": "py:property"}, "terms": {"": [5, 11, 17, 24, 45, 64, 65, 66, 67, 68], "0": [14, 45, 59, 64, 65, 66, 67, 68], "00": 64, "01": [26, 27, 64, 65, 67, 68], "012544": 67, "016": 68, "018": 68, "02": 67, "03": 65, "04": [64, 65, 66, 67, 68], "05": 65, "06": 67, "062": [67, 68], "063": 67, "071": 67, "072": 67, "079233": 68, "09": 65, "093352": 65, "1": [3, 11, 21, 22, 24, 26, 27, 29, 30, 31, 32, 34, 45, 50, 63], "10": [49, 63, 68], "100": [63, 66, 67, 68], "1000": 67, "1000000": 11, "101": 63, "108410": 66, "11": [64, 66, 67, 68], "12": 68, "133449": 68, "14": 66, "145693": 65, "146": 67, "147": 67, "15": 68, "158988": 64, "17": 65, "18": [64, 66, 67, 68], "187926": 66, "189734": 65, "19": [65, 67], "197": 68, "1a": 63, "1b": 63, "1c": 63, "2": [3, 14, 22, 24, 31, 32, 59, 63, 65], "20": 63, "2009": 63, "2010": 63, "2011": 68, "2012": 68, "2013": 68, "2014": [63, 68], "2015": [63, 68], "2016": [63, 68], "2017": 68, "2018": 68, "2019": [33, 68], "2020": [26, 27, 33, 63], "2021": [63, 68], "2022": 68, "2023": [65, 68], "2024": [64, 66, 67, 68], "21": 65, "22": 66, "239": 64, "242": 64, "251988": 67, "26": [65, 68], "27": 68, "2a": 63, "3": [63, 65, 68], "305880": 67, "31": 63, "311": 68, "313": 68, "32567": 65, "33": 68, "330467": 67, "336015": 64, "356768": 66, "359": 66, "361": 66, "39": [64, 65, 66, 67, 68], "390": 67, "392": 67, "4": [63, 65, 68], "40": [66, 68], "437": 66, "449": 65, "45": 65, "465": 67, "466": 67, "475": 66, "477": 66, "481393": 64, "49": [64, 67], "5": [63, 64, 65, 66, 68], "50": [64, 66], "505": 67, "506": [65, 67], "51": 65, "515327": 68, "52": [65, 67], "522759": 67, "533433": 67, "54": 67, "5432": [3, 17, 64, 66, 67, 68], "556": 68, "57": [64, 66, 67, 68], "58": [64, 67, 68], "5815": 68, "591": 65, "592": 65, "596": 66, "598": 66, "6": [63, 65, 66, 68], "613": 64, "615": 64, "623": 64, "624": 64, "669": 67, "671": 67, "675141": 65, "676533": 67, "7": [63, 65, 68], "700": 68, "702": 68, "711404": 68, "717": 67, "719": 67, "725": 64, "727": 64, "728": 64, "8": [63, 68], "809877": 66, "814": 65, "815": 65, "82": 67, "853": 67, "856": 65, "857": 65, "867": 66, "9": 63, "902": 65, "903": 65, "9305": 65, "939296": 65, "951092": 64, "952": 66, "954": 66, "969": 68, "972": 68, "983342": 67, "999": 67, "A": [10, 11, 21, 26, 27, 47], "And": [0, 67], "For": [1, 17], "If": [1, 17, 19, 20, 21, 22, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 52, 60], "In": 3, "It": [3, 24, 63], "No": [11, 68], "Not": 5, "OR": 51, "Or": 0, "The": [1, 3, 5, 11, 15, 20, 24, 48, 62, 63, 64, 66, 67, 68], "To": 1, "__add__": [0, 58], "__call__": [0, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61], "__init__": [0, 11, 58], "aado2": 63, "abov": 63, "abstract": 53, "accord": [17, 64, 66, 67, 68], "accordingli": [64, 66, 67, 68], "activ": 3, "ad": [11, 19, 20, 21, 22, 58], "add": [19, 20, 21, 22, 50, 58], "add_to": [19, 20, 21, 22], "addcolumn": 0, "adddeltacolumn": [0, 67], "adddeltaconst": 0, "addnumer": 0, "address": 5, "adjust": 15, "admdad": 65, "admiss": [63, 66], "admissiondrug": 64, "admissiondx": 64, "admittim": 67, "admitting_concept_id": 68, "advanc": 63, "after": [5, 15, 24, 26, 57, 58, 63], "aggfunc": 46, "aggreg": [3, 46], "aggsep": 46, "all": [1, 3, 11, 38, 52, 55, 61, 63, 65], "all_visit": 68, "allergi": 64, "allow": [5, 7, 9, 13, 15, 17, 63], "along": 1, "also": 24, "an": [1, 9, 11, 13, 15, 17, 20, 23, 47, 51, 55], "analysi": 1, "analyz": 54, "anchor_year": 15, "anchor_year_differ": 67, "anchor_year_group": 15, "ani": [11, 20, 28, 29, 30, 31, 34, 37, 38, 45, 50], "anoth": [11, 47, 55, 58], "any_": 38, "apacheapsvar": 64, "apachepatientresult": 64, "apachepredvar": 64, "api": [2, 3, 5, 7, 9, 13, 15, 16, 17, 63], "append": [0, 58], "appli": [0, 1, 15, 19, 20, 21, 22, 60], "approx": 63, "approxim": 15, "apr": 63, "april": 63, "ar": [5, 15, 24, 47], "arg": [53, 54, 58], "argument": [20, 28, 29, 30, 31, 34, 37, 38], "around": [3, 63], "ascend": [52, 65], "assign": 17, "assign_all_visit_id": 68, "assum": [24, 64, 66, 67, 68], "attent": 19, "attribut": 11, "automat": 5, "b": 38, "backend": 11, "base": [0, 3, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61], "batch": [11, 63], "batch_mod": [11, 67], "batch_siz": [11, 67], "becom": [11, 54], "befor": [1, 27, 47], "being": [19, 20, 21, 22, 26, 27, 29, 32, 33], "between": 63, "bin": 3, "binarize_col": [26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38], "binaryexpress": [11, 47], "black": 1, "bool": [5, 7, 9, 11, 13, 15, 17, 19, 20, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 51, 52, 55, 61], "boolean": [26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38], "both": 47, "build": [5, 63], "built": 3, "ca": 65, "call": 53, "callabl": 24, "can": [1, 3, 5, 7, 9, 13, 15, 17, 24, 38], "cannot": 54, "care": [9, 15], "care_sit": 68, "care_unit": [0, 9], "careplancareprovid": 64, "careplaneol": 64, "careplangener": 64, "careplango": 64, "careplaninfectiousdiseas": 64, "carevu": 63, "cartesian": 47, "cast": [0, 5, 7, 9, 11, 13, 15, 17, 65, 67], "cast_timestamp_col": [5, 7, 9, 13, 15, 17], "categori": 67, "cd": 3, "cdm_sourc": 68, "cdm_synthea10": 68, "certain": 54, "chain": [11, 58], "chart": [15, 63], "chart_ev": [66, 67], "chartev": [0, 13, 15, 66, 67], "chartevents_op": 66, "check": [1, 55], "check_exist": 55, "chronic": 63, "class": [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62], "clear": 11, "clear_data": [0, 11], "code": [2, 64, 66, 67, 68], "codestyl": 3, "cohort": 68, "cohort_definit": 68, "col": [19, 24, 25, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 48, 50, 52, 56, 57, 59, 60], "col1": [3, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 41, 42, 43, 44, 45, 47, 48, 50, 52, 55, 56, 57, 58, 59, 60], "col1_bool": [26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38], "col1_new": [24, 45, 55], "col1_plus_1": [21, 22], "col1_plus_col2": [19, 20], "col1_plus_col3": 19, "col1_substr": 59, "col1_trim": 60, "col2": [3, 19, 20, 21, 22, 24, 25, 41, 42, 43, 45, 47, 48, 52, 56, 57, 58, 60], "col2_new": [24, 45], "col2_plus_1": 22, "col2_plus_col3": 19, "col2_trim": 60, "col3": [3, 19, 20, 47, 57], "collection_date_tim": 65, "column": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 52, 55, 56, 57, 59, 60], "combin": [19, 23, 51], "come": 57, "commit": 2, "common": 68, "commun": 63, "complet": 56, "compon": 44, "comput": 11, "concept": [17, 68], "concept_ancestor": 68, "concept_class": 68, "concept_relationship": 68, "concept_synonym": 68, "cond": [11, 47], "cond_kwarg": [28, 29, 30, 31, 34, 37, 38], "cond_op": [23, 51], "condit": [3, 11, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 51, 68], "condition_concept_id": 68, "condition_concept_nam": 68, "condition_era": 68, "condition_occurr": 68, "conditionafterd": [0, 65, 67, 68], "conditionbefored": [0, 65], "conditionendswith": 0, "conditionequ": [0, 64, 65, 66, 67], "conditiongreaterthan": 0, "conditionin": [0, 3, 23, 51], "conditioninmonth": 0, "conditioninyear": [0, 67], "conditionlessthan": [0, 66], "conditionlik": [0, 23, 51, 67], "conditionregexmatch": [0, 63], "conditionstartswith": 0, "conditionsubstr": [0, 3, 64, 65, 66, 67, 68], "config": [64, 66, 67, 68], "consid": 17, "construct": [9, 13, 15, 17, 20, 21], "contain": [11, 63], "contribut": 2, "convers": 25, "convert": [25, 47], "correspond": [17, 42, 43], "cost": 68, "count": [0, 46, 65, 68], "crd": [2, 6, 63], "creat": [3, 5, 11, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 60, 63], "csv": [11, 68], "current": 25, "custom": [5, 7, 9, 13, 15, 17, 66], "customlab": 64, "cycqueri": [0, 63, 64, 65, 66, 68], "d": 3, "dai": 21, "dask": 11, "data": [0, 3, 9, 11, 13, 15, 54, 67, 68], "databas": [2, 5, 7, 9, 10, 11, 13, 15, 17, 62, 63, 64, 65, 66, 67, 68], "dataclass": 11, "datafram": [3, 11], "dataset": [0, 5, 7, 9, 11, 13, 15, 17, 63], "datasetqueri": [0, 3, 7, 9, 13, 15, 17], "date": [25, 26, 27], "datetim": [5, 7, 9, 13, 15, 17, 21, 26, 27], "db": [0, 5, 65, 67], "dbm": [3, 5, 7, 9, 13, 15, 17, 64, 66, 67, 68], "dbname": 3, "dbsourc": 66, "dbtabl": [11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 58, 59, 60, 61], "dd": [26, 27], "death": 68, "default": [5, 11, 37], "defin": 11, "delirium_v4_0_1": 65, "delta": 21, "delta_kwarg": 20, "depend": 3, "derived_vari": 65, "descend": 52, "develop": 2, "device_exposur": 68, "df": 3, "di": 68, "diagnos": [0, 9, 13, 63], "diagnoses_icd": [0, 15, 67], "diagnoses_op": 67, "diagnosi": [9, 13, 15, 64], "diagnosisstr": 63, "dict": [46, 55], "dictionari": 46, "differ": [38, 47], "disabl": 24, "discharg": 63, "discharge_date_tim": 63, "discharge_to_concept_id": 68, "discharge_to_concept_nam": 68, "dischtim": 67, "distinct": [0, 3, 65], "doc": 3, "docstr": 1, "dod": 15, "domain": 68, "don": 1, "dose_era": 68, "downstream": [5, 7, 9, 13, 15, 17], "drop": [0, 58], "dropempti": [0, 65], "dropnul": [0, 3], "drug_era": 68, "drug_exposur": 68, "drug_strength": 68, "drugnam": 64, "dst_col": 17, "dt": 68, "dtype": 68, "dtype_backend": 11, "e": [3, 5, 44, 47, 50], "e501": 24, "each": [17, 24, 52, 63, 64, 66, 67, 68], "ehr": [3, 5, 62, 63, 68], "eicu": [0, 2, 63], "eicu_crd": 64, "eicuqueri": [0, 63], "electron": 3, "empti": [5, 42], "encount": [9, 63], "encounters_lab": 65, "encounters_per_sit": 65, "encounters_queri": 65, "end": [28, 58, 63], "env": 3, "environ": [1, 3], "episod": 68, "episode_ev": 68, "equal": [29, 30, 34], "er": 65, "erdiagnosi": 65, "erintervent": 65, "error": 1, "etl": 68, "event": [15, 63], "exampl": [19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 58, 59, 60, 61, 63], "execut": [58, 64, 65, 66, 67, 68], "exist": [19, 20, 21, 22, 55, 60], "expens": 47, "expire_flag": 66, "express": 36, "extend": [0, 58], "extract": [44, 59, 64, 65, 66, 67, 68], "extract_str": 44, "extracttimestampcompon": 0, "f": [64, 65, 66, 67, 68], "fact_relationship": 68, "fals": [11, 19, 20, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 51, 52, 61, 65], "femal": 63, "fetch": [9, 11], "fhir_etl": 67, "fhir_trm": 67, "file": [1, 5, 11], "file_format": 11, "fill": [1, 45], "fill_valu": 45, "fillnul": 0, "filter": [3, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 51, 63], "final": 58, "final_visit_id": 68, "finish": [64, 65, 66, 67, 68], "first": [61, 64, 66, 67, 68], "fix": 1, "flag": 47, "float": [22, 25], "follow": [57, 68], "forget": 1, "format": [1, 11, 26, 27, 47, 68], "framework": 11, "from": [3, 9, 11, 15, 17, 44, 47, 55, 60, 63, 64, 66, 68], "func": 24, "function": [15, 19, 20, 21, 22, 24, 46, 53, 60, 63, 64, 65, 66, 67, 68], "further": 1, "g": [3, 5, 44, 47, 50], "gastroenter": 63, "gemini": [0, 2, 63], "geminiqueri": [0, 63], "genc_id": 65, "gender": [64, 66, 67], "gender_concept_nam": 68, "gener": [11, 68], "get": [2, 5, 7, 9, 11, 13, 15, 17, 40, 59, 63], "get_tabl": [0, 5, 7, 9, 13, 15, 17], "given": [45, 58], "glucos": 63, "googl": 1, "greater": [30, 34], "group": 46, "groupbi": 3, "groupby_col": 46, "groupbyaggreg": [0, 65], "guid": 1, "guidelin": [2, 3], "ha": 59, "hadm_id": [66, 67], "have": [5, 7, 9, 13, 15, 17, 31, 38, 47, 63], "hba1c": [23, 35, 51], "health": 3, "hemoglobin": 63, "henc": 3, "hint": 1, "hook": 2, "hospit": [15, 63], "hospital_num": 65, "hospitaldischargeyear": 64, "hospitalid": 64, "host": [3, 5, 7, 9, 13, 15, 17, 64, 65, 66, 67, 68], "hous": 68, "how": [63, 64, 66, 67, 68], "hpc": 65, "html": 3, "i": [1, 3, 5, 11, 15, 17, 19, 20, 21, 22, 24, 38, 42, 43, 47, 54, 63, 64, 66, 67, 68], "icd": 63, "icd_vers": 67, "icu": 15, "id": 17, "iii": [2, 12, 13, 63, 68], "imag": [0, 9], "implement": 53, "import": [3, 63], "includ": [3, 30, 34], "index": [11, 58, 59, 63], "index_col": [11, 67], "infecti": 63, "infer": 15, "info": [3, 9, 64, 65, 66, 67, 68], "inform": 44, "information_schema": [67, 68], "infusiondrug": 64, "initi": [11, 58], "input": 24, "insert": [0, 58], "instal": 2, "instanti": [5, 63], "instead": [23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 51], "instruct": [64, 66, 67, 68], "int": [5, 11, 22, 25, 32, 33, 47, 49, 58, 59], "int64": 68, "intakeoutput": 64, "integ": 50, "integr": 3, "intend": 5, "interest": 1, "interfac": [0, 9, 13, 15, 17], "interv": 20, "ip_admin": [0, 9], "ipdiagnosi": 65, "ipintervent": 65, "ipscu": 65, "isout": [11, 47, 68], "issu": 1, "iv": [2, 14, 63], "jane": [23, 51], "john": [23, 51], "join": [0, 3, 11, 15, 64, 65, 66, 67, 68], "join_tabl": [11, 47, 64, 66, 67, 68], "join_table_col": [11, 47], "just": 38, "keep": [0, 47, 63], "kei": [46, 55, 58], "keyword": [28, 29, 30, 31, 34, 37, 38, 61, 63], "kwarg": [53, 54], "lab": [15, 63, 65], "lab_nam": [23, 35, 46, 51], "lab_name_agg": 46, "lab_name_bool": 35, "lab_op": 65, "label": [19, 20, 21, 22, 44, 46, 50, 60, 66, 67], "labev": [0, 13, 15, 66], "labnam": 64, "lambda": 24, "larg": 54, "last": 1, "later": 63, "least": 1, "left": 47, "len": [64, 65, 66, 67, 68], "less": [34, 63], "like": [3, 17, 35], "limit": [0, 11, 54, 63, 66, 67, 68], "line": 24, "link": 1, "list": [3, 5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 24, 25, 31, 32, 33, 38, 40, 41, 42, 43, 45, 46, 47, 48, 51, 52, 56, 57, 58, 60, 64, 65, 66, 67, 68], "list_column": [0, 5, 7, 9, 13, 15, 17], "list_custom_t": [0, 5, 7, 9, 13, 15, 17, 66], "list_schema": [0, 5, 7, 9, 13, 15, 17, 67, 68], "list_tabl": [0, 3, 5, 7, 9, 13, 15, 17, 64, 65, 68], "liter": [0, 11], "load": 68, "local": 3, "localhost": [3, 17, 64, 66, 67, 68], "locality_vari": 65, "locat": 68, "long": [24, 63], "long_titl": [66, 67], "lookup_cci": 65, "lookup_ccsr": 65, "lookup_diagnosi": 65, "lookup_er_administr": 65, "lookup_hospital_num": 65, "lookup_icd10_ca_descript": 65, "lookup_icd10_ca_to_ccsr": 65, "lookup_imag": 65, "lookup_ip_administr": 65, "lookup_ip_scu": 65, "lookup_lab_concept": 65, "lookup_pharmacy_concept": 65, "lookup_pharmacy_rout": 65, "lookup_phy_characterist": 65, "lookup_room_transf": 65, "lookup_statcan": 65, "lookup_transf": 65, "lookup_transfusion_concept": 65, "lookup_vitals_concept": 65, "lymphadenopathi": 63, "m": [3, 66], "mai": 63, "make": [3, 38], "male": 63, "manag": 5, "mani": [3, 63], "map": [5, 7, 9, 13, 15, 17, 55], "map_concept_ids_to_nam": [0, 17, 68], "march": 63, "match": [3, 36, 68], "measur": [0, 17, 63], "measurement_concept_nam": 68, "medic": 63, "metadata": 68, "method": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 66], "microlab": 64, "million": 11, "mimic": [2, 12, 13, 14, 15, 63, 68], "mimic_fhir": 67, "mimiciii": [0, 66, 68], "mimiciiiqueri": [0, 63, 68], "mimiciv": [0, 67], "mimiciv_": 67, "mimiciv_deriv": 67, "mimiciv_hosp": 67, "mimiciv_icu": 67, "mimiciv_not": 67, "mimicivqueri": [0, 63], "mm": [26, 27], "mode": 11, "model": 68, "modul": [6, 8, 12, 14, 15], "month": [32, 44], "more": 3, "mortal": 63, "most": 63, "multipl": [9, 23, 24, 46, 51], "must": [25, 31, 32, 33, 38, 46], "mypi": 1, "mysql": 5, "name": [5, 7, 9, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 51, 55, 56, 57, 59, 68], "nbsphinx_allow_error": 3, "need": [1, 59], "neg": [19, 20], "negat": [26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38], "neither": 47, "new": [19, 20, 21, 22, 24, 45, 46, 50, 56, 59, 60], "new_col": 24, "new_col_label": [19, 20, 21, 22, 59, 60], "new_col_nam": [45, 59], "next": 67, "none": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 52, 59, 60], "noqa": 24, "nor": 47, "not_": [26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38], "note": [5, 15, 64, 68], "note_nlp": 68, "notebook": [64, 65, 66, 67, 68], "null": [43, 45], "number": [5, 39, 49, 57, 63], "numer": 22, "numpi": 1, "nurseassess": 64, "nursecar": 64, "nursechart": 64, "object": [5, 9, 10, 11, 13, 15, 17, 20, 21, 24, 26, 27, 46, 53, 58, 63], "observ": [0, 17, 68], "observation_period": 68, "occur": 63, "omop": [0, 2, 63], "omopqueri": [0, 63], "on_to_typ": [11, 47], "onc": 1, "one": [38, 63], "onli": [38, 47, 48, 63], "op": [0, 3, 11, 15, 63, 64, 65, 66, 68], "op_": 58, "oper": [3, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61], "oppos": 47, "option": [5, 7, 9, 11, 13, 15, 17, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 61], "order": [3, 11, 52, 54, 56, 57], "orderbi": [0, 65], "ordereddict": 58, "origin": 11, "orm": [5, 11, 63, 64, 65, 66, 67, 68], "other": [11, 19, 57, 58], "otherwis": [19, 20, 21, 22, 60], "our": 1, "out": 1, "outcom": 63, "outer": [11, 47], "over": 46, "pai": 19, "pair": 46, "panda": [3, 11, 68], "paramet": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 58, 59, 60, 61, 64, 66, 67, 68], "parquet": 11, "partit": [11, 63], "pass": [64, 66, 67, 68], "password": [3, 5, 7, 9, 13, 15, 17, 64, 65, 66, 67, 68], "pasthistori": 64, "path": [3, 5, 11], "patient": [0, 9, 15, 63], "patient_admiss": [66, 67], "patient_admissions_df": 67, "patient_admissions_diagnos": [66, 67], "patient_admissions_lab": 67, "patient_admissions_radiology_not": 67, "patient_admissions_vit": 67, "patient_chart_ev": 66, "patient_diagnos": 64, "patient_id_hash": 63, "patient_lab": [64, 66], "patient_med": 64, "patientunitstayid": 64, "pattern": 35, "payer_plan_period": 68, "pd": 68, "per": 63, "perform": [3, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 59, 60, 61, 68], "person": [0, 17, 68], "person_id": [39, 40, 46, 68], "person_visit": 68, "person_visits_condit": 68, "person_visits_conditions_measur": 68, "pharmaci": 65, "physicalexam": 64, "pip": 2, "place": 63, "pleas": 1, "poetri": 2, "pop": [0, 58], "port": [3, 5, 7, 9, 13, 15, 17, 64, 66, 67, 68], "possibli": [5, 7, 9, 13, 15, 17], "postgr": [64, 66, 67, 68], "postgresql": [2, 5, 17, 63, 64, 66, 67, 68], "potassium": 63, "pr": 1, "pre": 2, "prevent": 46, "print": [64, 65, 66, 67, 68], "procedur": 15, "procedure_occurr": 68, "procedures_icd": [0, 15], "process": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 59, 60, 61], "product": 47, "profil": [64, 65, 66, 67, 68], "properti": 11, "provid": [5, 7, 9, 13, 15, 17, 24, 38, 45, 46, 52, 62, 68], "public": [65, 67, 68], "pwd": [5, 64, 66, 67, 68], "pyarrow": [11, 68], "pylint": 24, "python": [1, 3, 63], "python3": 3, "qo": [3, 64, 65, 66, 67, 68], "queri": [2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 49, 51, 53, 58, 62, 63, 64, 65, 66, 67, 68], "querier": [3, 4, 7, 9, 13, 15, 17, 64, 65, 66, 67, 68], "queryinterfac": [0, 9, 13, 15, 17], "queryop": [0, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 58, 59, 60, 61], "quick": [64, 66, 67, 68], "quit": 54, "r": 67, "radiologi": [63, 65], "radiology_not": 67, "radiology_notes_op": 67, "random": 54, "randomizeord": 0, "rather": [19, 20], "raw": 63, "readi": [64, 65, 66, 67, 68], "receiv": 15, "recent": 63, "recogn": [5, 7, 9, 13, 15, 17], "recommend": 1, "record": [3, 63], "refer": 2, "regex": 36, "regular": 36, "relat": 3, "relationship": 68, "releas": 68, "remov": [42, 43], "renam": 0, "rename_map": 55, "reorder": [0, 57], "reorderaft": 0, "repo": 68, "report": [9, 63], "repres": 47, "respiratorycar": 64, "respiratorychart": 64, "result": [11, 58, 64, 66, 67, 68], "return": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 65, 66, 68], "return_cond": [23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 51], "room": 9, "room_transf": [0, 9], "roomtransf": 65, "routin": 63, "row": [11, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 49, 52, 54, 63, 65, 66, 67, 68], "ruff": 1, "run": [0, 1, 3, 5, 11, 63, 64, 65, 66, 68], "run_queri": [64, 65, 66, 67, 68], "sai": 47, "same": [46, 47], "save": [0, 11], "schema": [3, 5, 7, 9, 13, 15, 17, 67, 68], "schema_nam": [5, 7, 9, 13, 15, 17, 68], "schizophrenia": 63, "search": 63, "see": 3, "seen": 54, "select": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 58, 59, 60, 61, 67], "self": 5, "separ": 46, "sepsi": 63, "sequenc": [46, 58], "sequenti": [0, 3, 11, 64, 65, 66, 67, 68], "server": 11, "set": [3, 11, 63], "setup": [1, 64, 65, 66, 67, 68], "should": 11, "show": [1, 64, 65, 66, 67, 68], "showcas": 68, "sign": 63, "simpl": 3, "singl": 24, "size": 11, "slice": 58, "slow": 54, "so": 54, "sodium": 63, "sodium_test": 65, "some": [3, 19, 20, 21, 22, 26, 27, 28, 29, 30, 34, 37, 41, 42, 43, 52, 55, 60], "somecol_concept_id": 17, "somecol_concept_nam": 17, "somet": 3, "sort": [52, 63], "sort_index": 68, "sourc": [3, 5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61], "source_to_concept_map": 68, "source_to_source_vocab_map": 68, "source_to_standard_vocab_map": 68, "specif": 3, "specifi": [17, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 46, 47, 48, 57, 60], "specimen": 68, "sphinx": 3, "sphinxopt": 3, "sql": [3, 5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 59, 60, 61, 63], "sqlalchemi": [3, 5, 7, 9, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 59, 60, 61, 63], "sqlite": 5, "src_col": 17, "src_tabl": 17, "standard": [5, 7, 9, 13, 15, 17], "start": [2, 37, 59], "start_index": 59, "static": 1, "stop": 59, "stop_index": 59, "str": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 52, 55, 56, 57, 58, 59, 60, 67], "string": [28, 37, 46, 47, 50, 59, 60, 63], "string_agg": 46, "string_aggfunc": 46, "style": [1, 47], "subclass": 5, "subject_id": [63, 66], "submit": 1, "subqueri": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61], "subset": 63, "substr": [0, 3, 38, 63], "subtract": [19, 20], "successfulli": [64, 65, 66, 67, 68], "suggest": 47, "suppli": 15, "support": [6, 12, 14, 25], "sure": 3, "synthea": 68, "synthea_integration_test": 68, "system": 5, "t": 1, "tabl": [3, 5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 66, 68], "table1": [47, 61], "table2": [47, 61], "table_col": [11, 47], "table_nam": [5, 7, 9, 13, 15, 17], "take": [24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 63], "teach": 63, "teachingstatu": 64, "templat": 1, "test": [3, 63], "test_type_map": 65, "text": 67, "than": [19, 20, 30, 34, 63], "thank": 1, "them": 11, "thi": [5, 22, 38, 46, 47, 64, 65, 66, 67, 68], "thu": 11, "time": 44, "timedelta": 21, "timestamp": [5, 7, 9, 13, 15, 17, 25, 26, 27, 32, 33, 44, 65], "timestamp_col": [26, 27, 32, 33, 44], "titl": 63, "to_datetim": 68, "togeth": 63, "too": 24, "tool": [1, 3, 63, 64, 65, 66, 67, 68], "total": 63, "transfer": 9, "transfus": 65, "treatment": 64, "trim": 0, "true": [3, 5, 7, 9, 11, 13, 15, 17, 19, 20, 35, 38, 52, 55, 61, 64, 65, 67, 68], "tupl": [11, 47], "tutori": 2, "two": [47, 58, 61], "type": [1, 5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61], "type_": 25, "union": [0, 5, 11, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 58, 59, 60], "union_al": [0, 11, 61], "union_t": 61, "unit": [3, 9], "up": 3, "updat": [64, 66, 67, 68], "upstream": 11, "us": [1, 2, 5, 7, 9, 11, 13, 15, 17, 20, 23, 40, 46, 47, 51, 54, 61, 63, 64, 65, 66, 68], "usenam": 3, "user": [3, 5, 7, 9, 13, 15, 17, 64, 65, 66, 67, 68], "usernam": [5, 64, 65, 66, 67, 68], "util": [64, 65, 66, 67, 68], "v1": [66, 68], "v2": [67, 68], "valu": [22, 29, 30, 31, 34, 42, 43, 45, 46, 47, 50], "value_count": 68, "valuenum": 63, "virtual": 1, "visit": 63, "visit_count": 46, "visit_detail": [0, 17, 68], "visit_id": 40, "visit_occurr": [0, 17, 68], "visit_occurrence_id": 68, "visit_start_d": 68, "visits_concept_map": 68, "visits_concept_mapped_di": 68, "visits_measur": 68, "vital": [63, 65], "vitalaperiod": 64, "vitalperiod": 64, "vocabulari": 68, "we": [1, 68], "welcom": 3, "were": 63, "when": [5, 38, 47, 54], "where": [11, 59], "wherea": 19, "whether": [5, 7, 9, 11, 13, 15, 17, 38, 52, 55, 61], "which": [1, 5, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 59, 60, 61, 68], "whitespac": 60, "who": 63, "work": 19, "wrap": [9, 10, 11, 13, 15, 17], "wrapper": [3, 63], "write": 3, "x": 24, "y": 24, "year": [15, 32, 33, 44, 63, 68], "you": [1, 63], "your": 1, "yyyi": [26, 27]}, "titles": ["API Reference", "Contributing to cycquery", "Welcome to cycquery\u2019s documentation!", "cycquery", "cycquery.base", "cycquery.base.DatasetQuerier", "cycquery.eicu", "cycquery.eicu.EICUQuerier", "cycquery.gemini", "cycquery.gemini.GEMINIQuerier", "cycquery.interface", "cycquery.interface.QueryInterface", "cycquery.mimiciii", "cycquery.mimiciii.MIMICIIIQuerier", "cycquery.mimiciv", "cycquery.mimiciv.MIMICIVQuerier", "cycquery.omop", "cycquery.omop.OMOPQuerier", "cycquery.ops", "cycquery.ops.AddColumn", "cycquery.ops.AddDeltaColumn", "cycquery.ops.AddDeltaConstant", "cycquery.ops.AddNumeric", "cycquery.ops.And", "cycquery.ops.Apply", "cycquery.ops.Cast", "cycquery.ops.ConditionAfterDate", "cycquery.ops.ConditionBeforeDate", "cycquery.ops.ConditionEndsWith", "cycquery.ops.ConditionEquals", "cycquery.ops.ConditionGreaterThan", "cycquery.ops.ConditionIn", "cycquery.ops.ConditionInMonths", "cycquery.ops.ConditionInYears", "cycquery.ops.ConditionLessThan", "cycquery.ops.ConditionLike", "cycquery.ops.ConditionRegexMatch", "cycquery.ops.ConditionStartsWith", "cycquery.ops.ConditionSubstring", "cycquery.ops.Count", "cycquery.ops.Distinct", "cycquery.ops.Drop", "cycquery.ops.DropEmpty", "cycquery.ops.DropNulls", "cycquery.ops.ExtractTimestampComponent", "cycquery.ops.FillNull", "cycquery.ops.GroupByAggregate", "cycquery.ops.Join", "cycquery.ops.Keep", "cycquery.ops.Limit", "cycquery.ops.Literal", "cycquery.ops.Or", "cycquery.ops.OrderBy", "cycquery.ops.QueryOp", "cycquery.ops.RandomizeOrder", "cycquery.ops.Rename", "cycquery.ops.Reorder", "cycquery.ops.ReorderAfter", "cycquery.ops.Sequential", "cycquery.ops.Substring", "cycquery.ops.Trim", "cycquery.ops.Union", "cycquery", "Tutorials", "eICU-CRD tutorial", "GEMINI tutorial", "MIMIC-III tutorial", "MIMIC-IV tutorial", "OMOP tutorial"], "titleterms": {"": 2, "1": [64, 65, 66, 67, 68], "10": 67, "100": 64, "101": 65, "1a": 65, "1b": 65, "1c": 65, "2": [64, 66, 67, 68], "20": 66, "2009": 67, "2010": 68, "2014": 64, "2015": [64, 65, 67], "2016": 65, "2020": 68, "2021": 67, "2a": 65, "3": [64, 66, 67], "31": 65, "4": [64, 66, 67], "5": 67, "6": 67, "7": 67, "8": 67, "9": [66, 67], "And": 23, "Or": 51, "aado2": 66, "abov": 65, "addcolumn": 19, "adddeltacolumn": 20, "adddeltaconst": 21, "addnumer": 22, "admiss": [65, 67], "advanc": 67, "after": 68, "all": [64, 66, 67, 68], "api": [0, 62], "appli": 24, "approx": 67, "apr": 65, "april": 65, "base": [4, 5], "batch": 67, "between": 65, "carevu": 66, "cast": 25, "chart": 66, "chronic": 67, "code": 1, "commit": 1, "conditionafterd": 26, "conditionbefored": 27, "conditionendswith": 28, "conditionequ": 29, "conditiongreaterthan": 30, "conditionin": 31, "conditioninmonth": 32, "conditioninyear": 33, "conditionlessthan": 34, "conditionlik": 35, "conditionregexmatch": [36, 67], "conditionstartswith": 37, "conditionsubstr": 38, "contain": 67, "content": 2, "contribut": [1, 3], "count": 39, "crd": 64, "creat": 65, "cycqueri": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 67], "databas": 3, "dataset": [62, 65], "datasetqueri": 5, "develop": 3, "diagnos": [64, 66, 67, 68], "diagnosisstr": 64, "discharg": [64, 65], "discharge_date_tim": 65, "distinct": 40, "document": [2, 3], "drop": 41, "dropempti": 42, "dropnul": 43, "each": 65, "eicu": [6, 7, 64], "eicuqueri": [7, 64], "encount": [64, 65, 66, 67], "end": 68, "event": 66, "exampl": [64, 65, 66, 67, 68], "extracttimestampcompon": 44, "femal": [64, 66, 67, 68], "fillnul": 45, "filter": 67, "from": [65, 67], "gastroenter": 66, "gemini": [8, 9, 65], "geminiqueri": [9, 65], "get": [3, 64, 65, 66, 67, 68], "glucos": 64, "groupbyaggreg": 46, "guidelin": 1, "have": 66, "hemoglobin": 67, "hook": 1, "hospit": [64, 65], "how": 65, "icd": [66, 67], "iii": 66, "import": [64, 65, 66, 67, 68], "index": 67, "infecti": 67, "instal": 3, "instanti": [64, 65, 66, 67, 68], "interfac": [10, 11], "iv": 67, "join": 47, "keep": [48, 65], "keyword": 67, "lab": [64, 66, 67], "later": 67, "less": 66, "limit": [49, 64], "liter": 50, "long": [66, 67], "lymphadenopathi": 67, "mai": 65, "male": 66, "mani": 65, "march": 65, "measur": 68, "medic": 64, "mimic": [66, 67], "mimiciii": [12, 13], "mimiciiiqueri": [13, 66], "mimiciv": [14, 15], "mimicivqueri": [15, 67], "mortal": [66, 68], "most": 65, "number": 65, "occur": 67, "omop": [16, 17, 68], "omopqueri": [17, 68], "one": 65, "onli": 65, "op": [18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 67], "orderbi": 52, "outcom": [66, 68], "partit": 67, "patient": [64, 65, 66, 67, 68], "patient_id_hash": 65, "per": 65, "pip": 3, "place": 65, "poetri": 3, "postgresql": 3, "potassium": [64, 66], "pre": 1, "queri": 3, "queryinterfac": 11, "queryop": 53, "radiologi": 67, "randomizeord": 54, "raw": 67, "recent": 65, "record": 65, "refer": 0, "renam": 55, "reorder": 56, "reorderaft": 57, "report": 67, "return": 67, "routin": 67, "row": 64, "run": 67, "schizophrenia": [64, 67], "search": 64, "sepsi": 68, "sequenti": 58, "set": 65, "sign": 67, "sodium": 65, "sort": 65, "sql": 67, "start": 3, "string": 67, "subject_id": 67, "subset": 65, "substr": [59, 64], "tabl": 65, "take": 65, "teach": 64, "test": [64, 65, 66, 67], "than": 66, "titl": [66, 67], "togeth": 67, "total": 65, "trim": 60, "tutori": [63, 64, 65, 66, 67, 68], "union": 61, "us": [3, 67], "valuenum": 66, "visit": 68, "vital": 67, "welcom": 2, "were": 65, "who": 65, "year": [64, 67]}}) \ No newline at end of file diff --git a/tutorials/eicu.html b/tutorials/eicu.html index e9e5966..4f1fbcc 100644 --- a/tutorials/eicu.html +++ b/tutorials/eicu.html @@ -615,7 +615,7 @@

Imports and instantiate
-2024-04-18 11:27:55,239 INFO cycquery.orm    - Database setup, ready to run queries!
+2024-04-18 11:49:57,728 INFO cycquery.orm    - Database setup, ready to run queries!
 
@@ -722,7 +722,7 @@

Example 2. Get all patient encounters with diagnoses (
-2024-04-18 11:27:57,101 INFO cycquery.orm    - Query returned successfully!
+2024-04-18 11:50:00,239 INFO cycquery.orm    - Query returned successfully!
 

@@ -730,7 +730,7 @@

Example 2. Get all patient encounters with diagnoses (
-2024-04-18 11:27:57,103 INFO cycquery.utils.profile - Finished executing function run_query in 0.820597 s
+2024-04-18 11:50:00,242 INFO cycquery.utils.profile - Finished executing function run_query in 1.481393 s
 

@@ -771,7 +771,7 @@

Example 3. Get potassium lab tests for patients discharged in the year 2014,

-2024-04-18 11:27:57,416 INFO cycquery.orm    - Query returned successfully!
+2024-04-18 11:50:00,623 INFO cycquery.orm    - Query returned successfully!
 
@@ -779,7 +779,7 @@

Example 3. Get potassium lab tests for patients discharged in the year 2014,

-2024-04-18 11:27:57,418 INFO cycquery.utils.profile - Finished executing function run_query in 0.270279 s
+2024-04-18 11:50:00,624 INFO cycquery.utils.profile - Finished executing function run_query in 0.336015 s
 
@@ -818,7 +818,7 @@

Example 4. Get glucose medications (substring search) for female patients di

-2024-04-18 11:27:58,060 INFO cycquery.orm    - Query returned successfully!
+2024-04-18 11:50:01,613 INFO cycquery.orm    - Query returned successfully!
 
@@ -826,7 +826,7 @@

Example 4. Get glucose medications (substring search) for female patients di

-2024-04-18 11:27:58,062 INFO cycquery.utils.profile - Finished executing function run_query in 0.605530 s
+2024-04-18 11:50:01,615 INFO cycquery.utils.profile - Finished executing function run_query in 0.951092 s
 
diff --git a/tutorials/eicu.ipynb b/tutorials/eicu.ipynb index b5c3ce5..e638c89 100644 --- a/tutorials/eicu.ipynb +++ b/tutorials/eicu.ipynb @@ -35,10 +35,10 @@ "id": "75a140e0-fb27-4319-862f-be54397abe5c", "metadata": { "execution": { - "iopub.execute_input": "2024-04-18T15:27:51.905530Z", - "iopub.status.busy": "2024-04-18T15:27:51.904077Z", - "iopub.status.idle": "2024-04-18T15:27:55.962358Z", - "shell.execute_reply": "2024-04-18T15:27:55.960477Z" + "iopub.execute_input": "2024-04-18T15:49:55.705840Z", + "iopub.status.busy": "2024-04-18T15:49:55.704785Z", + "iopub.status.idle": "2024-04-18T15:49:58.544771Z", + "shell.execute_reply": "2024-04-18T15:49:58.542771Z" }, "tags": [] }, @@ -47,7 +47,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:27:55,239 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" + "2024-04-18 11:49:57,728 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" ] }, { @@ -124,10 +124,10 @@ "id": "c1efa964-8978-4a0e-9892-5ea4ce9953a3", "metadata": { "execution": { - "iopub.execute_input": "2024-04-18T15:27:55.970164Z", - "iopub.status.busy": "2024-04-18T15:27:55.968863Z", - "iopub.status.idle": "2024-04-18T15:27:56.258692Z", - "shell.execute_reply": "2024-04-18T15:27:56.256831Z" + "iopub.execute_input": "2024-04-18T15:49:58.553316Z", + "iopub.status.busy": "2024-04-18T15:49:58.551443Z", + "iopub.status.idle": "2024-04-18T15:49:58.735570Z", + "shell.execute_reply": "2024-04-18T15:49:58.733602Z" }, "tags": [] }, @@ -136,14 +136,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:27:56,249 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-18 11:49:58,725 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:27:56,250 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.267212 s\n" + "2024-04-18 11:49:58,727 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.158988 s\n" ] }, { @@ -180,10 +180,10 @@ "id": "a7ab5fa3-e26b-47a7-818f-1bf367a55760", "metadata": { "execution": { - "iopub.execute_input": "2024-04-18T15:27:56.266700Z", - "iopub.status.busy": "2024-04-18T15:27:56.265227Z", - "iopub.status.idle": "2024-04-18T15:27:57.110670Z", - "shell.execute_reply": "2024-04-18T15:27:57.108809Z" + "iopub.execute_input": "2024-04-18T15:49:58.743169Z", + "iopub.status.busy": "2024-04-18T15:49:58.741993Z", + "iopub.status.idle": "2024-04-18T15:50:00.249238Z", + "shell.execute_reply": "2024-04-18T15:50:00.247357Z" }, "tags": [] }, @@ -192,14 +192,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:27:57,101 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-18 11:50:00,239 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:27:57,103 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.820597 s\n" + "2024-04-18 11:50:00,242 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.481393 s\n" ] }, { @@ -236,10 +236,10 @@ "id": "24043abc-1878-4e00-8229-36d4a0368b98", "metadata": { "execution": { - "iopub.execute_input": "2024-04-18T15:27:57.118196Z", - "iopub.status.busy": "2024-04-18T15:27:57.117110Z", - "iopub.status.idle": "2024-04-18T15:27:57.425866Z", - "shell.execute_reply": "2024-04-18T15:27:57.423990Z" + "iopub.execute_input": "2024-04-18T15:50:00.257242Z", + "iopub.status.busy": "2024-04-18T15:50:00.255696Z", + "iopub.status.idle": "2024-04-18T15:50:00.631685Z", + "shell.execute_reply": "2024-04-18T15:50:00.630022Z" }, "tags": [] }, @@ -248,14 +248,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:27:57,416 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-18 11:50:00,623 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:27:57,418 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.270279 s\n" + "2024-04-18 11:50:00,624 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.336015 s\n" ] }, { @@ -298,10 +298,10 @@ "id": "f6142f27-e8d1-453c-bfe2-2265d9ff1914", "metadata": { "execution": { - "iopub.execute_input": "2024-04-18T15:27:57.433326Z", - "iopub.status.busy": "2024-04-18T15:27:57.432264Z", - "iopub.status.idle": "2024-04-18T15:27:58.070042Z", - "shell.execute_reply": "2024-04-18T15:27:58.068146Z" + "iopub.execute_input": "2024-04-18T15:50:00.639305Z", + "iopub.status.busy": "2024-04-18T15:50:00.638032Z", + "iopub.status.idle": "2024-04-18T15:50:01.622558Z", + "shell.execute_reply": "2024-04-18T15:50:01.620823Z" }, "tags": [] }, @@ -310,14 +310,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:27:58,060 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-18 11:50:01,613 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:27:58,062 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.605530 s\n" + "2024-04-18 11:50:01,615 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.951092 s\n" ] }, { diff --git a/tutorials/mimiciii.html b/tutorials/mimiciii.html index 509bc0b..a0fcb12 100644 --- a/tutorials/mimiciii.html +++ b/tutorials/mimiciii.html @@ -615,7 +615,7 @@

Imports and instantiate
-2024-04-18 11:28:10,924 INFO cycquery.orm    - Database setup, ready to run queries!
+2024-04-18 11:50:14,867 INFO cycquery.orm    - Database setup, ready to run queries!
 

@@ -697,7 +697,7 @@

Example 2. Get all female patient encounters with diagnoses (
-2024-04-18 11:28:19,416 INFO cycquery.orm    - Query returned successfully!
+2024-04-18 11:50:22,359 INFO cycquery.orm    - Query returned successfully!
 

@@ -705,7 +705,7 @@

Example 2. Get all female patient encounters with diagnoses (
-2024-04-18 11:28:19,419 INFO cycquery.utils.profile - Finished executing function run_query in 2.245811 s
+2024-04-18 11:50:22,361 INFO cycquery.utils.profile - Finished executing function run_query in 1.356768 s
 

@@ -782,7 +782,7 @@

Example 4. Get AaDO2 carevue chart events for male patients that have a
-2024-04-18 11:39:53,732 INFO cycquery.orm    - Query returned successfully!
+2024-04-18 11:57:40,475 INFO cycquery.orm    - Query returned successfully!
 

@@ -790,7 +790,7 @@

Example 4. Get AaDO2 carevue chart events for male patients that have a
-2024-04-18 11:39:53,734 INFO cycquery.utils.profile - Finished executing function run_query in 693.847932 s
+2024-04-18 11:57:40,477 INFO cycquery.utils.profile - Finished executing function run_query in 437.809877 s
 

diff --git a/tutorials/mimiciii.ipynb b/tutorials/mimiciii.ipynb index c5b688f..313b814 100644 --- a/tutorials/mimiciii.ipynb +++ b/tutorials/mimiciii.ipynb @@ -35,10 +35,10 @@ "id": "75a140e0-fb27-4319-862f-be54397abe5c", "metadata": { "execution": { - "iopub.execute_input": "2024-04-18T15:28:03.644795Z", - "iopub.status.busy": "2024-04-18T15:28:03.643680Z", - "iopub.status.idle": "2024-04-18T15:28:16.958728Z", - "shell.execute_reply": "2024-04-18T15:28:16.956835Z" + "iopub.execute_input": "2024-04-18T15:50:07.333083Z", + "iopub.status.busy": "2024-04-18T15:50:07.331982Z", + "iopub.status.idle": "2024-04-18T15:50:20.828781Z", + "shell.execute_reply": "2024-04-18T15:50:20.826850Z" }, "tags": [] }, @@ -47,7 +47,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:28:10,924 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" + "2024-04-18 11:50:14,867 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" ] }, { @@ -94,10 +94,10 @@ "id": "c1efa964-8978-4a0e-9892-5ea4ce9953a3", "metadata": { "execution": { - "iopub.execute_input": "2024-04-18T15:28:16.967253Z", - "iopub.status.busy": "2024-04-18T15:28:16.965511Z", - "iopub.status.idle": "2024-04-18T15:28:17.127541Z", - "shell.execute_reply": "2024-04-18T15:28:17.125745Z" + "iopub.execute_input": "2024-04-18T15:50:20.836500Z", + "iopub.status.busy": "2024-04-18T15:50:20.835504Z", + "iopub.status.idle": "2024-04-18T15:50:20.961645Z", + "shell.execute_reply": "2024-04-18T15:50:20.959787Z" }, "tags": [] }, @@ -106,14 +106,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:28:17,118 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-18 11:50:20,952 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:28:17,120 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.144103 s\n" + "2024-04-18 11:50:20,954 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.108410 s\n" ] }, { @@ -150,10 +150,10 @@ "id": "a7ab5fa3-e26b-47a7-818f-1bf367a55760", "metadata": { "execution": { - "iopub.execute_input": "2024-04-18T15:28:17.134933Z", - "iopub.status.busy": "2024-04-18T15:28:17.133791Z", - "iopub.status.idle": "2024-04-18T15:28:19.425873Z", - "shell.execute_reply": "2024-04-18T15:28:19.424225Z" + "iopub.execute_input": "2024-04-18T15:50:20.968679Z", + "iopub.status.busy": "2024-04-18T15:50:20.967640Z", + "iopub.status.idle": "2024-04-18T15:50:22.369500Z", + "shell.execute_reply": "2024-04-18T15:50:22.367644Z" }, "tags": [] }, @@ -162,14 +162,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:28:19,416 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-18 11:50:22,359 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:28:19,419 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 2.245811 s\n" + "2024-04-18 11:50:22,361 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.356768 s\n" ] }, { @@ -211,10 +211,10 @@ "id": "24043abc-1878-4e00-8229-36d4a0368b98", "metadata": { "execution": { - "iopub.execute_input": "2024-04-18T15:28:19.432708Z", - "iopub.status.busy": "2024-04-18T15:28:19.431747Z", - "iopub.status.idle": "2024-04-18T15:28:19.829082Z", - "shell.execute_reply": "2024-04-18T15:28:19.827438Z" + "iopub.execute_input": "2024-04-18T15:50:22.376446Z", + "iopub.status.busy": "2024-04-18T15:50:22.375532Z", + "iopub.status.idle": "2024-04-18T15:50:22.605722Z", + "shell.execute_reply": "2024-04-18T15:50:22.603842Z" }, "tags": [] }, @@ -223,14 +223,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:28:19,820 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-18 11:50:22,596 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:28:19,821 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.355687 s\n" + "2024-04-18 11:50:22,598 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.187926 s\n" ] }, { @@ -264,10 +264,10 @@ "id": "f6142f27-e8d1-453c-bfe2-2265d9ff1914", "metadata": { "execution": { - "iopub.execute_input": "2024-04-18T15:28:19.836150Z", - "iopub.status.busy": "2024-04-18T15:28:19.835162Z", - "iopub.status.idle": "2024-04-18T15:39:53.742670Z", - "shell.execute_reply": "2024-04-18T15:39:53.740900Z" + "iopub.execute_input": "2024-04-18T15:50:22.612709Z", + "iopub.status.busy": "2024-04-18T15:50:22.611797Z", + "iopub.status.idle": "2024-04-18T15:57:40.485339Z", + "shell.execute_reply": "2024-04-18T15:57:40.483565Z" }, "tags": [] }, @@ -276,14 +276,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:39:53,732 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-18 11:57:40,475 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:39:53,734 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 693.847932 s\n" + "2024-04-18 11:57:40,477 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 437.809877 s\n" ] }, { diff --git a/tutorials/mimiciv.html b/tutorials/mimiciv.html index be65abc..562d405 100644 --- a/tutorials/mimiciv.html +++ b/tutorials/mimiciv.html @@ -615,7 +615,7 @@

Imports and instantiate
-2024-04-18 11:40:03,490 INFO cycquery.orm    - Database setup, ready to run queries!
+2024-04-18 11:57:49,853 INFO cycquery.orm    - Database setup, ready to run queries!
 

@@ -660,7 +660,7 @@

Example 1. Get all patient admissions from 2021 or later (approx year of adm

-2024-04-18 11:40:05,988 INFO cycquery.orm    - Query returned successfully!
+2024-04-18 11:57:52,390 INFO cycquery.orm    - Query returned successfully!
 
@@ -668,7 +668,7 @@

Example 1. Get all patient admissions from 2021 or later (approx year of adm

-2024-04-18 11:40:05,989 INFO cycquery.utils.profile - Finished executing function run_query in 0.282214 s
+2024-04-18 11:57:52,392 INFO cycquery.utils.profile - Finished executing function run_query in 0.305880 s
 
@@ -713,7 +713,7 @@

Example 2. Get all patient encounters with diagnoses (
-2024-04-18 11:40:09,010 INFO cycquery.orm    - Query returned successfully!
+2024-04-18 11:57:54,717 INFO cycquery.orm    - Query returned successfully!
 

@@ -721,7 +721,7 @@

Example 2. Get all patient encounters with diagnoses (
-2024-04-18 11:40:09,012 INFO cycquery.utils.profile - Finished executing function run_query in 2.946522 s
+2024-04-18 11:57:54,719 INFO cycquery.utils.profile - Finished executing function run_query in 2.251988 s
 

@@ -766,7 +766,7 @@

Example 3. Advanced - uses
-2024-04-18 11:40:13,018 INFO cycquery.orm    - Query returned successfully!
+2024-04-18 11:57:58,465 INFO cycquery.orm    - Query returned successfully!
 

@@ -774,7 +774,7 @@

Example 3. Advanced - uses
-2024-04-18 11:40:13,020 INFO cycquery.utils.profile - Finished executing function run_query in 3.936798 s
+2024-04-18 11:57:58,466 INFO cycquery.utils.profile - Finished executing function run_query in 3.676533 s
 

@@ -919,7 +919,7 @@

Example 6. Get radiology reports and filter on keywords
-2024-04-18 11:40:33,180 INFO cycquery.orm    - Query returned successfully!
+2024-04-18 11:58:18,062 INFO cycquery.orm    - Query returned successfully!
 

@@ -927,7 +927,7 @@

Example 6. Get radiology reports and filter on keywords
-2024-04-18 11:40:33,182 INFO cycquery.utils.profile - Finished executing function run_query in 11.322607 s
+2024-04-18 11:58:18,063 INFO cycquery.utils.profile - Finished executing function run_query in 11.330467 s
 

@@ -970,7 +970,7 @@

Example 7. Get all female patient encounters from year 2015, and return batc

-2024-04-18 11:40:34,314 INFO cycquery.orm    - Query returned successfully!
+2024-04-18 11:58:19,146 INFO cycquery.orm    - Query returned successfully!
 
@@ -978,7 +978,7 @@

Example 7. Get all female patient encounters from year 2015, and return batc

-2024-04-18 11:40:34,317 INFO cycquery.utils.profile - Finished executing function run_query in 1.030955 s
+2024-04-18 11:58:19,147 INFO cycquery.utils.profile - Finished executing function run_query in 0.983342 s
 
diff --git a/tutorials/mimiciv.ipynb b/tutorials/mimiciv.ipynb index 3c163ab..a0d592e 100644 --- a/tutorials/mimiciv.ipynb +++ b/tutorials/mimiciv.ipynb @@ -35,10 +35,10 @@ "id": "53009e6b", "metadata": { "execution": { - "iopub.execute_input": "2024-04-18T15:39:58.323475Z", - "iopub.status.busy": "2024-04-18T15:39:58.322223Z", - "iopub.status.idle": "2024-04-18T15:40:05.663901Z", - "shell.execute_reply": "2024-04-18T15:40:05.662249Z" + "iopub.execute_input": "2024-04-18T15:57:45.701081Z", + "iopub.status.busy": "2024-04-18T15:57:45.700105Z", + "iopub.status.idle": "2024-04-18T15:57:52.041768Z", + "shell.execute_reply": "2024-04-18T15:57:52.040031Z" }, "tags": [] }, @@ -47,7 +47,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:40:03,490 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" + "2024-04-18 11:57:49,853 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" ] }, { @@ -105,10 +105,10 @@ "id": "cdfadaa4-6fd6-4fd7-85cf-e012aa0799e1", "metadata": { "execution": { - "iopub.execute_input": "2024-04-18T15:40:05.671417Z", - "iopub.status.busy": "2024-04-18T15:40:05.669944Z", - "iopub.status.idle": "2024-04-18T15:40:05.996760Z", - "shell.execute_reply": "2024-04-18T15:40:05.995088Z" + "iopub.execute_input": "2024-04-18T15:57:52.049607Z", + "iopub.status.busy": "2024-04-18T15:57:52.048050Z", + "iopub.status.idle": "2024-04-18T15:57:52.399337Z", + "shell.execute_reply": "2024-04-18T15:57:52.397697Z" } }, "outputs": [ @@ -116,14 +116,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:40:05,988 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-18 11:57:52,390 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:40:05,989 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.282214 s\n" + "2024-04-18 11:57:52,392 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.305880 s\n" ] }, { @@ -160,10 +160,10 @@ "id": "a89a9cf0", "metadata": { "execution": { - "iopub.execute_input": "2024-04-18T15:40:06.003930Z", - "iopub.status.busy": "2024-04-18T15:40:06.002653Z", - "iopub.status.idle": "2024-04-18T15:40:09.019118Z", - "shell.execute_reply": "2024-04-18T15:40:09.017503Z" + "iopub.execute_input": "2024-04-18T15:57:52.406704Z", + "iopub.status.busy": "2024-04-18T15:57:52.405459Z", + "iopub.status.idle": "2024-04-18T15:57:54.726296Z", + "shell.execute_reply": "2024-04-18T15:57:54.724676Z" } }, "outputs": [ @@ -171,14 +171,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:40:09,010 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-18 11:57:54,717 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:40:09,012 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 2.946522 s\n" + "2024-04-18 11:57:54,719 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 2.251988 s\n" ] }, { @@ -225,10 +225,10 @@ "id": "03936cee", "metadata": { "execution": { - "iopub.execute_input": "2024-04-18T15:40:09.026281Z", - "iopub.status.busy": "2024-04-18T15:40:09.024974Z", - "iopub.status.idle": "2024-04-18T15:40:13.028021Z", - "shell.execute_reply": "2024-04-18T15:40:13.026369Z" + "iopub.execute_input": "2024-04-18T15:57:54.733842Z", + "iopub.status.busy": "2024-04-18T15:57:54.732541Z", + "iopub.status.idle": "2024-04-18T15:57:58.474544Z", + "shell.execute_reply": "2024-04-18T15:57:58.472879Z" } }, "outputs": [ @@ -236,14 +236,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:40:13,018 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-18 11:57:58,465 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:40:13,020 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 3.936798 s\n" + "2024-04-18 11:57:58,466 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 3.676533 s\n" ] }, { @@ -290,10 +290,10 @@ "id": "56a72377", "metadata": { "execution": { - "iopub.execute_input": "2024-04-18T15:40:13.035256Z", - "iopub.status.busy": "2024-04-18T15:40:13.033966Z", - "iopub.status.idle": "2024-04-18T15:40:17.688619Z", - "shell.execute_reply": "2024-04-18T15:40:17.686931Z" + "iopub.execute_input": "2024-04-18T15:57:58.481241Z", + "iopub.status.busy": "2024-04-18T15:57:58.480543Z", + "iopub.status.idle": "2024-04-18T15:58:02.080174Z", + "shell.execute_reply": "2024-04-18T15:58:02.078501Z" } }, "outputs": [ @@ -301,14 +301,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:40:17,679 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-18 11:58:02,071 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:40:17,681 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 4.587958 s\n" + "2024-04-18 11:58:02,072 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 3.533433 s\n" ] }, { @@ -351,10 +351,10 @@ "id": "bce11f81", "metadata": { "execution": { - "iopub.execute_input": "2024-04-18T15:40:17.695933Z", - "iopub.status.busy": "2024-04-18T15:40:17.694711Z", - "iopub.status.idle": "2024-04-18T15:40:21.804585Z", - "shell.execute_reply": "2024-04-18T15:40:21.802914Z" + "iopub.execute_input": "2024-04-18T15:58:02.087741Z", + "iopub.status.busy": "2024-04-18T15:58:02.086456Z", + "iopub.status.idle": "2024-04-18T15:58:06.678478Z", + "shell.execute_reply": "2024-04-18T15:58:06.676835Z" } }, "outputs": [ @@ -362,14 +362,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:40:21,795 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-18 11:58:06,669 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:40:21,797 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 4.043617 s\n" + "2024-04-18 11:58:06,671 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 4.522759 s\n" ] }, { @@ -412,10 +412,10 @@ "id": "f00d270c-d78f-4dc0-8dae-ff4d52958c8b", "metadata": { "execution": { - "iopub.execute_input": "2024-04-18T15:40:21.811786Z", - "iopub.status.busy": "2024-04-18T15:40:21.810462Z", - "iopub.status.idle": "2024-04-18T15:40:33.189389Z", - "shell.execute_reply": "2024-04-18T15:40:33.187770Z" + "iopub.execute_input": "2024-04-18T15:58:06.686134Z", + "iopub.status.busy": "2024-04-18T15:58:06.684789Z", + "iopub.status.idle": "2024-04-18T15:58:18.070793Z", + "shell.execute_reply": "2024-04-18T15:58:18.069162Z" }, "tags": [] }, @@ -424,14 +424,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:40:33,180 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-18 11:58:18,062 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:40:33,182 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 11.322607 s\n" + "2024-04-18 11:58:18,063 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 11.330467 s\n" ] }, { @@ -480,10 +480,10 @@ "id": "28683d70-376e-4d9b-883d-1a7de634e455", "metadata": { "execution": { - "iopub.execute_input": "2024-04-18T15:40:33.198425Z", - "iopub.status.busy": "2024-04-18T15:40:33.197400Z", - "iopub.status.idle": "2024-04-18T15:40:34.668254Z", - "shell.execute_reply": "2024-04-18T15:40:34.666275Z" + "iopub.execute_input": "2024-04-18T15:58:18.078311Z", + "iopub.status.busy": "2024-04-18T15:58:18.077017Z", + "iopub.status.idle": "2024-04-18T15:58:19.484539Z", + "shell.execute_reply": "2024-04-18T15:58:19.482823Z" } }, "outputs": [ @@ -491,14 +491,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:40:34,314 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-18 11:58:19,146 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:40:34,317 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.030955 s\n" + "2024-04-18 11:58:19,147 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.983342 s\n" ] }, { @@ -543,10 +543,10 @@ "id": "a853deec", "metadata": { "execution": { - "iopub.execute_input": "2024-04-18T15:40:34.676201Z", - "iopub.status.busy": "2024-04-18T15:40:34.674613Z", - "iopub.status.idle": "2024-04-18T15:40:34.699461Z", - "shell.execute_reply": "2024-04-18T15:40:34.697717Z" + "iopub.execute_input": "2024-04-18T15:58:19.491580Z", + "iopub.status.busy": "2024-04-18T15:58:19.490552Z", + "iopub.status.idle": "2024-04-18T15:58:19.513388Z", + "shell.execute_reply": "2024-04-18T15:58:19.511711Z" }, "tags": [] }, @@ -555,14 +555,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:40:34,690 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-18 11:58:19,505 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:40:34,692 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.013542 s\n" + "2024-04-18 11:58:19,506 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.012544 s\n" ] }, { diff --git a/tutorials/omop.html b/tutorials/omop.html index fe14592..8b104ca 100644 --- a/tutorials/omop.html +++ b/tutorials/omop.html @@ -623,7 +623,7 @@

Imports and instantiate
-2024-04-18 11:40:41,216 INFO cycquery.orm    - Database setup, ready to run queries!
+2024-04-18 11:58:26,062 INFO cycquery.orm    - Database setup, ready to run queries!
 

@@ -818,7 +818,7 @@

Imports and instantiate
-2024-04-18 11:40:49,583 INFO cycquery.orm    - Database setup, ready to run queries!
+2024-04-18 11:58:33,556 INFO cycquery.orm    - Database setup, ready to run queries!
 

@@ -858,7 +858,7 @@

Example 1. Get all patient visits that ended in a mortality outcome in or af

-2024-04-18 11:40:56,215 INFO cycquery.orm    - Query returned successfully!
+2024-04-18 11:58:40,016 INFO cycquery.orm    - Query returned successfully!
 
@@ -866,7 +866,7 @@

Example 1. Get all patient visits that ended in a mortality outcome in or af

-2024-04-18 11:40:56,217 INFO cycquery.utils.profile - Finished executing function run_query in 0.668646 s
+2024-04-18 11:58:40,018 INFO cycquery.utils.profile - Finished executing function run_query in 0.515327 s
 
@@ -922,7 +922,7 @@

Example 2. Get all measurements for female patient visits with
-2024-04-18 11:44:19,561 INFO cycquery.orm    - Query returned successfully!
+2024-04-18 12:01:57,969 INFO cycquery.orm    - Query returned successfully!
 

@@ -930,7 +930,7 @@

Example 2. Get all measurements for female patient visits with
-2024-04-18 11:44:19,563 INFO cycquery.utils.profile - Finished executing function run_query in 203.103100 s
+2024-04-18 12:01:57,972 INFO cycquery.utils.profile - Finished executing function run_query in 197.711404 s
 

@@ -956,8 +956,7 @@

Example 2. Get all measurements for female patient visits with
 measurement_concept_name
-Body weight            51
-No matching concept    49
+No matching concept    100
 Name: count, dtype: int64[pyarrow]
 

diff --git a/tutorials/omop.ipynb b/tutorials/omop.ipynb index fd0e4f9..e30491b 100644 --- a/tutorials/omop.ipynb +++ b/tutorials/omop.ipynb @@ -45,10 +45,10 @@ "id": "53009e6b", "metadata": { "execution": { - "iopub.execute_input": "2024-04-18T15:40:38.676848Z", - "iopub.status.busy": "2024-04-18T15:40:38.675913Z", - "iopub.status.idle": "2024-04-18T15:40:42.356896Z", - "shell.execute_reply": "2024-04-18T15:40:42.355236Z" + "iopub.execute_input": "2024-04-18T15:58:23.506589Z", + "iopub.status.busy": "2024-04-18T15:58:23.505642Z", + "iopub.status.idle": "2024-04-18T15:58:27.183069Z", + "shell.execute_reply": "2024-04-18T15:58:27.181364Z" } }, "outputs": [ @@ -56,7 +56,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:40:41,216 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" + "2024-04-18 11:58:26,062 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" ] }, { @@ -151,10 +151,10 @@ "id": "3a3d9cb9-fe40-45b8-ba2f-8de52a3b7f4f", "metadata": { "execution": { - "iopub.execute_input": "2024-04-18T15:40:42.368537Z", - "iopub.status.busy": "2024-04-18T15:40:42.367042Z", - "iopub.status.idle": "2024-04-18T15:40:42.837841Z", - "shell.execute_reply": "2024-04-18T15:40:42.836234Z" + "iopub.execute_input": "2024-04-18T15:58:27.190589Z", + "iopub.status.busy": "2024-04-18T15:58:27.189137Z", + "iopub.status.idle": "2024-04-18T15:58:27.457191Z", + "shell.execute_reply": "2024-04-18T15:58:27.455556Z" } }, "outputs": [ @@ -162,14 +162,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:40:42,751 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-18 11:58:27,311 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:40:42,753 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.343278 s\n" + "2024-04-18 11:58:27,313 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.079233 s\n" ] }, { @@ -227,10 +227,10 @@ "id": "030e2491-a7cc-42f3-a1ca-618212b3524c", "metadata": { "execution": { - "iopub.execute_input": "2024-04-18T15:40:42.844948Z", - "iopub.status.busy": "2024-04-18T15:40:42.843651Z", - "iopub.status.idle": "2024-04-18T15:40:43.534242Z", - "shell.execute_reply": "2024-04-18T15:40:43.532632Z" + "iopub.execute_input": "2024-04-18T15:58:27.464684Z", + "iopub.status.busy": "2024-04-18T15:58:27.463355Z", + "iopub.status.idle": "2024-04-18T15:58:27.709222Z", + "shell.execute_reply": "2024-04-18T15:58:27.707570Z" } }, "outputs": [ @@ -238,14 +238,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:40:43,525 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-18 11:58:27,700 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:40:43,527 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.585587 s\n" + "2024-04-18 11:58:27,702 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.133449 s\n" ] }, { @@ -303,10 +303,10 @@ "id": "0622b3df-2864-4f32-bd98-806019f59c50", "metadata": { "execution": { - "iopub.execute_input": "2024-04-18T15:40:43.541576Z", - "iopub.status.busy": "2024-04-18T15:40:43.540295Z", - "iopub.status.idle": "2024-04-18T15:40:55.479748Z", - "shell.execute_reply": "2024-04-18T15:40:55.478050Z" + "iopub.execute_input": "2024-04-18T15:58:27.716882Z", + "iopub.status.busy": "2024-04-18T15:58:27.715554Z", + "iopub.status.idle": "2024-04-18T15:58:39.434419Z", + "shell.execute_reply": "2024-04-18T15:58:39.432742Z" }, "tags": [] }, @@ -315,7 +315,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:40:49,583 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" + "2024-04-18 11:58:33,556 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n" ] }, { @@ -357,10 +357,10 @@ "id": "40ff2e83-75e4-4119-aa33-26f95e63ddaa", "metadata": { "execution": { - "iopub.execute_input": "2024-04-18T15:40:55.486755Z", - "iopub.status.busy": "2024-04-18T15:40:55.485756Z", - "iopub.status.idle": "2024-04-18T15:40:56.224438Z", - "shell.execute_reply": "2024-04-18T15:40:56.222814Z" + "iopub.execute_input": "2024-04-18T15:58:39.441816Z", + "iopub.status.busy": "2024-04-18T15:58:39.440485Z", + "iopub.status.idle": "2024-04-18T15:58:40.025063Z", + "shell.execute_reply": "2024-04-18T15:58:40.023455Z" }, "tags": [] }, @@ -369,14 +369,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:40:56,215 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-18 11:58:40,016 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:40:56,217 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.668646 s\n" + "2024-04-18 11:58:40,018 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.515327 s\n" ] }, { @@ -419,10 +419,10 @@ "id": "46fd771c-5da7-4bce-aec7-08a5210a069b", "metadata": { "execution": { - "iopub.execute_input": "2024-04-18T15:40:56.231225Z", - "iopub.status.busy": "2024-04-18T15:40:56.230251Z", - "iopub.status.idle": "2024-04-18T15:44:19.571701Z", - "shell.execute_reply": "2024-04-18T15:44:19.569921Z" + "iopub.execute_input": "2024-04-18T15:58:40.032210Z", + "iopub.status.busy": "2024-04-18T15:58:40.031007Z", + "iopub.status.idle": "2024-04-18T16:01:57.979452Z", + "shell.execute_reply": "2024-04-18T16:01:57.977776Z" }, "tags": [] }, @@ -431,14 +431,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:44:19,561 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" + "2024-04-18 12:01:57,969 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "2024-04-18 11:44:19,563 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 203.103100 s\n" + "2024-04-18 12:01:57,972 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 197.711404 s\n" ] }, { @@ -488,10 +488,10 @@ "id": "d20a2581-f613-4ab8-9feb-3e84b8835db1", "metadata": { "execution": { - "iopub.execute_input": "2024-04-18T15:44:19.578967Z", - "iopub.status.busy": "2024-04-18T15:44:19.578212Z", - "iopub.status.idle": "2024-04-18T15:44:19.737797Z", - "shell.execute_reply": "2024-04-18T15:44:19.736052Z" + "iopub.execute_input": "2024-04-18T16:01:57.986229Z", + "iopub.status.busy": "2024-04-18T16:01:57.985501Z", + "iopub.status.idle": "2024-04-18T16:01:58.186112Z", + "shell.execute_reply": "2024-04-18T16:01:58.184452Z" }, "tags": [] }, @@ -500,8 +500,7 @@ "data": { "text/plain": [ "measurement_concept_name\n", - "Body weight 51\n", - "No matching concept 49\n", + "No matching concept 100\n", "Name: count, dtype: int64[pyarrow]" ] },