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  "Description": "Identify the characteristics of patients in data mapped to\nthe Observational Medical Outcomes Partnership (OMOP) common\ndata model.",
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  "Date/Publication": "2026-02-26 08:39:12 UTC",
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    "addBirthdayQuery",
    "addCategories",
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    "addCohortIntersectCount",
    "addCohortIntersectDate",
    "addCohortIntersectDays",
    "addCohortIntersectField",
    "addCohortIntersectFlag",
    "addCohortName",
    "addConceptIntersectCount",
    "addConceptIntersectDate",
    "addConceptIntersectDays",
    "addConceptIntersectField",
    "addConceptIntersectFlag",
    "addConceptName",
    "addDateOfBirth",
    "addDateOfBirthQuery",
    "addDeathDate",
    "addDeathDays",
    "addDeathFlag",
    "addDemographics",
    "addDemographicsQuery",
    "addFutureObservation",
    "addFutureObservationQuery",
    "addInObservation",
    "addInObservationQuery",
    "addObservationPeriodId",
    "addObservationPeriodIdQuery",
    "addPriorObservation",
    "addPriorObservationQuery",
    "addSex",
    "addSexQuery",
    "addTableIntersectCount",
    "addTableIntersectDate",
    "addTableIntersectDays",
    "addTableIntersectField",
    "addTableIntersectFlag",
    "availableEstimates",
    "benchmarkPatientProfiles",
    "endDateColumn",
    "filterCohortId",
    "filterInObservation",
    "mockDisconnect",
    "mockPatientProfiles",
    "settings",
    "sourceConceptIdColumn",
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    "startDateColumn",
    "summariseResult",
    "suppress",
    "variableTypes"
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      "page": "addAge",
      "title": "Compute the age of the individuals at a certain date",
      "topics": [
        "addAge"
      ]
    },
    {
      "page": "addAgeQuery",
      "title": "Query to add the age of the individuals at a certain date",
      "topics": [
        "addAgeQuery"
      ]
    },
    {
      "page": "addBirthday",
      "title": "Add the birth day of an individual to a table",
      "topics": [
        "addBirthday"
      ]
    },
    {
      "page": "addBirthdayQuery",
      "title": "Add the birth day of an individual to a table",
      "topics": [
        "addBirthdayQuery"
      ]
    },
    {
      "page": "addCategories",
      "title": "Categorize a numeric variable",
      "topics": [
        "addCategories"
      ]
    },
    {
      "page": "addCdmName",
      "title": "Add cdm name",
      "topics": [
        "addCdmName"
      ]
    },
    {
      "page": "addCohortIntersectCount",
      "title": "It creates columns to indicate number of occurrences of intersection with a cohort",
      "topics": [
        "addCohortIntersectCount"
      ]
    },
    {
      "page": "addCohortIntersectDate",
      "title": "Date of cohorts that are present in a certain window",
      "topics": [
        "addCohortIntersectDate"
      ]
    },
    {
      "page": "addCohortIntersectDays",
      "title": "It creates columns to indicate the number of days between the current table and a target cohort",
      "topics": [
        "addCohortIntersectDays"
      ]
    },
    {
      "page": "addCohortIntersectField",
      "title": "It creates a column with the field of a desired intersection",
      "topics": [
        "addCohortIntersectField"
      ]
    },
    {
      "page": "addCohortIntersectFlag",
      "title": "It creates columns to indicate the presence of cohorts",
      "topics": [
        "addCohortIntersectFlag"
      ]
    },
    {
      "page": "addCohortName",
      "title": "Add cohort name for each cohort_definition_id",
      "topics": [
        "addCohortName"
      ]
    },
    {
      "page": "addConceptIntersectCount",
      "title": "It creates column to indicate the count overlap information between a table and a concept",
      "topics": [
        "addConceptIntersectCount"
      ]
    },
    {
      "page": "addConceptIntersectDate",
      "title": "It creates column to indicate the date overlap information between a table and a concept",
      "topics": [
        "addConceptIntersectDate"
      ]
    },
    {
      "page": "addConceptIntersectDays",
      "title": "It creates column to indicate the days of difference from an index date to a concept",
      "topics": [
        "addConceptIntersectDays"
      ]
    },
    {
      "page": "addConceptIntersectField",
      "title": "It adds a custom column (field) from the intersection with a certain table subsetted by concept id. In general it is used to add the first value of a certain measurement.",
      "topics": [
        "addConceptIntersectField"
      ]
    },
    {
      "page": "addConceptIntersectFlag",
      "title": "It creates column to indicate the flag overlap information between a table and a concept",
      "topics": [
        "addConceptIntersectFlag"
      ]
    },
    {
      "page": "addConceptName",
      "title": "Add concept name for each concept_id",
      "topics": [
        "addConceptName"
      ]
    },
    {
      "page": "addDateOfBirth",
      "title": "Add a column with the individual birth date",
      "topics": [
        "addDateOfBirth"
      ]
    },
    {
      "page": "addDateOfBirthQuery",
      "title": "Query to add a column with the individual birth date",
      "topics": [
        "addDateOfBirthQuery"
      ]
    },
    {
      "page": "addDeathDate",
      "title": "Add date of death for individuals. Only death within the same observation period than 'indexDate' will be observed.",
      "topics": [
        "addDeathDate"
      ]
    },
    {
      "page": "addDeathDays",
      "title": "Add days to death for individuals. Only death within the same observation period than 'indexDate' will be observed.",
      "topics": [
        "addDeathDays"
      ]
    },
    {
      "page": "addDeathFlag",
      "title": "Add flag for death for individuals. Only death within the same observation period than 'indexDate' will be observed.",
      "topics": [
        "addDeathFlag"
      ]
    },
    {
      "page": "addDemographics",
      "title": "Compute demographic characteristics at a certain date",
      "topics": [
        "addDemographics"
      ]
    },
    {
      "page": "addDemographicsQuery",
      "title": "Query to add demographic characteristics at a certain date",
      "topics": [
        "addDemographicsQuery"
      ]
    },
    {
      "page": "addFutureObservation",
      "title": "Compute the number of days till the end of the observation period at a certain date",
      "topics": [
        "addFutureObservation"
      ]
    },
    {
      "page": "addFutureObservationQuery",
      "title": "Query to add the number of days till the end of the observation period at a certain date",
      "topics": [
        "addFutureObservationQuery"
      ]
    },
    {
      "page": "addInObservation",
      "title": "Indicate if a certain record is within the observation period",
      "topics": [
        "addInObservation"
      ]
    },
    {
      "page": "addInObservationQuery",
      "title": "Query to add a new column to indicate if a certain record is within the observation period",
      "topics": [
        "addInObservationQuery"
      ]
    },
    {
      "page": "addObservationPeriodId",
      "title": "Add the ordinal number of the observation period associated that a given date is in.",
      "topics": [
        "addObservationPeriodId"
      ]
    },
    {
      "page": "addObservationPeriodIdQuery",
      "title": "Add the ordinal number of the observation period associated that a given date is in. Result is not computed, only query is added.",
      "topics": [
        "addObservationPeriodIdQuery"
      ]
    },
    {
      "page": "addPriorObservation",
      "title": "Compute the number of days of prior observation in the current observation period at a certain date",
      "topics": [
        "addPriorObservation"
      ]
    },
    {
      "page": "addPriorObservationQuery",
      "title": "Query to add the number of days of prior observation in the current observation period at a certain date",
      "topics": [
        "addPriorObservationQuery"
      ]
    },
    {
      "page": "addSex",
      "title": "Compute the sex of the individuals",
      "topics": [
        "addSex"
      ]
    },
    {
      "page": "addSexQuery",
      "title": "Query to add the sex of the individuals",
      "topics": [
        "addSexQuery"
      ]
    },
    {
      "page": "addTableIntersectCount",
      "title": "Compute number of intersect with an omop table.",
      "topics": [
        "addTableIntersectCount"
      ]
    },
    {
      "page": "addTableIntersectDate",
      "title": "Compute date of intersect with an omop table.",
      "topics": [
        "addTableIntersectDate"
      ]
    },
    {
      "page": "addTableIntersectDays",
      "title": "Compute time to intersect with an omop table.",
      "topics": [
        "addTableIntersectDays"
      ]
    },
    {
      "page": "addTableIntersectField",
      "title": "Intersecting the cohort with columns of an OMOP table of user's choice. It will add an extra column to the cohort, indicating the intersected entries with the target columns in a window of the user's choice.",
      "topics": [
        "addTableIntersectField"
      ]
    },
    {
      "page": "addTableIntersectFlag",
      "title": "Compute a flag intersect with an omop table.",
      "topics": [
        "addTableIntersectFlag"
      ]
    },
    {
      "page": "availableEstimates",
      "title": "Show the available estimates that can be used for the different variable_type supported.",
      "topics": [
        "availableEstimates"
      ]
    },
    {
      "page": "benchmarkPatientProfiles",
      "title": "Benchmark intersections and demographics functions for a certain source (cdm).",
      "topics": [
        "benchmarkPatientProfiles"
      ]
    },
    {
      "page": "endDateColumn",
      "title": "Get the name of the end date column for a certain table in the cdm",
      "topics": [
        "endDateColumn"
      ]
    },
    {
      "page": "filterCohortId",
      "title": "Filter a cohort according to cohort_definition_id column, the result is not computed into a table. only a query is added. Used usually as internal functions of other packages.",
      "topics": [
        "filterCohortId"
      ]
    },
    {
      "page": "filterInObservation",
      "title": "Filter the rows of a 'cdm_table' to the ones in observation that 'indexDate' is in observation.",
      "topics": [
        "filterInObservation"
      ]
    },
    {
      "page": "mockDisconnect",
      "title": "Deprecated",
      "topics": [
        "mockDisconnect"
      ]
    },
    {
      "page": "mockPatientProfiles",
      "title": "It creates a mock database for testing PatientProfiles package",
      "topics": [
        "mockPatientProfiles"
      ]
    },
    {
      "page": "sourceConceptIdColumn",
      "title": "Get the name of the source concept_id column for a certain table in the cdm",
      "topics": [
        "sourceConceptIdColumn"
      ]
    },
    {
      "page": "standardConceptIdColumn",
      "title": "Get the name of the standard concept_id column for a certain table in the cdm",
      "topics": [
        "standardConceptIdColumn"
      ]
    },
    {
      "page": "startDateColumn",
      "title": "Get the name of the start date column for a certain table in the cdm",
      "topics": [
        "startDateColumn"
      ]
    },
    {
      "page": "summariseResult",
      "title": "Summarise variables using a set of estimate functions. The output will be a formatted summarised_result object.",
      "topics": [
        "summariseResult"
      ]
    },
    {
      "page": "variableTypes",
      "title": "Classify the variables between 5 types: \"numeric\", \"categorical\", \"logical\", \"date\", \"integer\", or NA.",
      "topics": [
        "variableTypes"
      ]
    }
  ],
  "_pkglogo": "https://github.com/darwin-eu/patientprofiles/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/darwin-eu/patientprofiles/raw/HEAD/README.md",
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      "source": "cohort-intersect.Rmd",
      "filename": "cohort-intersect.html",
      "title": "Adding cohort intersections",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Identifying cohort intersections",
        "Options for identifying cohort intersection",
        "Naming conventions for new variables"
      ],
      "created": "2024-04-09 11:54:26",
      "modified": "2025-10-02 13:59:21",
      "commits": 6
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    {
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      "filename": "concept-intersect.html",
      "title": "Adding concept intersections",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Adding variables from concept sets",
        "Adding multiple concept based variables",
        "Cohort-based versus concept-based intersections"
      ],
      "created": "2024-04-09 11:54:26",
      "modified": "2025-10-02 13:59:21",
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    {
      "source": "demographics.rmd",
      "filename": "demographics.html",
      "title": "Adding patient demographics",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Adding characteristics to OMOP CDM tables",
        "Adding characteristics to a cohort tables",
        "Getting multiple characteristics at once"
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      "created": "2024-04-09 11:54:26",
      "modified": "2025-10-02 13:59:21",
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    {
      "source": "summarise.Rmd",
      "filename": "summarise.html",
      "title": "Summarise result",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Variables type",
        "Estimates names",
        "Summarise our first table"
      ],
      "created": "2024-04-09 11:54:26",
      "modified": "2025-10-02 13:59:21",
      "commits": 7
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    {
      "source": "table-intersect.Rmd",
      "filename": "table-intersect.html",
      "title": "Adding table intersections",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2024-04-09 11:54:26",
      "modified": "2025-10-02 13:59:21",
      "commits": 6
    }
  ],
  "_score": 9.609465488928944,
  "_indexed": true,
  "_nocasepkg": "patientprofiles",
  "_universes": [
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    "catalamarti"
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