Methods and Classes for the OMOP Common Data Model
Required columns for each of the achilles result tables
Names of the tables that contain the results of achilles analyses
Identify variables in additional_name column
Add settings columns to a <summarised_result> object
Assert that an object is a character and fulfill certain conditions.
Assert that an object is within a certain oprtions.
Assert that an object has a certain class.
Assert Date
Assert that an object is a list.
Assert that an object is a logical.
Assert that an object is a numeric.
Assert that an object is a table.
Assert that an expression is TRUE.
Get cohort attrition from a cohort_table object.
Get attrition from an object.
Bind two or more cohort tables
Bind two or more objects of the same class.
Bind two or summarised_result objects
Subset a cdm reference object.
Assign an table to a cdm reference.
Separate the cdm tables in classes
Disconnect from a cdm object.
Create a cdm object from local tables
Get the name of a cdm_reference associated object
Get the cdm_reference of a cdm_table.
Restrict the cdm object to a subset of tables.
Get the cdmSource of an object.
Get the source type of a cdm_reference object.
This is an internal developer focused function that creates a cdm_tabl...
Get the version of an object.
Check whether a cohort table satisfies requirements
Get codelist from a cohort_table object.
Required columns for a generated cohort set.
Get cohort counts from a cohort_table object.
Cohort tables that a cdm reference can contain in the OMOP Common Data...
Retrieves the cdm reference into a local cdm.
To collect a cohort_table object.
Provide all combinations of strata levels.
Store results in a table.
Create the missing indexes
Create a log file
Create a table index
Drop a table from a cdm object.
Drop a table from a cdm object.
Create an empty achilles table
Create an empty cdm_reference
Empty codelist object.
Empty codelist object.
Create an empty cohort_table object
Empty concept_set_expression object.
Create an empty omop table
Empty summarised_result object.
Choices that can be present in estimate_type column.
Existing indexes in a cdm object
Expected indexes in a cdm object
Export a codelist object.
Export a concept set expression.
Export a summarised_result object to a csv file.
Filter the additional_name-additional_level pair in a summarised_resul...
Filter the group_name-group_level pair in a summarised_result
Filter a <summarised_result> using the settings
Filter the strata_name-strata_level pair in a summarised_result
Get the cohort definition id of a certain name
Get the cohort name of a certain cohort definition id
Get the column name with the person identifier from a table (either su...
Identify variables in group_name column
Import a codelist.
Import a concept set expression.
Import a set of summarised results.
Insert a cdm_reference object to a different source.
Convert a table that is not a cdm_table but have the same original sou...
Insert a table to a cdm object.
To check whether an object is already suppressed to a certain min cell...
Check if a table is empty or not
List tables that can be accessed though a cdm object.
Log a message to a logFile
Create an achilles table from a cdm_table.
cdm_reference objects constructor
Create a cdm source object.
Create an cdm table.
'codelist' object constructor
'codelist' object constructor
cohort_table objects constructor.
'concept_set_expression' object constructor
A new local source for the cdm
Create an omop table from a cdm table.
'summarised_results' object constructor
Count the number of records that a cdm_table has.
Count the number of subjects that a cdm_table has.
Required columns that the standard tables in the OMOP Common Data Mode...
Check or set the OMOP_DATA_FOLDER where the OMOP related data is store...
omopgenerics: Methods and Classes for the OMOP Common Data Model
Return a table of omop cdm fields informations
Standard tables that a cdm reference can contain in the OMOP Common Da...
Set estimates as columns
Print a CDM reference object
Print a codelist with details
Print a codelist
Print a concept set expression
Read a table from the cdm_source and add it to to the cdm.
Update cohort attrition.
Objects exported from other packages
Required columns that the result tables must have.
Check if different packages version are used for summarise_results obj...
Get cohort settings from a cohort_table object.
Get settings from an object.
Get settings from a summarised_result object.
Identify settings columns of a <summarised_result>
Get the source type of an object.
Split additional_name and additional_level columns
Split all pairs name-level into columns.
Split group_name and group_level columns
Split strata_name and strata_level columns
Status of the indexes
Identify variables in strata_name column
Subset a cdm reference object.
Assign a table to a cdm reference.
Summarise and extract the information of a log file into a `summarised...
Summary a cdm reference
Summarise a cdm_source object
Summary a generated cohort set
Summary a summarised_result
Function to suppress counts in result objects
Function to suppress counts in result objects
Get the table name of a cdm_table.
Get the table source of a cdm_table.
Turn a <summarised_result> object into a tidy tibble
Identify tidy columns of a <summarised_result>
Create a temporary prefix for tables, that contains a unique prefix th...
Convert a character vector to snake case
Create a <summarised_result> object from a data.frame, given a set of ...
Get a unique Identifier with a certain number of characters and a pref...
Create a unique table name
Unite one or more columns in additional_name-additional_level format
Unite one or more columns in group_name-group_level format
Unite one or more columns in strata_name-strata_level format
Validate if a cdm_table is a valid achilles table.
Validate the ageGroup argument. It must be a list of two integerish nu...
Validate if an object in a valid cdm_reference.
Validate if a table is a valid cdm_table object.
Validate a cohort table input.
Validate cohortId argument. CohortId can either be a cohort_definition...
Validate whether a variable points to a certain exiting column in a ta...
Validate conceptSet argument. It can either be a list, a codelist, a c...
Validate name argument. It must be a snake_case character vector. You ...
Validate if two columns are valid Name-Level pair.
Validate nameStyle argument. If any of the element in ... has leng...
Validate a new column of a table
Validate an omop_table
Validate if a an object is a valid 'summarised_result' object.
To validate a strata list. It makes sure that elements are unique and ...
Validate a window argument. It must be a list of two elements (window ...
Provides definitions of core classes and methods used by analytic pipelines that query the OMOP (Observational Medical Outcomes Partnership) common data model.
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