Methods and Classes for the OMOP Common Data Model

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Documentation for package ‘omopgenerics’ version 1.2.0

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A B C D E F G I L N O P R S T U V misc

-- A --

achillesColumns Required columns for each of the achilles result tables
achillesTables Names of the tables that contain the results of achilles analyses
additionalColumns Identify variables in additional_name column
addSettings Add settings columns to a <summarised_result> object
assertCharacter Assert that an object is a character and fulfill certain conditions.
assertChoice Assert that an object is within a certain oprtions.
assertClass Assert that an object has a certain class.
assertDate Assert Date
assertList Assert that an object is a list.
assertLogical Assert that an object is a logical.
assertNumeric Assert that an object is a numeric.
assertTable Assert that an object is a table.
assertTrue Assert that an expression is TRUE.
attrition Get attrition from an object.
attrition.cohort_table Get cohort attrition from a cohort_table object.

-- B --

bind Bind two or more objects of the same class.
bind.cohort_table Bind two or more cohort tables
bind.summarised_result Bind two or summarised_result objects

-- C --

cdmDisconnect Disconnect from a cdm object.
cdmFromTables Create a cdm object from local tables
cdmName Get the name of a cdm_reference associated object
cdmReference Get the 'cdm_reference' of a 'cdm_table'.
cdmSelect Restrict the cdm object to a subset of tables.
cdmSource Get the cdmSource of an object.
cdmSourceType Get the source type of a cdm_reference object.
cdmTableFromSource This is an internal developer focused function that creates a cdm_table from a table that shares the source but it is not a cdm_table. Please use insertTable if you want to insert a table to a cdm_reference object.
cdmVersion Get the version of an object.
checkCohortRequirements Check whether a cohort table satisfies requirements
cohortCodelist Get codelist from a cohort_table object.
cohortColumns Required columns for a generated cohort set.
cohortCount Get cohort counts from a cohort_table object.
cohortTables Cohort tables that a cdm reference can contain in the OMOP Common Data Model.
collect.cdm_reference Retrieves the cdm reference into a local cdm.
collect.cohort_table To collect a 'cohort_table' object.
combineStrata Provide all combinations of strata levels.
compute.cdm_table Store results in a table.
createLogFile Create a log file

-- D --

dropSourceTable Drop a table from a cdm object.
dropTable Drop a table from a cdm object. *[Deprecated]*

-- E --

emptyAchillesTable Create an empty achilles table
emptyCdmReference Create an empty cdm_reference
emptyCodelist Empty 'codelist' object.
emptyCodelistWithDetails Empty 'codelist' object.
emptyCohortTable Create an empty cohort_table object
emptyOmopTable Create an empty omop table
emptySummarisedResult Empty 'summarised_result' object.
estimateTypeChoices Choices that can be present in 'estimate_type' column.
exportCodelist Export a codelist object.
exportConceptSetExpression Export a concept set expression.
exportSummarisedResult Export a summarised_result object to a csv file.

-- F --

filterAdditional Filter the additional_name-additional_level pair in a summarised_result
filterGroup Filter the group_name-group_level pair in a summarised_result
filterSettings Filter a <summarised_result> using the settings
filterStrata Filter the strata_name-strata_level pair in a summarised_result

-- G --

getCohortId Get the cohort definition id of a certain name
getCohortName Get the cohort name of a certain cohort definition id
getPersonIdentifier Get the column name with the person identifier from a table (either subject_id or person_id), it will throw an error if it contains both or neither.
groupColumns Identify variables in group_name column

-- I --

importCodelist Import a codelist.
importConceptSetExpression Import a concept set expression.
importSummarisedResult Import a set of summarised results.
insertCdmTo Insert a cdm_reference object to a different source.
insertFromSource Convert a table that is not a cdm_table but have the same original source to a cdm_table. This Table is not meant to be used to insert tables in the cdm, please use insertTable instead.
insertTable Insert a table to a cdm object.
isResultSuppressed To check whether an object is already suppressed to a certain min cell count.
isTableEmpty Check if a table is empty or not

-- L --

listSourceTables List tables that can be accessed though a cdm object.
logMessage Log a message to a logFile

-- N --

newAchillesTable Create an achilles table from a cdm_table.
newCdmReference 'cdm_reference' objects constructor
newCdmSource Create a cdm source object.
newCdmTable Create an cdm table.
newCodelist 'codelist' object constructor
newCodelistWithDetails 'codelist' object constructor
newCohortTable 'cohort_table' objects constructor.
newConceptSetExpression 'conceptSetExpression' object constructor
newLocalSource A new local source for the cdm
newOmopTable Create an omop table from a cdm table.
newSummarisedResult 'summarised_results' object constructor
numberRecords Count the number of records that a 'cdm_table' has.
numberSubjects Count the number of subjects that a 'cdm_table' has.

-- O --

omopColumns Required columns that the standard tables in the OMOP Common Data Model must have.
omopTableFields Return a table of omop cdm fields informations
omopTables Standard tables that a cdm reference can contain in the OMOP Common Data Model.

-- P --

pivotEstimates Set estimates as columns
print.cdm_reference Print a CDM reference object
print.codelist Print a codelist
print.codelist_with_details Print a codelist with details
print.conceptSetExpression Print a concept set expression

-- R --

readSourceTable Read a table from the cdm_source and add it to to the cdm.
recordCohortAttrition Update cohort attrition.
resultColumns Required columns that the result tables must have.
resultPackageVersion Check if different packages version are used for summarise_results object

-- S --

settings Get settings from an object.
settings.cohort_table Get cohort settings from a cohort_table object.
settings.summarised_result Get settings from a summarised_result object.
settingsColumns Identify settings columns of a <summarised_result>
sourceType Get the source type of an object.
splitAdditional Split additional_name and additional_level columns
splitAll Split all pairs name-level into columns.
splitGroup Split group_name and group_level columns
splitStrata Split strata_name and strata_level columns
strataColumns Identify variables in strata_name column
summariseLogFile Summarise and extract the information of a log file into a 'summarised_result' object.
summary.cdm_reference Summary a cdm reference
summary.cohort_table Summary a generated cohort set
summary.summarised_result Summary a summarised_result
suppress Function to suppress counts in result objects
suppress.summarised_result Function to suppress counts in result objects

-- T --

tableName Get the table name of a 'cdm_table'.
tableSource Get the table source of a 'cdm_table'.
tidy.summarised_result Turn a <summarised_result> object into a tidy tibble
tidyColumns Identify tidy columns of a <summarised_result>
tmpPrefix Create a temporary prefix for tables, that contains a unique prefix that starts with tmp.
toSnakeCase Convert a character vector to snake case
transformToSummarisedResult Create a <summarised_result> object from a data.frame, given a set of specifications.

-- U --

uniqueId Get a unique Identifier with a certain number of characters and a prefix.
uniqueTableName Create a unique table name
uniteAdditional Unite one or more columns in additional_name-additional_level format
uniteGroup Unite one or more columns in group_name-group_level format
uniteStrata Unite one or more columns in strata_name-strata_level format

-- V --

validateAchillesTable Validate if a cdm_table is a valid achilles table.
validateAgeGroupArgument Validate the ageGroup argument. It must be a list of two integerish numbers lower age and upper age, both of the must be greater or equal to 0 and lower age must be lower or equal to the upper age. If not named automatic names will be given in the output list.
validateCdmArgument Validate if an object in a valid cdm_reference.
validateCdmTable Validate if a table is a valid cdm_table object.
validateCohortArgument Validate a cohort table input.
validateCohortIdArgument Validate cohortId argument. CohortId can either be a cohort_definition_id value, a cohort_name or a tidyselect expression referinc to cohort_names. If you want to support tidyselect expressions please use the function as: 'validateCohortIdArgument({{cohortId}}, cohort)'.
validateColumn Validate whether a variable points to a certain exiting column in a table.
validateConceptSetArgument Validate conceptSet argument. It can either be a list, a codelist, a conceptSetExpression or a codelist with details. The output will always be a codelist.
validateNameArgument Validate name argument. It must be a snake_case character vector. You can add the a cdm object to check 'name' is not already used in that cdm.
validateNameLevel Validate if two columns are valid Name-Level pair.
validateNameStyle Validate 'nameStyle' argument. If any of the element in '...' has length greater than 1 it must be contained in nameStyle. Note that snake case notation is used.
validateNewColumn Validate a new column of a table
validateOmopTable Validate an omop_table
validateResultArgument Validate if a an object is a valid 'summarised_result' object.
validateStrataArgument To validate a strata list. It makes sure that elements are unique and point to columns in table.
validateWindowArgument Validate a window argument. It must be a list of two elements (window start and window end), both must be integerish and window start must be lower or equal than window end.

-- misc --

$.cdm_reference Subset a cdm reference object.
$<-.cdm_reference Assign an table to a cdm reference.
[[.cdm_reference Subset a cdm reference object.
[[<-.cdm_reference Assign a table to a cdm reference.