Glossary

argument

A value given to a function or program when it runs. The term is often used interchangeably (and inconsistently) with parameter.

assign

To give a value a name by associating a variable with it. In R, this is typically done using the <- operator (e.g., x <- 5).

body

(of a function): the statements that are executed when a function runs.

CDM

Common Data Model - a standardized data structure that organizes healthcare data into a consistent format. The OMOP CDM is one of the most widely used healthcare CDMs.

clinical event

Any observation or occurrence in a patient’s healthcare journey, such as a diagnosis, procedure, drug exposure, or measurement.

cohort

A group of patients who share a common characteristic or experience within a defined time period. In OMOP, cohorts are often defined using specific inclusion and exclusion criteria.

comment

A remark in a program that is intended to help human readers understand what is going on, but is ignored by the computer. Comments in R start with a # character and run to the end of the line.

comma-separated values

(CSV) A common textual representation for tables in which the values in each row are separated by commas.

concept

In OMOP, a standardized clinical term with a unique identifier that represents medical entities like conditions, drugs, or procedures.

conceptid

A unique numerical identifier assigned to each concept in the OMOP vocabulary.

data frame

In R, a two-dimensional data structure similar to a table or spreadsheet, where each column can contain different data types.

delimiter

A character or characters used to separate individual values, such as the commas between columns in a CSV file.

documentation

Human-language text written to explain what software does, how it works, or how to use it.

domain

In OMOP, a high-level category that classifies clinical data (e.g., Condition, Drug, Procedure, Measurement).

EHR

Electronic Health Record - a digital version of a patient’s medical history maintained by healthcare providers.

floating-point number

A number containing a fractional part and an exponent. See also: integer.

for loop

A loop that is executed once for each value in some kind of set, list, or range. See also: while loop.

function call

A use of a function in another piece of code.

index

A subscript that specifies the location of a single value in a collection, such as a single pixel in an image or a row in a data frame.

integer

A whole number, such as -12343. See also: floating-point number.

library

In R, the directory(ies) where packages are stored.

observational data

Healthcare data collected during routine clinical practice, as opposed to data from controlled clinical trials.

OMOP

Observational Medical Outcomes Partnership - a common data model for healthcare data developed to standardize the structure and content of observational data.

package

A collection of R functions, data and compiled code in a well-defined format. Packages are stored in a library and loaded using the library() function.

parameter

A variable named in the function’s declaration that is used to hold a value passed into the call. The term is often used interchangeably (and inconsistently) with argument.

personid

A unique identifier for each patient in the OMOP CDM that links all clinical events for an individual across different tables.

return statement

A statement that causes a function to stop executing and return a value to its caller immediately.

sequence

A collection of information that is presented in a specific order.

shape

An array’s dimensions, represented as a vector. For example, a 5×3 array’s shape is (5,3).

standard concept

In OMOP, a concept designated as the preferred term for representing clinical information in analyses.

string

Short for “character string”, a sequence of zero or more characters.

syntax error

A programming error that occurs when statements are in an order or contain characters not expected by the programming language.

tibble

A modern reimagining of the data frame in R (from the tidyverse), with some improved behaviors for displaying and subsetting data.

type

The classification of something in a program (for example, the contents of a variable) as a kind of number (e.g. floating-point number, integer), string, or something else. In R the command typeof() is used to query a variable’s type.

variable

A named storage location in a program that can hold a value which may change during program execution.

vector

In R, a basic data structure that contains elements of the same type (e.g., all numbers or all characters).

vocabulary

In OMOP, a standardized terminology system (such as SNOMED, LOINC, or RxNorm) used to code clinical concepts.

while loop

A loop that keeps executing as long as some condition is true. See also: for loop. ``