The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.

2 Introduction

In this vignette, we will explore the OmopSketch function summariseTrend(), which summarises temporal trends from OMOP CDM tables. This function allows you to visualise how key measures (such as number of records, number of persons, person-days, age, or sex distribution) change over time.

2.1 Create a mock cdm

Let’s start by loading essential packages and creating a mock CDM using the R package omock

library(omock)
library(OmopSketch)
library(dplyr)
library(visOmopResults)

cdm <- mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")
#> ℹ Reading GiBleed tables.
#> ℹ Adding drug_strength table.
#> ℹ Creating local <cdm_reference> object.
#> ℹ Inserting <cdm_reference> into duckdb.

cdm
#> 
#> ── # OMOP CDM reference (duckdb) of GiBleed ────────────────────────────────────
#> • omop tables: care_site, cdm_source, concept, concept_ancestor, concept_class,
#> concept_relationship, concept_synonym, condition_era, condition_occurrence,
#> cost, death, device_exposure, domain, dose_era, drug_era, drug_exposure,
#> drug_strength, fact_relationship, location, measurement, metadata, note,
#> note_nlp, observation, observation_period, payer_plan_period, person,
#> procedure_occurrence, provider, relationship, source_to_concept_map, specimen,
#> visit_detail, visit_occurrence, vocabulary
#> • cohort tables: -
#> • achilles tables: -
#> • other tables: -

4 Tidy the summarised object with tableTrend

tableTrend() helps you convert a summarised result into a nicely formatted table for reporting or inspection (for example gt (default), flextable, reactable, or DT::datatable). It formats time intervals, strata and estimate columns so the results are easy to read and export.

result <- summariseTrend(
  cdm = cdm,
  event = "condition_occurrence",
  episode = "drug_exposure",
  output = "age",
  interval = "years"
)
tableTrend(result = result)
Summary of Age by years in condition_occurrence, drug_exposure tables
Variable name Time interval Estimate name
Database name
GiBleed
event; condition_occurrence
Age 1908-01-01 to 1908-12-31 Median 0.00
1909-01-01 to 1909-12-31 Median 0.00
1910-01-01 to 1910-12-31 Median 1.00
1911-01-01 to 1911-12-31 Median 1.00
1912-01-01 to 1912-12-31 Median 1.00
1913-01-01 to 1913-12-31 Median 1.00
1914-01-01 to 1914-12-31 Median 3.00
1915-01-01 to 1915-12-31 Median 3.00
1916-01-01 to 1916-12-31 Median 4.00
1917-01-01 to 1917-12-31 Median 5.00
1918-01-01 to 1918-12-31 Median 6.00
1919-01-01 to 1919-12-31 Median 6.00
1920-01-01 to 1920-12-31 Median 6.00
1921-01-01 to 1921-12-31 Median 4.00
1922-01-01 to 1922-12-31 Median 4.00
1923-01-01 to 1923-12-31 Median 5.00
1924-01-01 to 1924-12-31 Median 4.00
1925-01-01 to 1925-12-31 Median 5.00
1926-01-01 to 1926-12-31 Median 6.00
1927-01-01 to 1927-12-31 Median 7.00
1928-01-01 to 1928-12-31 Median 8.00
1929-01-01 to 1929-12-31 Median 9.00
1930-01-01 to 1930-12-31 Median 9.00
1931-01-01 to 1931-12-31 Median 9.00
1932-01-01 to 1932-12-31 Median 11.00
1933-01-01 to 1933-12-31 Median 11.00
1934-01-01 to 1934-12-31 Median 13.00
1935-01-01 to 1935-12-31 Median 11.00
1936-01-01 to 1936-12-31 Median 11.00
1937-01-01 to 1937-12-31 Median 7.00
1938-01-01 to 1938-12-31 Median 11.00
1939-01-01 to 1939-12-31 Median 6.00
1940-01-01 to 1940-12-31 Median 5.00
1941-01-01 to 1941-12-31 Median 5.00
1942-01-01 to 1942-12-31 Median 7.00
1943-01-01 to 1943-12-31 Median 7.00
1944-01-01 to 1944-12-31 Median 8.00
1945-01-01 to 1945-12-31 Median 7.00
1946-01-01 to 1946-12-31 Median 7.00
1947-01-01 to 1947-12-31 Median 8.00
1948-01-01 to 1948-12-31 Median 9.00
1949-01-01 to 1949-12-31 Median 8.00
1950-01-01 to 1950-12-31 Median 6.00
1951-01-01 to 1951-12-31 Median 6.00
1952-01-01 to 1952-12-31 Median 6.00
1953-01-01 to 1953-12-31 Median 7.00
1954-01-01 to 1954-12-31 Median 7.00
1955-01-01 to 1955-12-31 Median 8.00
1956-01-01 to 1956-12-31 Median 7.00
1957-01-01 to 1957-12-31 Median 9.00
1958-01-01 to 1958-12-31 Median 7.00
1959-01-01 to 1959-12-31 Median 8.00
1960-01-01 to 1960-12-31 Median 8.00
1961-01-01 to 1961-12-31 Median 8.00
1962-01-01 to 1962-12-31 Median 8.00
1963-01-01 to 1963-12-31 Median 9.00
1964-01-01 to 1964-12-31 Median 9.00
1965-01-01 to 1965-12-31 Median 9.00
1966-01-01 to 1966-12-31 Median 10.00
1967-01-01 to 1967-12-31 Median 10.00
1968-01-01 to 1968-12-31 Median 11.00
1969-01-01 to 1969-12-31 Median 11.00
1970-01-01 to 1970-12-31 Median 11.00
1971-01-01 to 1971-12-31 Median 12.00
1972-01-01 to 1972-12-31 Median 13.00
1973-01-01 to 1973-12-31 Median 12.00
1974-01-01 to 1974-12-31 Median 13.00
1975-01-01 to 1975-12-31 Median 14.00
1976-01-01 to 1976-12-31 Median 15.00
1977-01-01 to 1977-12-31 Median 16.00
1978-01-01 to 1978-12-31 Median 17.00
1979-01-01 to 1979-12-31 Median 17.00
1980-01-01 to 1980-12-31 Median 20.00
1981-01-01 to 1981-12-31 Median 19.00
1982-01-01 to 1982-12-31 Median 21.00
1983-01-01 to 1983-12-31 Median 22.00
1984-01-01 to 1984-12-31 Median 22.00
1985-01-01 to 1985-12-31 Median 24.00
1986-01-01 to 1986-12-31 Median 25.00
1987-01-01 to 1987-12-31 Median 27.00
1988-01-01 to 1988-12-31 Median 27.00
1989-01-01 to 1989-12-31 Median 29.00
1990-01-01 to 1990-12-31 Median 29.00
1991-01-01 to 1991-12-31 Median 30.00
1992-01-01 to 1992-12-31 Median 33.00
1993-01-01 to 1993-12-31 Median 33.00
1994-01-01 to 1994-12-31 Median 34.00
1995-01-01 to 1995-12-31 Median 35.00
1996-01-01 to 1996-12-31 Median 36.00
1997-01-01 to 1997-12-31 Median 37.00
1998-01-01 to 1998-12-31 Median 37.00
1999-01-01 to 1999-12-31 Median 38.00
2000-01-01 to 2000-12-31 Median 38.00
2001-01-01 to 2001-12-31 Median 39.00
2002-01-01 to 2002-12-31 Median 40.00
2003-01-01 to 2003-12-31 Median 41.00
2004-01-01 to 2004-12-31 Median 41.00
2005-01-01 to 2005-12-31 Median 41.00
2006-01-01 to 2006-12-31 Median 42.00
2007-01-01 to 2007-12-31 Median 42.00
2008-01-01 to 2008-12-31 Median 43.00
2009-01-01 to 2009-12-31 Median 45.00
2010-01-01 to 2010-12-31 Median 46.00
2011-01-01 to 2011-12-31 Median 48.00
2012-01-01 to 2012-12-31 Median 48.00
2013-01-01 to 2013-12-31 Median 49.00
2014-01-01 to 2014-12-31 Median 50.00
2015-01-01 to 2015-12-31 Median 51.00
2016-01-01 to 2016-12-31 Median 52.00
2017-01-01 to 2017-12-31 Median 54.00
2018-01-01 to 2018-12-31 Median 55.00
2019-01-01 to 2019-12-31 Median 56.00
overall Median 29.00
episode; drug_exposure
Age 1909-01-01 to 1909-12-31 Median 0.00
1910-01-01 to 1910-12-31 Median 1.00
1911-01-01 to 1911-12-31 Median 1.00
1912-01-01 to 1912-12-31 Median 1.00
1913-01-01 to 1913-12-31 Median 1.00
1914-01-01 to 1914-12-31 Median 3.00
1915-01-01 to 1915-12-31 Median 3.00
1916-01-01 to 1916-12-31 Median 4.00
1917-01-01 to 1917-12-31 Median 4.00
1918-01-01 to 1918-12-31 Median 6.00
1919-01-01 to 1919-12-31 Median 6.00
1920-01-01 to 1920-12-31 Median 5.00
1921-01-01 to 1921-12-31 Median 4.00
1922-01-01 to 1922-12-31 Median 3.00
1923-01-01 to 1923-12-31 Median 3.00
1924-01-01 to 1924-12-31 Median 4.00
1925-01-01 to 1925-12-31 Median 5.00
1926-01-01 to 1926-12-31 Median 7.00
1927-01-01 to 1927-12-31 Median 7.00
1928-01-01 to 1928-12-31 Median 6.00
1929-01-01 to 1929-12-31 Median 7.00
1930-01-01 to 1930-12-31 Median 8.00
1931-01-01 to 1931-12-31 Median 9.00
1932-01-01 to 1932-12-31 Median 11.00
1933-01-01 to 1933-12-31 Median 10.00
1934-01-01 to 1934-12-31 Median 11.00
1935-01-01 to 1935-12-31 Median 11.00
1936-01-01 to 1936-12-31 Median 8.00
1937-01-01 to 1937-12-31 Median 4.00
1938-01-01 to 1938-12-31 Median 14.00
1939-01-01 to 1939-12-31 Median 3.00
1940-01-01 to 1940-12-31 Median 5.00
1941-01-01 to 1941-12-31 Median 4.00
1942-01-01 to 1942-12-31 Median 5.00
1943-01-01 to 1943-12-31 Median 6.00
1944-01-01 to 1944-12-31 Median 7.00
1945-01-01 to 1945-12-31 Median 5.00
1946-01-01 to 1946-12-31 Median 4.00
1947-01-01 to 1947-12-31 Median 5.00
1948-01-01 to 1948-12-31 Median 4.00
1949-01-01 to 1949-12-31 Median 5.00
1950-01-01 to 1950-12-31 Median 4.00
1951-01-01 to 1951-12-31 Median 4.00
1952-01-01 to 1952-12-31 Median 4.00
1953-01-01 to 1953-12-31 Median 5.00
1954-01-01 to 1954-12-31 Median 4.00
1955-01-01 to 1955-12-31 Median 2.00
1956-01-01 to 1956-12-31 Median 2.00
1957-01-01 to 1957-12-31 Median 3.00
1958-01-01 to 1958-12-31 Median 3.00
1959-01-01 to 1959-12-31 Median 3.00
1960-01-01 to 1960-12-31 Median 2.00
1961-01-01 to 1961-12-31 Median 3.00
1962-01-01 to 1962-12-31 Median 4.00
1963-01-01 to 1963-12-31 Median 4.00
1964-01-01 to 1964-12-31 Median 4.00
1965-01-01 to 1965-12-31 Median 4.00
1966-01-01 to 1966-12-31 Median 4.00
1967-01-01 to 1967-12-31 Median 4.00
1968-01-01 to 1968-12-31 Median 4.00
1969-01-01 to 1969-12-31 Median 4.00
1970-01-01 to 1970-12-31 Median 4.00
1971-01-01 to 1971-12-31 Median 4.00
1972-01-01 to 1972-12-31 Median 4.00
1973-01-01 to 1973-12-31 Median 4.00
1974-01-01 to 1974-12-31 Median 5.00
1975-01-01 to 1975-12-31 Median 7.00
1976-01-01 to 1976-12-31 Median 7.00
1977-01-01 to 1977-12-31 Median 4.00
1978-01-01 to 1978-12-31 Median 5.00
1979-01-01 to 1979-12-31 Median 10.00
1980-01-01 to 1980-12-31 Median 11.00
1981-01-01 to 1981-12-31 Median 14.00
1982-01-01 to 1982-12-31 Median 15.00
1983-01-01 to 1983-12-31 Median 16.00
1984-01-01 to 1984-12-31 Median 13.00
1985-01-01 to 1985-12-31 Median 19.00
1986-01-01 to 1986-12-31 Median 21.00
1987-01-01 to 1987-12-31 Median 22.00
1988-01-01 to 1988-12-31 Median 22.00
1989-01-01 to 1989-12-31 Median 22.00
1990-01-01 to 1990-12-31 Median 22.00
1991-01-01 to 1991-12-31 Median 23.00
1992-01-01 to 1992-12-31 Median 31.00
1993-01-01 to 1993-12-31 Median 30.00
1994-01-01 to 1994-12-31 Median 31.00
1995-01-01 to 1995-12-31 Median 31.00
1996-01-01 to 1996-12-31 Median 35.00
1997-01-01 to 1997-12-31 Median 37.00
1998-01-01 to 1998-12-31 Median 38.00
1999-01-01 to 1999-12-31 Median 38.00
2000-01-01 to 2000-12-31 Median 40.00
2001-01-01 to 2001-12-31 Median 41.00
2002-01-01 to 2002-12-31 Median 41.00
2003-01-01 to 2003-12-31 Median 42.00
2004-01-01 to 2004-12-31 Median 41.00
2005-01-01 to 2005-12-31 Median 42.00
2006-01-01 to 2006-12-31 Median 49.00
2007-01-01 to 2007-12-31 Median 48.00
2008-01-01 to 2008-12-31 Median 44.00
2009-01-01 to 2009-12-31 Median 47.00
2010-01-01 to 2010-12-31 Median 50.00
2011-01-01 to 2011-12-31 Median 50.00
2012-01-01 to 2012-12-31 Median 50.00
2013-01-01 to 2013-12-31 Median 50.00
2014-01-01 to 2014-12-31 Median 51.00
2015-01-01 to 2015-12-31 Median 51.00
2016-01-01 to 2016-12-31 Median 51.00
2017-01-01 to 2017-12-31 Median 51.00
2018-01-01 to 2018-12-31 Median 51.00
2019-01-01 to 2019-12-31 Median 51.00
overall Median 24.00

6 Disconnect from CDM

Finally, disconnect from the mock CDM.

cdmDisconnect(cdm = cdm)

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.