Table of incidence results

Usage

tableIncidence(
  result,
  type = "gt",
  header = c("estimate_name"),
  groupColumn = character(),
  settingsColumns = colnames(settings(result)),
  hide = character(),
  .options = list()
)

Arguments

result: Incidence results
type: Type of table. Can be "gt", "flextable", or "tibble"
header: A vector specifying the elements to include in the header. The order of elements matters, with the first being the topmost header. The header vector can contain one of the following variables: "cdm_name", "denominator_cohort_name", "outcome_cohort_name", "incidence_start_date", "incidence_end_date", "estimate_name", variables in the strata_name column, and any of the settings columns specified in settingsColumns argument. The header can also include other names to use as overall header labels
groupColumn: Variables to use as group labels. Allowed columns are the same as in header
settingsColumns: Variables from the settings atribute to dispaly in the table
hide: Table columns to exclude, options are the ones described in header
.options: Table options to apply

Value

Table of results

Examples

# \donttest{
cdm <- mockIncidencePrevalenceRef(sampleSize = 1000)
cdm <- generateDenominatorCohortSet(
  cdm = cdm, name = "denominator",
  cohortDateRange = c(as.Date("2008-01-01"), as.Date("2018-01-01"))
)
#> ℹ Creating denominator cohorts
#> ✔ Cohorts created in 0 min and 3 sec
inc <- estimateIncidence(
  cdm = cdm,
  denominatorTable = "denominator",
  outcomeTable = "outcome"
)
#> Getting incidence for analysis 1 of 1
#> Overall time taken: 0 mins and 1 secs
tableIncidence(inc)


  Database name
      Denominator cohort name
      Outcome cohort name
      Incidence start date
      Incidence end date
      Result type
      Package name
      Package version
      Analysis outcome washout
      Analysis repeated events
      Analysis interval
      Analysis complete database intervals
      Denominator age group
      Denominator sex
      Denominator days prior observation
      Denominator start date
      Denominator end date
      Denominator target cohort name
      Denominator time at risk
      Min cell count
      
        Estimate name
      
    
Denominator (N)
      Person-years
      Outcome (N)
      Incidence 100 person-years [95% CI]
    
mock
denominator_cohort_1
cohort_1
2008-01-01
2008-12-31
incidence
IncidencePrevalence
0.8.1
inf
FALSE
years
TRUE
0 to 150
Both
0
2008-01-01
2018-01-01
None
0 to Inf
5
42
33.05
9
27,230.64 (12,451.58 -
      51,692.24)



2009-01-01
2009-12-31
incidence
IncidencePrevalence
0.8.1
inf
FALSE
years
TRUE
0 to 150
Both
0
2008-01-01
2018-01-01
None
0 to Inf
5
38
28.74
13
45,229.98 (24,083.06 -
      77,344.64)



2010-01-01
2010-12-31
incidence
IncidencePrevalence
0.8.1
inf
FALSE
years
TRUE
0 to 150
Both
0
2008-01-01
2018-01-01
None
0 to Inf
5
25
19.69
8
40,623.57 (17,538.37 -
      80,044.63)



2011-01-01
2011-12-31
incidence
IncidencePrevalence
0.8.1
inf
FALSE
years
TRUE
0 to 150
Both
0
2008-01-01
2018-01-01
None
0 to Inf
5
17
11.57
7
60,485.61 (24,318.35 -
      124,623.48)



2012-01-01
2012-12-31
incidence
IncidencePrevalence
0.8.1
inf
FALSE
years
TRUE
0 to 150
Both
0
2008-01-01
2018-01-01
None
0 to Inf
5
10
<5
<5
<5 (<5 -
      <5)



2013-01-01
2013-12-31
incidence
IncidencePrevalence
0.8.1
inf
FALSE
years
TRUE
0 to 150
Both
0
2008-01-01
2018-01-01
None
0 to Inf
5
9
<5
<5
<5 (<5 -
      <5)



2014-01-01
2014-12-31
incidence
IncidencePrevalence
0.8.1
inf
FALSE
years
TRUE
0 to 150
Both
0
2008-01-01
2018-01-01
None
0 to Inf
5
8
<5
<5
<5 (<5 -
      <5)



2015-01-01
2015-12-31
incidence
IncidencePrevalence
0.8.1
inf
FALSE
years
TRUE
0 to 150
Both
0
2008-01-01
2018-01-01
None
0 to Inf
5
6
<5
<5
<5 (<5 -
      <5)



2016-01-01
2016-12-31
incidence
IncidencePrevalence
0.8.1
inf
FALSE
years
TRUE
0 to 150
Both
0
2008-01-01
2018-01-01
None
0 to Inf
5
<5
<5
<5
<5 (<5 -
      <5)
# }

Database name	Denominator cohort name	Outcome cohort name	Incidence start date	Incidence end date	Result type	Package name	Package version	Analysis outcome washout	Analysis repeated events	Analysis interval	Analysis complete database intervals	Denominator age group	Denominator sex	Denominator days prior observation	Denominator start date	Denominator end date	Denominator target cohort name	Denominator time at risk	Min cell count	Estimate name
Database name	Denominator cohort name	Outcome cohort name	Incidence start date	Incidence end date	Result type	Package name	Package version	Analysis outcome washout	Analysis repeated events	Analysis interval	Analysis complete database intervals	Denominator age group	Denominator sex	Denominator days prior observation	Denominator start date	Denominator end date	Denominator target cohort name	Denominator time at risk	Min cell count	Denominator (N)	Person-years	Outcome (N)	Incidence 100 person-years [95% CI]
mock	denominator_cohort_1	cohort_1	2008-01-01	2008-12-31	incidence	IncidencePrevalence	0.8.1	inf	FALSE	years	TRUE	0 to 150	Both	0	2008-01-01	2018-01-01	None	0 to Inf	5	42	33.05	9	27,230.64 (12,451.58 - 51,692.24)
			2009-01-01	2009-12-31	incidence	IncidencePrevalence	0.8.1	inf	FALSE	years	TRUE	0 to 150	Both	0	2008-01-01	2018-01-01	None	0 to Inf	5	38	28.74	13	45,229.98 (24,083.06 - 77,344.64)
			2010-01-01	2010-12-31	incidence	IncidencePrevalence	0.8.1	inf	FALSE	years	TRUE	0 to 150	Both	0	2008-01-01	2018-01-01	None	0 to Inf	5	25	19.69	8	40,623.57 (17,538.37 - 80,044.63)
			2011-01-01	2011-12-31	incidence	IncidencePrevalence	0.8.1	inf	FALSE	years	TRUE	0 to 150	Both	0	2008-01-01	2018-01-01	None	0 to Inf	5	17	11.57	7	60,485.61 (24,318.35 - 124,623.48)
			2012-01-01	2012-12-31	incidence	IncidencePrevalence	0.8.1	inf	FALSE	years	TRUE	0 to 150	Both	0	2008-01-01	2018-01-01	None	0 to Inf	5	10	<5	<5	<5 (<5 - <5)
			2013-01-01	2013-12-31	incidence	IncidencePrevalence	0.8.1	inf	FALSE	years	TRUE	0 to 150	Both	0	2008-01-01	2018-01-01	None	0 to Inf	5	9	<5	<5	<5 (<5 - <5)
			2014-01-01	2014-12-31	incidence	IncidencePrevalence	0.8.1	inf	FALSE	years	TRUE	0 to 150	Both	0	2008-01-01	2018-01-01	None	0 to Inf	5	8	<5	<5	<5 (<5 - <5)
			2015-01-01	2015-12-31	incidence	IncidencePrevalence	0.8.1	inf	FALSE	years	TRUE	0 to 150	Both	0	2008-01-01	2018-01-01	None	0 to Inf	5	6	<5	<5	<5 (<5 - <5)
			2016-01-01	2016-12-31	incidence	IncidencePrevalence	0.8.1	inf	FALSE	years	TRUE	0 to 150	Both	0	2008-01-01	2018-01-01	None	0 to Inf	5	<5	<5	<5	<5 (<5 - <5)