Table of incidence results

Table of incidence results

Usage

tableIncidence(
  result,
  type = "gt",
  header = c("estimate_name"),
  groupColumn = character(),
  settingsColumn = omopgenerics::settingsColumns(result),
  hide = character(),
  .options = list(),
  settingsColumns = lifecycle::deprecated()
)

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 settingsColumn 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

settingsColumn

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

settingsColumns

Value

Table of results

Examples

# \donttest{
cdm <- mockIncidencePrevalence(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
      
Analysis interval
      
Analysis complete database intervals
      
Analysis outcome washout
      
Analysis repeated events
      
Denominator age group
      
Denominator days prior observation
      
Denominator end date
      
Denominator sex
      
Denominator start date
      
Denominator target cohort name
      
Denominator time at risk
      

        
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
years
TRUE
inf
FALSE
0 to 150
0
2018-01-01
Both
2008-01-01
None
0 to Inf
42
33.05
9
27,230.64 (12,451.58 -
      51,692.24)



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



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



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



2012-01-01
2012-12-31
years
TRUE
inf
FALSE
0 to 150
0
2018-01-01
Both
2008-01-01
None
0 to Inf
10
9.86
1
10,137.88 (256.67 -
      56,484.62)



2013-01-01
2013-12-31
years
TRUE
inf
FALSE
0 to 150
0
2018-01-01
Both
2008-01-01
None
0 to Inf
9
8.74
1
11,446.89 (289.81 -
      63,777.97)



2014-01-01
2014-12-31
years
TRUE
inf
FALSE
0 to 150
0
2018-01-01
Both
2008-01-01
None
0 to Inf
8
6.36
2
31,461.38 (3,810.12 -
      113,649.33)



2015-01-01
2015-12-31
years
TRUE
inf
FALSE
0 to 150
0
2018-01-01
Both
2008-01-01
None
0 to Inf
6
3.86
4
103,761.35 (28,271.48 -
      265,670.26)



2016-01-01
2016-12-31
years
TRUE
inf
FALSE
0 to 150
0
2018-01-01
Both
2008-01-01
None
0 to Inf
2
1.11
1
90,415.91 (2,289.13 -
      503,765.23)
# }