Table of incidence results

Table of incidence results

Usage

tableIncidence(
  result,
  type = "gt",
  header = c("estimate_name"),
  groupColumn = c("cdm_name", "outcome_cohort_name"),
  settingsColumn = c("denominator_age_group", "denominator_sex"),
  hide = c("denominator_cohort_name", "analysis_interval"),
  .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 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 attribute to display 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 <- 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
#> ! cohort columns will be reordered to match the expected order:
#>   cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date.
#> ✔ Cohorts created in 0 min and 2 sec
inc <- estimateIncidence(
  cdm = cdm,
  denominatorTable = "denominator",
  outcomeTable = "outcome"
)
#> ℹ Getting incidence for analysis 1 of 1
#> ✔ Overall time taken: 0 mins and 1 secs
tableIncidence(inc)


  
Incidence start date
      
Incidence end date
      
Denominator age group
      
Denominator sex
      

        
Estimate name
      
    
Denominator (N)
      
Person-years
      
Outcome (N)
      
Incidence 100,000 person-years [95% CI]
    
mock; cohort_1
    
2008-01-01
2008-12-31
0 to 150
Both
42
33.05
9
27,230.64 (12,451.58 -
      51,692.24)
2009-01-01
2009-12-31
0 to 150
Both
38
28.74
13
45,229.98 (24,083.06 -
      77,344.64)
2010-01-01
2010-12-31
0 to 150
Both
25
19.69
8
40,623.57 (17,538.37 -
      80,044.63)
2011-01-01
2011-12-31
0 to 150
Both
17
11.57
7
60,485.61 (24,318.35 -
      124,623.48)
2012-01-01
2012-12-31
0 to 150
Both
10
9.86
1
10,137.88 (256.67 -
      56,484.62)
2013-01-01
2013-12-31
0 to 150
Both
9
8.74
1
11,446.89 (289.81 -
      63,777.97)
2014-01-01
2014-12-31
0 to 150
Both
8
6.36
2
31,461.38 (3,810.12 -
      113,649.33)
2015-01-01
2015-12-31
0 to 150
Both
6
3.86
4
103,761.35 (28,271.48 -
      265,670.26)
2016-01-01
2016-12-31
0 to 150
Both
2
1.11
1
90,415.91 (2,289.13 -
      503,765.23)
# }