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Table of prevalence results

tablePrevalence.Rd

Table of prevalence results

Usage

tablePrevalence(
  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

Prevalence 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", "prevalence_start_date", "prevalence_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 prevalence 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
prev <- estimatePointPrevalence(
  cdm = cdm,
  denominatorTable = "denominator",
  outcomeTable = "outcome",
  interval = "months"
)
#> ℹ Getting prevalence for analysis 1 of 1
#> ✔ Time taken: 0 mins and 1 secs
tablePrevalence(prev)



  
Prevalence start date
      Prevalence end date
      Denominator age group
      Denominator sex
      
        
Estimate name

      		
    
Denominator (N)
      Outcome (N)
      Prevalence [95% CI]
    
mock; cohort_1
    
2008-01-01
2008-01-01
0 to 150
Both
55
0
0.00 (0.00 - 0.07)
2008-02-01
2008-02-01
0 to 150
Both
55
0
0.00 (0.00 - 0.07)
2008-03-01
2008-03-01
0 to 150
Both
55
0
0.00 (0.00 - 0.07)
2008-04-01
2008-04-01
0 to 150
Both
56
0
0.00 (0.00 - 0.06)
2008-05-01
2008-05-01
0 to 150
Both
57
0
0.00 (0.00 - 0.06)
2008-06-01
2008-06-01
0 to 150
Both
57
0
0.00 (0.00 - 0.06)
2008-07-01
2008-07-01
0 to 150
Both
57
0
0.00 (0.00 - 0.06)
2008-08-01
2008-08-01
0 to 150
Both
59
0
0.00 (0.00 - 0.06)
2008-09-01
2008-09-01
0 to 150
Both
59
0
0.00 (0.00 - 0.06)
2008-10-01
2008-10-01
0 to 150
Both
59
1
0.02 (0.00 - 0.09)
2008-11-01
2008-11-01
0 to 150
Both
59
0
0.00 (0.00 - 0.06)
2008-12-01
2008-12-01
0 to 150
Both
59
0
0.00 (0.00 - 0.06)
2009-01-01
2009-01-01
0 to 150
Both
59
0
0.00 (0.00 - 0.06)
2009-02-01
2009-02-01
0 to 150
Both
59
0
0.00 (0.00 - 0.06)
2009-03-01
2009-03-01
0 to 150
Both
56
0
0.00 (0.00 - 0.06)
2009-04-01
2009-04-01
0 to 150
Both
56
0
0.00 (0.00 - 0.06)
2009-05-01
2009-05-01
0 to 150
Both
54
0
0.00 (0.00 - 0.07)
2009-06-01
2009-06-01
0 to 150
Both
54
0
0.00 (0.00 - 0.07)
2009-07-01
2009-07-01
0 to 150
Both
54
1
0.02 (0.00 - 0.10)
2009-08-01
2009-08-01
0 to 150
Both
54
2
0.04 (0.01 - 0.13)
2009-09-01
2009-09-01
0 to 150
Both
53
0
0.00 (0.00 - 0.07)
2009-10-01
2009-10-01
0 to 150
Both
52
0
0.00 (0.00 - 0.07)
2009-11-01
2009-11-01
0 to 150
Both
51
1
0.02 (0.00 - 0.10)
2009-12-01
2009-12-01
0 to 150
Both
53
0
0.00 (0.00 - 0.07)
2010-01-01
2010-01-01
0 to 150
Both
52
1
0.02 (0.00 - 0.10)
2010-02-01
2010-02-01
0 to 150
Both
52
0
0.00 (0.00 - 0.07)
2010-03-01
2010-03-01
0 to 150
Both
49
0
0.00 (0.00 - 0.07)
2010-04-01
2010-04-01
0 to 150
Both
46
0
0.00 (0.00 - 0.08)
2010-05-01
2010-05-01
0 to 150
Both
44
0
0.00 (0.00 - 0.08)
2010-06-01
2010-06-01
0 to 150
Both
44
0
0.00 (0.00 - 0.08)
2010-07-01
2010-07-01
0 to 150
Both
43
0
0.00 (0.00 - 0.08)
2010-08-01
2010-08-01
0 to 150
Both
42
0
0.00 (0.00 - 0.08)
2010-09-01
2010-09-01
0 to 150
Both
41
1
0.02 (0.00 - 0.13)
2010-10-01
2010-10-01
0 to 150
Both
41
1
0.02 (0.00 - 0.13)
2010-11-01
2010-11-01
0 to 150
Both
41
0
0.00 (0.00 - 0.09)
2010-12-01
2010-12-01
0 to 150
Both
41
0
0.00 (0.00 - 0.09)
2011-01-01
2011-01-01
0 to 150
Both
41
0
0.00 (0.00 - 0.09)
2011-02-01
2011-02-01
0 to 150
Both
39
1
0.03 (0.00 - 0.13)
2011-03-01
2011-03-01
0 to 150
Both
39
1
0.03 (0.00 - 0.13)
2011-04-01
2011-04-01
0 to 150
Both
37
0
0.00 (0.00 - 0.09)
2011-05-01
2011-05-01
0 to 150
Both
36
0
0.00 (0.00 - 0.10)
2011-06-01
2011-06-01
0 to 150
Both
36
0
0.00 (0.00 - 0.10)
2011-07-01
2011-07-01
0 to 150
Both
36
0
0.00 (0.00 - 0.10)
2011-08-01
2011-08-01
0 to 150
Both
35
0
0.00 (0.00 - 0.10)
2011-09-01
2011-09-01
0 to 150
Both
35
0
0.00 (0.00 - 0.10)
2011-10-01
2011-10-01
0 to 150
Both
35
0
0.00 (0.00 - 0.10)
2011-11-01
2011-11-01
0 to 150
Both
33
0
0.00 (0.00 - 0.10)
2011-12-01
2011-12-01
0 to 150
Both
33
0
0.00 (0.00 - 0.10)
2012-01-01
2012-01-01
0 to 150
Both
32
0
0.00 (0.00 - 0.11)
2012-02-01
2012-02-01
0 to 150
Both
31
0
0.00 (0.00 - 0.11)
2012-03-01
2012-03-01
0 to 150
Both
31
0
0.00 (0.00 - 0.11)
2012-04-01
2012-04-01
0 to 150
Both
29
0
0.00 (0.00 - 0.12)
2012-05-01
2012-05-01
0 to 150
Both
28
0
0.00 (0.00 - 0.12)
2012-06-01
2012-06-01
0 to 150
Both
27
0
0.00 (0.00 - 0.12)
2012-07-01
2012-07-01
0 to 150
Both
26
0
0.00 (0.00 - 0.13)
2012-08-01
2012-08-01
0 to 150
Both
26
0
0.00 (0.00 - 0.13)
2012-09-01
2012-09-01
0 to 150
Both
26
0
0.00 (0.00 - 0.13)
2012-10-01
2012-10-01
0 to 150
Both
26
0
0.00 (0.00 - 0.13)
2012-11-01
2012-11-01
0 to 150
Both
25
0
0.00 (0.00 - 0.13)
2012-12-01
2012-12-01
0 to 150
Both
25
0
0.00 (0.00 - 0.13)
2013-01-01
2013-01-01
0 to 150
Both
25
0
0.00 (0.00 - 0.13)
2013-02-01
2013-02-01
0 to 150
Both
24
0
0.00 (0.00 - 0.14)
2013-03-01
2013-03-01
0 to 150
Both
23
0
0.00 (0.00 - 0.14)
2013-04-01
2013-04-01
0 to 150
Both
22
0
0.00 (0.00 - 0.15)
2013-05-01
2013-05-01
0 to 150
Both
21
0
0.00 (0.00 - 0.15)
2013-06-01
2013-06-01
0 to 150
Both
21
0
0.00 (0.00 - 0.15)
2013-07-01
2013-07-01
0 to 150
Both
20
0
0.00 (0.00 - 0.16)
2013-08-01
2013-08-01
0 to 150
Both
20
0
0.00 (0.00 - 0.16)
2013-09-01
2013-09-01
0 to 150
Both
20
0
0.00 (0.00 - 0.16)
2013-10-01
2013-10-01
0 to 150
Both
18
1
0.06 (0.01 - 0.26)
2013-11-01
2013-11-01
0 to 150
Both
18
0
0.00 (0.00 - 0.18)
2013-12-01
2013-12-01
0 to 150
Both
18
0
0.00 (0.00 - 0.18)
2014-01-01
2014-01-01
0 to 150
Both
18
0
0.00 (0.00 - 0.18)
2014-02-01
2014-02-01
0 to 150
Both
18
0
0.00 (0.00 - 0.18)
2014-03-01
2014-03-01
0 to 150
Both
18
0
0.00 (0.00 - 0.18)
2014-04-01
2014-04-01
0 to 150
Both
18
1
0.06 (0.01 - 0.26)
2014-05-01
2014-05-01
0 to 150
Both
18
0
0.00 (0.00 - 0.18)
2014-06-01
2014-06-01
0 to 150
Both
18
0
0.00 (0.00 - 0.18)
2014-07-01
2014-07-01
0 to 150
Both
18
0
0.00 (0.00 - 0.18)
2014-08-01
2014-08-01
0 to 150
Both
17
0
0.00 (0.00 - 0.18)
2014-09-01
2014-09-01
0 to 150
Both
17
0
0.00 (0.00 - 0.18)
2014-10-01
2014-10-01
0 to 150
Both
17
0
0.00 (0.00 - 0.18)
2014-11-01
2014-11-01
0 to 150
Both
16
0
0.00 (0.00 - 0.19)
2014-12-01
2014-12-01
0 to 150
Both
16
0
0.00 (0.00 - 0.19)
2015-01-01
2015-01-01
0 to 150
Both
16
0
0.00 (0.00 - 0.19)
2015-02-01
2015-02-01
0 to 150
Both
16
0
0.00 (0.00 - 0.19)
2015-03-01
2015-03-01
0 to 150
Both
16
0
0.00 (0.00 - 0.19)
2015-04-01
2015-04-01
0 to 150
Both
16
0
0.00 (0.00 - 0.19)
2015-05-01
2015-05-01
0 to 150
Both
16
0
0.00 (0.00 - 0.19)
2015-06-01
2015-06-01
0 to 150
Both
16
1
0.06 (0.01 - 0.28)
2015-07-01
2015-07-01
0 to 150
Both
16
0
0.00 (0.00 - 0.19)
2015-08-01
2015-08-01
0 to 150
Both
15
0
0.00 (0.00 - 0.20)
2015-09-01
2015-09-01
0 to 150
Both
15
0
0.00 (0.00 - 0.20)
2015-10-01
2015-10-01
0 to 150
Both
15
0
0.00 (0.00 - 0.20)
2015-11-01
2015-11-01
0 to 150
Both
15
0
0.00 (0.00 - 0.20)
2015-12-01
2015-12-01
0 to 150
Both
14
0
0.00 (0.00 - 0.22)
2016-01-01
2016-01-01
0 to 150
Both
14
0
0.00 (0.00 - 0.22)
2016-02-01
2016-02-01
0 to 150
Both
13
0
0.00 (0.00 - 0.23)
2016-03-01
2016-03-01
0 to 150
Both
11
0
0.00 (0.00 - 0.26)
2016-04-01
2016-04-01
0 to 150
Both
11
0
0.00 (0.00 - 0.26)
2016-05-01
2016-05-01
0 to 150
Both
10
0
0.00 (0.00 - 0.28)
2016-06-01
2016-06-01
0 to 150
Both
10
0
0.00 (0.00 - 0.28)
2016-07-01
2016-07-01
0 to 150
Both
10
0
0.00 (0.00 - 0.28)
2016-08-01
2016-08-01
0 to 150
Both
10
0
0.00 (0.00 - 0.28)
2016-09-01
2016-09-01
0 to 150
Both
9
0
0.00 (0.00 - 0.30)
2016-10-01
2016-10-01
0 to 150
Both
8
0
0.00 (0.00 - 0.32)
2016-11-01
2016-11-01
0 to 150
Both
8
0
0.00 (0.00 - 0.32)
2016-12-01
2016-12-01
0 to 150
Both
8
0
0.00 (0.00 - 0.32)
2017-01-01
2017-01-01
0 to 150
Both
7
0
0.00 (0.00 - 0.35)
2017-02-01
2017-02-01
0 to 150
Both
7
0
0.00 (0.00 - 0.35)
2017-03-01
2017-03-01
0 to 150
Both
7
0
0.00 (0.00 - 0.35)
2017-04-01
2017-04-01
0 to 150
Both
7
0
0.00 (0.00 - 0.35)
2017-05-01
2017-05-01
0 to 150
Both
7
0
0.00 (0.00 - 0.35)
2017-06-01
2017-06-01
0 to 150
Both
7
0
0.00 (0.00 - 0.35)
2017-07-01
2017-07-01
0 to 150
Both
7
0
0.00 (0.00 - 0.35)
2017-08-01
2017-08-01
0 to 150
Both
7
0
0.00 (0.00 - 0.35)
2017-09-01
2017-09-01
0 to 150
Both
7
0
0.00 (0.00 - 0.35)
2017-10-01
2017-10-01
0 to 150
Both
7
0
0.00 (0.00 - 0.35)
2017-11-01
2017-11-01
0 to 150
Both
6
0
0.00 (0.00 - 0.39)
2017-12-01
2017-12-01
0 to 150
Both
6
0
0.00 (0.00 - 0.39)
2018-01-01
2018-01-01
0 to 150
Both
6
0
0.00 (0.00 - 0.39)
# }