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(C)omplete (S)chedule Coverage Upset Plot

Source: R/cs_upsetplot.R
cs_upsetplot.Rd

Generates an UpSet plot showing the number of individuals who received various combinations of vaccine doses defined in a vaccination schedule, for a given birth cohort. Individuals with a complete schedule are highlighted.

Usage

cs_upsetplot(
  data.EIR,
  data.schedule,
  birth_cohort,
  denominator = NULL,
  min_size = 1,
  set_order = NULL
)

Arguments

data.EIR

A data frame containing individual vaccination records. See pahoabc.EIR for expected structure.

data.schedule

A data frame defining the vaccination schedule. See pahoabc.schedule for expected structure.

birth_cohort

Numeric. A single birth year for which to calculate and visualize coverage.

denominator

The denominator to use. If NULL (default), then the number of unique IDs in data.EIR is used.

min_size

The minimum number of doses (as a percentage of the denominator) a group has to have in order to be shown in the plot. Default is 1 percent.

set_order

A vector containing the desired order of the doses as they will appear in the combination matrix. They must match the names in the dose column of data.EIR and data.schedule. If NULL, uses the default ordering scheme of ComplexUpset::upset().

Value

A ComplexUpset plot.