Compute cumulative 'incidence'

Source: R/cumulate.R

cumulate is an S3 generic to compute cumulative numbers, with methods for different types of objects:

cumulate(x)

# Default S3 method
cumulate(x)

# S3 method for class 'incidence'
cumulate(x)

Arguments

x

An incidence object.

Details

  • default method is a wrapper for cumsum

  • incidence objects: computes cumulative incidence over time

  • projections objects: same, for projections objects, implemented in the similarly named package; see ?cumulate.projections for more information, after loading the package

See also

The incidence() function to generate the 'incidence' objects.

Author

Thibaut Jombart thibautjombart@gmail.com

Examples

dat <- as.integer(c(0,1,2,2,3,5,7))
group <- factor(c(1, 2, 3, 3, 3, 3, 1))
i <- incidence(dat, groups = group)
i
#> <incidence object>
#> [7 cases from days 0 to 7]
#> [3 groups: 1, 2, 3]
#> 
#> $counts: matrix with 8 rows and 3 columns
#> $n: 7 cases in total
#> $dates: 8 dates marking the left-side of bins
#> $interval: 1 day
#> $timespan: 8 days
#> $cumulative: FALSE
#> 
plot(i)


i_cum <- cumulate(i)
i_cum
#> <incidence object>
#> [7 cases from days 0 to 7]
#> [3 groups: 1, 2, 3]
#> 
#> $counts: matrix with 8 rows and 3 columns
#> $n: 7 cases in total
#> $dates: 8 dates marking the left-side of bins
#> $interval: 1 day
#> $timespan: 8 days
#> $cumulative: TRUE
#> 
plot(i_cum)