Pool 'incidence' across groups

This function pools incidence across all groups of an incidence object. The resulting incidence() object will contains counts summed over all groups present in the input.

pool(x)

Arguments

x

An 'incidence' object.

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
#> $cumulative: FALSE
#> 
i$counts
#>      1 2 3
#> [1,] 1 0 0
#> [2,] 0 1 0
#> [3,] 0 0 2
#> [4,] 0 0 1
#> [5,] 0 0 0
#> [6,] 0 0 1
#> [7,] 0 0 0
#> [8,] 1 0 0

## pool all groups
pool(i)
#> <incidence object>
#> [7 cases from days 0 to 7]
#> 
#> $counts: matrix with 8 rows and 1 columns
#> $n: 7 cases in total
#> $dates: 8 dates marking the left-side of bins
#> $interval: 1 day
#> $timespan: 8 days
#> $cumulative: FALSE
#> 
pool(i)$counts
#>      [,1]
#> [1,]    1
#> [2,]    1
#> [3,]    2
#> [4,]    1
#> [5,]    0
#> [6,]    1
#> [7,]    0
#> [8,]    1

## pool only groups 1 and 3
pool(i[,c(1,3)])
#> <incidence object>
#> [6 cases from days 0 to 7]
#> 
#> $counts: matrix with 8 rows and 1 columns
#> $n: 6 cases in total
#> $dates: 8 dates marking the left-side of bins
#> $interval: 1 day
#> $timespan: 8 days
#> $cumulative: FALSE
#> 
pool(i[,c(1,3)])$counts
#>      [,1]
#> [1,]    1
#> [2,]    0
#> [3,]    2
#> [4,]    1
#> [5,]    0
#> [6,]    1
#> [7,]    0
#> [8,]    1