Get counts from an incidence object

Get counts from an incidence object

get_counts(x, groups = NULL)

# S3 method for class 'incidence'
get_counts(x, groups = NULL)

Arguments

x

an incidence object.

groups

if there are groups, use this to specify a group or groups to subset. Defaults to NULL indicating that all groups are returned.

Value

a matrix of counts where each row represents a date bin

Examples

if (require(outbreaks)) { withAutoprint({
  dat  <- ebola_sim$linelist$date_of_onset
  gend <- ebola_sim$linelist$gender
  i    <- incidence(dat, interval = "week", groups = gend)
  
  ## Use with an object and no arguments gives the counts matrix
  head(get_counts(i))

  ## Specifying a position or group name will return a matrix subset to that
  ## group
  head(get_counts(i, 1L))
  head(get_counts(i, "f"))

  ## Specifying multiple groups allows you to rearrange columns
  head(get_counts(i, c("m", "f")))

  ## If you want a vector, you can use drop
  drop(get_counts(i, "f"))
})}
#> > dat <- ebola_sim$linelist$date_of_onset
#> > gend <- ebola_sim$linelist$gender
#> > i <- incidence(dat, interval = "week", groups = gend)
#> > head(get_counts(i))
#>      f  m
#> [1,] 1  0
#> [2,] 0  1
#> [3,] 4  1
#> [4,] 4  0
#> [5,] 9  3
#> [6,] 8 10
#> > head(get_counts(i, 1L))
#>      f
#> [1,] 1
#> [2,] 0
#> [3,] 4
#> [4,] 4
#> [5,] 9
#> [6,] 8
#> > head(get_counts(i, "f"))
#>      f
#> [1,] 1
#> [2,] 0
#> [3,] 4
#> [4,] 4
#> [5,] 9
#> [6,] 8
#> > head(get_counts(i, c("m", "f")))
#>       m f
#> [1,]  0 1
#> [2,]  1 0
#> [3,]  1 4
#> [4,]  0 4
#> [5,]  3 9
#> [6,] 10 8
#> > drop(get_counts(i, "f"))
#>  [1]   1   0   4   4   9   8   8   9  13   7  15  12  11  18  35  38  45  45  57
#> [20]  65  74 115 123 167 156 160 135 135 117 129 111  91  75  79  69  67  62  62
#> [39]  41  47  63  49  42  44  36  40  38  38  28  29  34  29  18  27  18  10