Subsetting 'incidence' objects

Two functions can be used to subset incidence objects. The function subset permits to retain dates within a specified range and, optionally, specific groups. The operator "[" can be used as for matrices, using the syntax x[i,j] where 'i' is a subset of dates, and 'j' is a subset of groups.

# S3 method for class 'incidence'
subset(x, ..., from = min(x$dates), to = max(x$dates), groups = TRUE)

# S3 method for class 'incidence'
x[i, j]

Arguments

x

An incidence object, generated by the function incidence().

...

Further arguments passed to other methods (not used).

from

The starting date; data strictly before this date are discarded.

to

The ending date; data strictly after this date are discarded.

groups

(optional) The groups to retained, indicated as subsets of the columns of x$counts.

i

a subset of dates to retain

j

a subset of groups to retain

See also

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

Author

Thibaut Jombart thibautjombart@gmail.com

Examples

## example using simulated dataset
if(require(outbreaks)) { withAutoprint({
  onset <- ebola_sim$linelist$date_of_onset

  ## weekly incidence
  inc <- incidence(onset, interval = 7)
  inc
  inc[1:10] # first 10 weeks
  plot(inc[1:10])
  inc[-c(11:15)] # remove weeks 11-15
  plot(inc[-c(11:15)])
})}
#> > onset <- ebola_sim$linelist$date_of_onset
#> > inc <- incidence(onset, interval = 7)
#> > inc
#> <incidence object>
#> [5888 cases from days 2014-04-07 to 2015-04-27]
#> [5888 cases from ISO weeks 2014-W15 to 2015-W18]
#> 
#> $counts: matrix with 56 rows and 1 columns
#> $n: 5888 cases in total
#> $dates: 56 dates marking the left-side of bins
#> $interval: 7 days
#> $timespan: 386 days
#> $cumulative: FALSE
#> 
#> > inc[1:10]
#> <incidence object>
#> [121 cases from days 2014-04-07 to 2014-06-09]
#> [121 cases from ISO weeks 2014-W15 to 2014-W24]
#> 
#> $counts: matrix with 10 rows and 1 columns
#> $n: 121 cases in total
#> $dates: 10 dates marking the left-side of bins
#> $interval: 7 days
#> $timespan: 64 days
#> $cumulative: FALSE
#> 
#> > plot(inc[1:10])

#> > inc[-c(11:15)]
#> <incidence object>
#> [5701 cases from days 2014-04-07 to 2015-04-27]
#> [5701 cases from ISO weeks 2014-W15 to 2015-W18]
#> 
#> $counts: matrix with 51 rows and 1 columns
#> $n: 5701 cases in total
#> $dates: 51 dates marking the left-side of bins
#> $interval: 7 days
#> $timespan: 386 days
#> $cumulative: FALSE
#> 
#> > plot(inc[-c(11:15)])