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 incidence
subset(x, ..., from = min(x$dates),
  to = max(x$dates), groups = TRUE)

# S3 method for 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.

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)])