subset.Rd
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)
x  An incidence object, generated by the function


...  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$counts. 
i  a subset of dates to retain 
j  a subset of groups to retain 
The incidence()
function to generate the 'incidence'
objects.
## example using simulated dataset if(require(outbreaks)) { withAutoprint({ onset < ebola_sim$linelist$date_of_onset ## weekly incidence inc < incidence(onset, interval = 7) inc inc[1:10] # first 10 weeks plot(inc[1:10]) inc[c(11:15)] # remove weeks 1115 plot(inc[c(11:15)]) })}#> > onset < ebola_sim$linelist$date_of_onset #> > inc < incidence(onset, interval = 7) #> > inc #> <incidence object> #> [5888 cases from days 20140407 to 20150427] #> [5888 cases from ISO weeks 2014W15 to 2015W18] #> #> $counts: matrix with 56 rows and 1 columns #> $n: 5888 cases in total #> $dates: 56 dates marking the leftside of bins #> $interval: 7 days #> $timespan: 386 days #> $cumulative: FALSE #> #> > inc[1:10] #> <incidence object> #> [121 cases from days 20140407 to 20140609] #> [121 cases from ISO weeks 2014W15 to 2014W24] #> #> $counts: matrix with 10 rows and 1 columns #> $n: 121 cases in total #> $dates: 10 dates marking the leftside of bins #> $interval: 7 days #> $timespan: 64 days #> $cumulative: FALSE #> #> > plot(inc[1:10])#> > inc[c(11:15)] #> <incidence object> #> [5701 cases from days 20140407 to 20150427] #> [5701 cases from ISO weeks 2014W15 to 2015W18] #> #> $counts: matrix with 51 rows and 1 columns #> $n: 5701 cases in total #> $dates: 51 dates marking the leftside of bins #> $interval: 7 days #> $timespan: 386 days #> $cumulative: FALSE #> #> > plot(inc[c(11:15)])