The []
and [[]]
operators for linelist
objects behaves like for regular
data.frame
or tibble
, but check that tagged variables are not lost, and
takes the appropriate action if this is the case (warning, error, or ignore,
depending on the general option set via lost_tags_action()
) .
Usage
# S3 method for class 'linelist'
x[i, j, drop = FALSE]
# S3 method for class 'linelist'
x[i, j] <- value
# S3 method for class 'linelist'
x[[i, j]] <- value
# S3 method for class 'linelist'
x$name <- value
Arguments
- x
a
linelist
object- i
a vector of
integer
orlogical
to subset the rows of thelinelist
- j
a vector of
character
,integer
, orlogical
to subset the columns of thelinelist
- drop
a
logical
indicating if, when a single column is selected, thedata.frame
class should be dropped to return a simple vector, in which case thelinelist
class is lost as well; defaults toFALSE
- value
the replacement to be used for the entries identified in
x
- name
a literal character string or a name (possibly backtick quoted). For extraction, this is normally (see under ‘Environments’) partially matched to the
names
of the object.
See also
lost_tags_action()
to set the behaviour to adopt when tags are lost through subsetting; default is to issue a warningget_lost_tags_action()
to check the current the behaviour
Examples
if (require(outbreaks) && require(dplyr)) {
## create a linelist
x <- measles_hagelloch_1861 |>
make_linelist(
id = "case_ID",
date_onset = "date_of_prodrome",
age = "age",
gender = "gender"
) |>
mutate(result = if_else(is.na(date_of_death), "survived", "died")) |>
set_tags(outcome = "result") |>
rename(identifier = case_ID)
x
## dangerous removal of a tagged column setting it to NULL issues a warning
x[, 1] <- NULL
x
x[[2]] <- NULL
x
x$age <- NULL
x
}
#> Warning: The following tags have lost their variable:
#> id:identifier
#> Warning: The following tags have lost their variable:
#> date_onset:date_of_prodrome
#> Warning: The following tags have lost their variable:
#> age:age
#>
#> // linelist object
#> infector date_of_rash date_of_death gender family_ID class complications
#> 1 45 1861-11-25 <NA> f 41 1 yes
#> 2 45 1861-11-27 <NA> f 41 1 yes
#> 3 172 1861-12-02 <NA> f 41 0 yes
#> 4 180 1861-11-28 <NA> m 61 2 yes
#> 5 45 1861-11-27 <NA> f 42 1 yes
#> 6 180 1861-11-29 <NA> m 42 2 yes
#> 7 42 1861-11-28 <NA> m 26 0 yes
#> 8 45 1861-11-26 <NA> m 44 1 yes
#> 9 182 1861-11-30 <NA> m 44 2 yes
#> 10 45 1861-11-25 <NA> f 29 1 yes
#> 11 182 1861-11-30 <NA> f 27 2 yes
#> 12 45 1861-11-25 <NA> f 32 1 yes
#> 13 12 1861-12-05 <NA> m 32 2 yes
#> 14 181 1861-11-29 <NA> f 22 2 yes
#> 15 45 1861-11-29 <NA> m 22 1 yes
#> 16 181 1861-11-25 <NA> f 43 2 yes
#> 17 181 1861-11-25 <NA> f 43 2 yes
#> 18 175 1861-11-27 <NA> f 43 0 yes
#> 19 181 1861-11-24 <NA> m 11 2 yes
#> 20 181 1861-11-27 <NA> m 11 2 yes
#> 21 181 1861-11-29 <NA> f 11 2 yes
#> 22 45 1861-11-25 <NA> f 35 1 yes
#> 23 45 1861-11-25 <NA> f 35 1 yes
#> 24 22 1861-12-04 <NA> m 35 0 yes
#> 25 22 1861-12-04 <NA> f 35 2 yes
#> 26 45 1861-11-27 <NA> m 67 1 yes
#> 27 10 1861-12-02 1861-12-14 m 29 0 yes
#> 28 180 1861-11-30 <NA> f 65 2 yes
#> 29 31 1861-12-02 <NA> m 15 2 yes
#> 30 45 1861-11-29 <NA> f 15 2 yes
#> 31 45 1861-11-24 <NA> f 15 1 yes
#> 32 45 1861-11-24 <NA> m 15 1 yes
#> 33 45 1861-11-26 <NA> f 1 1 yes
#> 34 181 1861-11-26 <NA> m 1 2 yes
#> 35 182 1861-11-30 <NA> f 10 2 yes
#> 36 34 1861-12-05 <NA> m 46 2 yes
#> 37 182 1861-12-02 <NA> m 46 2 yes
#> 38 17 1861-12-05 <NA> <NA> 54 2 yes
#> 39 45 1861-11-26 <NA> m 5 1 yes
#> 40 93 1861-12-07 <NA> m 36 2 yes
#> 41 180 1861-11-29 <NA> m 59 2 yes
#> 42 178 1861-11-19 <NA> f 33 0 yes
#> 43 42 1861-11-30 <NA> m 33 0 yes
#> 44 45 1861-11-24 <NA> m 45 1 yes
#> 45 184 1861-11-13 <NA> m 48 1 yes
#> 46 45 1861-11-27 <NA> m 48 2 yes
#> 47 45 1861-11-27 <NA> f 48 2 yes
#> 48 10 1861-12-05 <NA> f 29 0 yes
#> 49 17 1861-12-06 <NA> m 49 2 yes
#> 50 8 1861-12-06 <NA> f 44 0 yes
#> 51 31 1861-12-05 <NA> m 15 0 yes
#> 52 17 1861-12-05 1861-12-12 m 43 2 yes
#> 53 17 1861-12-04 <NA> m 43 0 yes
#> 54 17 1861-12-05 1861-12-15 m 43 0 yes
#> 55 17 1861-12-05 <NA> f 43 2 yes
#> 56 45 1861-11-29 <NA> m 20 1 yes
#> 57 56 1861-12-05 <NA> m 20 0 yes
#> 58 45 1861-11-26 <NA> m 24 1 yes
#> 59 58 1861-12-04 <NA> f 24 2 yes
#> 60 58 1861-12-06 1861-12-12 m 24 0 yes
#> 61 186 1861-12-03 <NA> f 8 0 yes
#> 62 11 1861-12-06 <NA> m 8 2 yes
#> 63 19 1861-12-08 <NA> m 8 2 yes
#> 64 45 1861-11-27 <NA> m 30 1 yes
#> 65 64 1861-12-06 <NA> m 30 0 yes
#> 66 64 1861-12-05 <NA> f 30 0 yes
#> 67 11 1861-12-07 <NA> f 55 2 yes
#> 68 179 1861-12-02 <NA> f 16 0 yes
#> 69 54 1861-12-17 <NA> m 63 0 yes
#> 70 180 1861-12-03 <NA> m 21 2 yes
#> 71 10 1861-12-05 <NA> f 29 2 yes
#> 72 12 1861-12-06 <NA> f 32 2 yes
#> 73 180 1861-12-05 <NA> f 47 2 yes
#> 74 45 1861-11-26 <NA> f 23 1 yes
#> 75 74 1861-12-05 <NA> m 23 2 yes
#> 76 5 1861-12-06 <NA> m 42 0 yes
#> 77 180 1861-11-27 <NA> f 18 1 yes
#> 78 181 1861-11-26 <NA> f 18 2 yes
#> 79 179 1861-12-05 <NA> f 18 0 yes
#> 80 78 1861-12-05 1861-12-12 m 18 2 yes
#> 81 39 1861-12-04 <NA> m 5 2 yes
#> 82 45 1861-11-26 <NA> m 21 1 yes
#> 83 82 1861-12-05 <NA> f 21 2 yes
#> 84 82 1861-12-04 <NA> m 21 0 yes
#> 85 44 1861-12-05 <NA> f 45 0 yes
#> 86 1 1861-12-05 <NA> f 41 0 yes
#> 87 47 1861-12-07 <NA> f 60 2 yes
#> 88 47 1861-12-07 <NA> f 60 2 yes
#> 89 12 1861-12-05 <NA> f 32 0 yes
#> 90 93 1861-12-05 <NA> m 36 2 yes
#> 91 93 1861-12-05 <NA> f 36 0 yes
#> 92 93 1861-12-07 <NA> f 36 0 yes
#> 93 45 1861-11-26 <NA> m 36 1 yes
#> 94 183 1861-12-03 <NA> f 10 0 yes
#> 95 10 1861-12-07 <NA> m 29 0 yes
#> 96 97 1861-12-04 <NA> m 28 0 yes
#> 97 45 1861-11-25 <NA> m 28 1 yes
#> 98 64 1861-12-12 1861-12-17 m 27 0 yes
#> 99 11 1861-12-10 <NA> m 27 0 yes
#> 100 47 1861-12-07 <NA> m 69 2 yes
#> 101 7 1861-12-06 <NA> f 26 0 yes
#> 102 21 1861-12-07 <NA> m 68 2 yes
#> 103 37 1861-12-07 <NA> <NA> 54 2 yes
#> 104 58 1861-12-06 <NA> m 24 0 yes
#> 105 74 1861-12-08 <NA> m 23 0 yes
#> 106 42 1861-11-26 <NA> m 34 0 yes
#> 107 19 1861-12-07 <NA> f 34 2 yes
#> 108 106 1861-12-06 <NA> m 34 0 yes
#> 109 12 1861-12-07 <NA> f 32 0 yes
#> 110 18 1861-12-06 <NA> m 49 0 yes
#> 111 34 1861-12-05 <NA> m 2 2 yes
#> 112 21 1861-12-08 <NA> m 2 2 yes
#> 113 31 1861-12-07 <NA> f 15 0 yes
#> 114 78 1861-12-05 <NA> <NA> 52 2 yes
#> 115 16 1861-12-07 <NA> f 66 2 yes
#> 116 45 1861-11-25 <NA> m 40 1 yes
#> 117 116 1861-12-06 <NA> m 40 2 yes
#> 118 116 1861-12-06 <NA> f 40 0 yes
#> 119 116 1861-12-08 <NA> f 40 0 yes
#> 120 7 1861-12-08 <NA> m 26 0 yes
#> 121 11 1861-12-08 <NA> m 50 2 yes
#> 122 188 1861-12-10 <NA> f 50 0 yes
#> 123 7 1861-12-07 1861-12-13 f 25 0 yes
#> 124 7 1861-12-08 <NA> m 7 0 yes
#> 125 7 1861-12-09 <NA> f 7 0 yes
#> 126 37 1861-12-09 <NA> <NA> 54 0 yes
#> 127 106 1861-12-09 1861-12-15 m 34 0 yes
#> 128 7 1861-12-05 <NA> m 6 0 yes
#> 129 7 1861-12-07 <NA> f 6 0 yes
#> 130 56 1861-12-06 <NA> f 20 2 yes
#> 131 56 1861-12-06 <NA> m 20 0 yes
#> 132 14 1861-12-07 <NA> m 22 2 yes
#> 133 18 1861-12-08 <NA> f 53 0 yes
#> 134 78 1861-12-06 <NA> m 18 2 yes
#> 135 79 1861-12-07 <NA> m 18 0 yes
#> 136 17 1861-12-07 <NA> f 12 2 yes
#> 137 16 1861-12-06 <NA> f 12 2 yes
#> 138 34 1861-12-05 <NA> <NA> 3 2 yes
#> 139 4 1861-12-11 <NA> <NA> 3 2 yes
#> 140 6 1861-12-10 <NA> <NA> 58 0 yes
#> 141 NA 1862-01-27 <NA> f 50 0 yes
#> 142 145 1861-12-08 1861-12-09 m 39 0 yes
#> 143 145 1861-12-08 <NA> f 39 2 yes
#> 144 145 1861-12-08 <NA> m 39 0 yes
#> 145 45 1861-11-27 <NA> f 39 1 yes
#> 146 172 1861-12-07 <NA> f 13 0 yes
#> 147 18 1861-12-07 <NA> f 13 0 yes
#> 148 14 1861-12-07 <NA> f 19 2 yes
#> 149 39 1861-12-09 1861-12-15 m 19 0 yes
#> 150 148 1861-12-15 <NA> m 19 0 yes
#> 151 153 1861-12-11 <NA> f 37 0 yes
#> 152 153 1861-12-08 <NA> f 37 0 yes
#> 153 45 1861-11-27 <NA> f 37 1 yes
#> 154 153 1861-12-04 <NA> f 37 0 yes
#> 155 73 1861-12-13 <NA> m 47 2 yes
#> 156 45 1861-11-24 <NA> m 31 1 yes
#> 157 156 1861-12-07 <NA> f 31 0 yes
#> 158 156 1861-12-07 <NA> f 31 0 yes
#> 159 37 1861-12-13 <NA> f 46 0 yes
#> 160 68 1861-12-13 <NA> f 16 0 yes
#> 161 148 1861-12-16 <NA> f 19 0 yes
#> 162 123 1861-12-16 <NA> f 25 0 yes
#> 163 123 1861-12-16 1861-12-28 f 25 0 yes
#> 164 102 1861-12-15 <NA> m 14 0 yes
#> 165 102 1861-12-19 <NA> m 14 0 yes
#> 166 153 1861-12-07 <NA> m 37 0 yes
#> 167 110 1861-12-18 <NA> m 49 0 yes
#> 168 98 1861-12-15 <NA> m 56 0 yes
#> 169 153 1861-12-07 <NA> m 38 0 yes
#> 170 153 1861-12-10 <NA> m 38 2 yes
#> 171 169 1861-12-17 <NA> m 38 0 yes
#> 172 174 1861-11-21 <NA> f 62 0 yes
#> 173 NA 1861-11-03 <NA> m 9 0 yes
#> 174 NA 1861-11-08 <NA> f 9 0 yes
#> 175 173 1861-11-15 <NA> m 9 0 yes
#> 176 146 1861-12-15 <NA> <NA> 64 0 yes
#> 177 184 1861-11-11 <NA> f 17 1 yes
#> 178 184 1861-11-11 <NA> m 17 0 yes
#> 179 177 1861-11-21 <NA> f 17 1 yes
#> 180 177 1861-11-21 <NA> m 17 2 yes
#> 181 184 1861-11-17 <NA> f 4 2 yes
#> 182 184 1861-11-18 1861-11-18 m 4 2 yes
#> 183 184 1861-11-15 <NA> m 4 0 yes
#> 184 NA 1861-11-06 <NA> <NA> 51 2 yes
#> 185 82 1861-12-07 <NA> m 21 0 yes
#> 186 45 1861-11-26 <NA> <NA> 57 0 yes
#> 187 82 1861-12-11 <NA> m 21 0 yes
#> 188 175 1861-11-27 <NA> <NA> 57 0 yes
#> x_loc y_loc result
#> 1 142.5 100.0 survived
#> 2 142.5 100.0 survived
#> 3 142.5 100.0 survived
#> 4 165.0 102.5 survived
#> 5 145.0 120.0 survived
#> 6 145.0 120.0 survived
#> 7 272.5 147.5 survived
#> 8 97.5 155.0 survived
#> 9 97.5 155.0 survived
#> 10 240.0 75.0 survived
#> 11 270.0 135.0 survived
#> 12 195.0 27.5 survived
#> 13 195.0 27.5 survived
#> 14 227.5 185.0 survived
#> 15 227.5 185.0 survived
#> 16 172.5 172.5 survived
#> 17 172.5 172.5 survived
#> 18 172.5 172.5 survived
#> 19 167.5 5.0 survived
#> 20 167.5 5.0 survived
#> 21 167.5 5.0 survived
#> 22 167.5 5.0 survived
#> 23 167.5 5.0 survived
#> 24 167.5 5.0 survived
#> 25 167.5 5.0 survived
#> 26 7.5 37.5 survived
#> 27 240.0 75.0 died
#> 28 15.0 47.5 survived
#> 29 125.0 187.5 survived
#> 30 125.0 187.5 survived
#> 31 125.0 187.5 survived
#> 32 125.0 187.5 survived
#> 33 125.0 187.5 survived
#> 34 125.0 187.5 survived
#> 35 190.0 115.0 survived
#> 36 280.0 192.5 survived
#> 37 280.0 192.5 survived
#> 38 280.0 192.5 survived
#> 39 227.5 217.5 survived
#> 40 162.5 47.5 survived
#> 41 185.0 80.0 survived
#> 42 170.0 17.5 survived
#> 43 170.0 17.5 survived
#> 44 150.0 15.0 survived
#> 45 75.0 55.0 survived
#> 46 75.0 55.0 survived
#> 47 75.0 55.0 survived
#> 48 240.0 75.0 survived
#> 49 175.0 140.0 survived
#> 50 97.5 155.0 survived
#> 51 125.0 187.5 survived
#> 52 172.5 172.5 died
#> 53 172.5 172.5 survived
#> 54 172.5 172.5 died
#> 55 172.5 172.5 survived
#> 56 265.0 225.0 survived
#> 57 265.0 225.0 survived
#> 58 250.0 210.0 survived
#> 59 250.0 210.0 survived
#> 60 250.0 210.0 died
#> 61 270.0 102.5 survived
#> 62 270.0 102.5 survived
#> 63 270.0 102.5 survived
#> 64 237.5 90.0 survived
#> 65 237.5 90.0 survived
#> 66 237.5 90.0 survived
#> 67 267.5 127.5 survived
#> 68 165.0 192.5 survived
#> 69 150.0 165.0 survived
#> 70 205.0 182.5 survived
#> 71 240.0 75.0 survived
#> 72 195.0 27.5 survived
#> 73 182.5 55.0 survived
#> 74 257.5 195.0 survived
#> 75 257.5 195.0 survived
#> 76 145.0 120.0 survived
#> 77 187.5 240.0 survived
#> 78 187.5 240.0 survived
#> 79 187.5 240.0 survived
#> 80 187.5 240.0 died
#> 81 227.5 217.5 survived
#> 82 205.0 182.5 survived
#> 83 205.0 182.5 survived
#> 84 205.0 182.5 survived
#> 85 150.0 15.0 survived
#> 86 142.5 100.0 survived
#> 87 77.5 42.5 survived
#> 88 77.5 42.5 survived
#> 89 195.0 27.5 survived
#> 90 162.5 47.5 survived
#> 91 162.5 47.5 survived
#> 92 162.5 47.5 survived
#> 93 162.5 47.5 survived
#> 94 190.0 115.0 survived
#> 95 240.0 75.0 survived
#> 96 230.0 120.0 survived
#> 97 230.0 120.0 survived
#> 98 270.0 135.0 died
#> 99 270.0 135.0 survived
#> 100 252.5 150.0 survived
#> 101 272.5 147.5 survived
#> 102 257.5 180.0 survived
#> 103 280.0 192.5 survived
#> 104 250.0 210.0 survived
#> 105 257.5 195.0 survived
#> 106 170.0 17.5 survived
#> 107 170.0 17.5 survived
#> 108 170.0 17.5 survived
#> 109 195.0 27.5 survived
#> 110 175.0 140.0 survived
#> 111 142.5 180.0 survived
#> 112 142.5 180.0 survived
#> 113 125.0 187.5 survived
#> 114 200.0 210.0 survived
#> 115 75.0 20.0 survived
#> 116 127.5 147.5 survived
#> 117 127.5 147.5 survived
#> 118 127.5 147.5 survived
#> 119 127.5 147.5 survived
#> 120 272.5 147.5 survived
#> 121 252.5 150.0 survived
#> 122 252.5 150.0 survived
#> 123 280.0 157.5 died
#> 124 280.0 167.5 survived
#> 125 280.0 167.5 survived
#> 126 280.0 192.5 survived
#> 127 170.0 17.5 died
#> 128 240.0 225.0 survived
#> 129 240.0 225.0 survived
#> 130 265.0 225.0 survived
#> 131 265.0 225.0 survived
#> 132 227.5 185.0 survived
#> 133 227.5 202.5 survived
#> 134 187.5 240.0 survived
#> 135 187.5 240.0 survived
#> 136 97.5 155.0 survived
#> 137 97.5 155.0 survived
#> 138 152.5 182.5 survived
#> 139 152.5 182.5 survived
#> 140 195.0 130.0 survived
#> 141 252.5 150.0 survived
#> 142 135.0 125.0 died
#> 143 135.0 125.0 survived
#> 144 135.0 125.0 survived
#> 145 135.0 125.0 survived
#> 146 72.5 152.5 survived
#> 147 72.5 152.5 survived
#> 148 255.0 230.0 survived
#> 149 255.0 230.0 died
#> 150 255.0 230.0 survived
#> 151 132.5 80.0 survived
#> 152 132.5 80.0 survived
#> 153 132.5 80.0 survived
#> 154 132.5 80.0 survived
#> 155 182.5 55.0 survived
#> 156 182.5 55.0 survived
#> 157 182.5 55.0 survived
#> 158 182.5 55.0 survived
#> 159 280.0 192.5 survived
#> 160 165.0 192.5 survived
#> 161 255.0 230.0 survived
#> 162 280.0 157.5 survived
#> 163 280.0 157.5 died
#> 164 257.5 180.0 survived
#> 165 257.5 180.0 survived
#> 166 132.5 80.0 survived
#> 167 175.0 140.0 survived
#> 168 267.5 127.5 survived
#> 169 132.5 80.0 survived
#> 170 132.5 80.0 survived
#> 171 132.5 80.0 survived
#> 172 185.0 175.0 survived
#> 173 212.5 107.5 survived
#> 174 212.5 107.5 survived
#> 175 212.5 107.5 survived
#> 176 72.5 152.5 survived
#> 177 182.5 200.0 survived
#> 178 182.5 200.0 survived
#> 179 182.5 200.0 survived
#> 180 182.5 200.0 survived
#> 181 182.5 200.0 survived
#> 182 182.5 200.0 died
#> 183 182.5 200.0 survived
#> 184 182.5 200.0 survived
#> 185 205.0 182.5 survived
#> 186 212.5 90.0 survived
#> 187 205.0 182.5 survived
#> 188 212.5 90.0 survived
#>
#> // tags: gender:gender, outcome:result