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$name <- valueArguments
- x
a
linelistobject- i
a vector of
integerorlogicalto subset the rows of thelinelist- j
a vector of
character,integer, orlogicalto subset the columns of thelinelist- drop
a
logicalindicating if, when a single column is selected, thedata.frameclass should be dropped to return a simple vector, in which case thelinelistclass is lost as well; defaults toFALSE- value
the replacement to be used for the entries identified in
x- name
a literal character string or a name (possibly backtick quoted). For extraction, this is normally (see under ‘Environments’) partially matched to the
namesof the object.
See also
lost_tags_action()to set the behaviour to adopt when tags are lost through subsetting; default is to issue a warningget_lost_tags_action()to check the current the behaviour
Examples
if (require(outbreaks) && require(dplyr)) {
## create a linelist
x <- measles_hagelloch_1861 |>
make_linelist(
id = "case_ID",
date_onset = "date_of_prodrome",
age = "age",
gender = "gender"
) |>
mutate(result = if_else(is.na(date_of_death), "survived", "died")) |>
set_tags(outcome = "result") |>
rename(identifier = case_ID)
x
## dangerous removal of a tagged column setting it to NULL issues a warning
x[, 1] <- NULL
x
x[[2]] <- NULL
x
x$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