![[Stable]](figures/lifecycle-stable.svg)
extract_tto() collects
all available time to onsets for a set of drug-adr pairs.
Arguments
- .data
A
linkdata.table. Seelink_.- adr_s
A character string. The name of the adr column. (see details)
- drug_s
A character string. The name of the drug column. (see details)
- tto_time_range
Incertitude range of Time to onset, in days. Defaults to 1 as recommended by umc
Value
A data.frame with
All available time to onsets for this combination (column
tto_max).adr_sanddrug_s, same as input.UMCReportId, the unique identifier of the case.
Details
Extraction of (maximum available) time between drug initiation
and event onset. This runs at the drug-adr pair level.
You will need a link data.table, see link_, on which
you have added drugs and adrs with add_drug() and add_adr().
Uppsala Monitoring Centre recommends to use only cases where the incertitude
on time to onset is less than 1 day. You can change this with tto_time_range.
You might want to use desc_tto() to obtain summary statistics of
time to onset, but extract_tto() is useful to get the raw data and plot it,
for instance with ggplot2.
Examples
link_ <-
link_ |>
add_drug(
d_code = ex_$d_groups_drecno,
drug_data = drug_
) |>
add_adr(
a_code = ex_$a_llt,
adr_data = adr_
)
#> ℹ `.data` detected as `link` table.
#> ℹ `.data` detected as `link` table.
extract_tto(.data = link_,
adr_s = "a_colitis",
drug_s = "pd1")
#> UMCReportId tto_max adr_s drug_s
#> 1 108846594 205 a_colitis pd1
#> 2 73027866 175 a_colitis pd1
#> 3 87966085 36 a_colitis pd1
#> 4 88371745 740 a_colitis pd1
#> 5 138643678 379 a_colitis pd1
#> 6 39936658 99 a_colitis pd1
#> 7 142848064 1207 a_colitis pd1
#> 8 140765885 5 a_colitis pd1
#> 9 11372968 62 a_colitis pd1
#> 10 24328271 88 a_colitis pd1
#> 11 63102481 57 a_colitis pd1
#> 12 34209616 8 a_colitis pd1
#> 13 21293261 59 a_colitis pd1
#> 14 81010378 27 a_colitis pd1
#> 15 67492542 78 a_colitis pd1
#> 16 58329610 541 a_colitis pd1
#> 17 109965210 1 a_colitis pd1
#> 18 84968360 4 a_colitis pd1
#> 19 37122185 11 a_colitis pd1
#> 20 77761414 3 a_colitis pd1
#> 21 26302027 137 a_colitis pd1
#> 22 38269558 393 a_colitis pd1
#> 23 85691581 490 a_colitis pd1
#> 24 112663221 7 a_colitis pd1
#> 25 610256 52 a_colitis pd1
#> 26 109716692 37 a_colitis pd1
#> 27 56986472 47 a_colitis pd1
#> 28 6112110 44 a_colitis pd1
#> 29 76401465 390 a_colitis pd1
#> 30 125056616 18 a_colitis pd1
#> 31 33942691 36 a_colitis pd1
#> 32 63782466 41 a_colitis pd1
#> 33 1261650 286 a_colitis pd1
#> 34 85774959 254 a_colitis pd1
#> 35 133088642 23 a_colitis pd1
#> 36 143881598 113 a_colitis pd1
#> 37 79620779 85 a_colitis pd1
#> 38 33962643 26 a_colitis pd1
#> 39 95759941 59 a_colitis pd1
extract_tto(.data = link_,
adr_s = c("a_colitis", "a_pneumonitis"),
drug_s = c("pd1", "ctla4"))
#> UMCReportId tto_max adr_s drug_s
#> 1 108846594 205 a_colitis pd1
#> 2 73027866 175 a_colitis pd1
#> 3 87966085 36 a_colitis pd1
#> 4 88371745 740 a_colitis pd1
#> 5 138643678 379 a_colitis pd1
#> 6 39936658 99 a_colitis pd1
#> 7 142848064 1207 a_colitis pd1
#> 8 140765885 5 a_colitis pd1
#> 9 11372968 62 a_colitis pd1
#> 10 24328271 88 a_colitis pd1
#> 11 63102481 57 a_colitis pd1
#> 12 34209616 8 a_colitis pd1
#> 13 21293261 59 a_colitis pd1
#> 14 81010378 27 a_colitis pd1
#> 15 67492542 78 a_colitis pd1
#> 16 58329610 541 a_colitis pd1
#> 17 109965210 1 a_colitis pd1
#> 18 84968360 4 a_colitis pd1
#> 19 37122185 11 a_colitis pd1
#> 20 77761414 3 a_colitis pd1
#> 21 26302027 137 a_colitis pd1
#> 22 38269558 393 a_colitis pd1
#> 23 85691581 490 a_colitis pd1
#> 24 112663221 7 a_colitis pd1
#> 25 610256 52 a_colitis pd1
#> 26 109716692 37 a_colitis pd1
#> 27 56986472 47 a_colitis pd1
#> 28 6112110 44 a_colitis pd1
#> 29 76401465 390 a_colitis pd1
#> 30 125056616 18 a_colitis pd1
#> 31 33942691 36 a_colitis pd1
#> 32 63782466 41 a_colitis pd1
#> 33 1261650 286 a_colitis pd1
#> 34 85774959 254 a_colitis pd1
#> 35 133088642 23 a_colitis pd1
#> 36 143881598 113 a_colitis pd1
#> 37 79620779 85 a_colitis pd1
#> 38 33962643 26 a_colitis pd1
#> 39 95759941 59 a_colitis pd1
#> 40 2626997 107 a_colitis ctla4
#> 41 140765885 5 a_colitis ctla4
#> 42 11372968 15 a_colitis ctla4
#> 43 12728402 76 a_colitis ctla4
#> 44 112663221 7 a_colitis ctla4
#> 45 109716692 37 a_colitis ctla4
#> 46 56986472 47 a_colitis ctla4
#> 47 125056616 18 a_colitis ctla4
#> 48 143881598 113 a_colitis ctla4
#> 49 95759941 59 a_colitis ctla4
#> 50 51868324 602 a_pneumonitis pd1
#> 51 141780031 43 a_pneumonitis pd1
#> 52 38542967 105 a_pneumonitis pd1
#> 53 46205163 90 a_pneumonitis pd1
#> 54 143915039 1050 a_pneumonitis pd1
#> 55 8037093 58 a_pneumonitis pd1
#> 56 51289899 6 a_pneumonitis pd1
#> 57 5827498 150 a_pneumonitis pd1
#> 58 109804882 32 a_pneumonitis pd1
#> 59 60410606 52 a_pneumonitis pd1
#> 60 28278690 470 a_pneumonitis pd1
#> 61 59468437 33 a_pneumonitis pd1
#> 62 68574533 49 a_pneumonitis pd1
#> 63 105702324 29 a_pneumonitis pd1
#> 64 55788241 125 a_pneumonitis pd1
#> 65 120048321 8 a_pneumonitis pd1
#> 66 91145758 21 a_pneumonitis pd1
#> 67 42289125 136 a_pneumonitis pd1
#> 68 49019818 77 a_pneumonitis pd1
#> 69 119065329 34 a_pneumonitis pd1
#> 70 11932941 58 a_pneumonitis pd1
#> 71 106102063 65 a_pneumonitis pd1
#> 72 82344156 52 a_pneumonitis pd1
#> 73 40884461 23 a_pneumonitis pd1
#> 74 63322168 523 a_pneumonitis pd1
#> 75 100871963 43 a_pneumonitis pd1
#> 76 140323054 18 a_pneumonitis pd1
#> 77 147304194 117 a_pneumonitis pd1
#> 78 12314086 69 a_pneumonitis pd1
#> 79 143881598 181 a_pneumonitis pd1
#> 80 3460652 138 a_pneumonitis pd1
#> 81 27273063 25 a_pneumonitis pd1
#> 82 84451753 1 a_pneumonitis pd1
#> 83 79620779 511 a_pneumonitis pd1
#> 84 103773756 52 a_pneumonitis pd1
#> 85 123322212 0 a_pneumonitis pd1
#> 86 135108556 183 a_pneumonitis pd1
#> 87 90067921 101 a_pneumonitis pd1
#> 88 95759941 73 a_pneumonitis pd1
#> 89 76017998 72 a_pneumonitis pd1
#> 90 38542967 106 a_pneumonitis ctla4
#> 91 46205163 90 a_pneumonitis ctla4
#> 92 82344156 52 a_pneumonitis ctla4
#> 93 40884461 23 a_pneumonitis ctla4
#> 94 12314086 69 a_pneumonitis ctla4
#> 95 143881598 181 a_pneumonitis ctla4
#> 96 103773756 52 a_pneumonitis ctla4
#> 97 95759941 73 a_pneumonitis ctla4