Overview
The objective of this tutorial is to generate a production-ready adverse events (AE) listing.
The AE listing offers comprehensive information on the desired adverse events. There are two essential functions for constructing AE listing tables with metalite.ae:
-
prepare_ae_listing(): prepare AE listing datasets. -
tlf_ae_listing(): transfer output datasets to RTF files.
An example output:
Example data
Within metalite.ae, we utilized the ADSL and ADAE datasets from the metalite package to create an illustrative dataset. The metadata structure remains consistent across all analysis examples within metalite.ae. Additional information can be accessed on the metalite package website.
meta <- meta_ae_example()Click to show the output
meta
#> ADaM metadata:
#> .$data_population Population data with 254 subjects
#> .$data_observation Observation data with 1191 records
#> .$plan Analysis plan with 18 plans
#>
#>
#> Analysis population type:
#> name id group var subset label
#> 1 'apat' 'USUBJID' 'TRTA' SAFFL == 'Y' 'All Participants as Treated'
#>
#>
#> Analysis observation type:
#> name id group var subset label
#> 1 'wk12' 'USUBJID' 'TRTA' SAFFL == 'Y' 'Weeks 0 to 12'
#> 2 'wk24' 'USUBJID' 'TRTA' AOCC01FL == 'Y' 'Weeks 0 to 24'
#>
#>
#> Analysis parameter type:
#> name label
#> 1 'rel' 'drug-related adverse events'
#> 2 'aeosi' 'adverse events of special interest'
#> 3 'any' 'any adverse events'
#> 4 'ser' 'serious adverse events'
#> subset
#> 1 AEREL %in% c('POSSIBLE', 'PROBABLE')
#> 2 AEOSI == 'Y'
#> 3
#> 4 AESER == 'Y'
#>
#>
#> Analysis function:
#> name label
#> 1 'ae_summary' 'Table: adverse event summary'
#> 2 'ae_listing' 'Listing: adverse event'
#> 3 'ae_exp_adj' 'Exposure Adjusted Incident Rate'
#> 4 'ae_specific' 'Table: specific adverse event'Analysis preparation
The function prepare_ae_listing() is used to create a
dataset for AE listing by utilizing predefined keywords specified in the
example data meta.
The resulting output of the function is an outdata
object, which comprises a collection of raw datasets for analysis and
reporting.
tbl <- prepare_ae_listing(
meta,
analysis = "ae_listing",
population = "apat",
observation = "wk12",
parameter = "ser"
)
head(tbl$tbl)
#> USUBJID ASTDY AEDECOD duration
#> 689 01-709-1424 5 SYNCOPE 1 Day
#> 1131 01-718-1170 27 SYNCOPE 2 Day
#> 1173 01-718-1371 38 PARTIAL SEIZURES WITH SECONDARY GENERALISATION 4 Day
#> AESEV AESER related action_taken outcome TRTA
#> 689 MODERATE Y Possible None Resolved High Dose
#> 1131 SEVERE Y Probable None Resolved Low Dose
#> 1173 SEVERE Y None None Resolved High Dose
#> subline
#> 689 Subject ID = 01-709-1424, Gender = M, Race = WHITE, AGE = 77 Years, TRT = High Dose
#> 1131 Subject ID = 01-718-1170, Gender = F, Race = WHITE, AGE = 80 Years, TRT = Low Dose
#> 1173 Subject ID = 01-718-1371, Gender = F, Race = WHITE, AGE = 69 Years, TRT = High Dose
head(tbl$col_name)
#> USUBJID ASTDY
#> "Unique Subject Identifier" "Analysis Start Relative Day"
#> AEDECOD duration
#> "Adverse Event" "Duration"
#> AESEV AESER
#> "Intensity" "Serious"RTF tables
The last step is to prepare the RTF table using
tlf_ae_listing().
footnote <- c(
"Related: Investigator-assessed relationship of the adverse event to study medication. Y = RELATED, N = NOT RELATED",
"Action Taken: Discontinued = DRUG WITHDRAWN, Interrupted = DRUG INTERRUPTED, Reduced = DOSE REDUCED, Increased = DOSE INCREASED, None = DOSE NOT CHANGED, N/A = NOT APPLICABLE.",
"Outcome: Resolved = RECOVERED/RESOLVED, Resolving = RECOVERING/RESOLVING, Sequelae = RECOVERED/RESOLVED WITH SEQUELAE, Not resolved = NOT RECOVERED/NOT RESOLVED.",
"Adverse event terms are from MedDRA Version 25.0."
)
tbl |> tlf_ae_listing(
footnotes = footnote,
orientation = "portrait",
source = "Source: [CDISCpilot: adam-adsl; adae]",
analysis = "ae_listing", # Provide analysis type defined in meta$analysis
path_outtable = "rtf/ae0listing0ser0wk12.rtf",
path_outdata = NULL
)
#> The output is saved in/home/runner/work/metalite.ae/metalite.ae/vignettes/rtf/ae0listing0ser0wk12.rtf