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Add Term1 and Term2 Example

Source: vignettes/add-term1-term2-example.Rmd
add-term1-term2-example.Rmd

Overview

The objective of this tutorial is to explain how users can add term1 and term2 parameters in the metalite.ae package to customize title and column labels for adverse event analyses. These parameters allow users to specify additional descriptive text that appears in generated tables and reports, providing more detail about the type of adverse events being analyzed.

Load the metalite.ae package

Create the example metadata object containing adverse event data and analysis definitions
- Verify that the AEOSI (Adverse Events of Special Interest) variable exists in the observation dataset
- Check if AEOSI exists

meta <- meta_ae_example()
"AEOSI" %in% names(meta$data_observation)

Result: FALSE → AEOSI variable is not present in the dataset
(TRUE would indicate that AEOSI exists in the original data).

Since AEOSI is missing in the current ADAE dataset, we need to create it manually:
 - Access the observation data from the meta object for modification
 - Define adverse events of special interest (e.g., DIARRHOEA, NAUSEA, VOMITING, HEADACHE, DIZZINESS, SOMNOLENCE, TREMOR)
 - Derive the AEOSI flag variable using conditional logic
 - Update the meta object by replacing its observation data with the modified dataset that now includes AEOSI

adae_modified <- meta$data_observation

special_interest_terms <- c(
  "DIARRHOEA", "NAUSEA", "VOMITING", "HEADACHE",
  "DIZZINESS", "SOMNOLENCE", "TREMOR"
)

adae_modified$AEOSI <- ifelse(
  adae_modified$AEDECOD %in% special_interest_terms,
  "Y",
  "N"
)

meta$data_observation <- adae_modified

Verify that the AEOSI variable now exists and count the number of records flagged as “Y”.

"AEOSI" %in% names(meta$data_observation)
#> [1] TRUE
table(meta$data_observation$AEOSI)
#> 
#>    N    Y 
#> 1069  122

Next, verify whether term1 and term2 values are already assigned in the meta_ae_example() metadata.
Extract the parameter mapping for aeosi0rel and review the existing values of term1 and term2.

param_info <- metalite::collect_adam_mapping(meta, "aeosi0rel")
print(param_info$term1)
#> NULL
print(param_info$term2)
#> NULL

The current parameter mapping shows that both term1 and term2 are NULL.
To proceed, we need to update the analysis plan and parameter definitions:
- Create a new plan that includes aeosi0rel under the ae_specific analysis parameters

new_plan <- plan(
  analysis = "ae_summary", population = "apat",
  observation = c("wk12", "wk24"), parameter = "any;rel;ser"
) |>
  add_plan(
    analysis = "ae_specific", population = "apat",
    observation = c("wk12", "wk24"),
    parameter = c("any", "aeosi", "rel", "ser", "dtc0rel", "aeosi0rel")
  ) |>
  add_plan(
    analysis = "ae_listing", population = "apat",
    observation = c("wk12", "wk24"), parameter = c("any", "rel", "ser")
  ) |>
  add_plan(
    analysis = "ae_exp_adj", population = "apat",
    observation = c("wk12", "wk24"), parameter = "any;rel;ser"
  )

Update the meta object with the new plan and define the aeosi0rel parameter

meta <- meta |>
  define_plan(plan = new_plan) |>
  define_parameter(
    name = "aeosi0rel",
    subset = quote(AEOSI == "Y"),
    var = "AEDECOD",
    soc = "AEBODSYS",
    term1 = " ",
    term2 = " ",
    label = "adverse events of special interest"
  ) |>
  meta_build()

Note: term1 and term2 are intentionally set to blank spaces to show difference between missing vs non missing term1 and term2 This serves as the “before” example, which will later be compared against a version with fully specified terms.

param_info <- metalite::collect_adam_mapping(meta, "aeosi0rel")
print(param_info$term1)
#> [1] " "
print(param_info$term2)
#> [1] " "

Analysis preparation

The function prepare_ae_specific() is used to create a dataset for AE summary analysis 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.

outdata <- prepare_ae_specific(
  meta,
  population = "apat",
  observation = "wk12",
  parameter = "aeosi0rel"
)

RTF tables

The last step is to prepare the RTF table using tlf_ae_specific().

outdata |>
  format_ae_specific() |>
  tlf_ae_specific(
    meddra_version = "24.0",
    source = "Source:  [CDISCpilot: adam-adsl; adae]",
    analysis = "ae_specific", # Provide analysis type defined in meta$analysis,
    orientation = "landscape",
    col_rel_width = c(6, rep(1, 8)),
    path_outtable = "rtf/ae0specific0aeosi0missing.rtf"
  )

We can observe in the current table that term1 and term2 are absent from both the title and the row/column labels. In the next step, we will demonstrate how to incorporate term1 and term2 into any output table based on our predefined keywords.

Update the meta object with the new plan and redefine the aeosi0rel parameter.
This time, we give term1 and term2 meaningful values instead of leaving them blank.
This is the “after” example, which we will compare with the earlier version to see how proper values change the table titles and row/column labels.

new_plan <- plan(
  analysis = "ae_summary", population = "apat",
  observation = c("wk12", "wk24"), parameter = "any;rel;ser"
) |>
  add_plan(
    analysis = "ae_specific", population = "apat",
    observation = c("wk12", "wk24"),
    parameter = c("any", "aeosi", "rel", "ser", "dtc0rel", "aeosi0rel")
  ) |>
  add_plan(
    analysis = "ae_listing", population = "apat",
    observation = c("wk12", "wk24"), parameter = c("any", "rel", "ser")
  ) |>
  add_plan(
    analysis = "ae_exp_adj", population = "apat",
    observation = c("wk12", "wk24"), parameter = "any;rel;ser"
  )
# Update the meta object with new plan
meta <- meta |>
  define_plan(plan = new_plan) |>
  define_parameter(
    name = "aeosi0rel",
    subset = quote(AEOSI == "Y" & AEREL == "Y"),
    var = "AEDECOD",
    soc = "AEBODSYS",
    term1 = " Drug-Related",
    term2 = " of Special Interest",
    label = "adverse events of special interest"
  ) |>
  meta_build()

Retrieve the parameter mapping for aeosi0rel and display term1 and term2 to confirm they match the values defined in the previous step.

param_info <- metalite::collect_adam_mapping(meta, "aeosi0rel")
print(param_info$term1)
#> [1] " Drug-Related"
print(param_info$term2)
#> [1] " of Special Interest"

Analysis preparation

Use the prepare_ae_specific() function to build the dataset for AE summary analysis.
This function applies the predefined keywords in meta and produces an outdata object, which contains the raw datasets needed for analysis and reporting.

outdata <- prepare_ae_specific(
  meta,
  population = "apat",
  observation = "wk12",
  parameter = "aeosi0rel"
)

RTF tables

The last step is to prepare the RTF table using tlf_ae_summary().

outdata |>
  format_ae_specific() |>
  tlf_ae_specific(
    meddra_version = "24.0",
    source = "Source:  [CDISCpilot: adam-adsl; adae]",
    analysis = "ae_specific", # Provide analysis type defined in meta$analysis,
    orientation = "landscape",
    col_rel_width = c(6, rep(1, 8)),
    path_outtable = "rtf/ae0specific0aeosi0rel.rtf"
  )

The generated table now includes term1 and term2 in both the title and row labels, showing the effect of assigning proper values compared to the earlier version where these fields were left blank.

  • In the title: term1 appears as “Drug Related” and term2 is appended as “of Special Interest”.
  • In the row labels:
    • “with one or more drug-related adverse events of special interest”
    • “with no drug-related adverse events of special interest”