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Standard components

Source: vignettes/Standard-components.Rmd
Standard-components.Rmd

This vignette serves as a temporary repository of the currently available standard components inside {mighty.component}.

ady: Analysis relative day

type: derivation

Derives the relative day compared to the treatment start date.

Parameters

name description
domain character Name of new domain being created
variable character Name of new variable to create
date character Name of date variable to use

Depends

domain column
{{domain}} {{date}}
{{domain}} TRTSDT

Outputs

  • {{variable}}

Code 

{{domain}} <- {{domain}} |>
  dplyr::mutate(
    {{variable}} = admiral::compute_duration(
      start_date = TRTSDT,
      end_date = {{date}},
      in_unit = "days",
      out_unit = "days",
      add_one = TRUE
    )
  )

aendt: Analysis end date

type: derivation

Derives analysis end date based on (incomplete) dates given as character

Parameters

name description
domain character Name of new domain being created
dtc character Name of date variable

Depends

domain column
{{domain}} {{dtc}}

Outputs

  • AENDT
  • AENDTF

Code 

{{domain}} <- {{domain}} |>
  dplyr::mutate(
    AENDT = admiral::convert_dtc_to_dt(
      dtc = {{dtc}},
      highest_imputation = "M",
      date_imputation = "last"
    ),
    AENDTF = admiral::compute_dtf(
      dtc = {{dtc}},
      dt = AENDT
    )
  )

assign: Assign

type: assigned

Assigns a single value to an entire column.

Parameters

name description
domain character Name of new domain being created
variable character Name of variable to create or modify
value Value to assign to the variable

Depends

domain column

Outputs

  • {{variable}}

Code 

{{domain}} <- {{domain}} |>
  dplyr::mutate(
    {{variable}} = {{{value}}}
  )

astdt: Analysis start date

type: derivation

Derives analysis start date based on (incomplete) dates given as character

Parameters

name description
domain character Name of new domain being created
dtc character Name of date variable

Depends

domain column
{{domain}} {{dtc}}

Outputs

  • ASTDT
  • ASTDTF

Code 

{{domain}} <- {{domain}} |>
  dplyr::mutate(
    ASTDT = admiral::convert_dtc_to_dt(
      dtc = {{dtc}},
      highest_imputation = "M",
      date_imputation = "first"
    ),
    ASTDTF = admiral::compute_dtf(
      dtc = {{dtc}},
      dt = ASTDT
    )
  )

predecessor: Predecessor

type: predecessor

Creates new column(s) based on a predecessor column(s).

Parameters

name description
domain character Name of new domain being created
source character Name of the data set the predecessor is from
variable character Name of variable(s) to use from source
by character name(s) of variable(s) to merge by

Depends

domain column
{{domain}} {{.}}
{{source}} {{.}}
{{source}} {{.}}

Outputs

  • {{.}}

Code 

{{domain}} <- {{domain}} |>
  dplyr::left_join(
    y = dplyr::select({{source}}, {{by}}, {{variable}}),
    by = dplyr::join_by({{by}})
  )

supp_sdtm: Add Supplementary Variable from SDTM

type: predecessor

Add a variable from a supplementary SDTM domain.

Parameters

name description
domain character Name of new domain being created
source character Name of the supplementary data set to use
qnam character Name of qualifier(s) to add from source

Depends

domain column
{{domain}} USUBJID
{{source}} USUBJID
{{source}} IDVAR
{{source}} IDVARVAL
{{source}} QNAM
{{source}} QVAL

Outputs

  • {{.}}

Code 

idvar <- unique({{source}}[["IDVAR"]])
idclass <- class({{domain}}[[idvar]])
idfunc <- get(paste0("as.", idclass))

supp_data <- {{source}} |>
  dplyr::select(USUBJID, IDVAR, IDVARVAL, QNAM, QVAL) |>
  tidyr::pivot_wider(names_from = QNAM, values_from = QVAL) |>
  dplyr::mutate(IDVARVAL = idfunc(IDVARVAL)) |>
  dplyr::select(USUBJID, IDVARVAL, {{qnam}})

{{domain}} <- {{domain}} |>
  dplyr::left_join(
    y = supp_data,
    by = dplyr::join_by(USUBJID, !!idvar == IDVARVAL)
  )

trtemfl: Treatment-emergent flag

type: derivation

Derives treatment emergent analysis flag.

Parameters

name description
domain character Name of new domain being created
end_window Passed along to admiral::end_window()

Depends

domain column
{{domain}} ASTDT
{{domain}} AENDT
{{domain}} TRTSDT
{{domain}} TRTEDT

Outputs

  • TRTEMFL

Code 

{{domain}} <- {{domain}} |>
  admiral::derive_var_trtemfl(
    start_date = ASTDT,
    end_date = AENDT,
    trt_start_date = TRTSDT,
    trt_end_date = TRTEDT,
    end_window = {{end_window}}
  )