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Adds a Parameter for Dose Intensity

Source: R/derive_param_doseint.R
derive_param_doseint.Rd

Adds a record for the dose intensity for each by group (e.g., subject and visit) where the source parameters are available.

Note: This is a wrapper function for the more generic derive_param_computed().

The analysis value of the new parameter is derived as Total Dose / Planned Dose * 100

Usage 

derive_param_doseint(
  dataset,
  by_vars,
  set_values_to = exprs(PARAMCD = "TNDOSINT"),
  tadm_code = "TNDOSE",
  tpadm_code = "TSNDOSE",
  zero_doses = "Inf",
  filter = NULL
)

Arguments

dataset

Input dataset

The variables specified by the by_vars argument are expected to be in the dataset. PARAMCD, and AVAL are expected as well.

The variable specified by by_vars and PARAMCD must be a unique key of the input dataset after restricting it by the filter condition (filter parameter) and to the parameters specified by tadm_code and padm_code.

by_vars

Grouping variables

Only variables specified in by_vars will be populated in the newly created records.

Permitted Values: list of variables created by exprs() e.g. exprs(USUBJID, VISIT)

set_values_to

Variables to be set

The specified variables are set to the specified values for the new observations. For example exprs(PARAMCD = "MAP") defines the parameter code for the new parameter.

Permitted Values: List of variable-value pairs

tadm_code

Total Doses Administered parameter code

The observations where PARAMCD equals the specified value are considered as the total dose administered. The AVAL associated with this PARAMCD will be the numerator of the dose intensity calculation.

Permitted Values: character value

tpadm_code

Total Doses Planned parameter code

The observations where PARAMCD equals the specified value are considered as the total planned dose. The AVAL associated with this PARAMCD will be the denominator of the dose intensity calculation.

Permitted Values: character value

zero_doses

Flag indicating logic for handling 0 planned or administered doses for a by_vars group

Default: Inf

Permitted Values: Inf, 100

No record is returned if either the planned (tpadm_code) or administered (tadm_code) AVAL are NA. No record is returned is a record does not exist for both tadm_code and tpadm_code for the specified by_var.

If zero_doses = Inf:

  1. If the planned dose (tpadm_code) is 0 and administered dose (tadm_code) is 0, NaN is returned.

  2. If the planned dose (tpadm_code) is 0 and the administered dose (tadm_code) is > 0, Inf is returned.

If zero_doses = 100 :

  1. If the planned dose (tpadm_code) is 0 and administered dose (tadm_code) is 0, 0 is returned.

  2. If the planned dose (tpadm_code) is 0 and the administered dose (tadm_code) is > 0, 100 is returned.

filter

Filter condition

The specified condition is applied to the input dataset before deriving the new parameter, i.e., only observations fulfilling the condition are taken into account.

Permitted Values: a condition

Value

The input dataset with the new parameter rows added. Note, a variable will only be populated in the new parameter rows if it is specified in by_vars.

See also

BDS-Findings Functions for adding Parameters/Records: default_qtc_paramcd(), derive_expected_records(), derive_extreme_event(), derive_extreme_records(), derive_locf_records(), derive_param_bmi(), derive_param_bsa(), derive_param_computed(), derive_param_exist_flag(), derive_param_exposure(), derive_param_framingham(), derive_param_map(), derive_param_qtc(), derive_param_rr(), derive_param_wbc_abs(), derive_summary_records()

Examples 

library(tibble)
library(lubridate, warn.conflicts = FALSE)

adex <- tribble(
  ~USUBJID, ~PARAMCD, ~VISIT, ~ANL01FL, ~ASTDT, ~AENDT, ~AVAL,
  "P001", "TNDOSE", "V1", "Y", ymd("2020-01-01"), ymd("2020-01-30"), 59,
  "P001", "TSNDOSE", "V1", "Y", ymd("2020-01-01"), ymd("2020-02-01"), 96,
  "P001", "TNDOSE", "V2", "Y", ymd("2020-02-01"), ymd("2020-03-15"), 88,
  "P001", "TSNDOSE", "V2", "Y", ymd("2020-02-05"), ymd("2020-03-01"), 88,
  "P002", "TNDOSE", "V1", "Y", ymd("2021-01-01"), ymd("2021-01-30"), 0,
  "P002", "TSNDOSE", "V1", "Y", ymd("2021-01-01"), ymd("2021-02-01"), 0,
  "P002", "TNDOSE", "V2", "Y", ymd("2021-02-01"), ymd("2021-03-15"), 52,
  "P002", "TSNDOSE", "V2", "Y", ymd("2021-02-05"), ymd("2021-03-01"), 0
)

derive_param_doseint(
  adex,
  by_vars = exprs(USUBJID, VISIT),
  set_values_to = exprs(PARAMCD = "TNDOSINT"),
  tadm_code = "TNDOSE",
  tpadm_code = "TSNDOSE"
)
#> # A tibble: 12 × 7
#>    USUBJID PARAMCD  VISIT ANL01FL ASTDT      AENDT       AVAL
#>    <chr>   <chr>    <chr> <chr>   <date>     <date>     <dbl>
#>  1 P001    TNDOSE   V1    Y       2020-01-01 2020-01-30  59  
#>  2 P001    TSNDOSE  V1    Y       2020-01-01 2020-02-01  96  
#>  3 P001    TNDOSE   V2    Y       2020-02-01 2020-03-15  88  
#>  4 P001    TSNDOSE  V2    Y       2020-02-05 2020-03-01  88  
#>  5 P002    TNDOSE   V1    Y       2021-01-01 2021-01-30   0  
#>  6 P002    TSNDOSE  V1    Y       2021-01-01 2021-02-01   0  
#>  7 P002    TNDOSE   V2    Y       2021-02-01 2021-03-15  52  
#>  8 P002    TSNDOSE  V2    Y       2021-02-05 2021-03-01   0  
#>  9 P001    TNDOSINT V1    NA      NA         NA          61.5
#> 10 P001    TNDOSINT V2    NA      NA         NA         100  
#> 11 P002    TNDOSINT V1    NA      NA         NA         NaN  
#> 12 P002    TNDOSINT V2    NA      NA         NA         Inf  

derive_param_doseint(
  adex,
  by_vars = exprs(USUBJID, VISIT),
  set_values_to = exprs(PARAMCD = "TDOSINT2"),
  tadm_code = "TNDOSE",
  tpadm_code = "TSNDOSE",
  zero_doses = "100"
)
#> # A tibble: 12 × 7
#>    USUBJID PARAMCD  VISIT ANL01FL ASTDT      AENDT       AVAL
#>    <chr>   <chr>    <chr> <chr>   <date>     <date>     <dbl>
#>  1 P001    TNDOSE   V1    Y       2020-01-01 2020-01-30  59  
#>  2 P001    TSNDOSE  V1    Y       2020-01-01 2020-02-01  96  
#>  3 P001    TNDOSE   V2    Y       2020-02-01 2020-03-15  88  
#>  4 P001    TSNDOSE  V2    Y       2020-02-05 2020-03-01  88  
#>  5 P002    TNDOSE   V1    Y       2021-01-01 2021-01-30   0  
#>  6 P002    TSNDOSE  V1    Y       2021-01-01 2021-02-01   0  
#>  7 P002    TNDOSE   V2    Y       2021-02-01 2021-03-15  52  
#>  8 P002    TSNDOSE  V2    Y       2021-02-05 2021-03-01   0  
#>  9 P001    TDOSINT2 V1    NA      NA         NA          61.5
#> 10 P001    TDOSINT2 V2    NA      NA         NA         100  
#> 11 P002    TDOSINT2 V1    NA      NA         NA           0  
#> 12 P002    TDOSINT2 V2    NA      NA         NA         100