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Convert XXTPT Strings to Hours

Source: R/convert_xxtpt_to_hours.R
convert_xxtpt_to_hours.Rd

[Experimental]

Converts CDISC timepoint strings (e.g., PCTPT, VSTPT, EGTPT, ISTPT, LBTPT) into numeric hours for analysis. The function handles common dose-centric formats including pre-dose, post-dose (hours/minutes), days, time ranges, and treatment-related time markers.

Usage 

convert_xxtpt_to_hours(
  xxtpt,
  treatment_duration = 0,
  range_method = "midpoint"
)

Arguments

xxtpt

A character vector of timepoint descriptions from SDTM --TPT variables (e.g., PCTPT, VSTPT, EGTPT, ISTPT, LBTPT). Can contain NA values.

Permitted values

character vector

Default value

none

treatment_duration

Numeric value(s) specifying the duration of treatment in hours. Used to convert "EOI/EOT" (End of Infusion/Treatment) patterns and patterns describing time after end of treatment. Must be non-negative. Can be either:

  • A single value (used for all timepoints), or

  • A vector of the same length as xxtpt (one value per timepoint)

Default is 0 hours (for instantaneous treatments like oral medications).

Permitted values

numeric scalar or vector (non-negative)

Default value

0

range_method

Method for converting time ranges to single values. Options are "midpoint" (default), "start", or "end". For example, "0-6h" with midpoint returns 3, with start returns 0, with end returns 6.

Permitted values

character scalar ("midpoint", "start", or "end")

Default value

"midpoint"

Value

A numeric vector of timepoints in hours. Returns NA_real_ for:

  • Input NA values

  • Unrecognized timepoint formats

  • Non-time descriptors (e.g., "Morning", "Evening")

Returns numeric(0) for empty input.

Details

The function recognizes the following patterns (all case-insensitive):

Special Cases:

  • "Screening" -> 0

  • "Pre-dose", "Predose", "Pre-treatment", "Pre-infusion", "Pre-inf", "Before", "Infusion", "0H" -> 0

  • "EOI", "EOT", "End of Infusion", "End of Treatment", "After End of Infusion", "After End of Treatment" -> treatment_duration (default: 0)

  • "Morning", "Evening" -> NA_real_

  • Unrecognized values -> NA_real_

Time Ranges: Time ranges are converted based on the range_method parameter:

  • "0-6h Post-dose" with range_method = "midpoint" (default) -> 3

  • "0-6h Post-dose" with range_method = "start" -> 0

  • "0-6h Post-dose" with range_method = "end" -> 6

  • "0-4H PRIOR START OF INFUSION" with midpoint -> -2 (negative for prior)

  • "8-16H POST START OF INFUSION" with midpoint -> 12

  • "0-4H AFTER EOI" with midpoint and treatment_duration=1 -> 3 (1 + 2)

  • "0-4H EOT" with midpoint and treatment_duration=0 -> 2

  • "4-8H AFTER END OF INFUSION" with midpoint and treatment_duration=1 -> 7 (1 + 6)

  • "4-8H POST INFUSION" with midpoint and treatment_duration=1 -> 7 (1 + 6)

  • "4-8H POST-INF" with midpoint and treatment_duration=1 -> 7 (1 + 6)

Time-based Conversions:

  • Days: "Day 1" -> 24, "2D" -> 48, "30 DAYS AFTER LAST" -> 720 (requires unit indicator; bare numbers like "2" return NA)

  • Hours + Minutes: "1H30M" -> 1.5

  • Hours: "2 hours" -> 2, "1 HOUR POST" -> 1

  • Minutes: "30M" -> 0.5, "30 MIN POST" -> 0.5

  • Predose: "5 MIN PREDOSE" -> -0.0833, "5 MIN PRE-DOSE" -> -0.0833

  • Before treatment: "5 MIN BEFORE" -> -0.0833

  • Post EOI/EOT: "1 HOUR POST EOI" -> treatment_duration + 1, "24 HR POST INF" -> treatment_duration + 24, "24 HR POST-INF" -> treatment_duration + 24, "1 HOUR AFTER EOT" -> treatment_duration + 1

  • After end: "30MIN AFTER END OF INFUSION" -> treatment_duration + 0.5

  • Start of infusion/treatment: "8H PRIOR START OF INFUSION" -> -8, "8H BEFORE START OF TREATMENT" -> -8

  • Pre EOI/EOT: "10MIN PRE EOI" -> treatment_duration - 1/6, "10MIN BEFORE EOT" -> treatment_duration - 1/6

Supported Unit Formats:

  • Hours: H, h, HR, hr, HOUR, hour (with optional plurals)

  • Minutes: M, m, MIN, min, MINUTE, minute (with optional plurals)

  • Days: D, d, DAY, day (with optional plurals)

  • Flexible whitespace and optional "Post-dose", "POST", "After last" suffixes

  • Hyphens in compound terms: "PRE-DOSE", "POST-INF", "POST-INFUSION"

Understanding POST/AFTER Patterns:

It's important to distinguish between patterns relative to treatment start versus treatment end:

  • Relative to START (treatment_duration NOT added):

    • "1H POST", "1H AFTER", "30M POST" -> Time from dose/treatment start

    • These patterns assume treatment starts at time 0

    • Example: "1H POST" -> 1 hour (regardless of treatment_duration)

  • Relative to END (treatment_duration IS added):

    • "1H POST EOI", "1H AFTER EOT", "1H POST INFUSION" -> Time from treatment end

    • These patterns account for when treatment ends (start + duration)

    • Example: "1H POST EOI" with treatment_duration=2 -> 3 hours (2 + 1)

This distinction follows standard pharmacokinetic conventions where "post-dose" refers to time from treatment initiation, while "post end of infusion" refers to time from treatment completion.

Vectorized Treatment Duration:

When treatment_duration is a vector, each timepoint uses its corresponding treatment duration value. This is useful when different records have different treatment durations (e.g., different infusion lengths).

See also

Date/Time Computation Functions that returns a vector: compute_age_years(), compute_dtf(), compute_duration(), compute_tmf(), convert_date_to_dtm(), convert_dtc_to_dt(), convert_dtc_to_dtm(), impute_dtc_dt(), impute_dtc_dtm()

Examples

Basic timepoint patterns

Convert basic dose-centric patterns to hours

convert_xxtpt_to_hours(c(
  "Screening",
  "Pre-dose",
  "Pre-treatment",
  "Before",
  "30M",
  "1H",
  "2H POSTDOSE",
  "Day 1"
))
#> [1]  0.0  0.0  0.0  0.0  0.5  1.0  2.0 24.0

Predose and before patterns

Convert predose/before patterns that return negative times

convert_xxtpt_to_hours(c("5 MIN PREDOSE", "5 MIN PRE-DOSE", "1 HOUR BEFORE"))
#> [1] -0.08333333 -0.08333333 -1.00000000

Treatment-related patterns (oral medications)

With default treatment_duration = 0 for oral medications

convert_xxtpt_to_hours(c(
  "EOT",
  "1 HOUR POST EOT",
  "1 HOUR AFTER EOT",
  "After End of Treatment"
))
#> [1] 0 1 1 0

With treatment_duration = 1 hour for IV infusions

convert_xxtpt_to_hours(
  c(
    "EOI",
    "1 HOUR POST EOI",
    "24 HR POST INF",
    "24 HR POST-INF",
    "30MIN AFTER END OF INFUSION",
    "8H PRIOR START OF INFUSION",
    "10MIN PRE EOI"
  ),
  treatment_duration = 1
)
#> [1]  1.0000000  2.0000000 25.0000000 25.0000000  1.5000000 -8.0000000  0.8333333

Vectorized treatment duration

Different treatment durations per timepoint

convert_xxtpt_to_hours(
  c("EOI", "1 HOUR POST EOI", "EOI", "1 HOUR POST EOI"),
  treatment_duration = c(1, 1, 2, 2)
)
#> [1] 1 2 2 3

Time ranges with midpoint method

Default midpoint method for ranges

convert_xxtpt_to_hours(c(
  "0-6h Post-dose",
  "0-4H PRIOR START OF INFUSION",
  "8-16H POST START OF INFUSION"
))
#> [1]  3 -2 12

Time ranges with custom methods

Specify start or end method for ranges

convert_xxtpt_to_hours("0-6h Post-dose", range_method = "end")
#> [1] 6
convert_xxtpt_to_hours("0-6h Post-dose", range_method = "start")
#> [1] 0

Ranges relative to EOI/EOT

Time ranges after end of infusion/treatment

convert_xxtpt_to_hours(
  c(
    "0-4H AFTER EOI",
    "0-4H POST EOI",
    "4-8H AFTER END OF INFUSION",
    "4-8H AFTER EOT",
    "4-8H POST INFUSION",
    "4-8H POST-INF"
  ),
  treatment_duration = 1
)
#> [1] 3 3 7 7 7 7

POST vs POST EOI distinction

Difference between POST (from start) and POST EOI (from end)

convert_xxtpt_to_hours(
  c("Pre-dose", "1H POST", "2H POST", "4H POST"),
  treatment_duration = 2
)
#> [1] 0 1 2 4

convert_xxtpt_to_hours(
  c("Pre-dose", "EOI", "1H POST EOI", "2H POST EOI"),
  treatment_duration = 2
)
#> [1] 0 2 3 4

convert_xxtpt_to_hours(
  c("1H POST", "1H POST EOI", "1H POST INFUSION"),
  treatment_duration = 2
)
#> [1] 1 3 3