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Impute Partial Date(-time) Portion of a --DTC Variable

Source: R/derive_vars_dtm.R
impute_dtc_dtm.Rd

Imputation partial date/time portion of a --DTC variable. based on user input.

Usage 

impute_dtc_dtm(
  dtc,
  highest_imputation = "h",
  date_imputation = "first",
  time_imputation = "first",
  min_dates = NULL,
  max_dates = NULL,
  preserve = FALSE
)

Arguments

dtc

The --DTC date to impute

A character date is expected in a format like yyyy-mm-dd or yyyy-mm-ddThh:mm:ss. Trailing components can be omitted and - is a valid "missing" value for any component.

Permitted values

a character date variable

Default value

none

highest_imputation

Highest imputation level

The highest_imputation argument controls which components of the --DTC value are imputed if they are missing. All components up to the specified level are imputed.

If a component at a higher level than the highest imputation level is missing, NA is returned. For example, for highest_imputation = "D" "2020" results in NA because the month is missing.

If "n" is specified, no imputation is performed, i.e., if any component is missing, NA is returned.

If "Y" is specified, date_imputation should be "first" or "last" and min_dates or max_dates should be specified respectively. Otherwise, NA is returned if the year component is missing.

Permitted values

"Y" (year, highest level), "M" (month), "D" (day), "h" (hour), "m" (minute), "s" (second), "n" (none, lowest level)

Default value

"h"

date_imputation

The value to impute the day/month when a datepart is missing.

A character value is expected.

  • The"first" and "last" keywords allow imputation to the first/last day/month. They can also be used to impute the year if used in conjunction with the min_dates or max_dates arguments. Some examples of this are available here.

  • When highest_imputation is "M" or "D", the "mid" keyword can also be specified to impute missing components to the middle of the possible range:

    • If both month and day are missing, they are imputed as "06-30" (middle of the year).

    • If only day is missing, it is imputed as "15" (middle of the month).

  • "<dd>" can be specified only if highest_imputation = "D". Missing days are imputed by the specified day, e.g. "10" for the 10th day of the month. The specified day should be valid for all months as otherwise an error might be issued. For example, date_imputation = "30" results in an invalid date of "2024-02-30" for the partial date "2024-02".

  • "<mm>-<dd>" can be specified only if highest_imputation is "M", e.g. "06-15" for the 15th of June.

Permitted values

a key-word, i.e. "first", "mid", "last", or "<mm>-<dd>" or "<dd>"

Default value

"first"

time_imputation

The value to impute the time when a timepart is missing.

A character value is expected, either as a

  • format with hour, min and sec specified as "hh:mm:ss": e.g. "00:00:00" for the start of the day,

  • or as a keyword: "first","last" to impute to the start/end of a day.

The argument is ignored if highest_imputation = "n".

Permitted values

"first", "last", or user-defined

Default value

"first"

min_dates

Minimum dates

A list of dates is expected. It is ensured that the imputed date is not before any of the specified dates, e.g., that the imputed adverse event start date is not before the first treatment date. Only dates which are in the range of possible dates of the dtc value are considered. The possible dates are defined by the missing parts of the dtc date (see example below). This ensures that the non-missing parts of the dtc date are not changed. A date or date-time object is expected. For example

impute_dtc_dtm(
  "2020-11",
  min_dates = list(
   ymd_hm("2020-12-06T12:12"),
   ymd_hm("2020-11-11T11:11")
  ),
  highest_imputation = "M"
)

returns "2020-11-11T11:11:11" because the possible dates for "2020-11" range from "2020-11-01T00:00:00" to "2020-11-30T23:59:59". Therefore "2020-12-06T12:12:12" is ignored. Returning "2020-12-06T12:12:12" would have changed the month although it is not missing (in the dtc date).

For date variables (not datetime) in the list the time is imputed to "00:00:00". Specifying date variables makes sense only if the date is imputed. If only time is imputed, date variables do not affect the result.

Permitted values

a list of dates, e.g. list(ymd_hms("2021-07-01T04:03:01"), ymd_hms("2022-05-12T13:57:23"))

Default value

NULL

max_dates

Maximum dates

A list of dates is expected. It is ensured that the imputed date is not after any of the specified dates, e.g., that the imputed date is not after the data cut off date. Only dates which are in the range of possible dates are considered. A date or date-time object is expected.

For date variables (not datetime) in the list the time is imputed to "23:59:59". Specifying date variables makes sense only if the date is imputed. If only time is imputed, date variables do not affect the result.

Permitted values

a list of dates, e.g. list(ymd_hms("2021-07-01T04:03:01"), ymd_hms("2022-05-12T13:57:23"))

Default value

NULL

preserve

Preserve lower level date/time part when higher order part is missing, e.g. preserve day if month is missing or preserve minute when hour is missing.

For example "2019---07" would return "2019-06-07 if preserve = TRUE (and date_imputation = "mid").

Permitted values

TRUE, FALSE

Default value

FALSE

Value

A character vector

Details

This is a vector-oriented helper and is not usually called directly on a data frame with %>%.

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(), convert_xxtpt_to_hours(), impute_dtc_dt()

Examples 

library(lubridate)

dates <- c(
  "2019-07-18T15:25:40",
  "2019-07-18T15:25",
  "2019-07-18T15",
  "2019-07-18",
  "2019-02",
  "2019",
  "2019",
  "2019---07",
  ""
)

# No date imputation (highest_imputation defaulted to "h")
# Missing time part imputed with 00:00:00 portion by default
impute_dtc_dtm(dtc = dates)
#> [1] "2019-07-18T15:25:40" "2019-07-18T15:25:00" "2019-07-18T15:00:00"
#> [4] "2019-07-18T00:00:00" NA                    NA                   
#> [7] NA                    NA                    NA                   

# No date imputation (highest_imputation defaulted to "h")
# Missing time part imputed with 23:59:59 portion
impute_dtc_dtm(
  dtc = dates,
  time_imputation = "23:59:59"
)
#> [1] "2019-07-18T15:25:40" "2019-07-18T15:25:59" "2019-07-18T15:59:59"
#> [4] "2019-07-18T23:59:59" NA                    NA                   
#> [7] NA                    NA                    NA                   

# Same as above
impute_dtc_dtm(
  dtc = dates,
  time_imputation = "last"
)
#> [1] "2019-07-18T15:25:40" "2019-07-18T15:25:59" "2019-07-18T15:59:59"
#> [4] "2019-07-18T23:59:59" NA                    NA                   
#> [7] NA                    NA                    NA                   

# Impute to first day/month if date is partial
# Missing time part imputed with 00:00:00 portion by default
impute_dtc_dtm(
  dtc = dates,
  highest_imputation = "M"
)
#> [1] "2019-07-18T15:25:40" "2019-07-18T15:25:00" "2019-07-18T15:00:00"
#> [4] "2019-07-18T00:00:00" "2019-02-01T00:00:00" "2019-01-01T00:00:00"
#> [7] "2019-01-01T00:00:00" "2019-01-01T00:00:00" NA                   
# same as above
impute_dtc_dtm(
  dtc = dates,
  highest_imputation = "M",
  date_imputation = "01-01"
)
#> [1] "2019-07-18T15:25:40" "2019-07-18T15:25:00" "2019-07-18T15:00:00"
#> [4] "2019-07-18T00:00:00" "2019-02-01T00:00:00" "2019-01-01T00:00:00"
#> [7] "2019-01-01T00:00:00" "2019-01-01T00:00:00" NA                   

# Impute to last day/month if date is partial
# Missing time part imputed with 23:59:59 portion
impute_dtc_dtm(
  dtc = dates,
  date_imputation = "last",
  time_imputation = "last"
)
#> [1] "2019-07-18T15:25:40" "2019-07-18T15:25:59" "2019-07-18T15:59:59"
#> [4] "2019-07-18T23:59:59" NA                    NA                   
#> [7] NA                    NA                    NA                   

# Impute to mid day/month if date is partial
# Missing time part imputed with 00:00:00 portion by default
impute_dtc_dtm(
  dtc = dates,
  highest_imputation = "M",
  date_imputation = "mid"
)
#> [1] "2019-07-18T15:25:40" "2019-07-18T15:25:00" "2019-07-18T15:00:00"
#> [4] "2019-07-18T00:00:00" "2019-02-15T00:00:00" "2019-06-30T00:00:00"
#> [7] "2019-06-30T00:00:00" "2019-06-30T00:00:00" NA                   

# Impute a date and ensure that the imputed date is not before a list of
# minimum dates
impute_dtc_dtm(
  "2020-12",
  min_dates = list(
    ymd_hm("2020-12-06T12:12"),
    ymd_hm("2020-11-11T11:11")
  ),
  highest_imputation = "M"
)
#> [1] "2020-12-06T12:12:00"

# Impute completely missing dates (only possible if min_dates or max_dates is specified)
impute_dtc_dtm(
  c("2020-12", NA_character_),
  min_dates = list(
    ymd_hm("2020-12-06T12:12", "2020-01-01T01:01"),
    ymd_hm("2020-11-11T11:11", NA)
  ),
  highest_imputation = "Y"
)
#> [1] "2020-12-06T12:12:00" "2020-01-01T01:01:00"