format_time: Parse date-time data to numeric time for use in respR...

In respR: Import, Process, Analyse, and Calculate Rates from Respirometry Data

Parse date-time data to numeric time for use in respR functions

Description

A function to parse class POSIX.ct or text strings of date-time data to numeric time for use in respR functions.

Usage

format_time(x, time = 1, format = "ymdHMS", start = 1)

Arguments

x	vector or data frame containing strings or class POSIX.ct date-time data to be converted to numeric.
time	numeric value or vector. Specifies column(s) containing date-time data. Default is 1.
format	string. Code describing structure of date-time data. See Details.
start	numeric. At what time (in seconds) should the formatted time data start? Default is 1.

Details

Regardless of input, all data are parsed to numeric time data in seconds duration from the first entry starting at 1. If you want the times to start at a different time, a start value can be specified, in which case the series starts at that number (in seconds) and all subsequent times are shifted forward by the same amount.

Input

Input can be a vector, or data frame. If a data frame, the column(s) of the date-time data are specified using the time input. By default the first column is assumed to contain the date-time data (i.e. time = 1).

If the date-time data is split over several columns (e.g. date in one column, time in another), multiple columns can be specified (e.g. time = c(1,2)). In this case, the format setting should reflect the correct order as entered in time.

Time only data

Time-only data, that is times which lack an associated date, can also be parsed. Normally, parsing time-only data will cause problems when the times cross midnight (i.e. 00:00:00). However, the function attempts to identify when this occurs and parse the data correctly.

Formatting

See the lubridate package for more detail on acceptable formatting.

Date-time data can be unspaced or separated by any combination of spaces, forward slashes, hyphens, dots, commas, colons, semicolons, or underscores. E.g. all these are parsed as the same date-time: ⁠"2010-02-28 13:10:23", "20100228131023", "2010,02/28 13.10;23", "2010 02 28 13_10-23"⁠.

• Times can be in 24H or 12H with AM/PM
  E.g. "2010-02-28 13:10:23" or "2010-02-28 1:10:23 PM"

• Times without initial zero are parsed as 24H time
  E.g. "1:10:23" is same as "1:10:23 AM" or "01:10:23"

• AM/PM take precedence over 24H formatting for 01-12h
  E.g. "1:10:23 PM" and "01:10:23 PM" are both same as "13:10:23"

• However, 24H formatting for 13-24h takes precedence over AM/PM
  E.g. "13:10:23 AM" is identified as "1:10:23 PM" or "13:10:23"

Syntax of 'format' input

Specify the order of year, month, day, and time in your date-time input.

d - Day of the month as decimal number (01–31 or 1–31).

m - Month of the year as decimal number (01–12 or 1–12).

y - Year (2010, 2001, 1989).

H - Hour as decimal number (00–24 or 0–24 or 00-12 (see p)).

M - Minute as decimal number (00–59 or 0–59).

S - Second as decimal number (00–59 or 0–59).

p - AM/PM indicator for 12-h date-time format (e.g. "01/12/2020 1:30:44 PM " would be "dmyHMSp").

Specify the order using the format input, using separators or not (optional): "dmyHMS"; "dmy_HMS" and "d m y H M S" are all the same. See Examples.

Single experimental datasets should never span different time zones, so if a time zone is present it is ignored for the purposes of calculating numeric times.

More

For additional help, documentation, vignettes, and more visit the respR website at https://januarharianto.github.io/respR/

Value

Output: If the input is a vector, output is a vector of equal length containing the numeric time data. For data frame inputs, an identical data frame is returned, with a new column named time_num added as the final column.

See Also

lubridate

Examples

# Convert year-month-day hour-min-sec
x <- c("09-02-03 01:11:11", "09-02-03 02:11:11","09-02-03 02:25:11")
format_time(x)

# Convert day-month-year hour-min, and use a separator in the format
x <- c("03-02-09 01:11", "03-02-09 02:11","03-02-09 02:25")
format_time(x, format = "dmy_HM")

# Convert when AM/PM is present
x <- c("09-02-03 11:11:11 AM", "09-02-03 12:11:11 PM","09-02-03 01:25:11 PM")
# This is WRONG - the AM/PM indicator is missing
format_time(x, format = "dmyHMS")
# This is correct
format_time(x, format = "dmyHMSp")

# Convert dataframe with year-month-day hour-min-sec (ymdHMS default)
x <- data.frame(
  x = c("09-02-03 01:11:11", "09-02-03 02:11:11","09-02-03 02:25:11"),
  y = c(23, 34, 45))
format_time(x, time = 1)

# Convert dataframe with time in a different column and non-default format
x <- data.frame(
  x = c(23, 34, 45),
  y = c("09-02-2018 11:11:11 AM", "09-02-2018 12:11:11 PM","09-02-2018 01:25:11 PM"),
  z = c(56, 67, 78))
format_time(x, time = 2, format = "dmyHMSp")

# Convert dataframe with separate date and time columns, and times crossing midnight
x <- data.frame(
  w = c("09-02-18", "09-02-18","10-02-18"),
  x = c("22:11:11", "23:11:11","00:25:11"),
  y = c(23, 34, 45),
  z = c(56, 67, 78))
# Crosses midnight, but parses correctly even without dates
format_time(x, time = 2, format = "HMS")
# Include dates to double check
format_time(x, time = 1:2, format = "dmyHMS")
# Input same as different column order & appropriate format order
format_time(x, time = 2:1, format = "HMSdmy")

# Convert a data frame with date and time split over multiple columns
x <- data.frame(
  u = c("09", "09","10"),
  v = c("02", "02","02"),
  w = c("2018", "2018","2018"),
  x = c("22:11:11", "23:11:11","00:25:11"),
  y = c(23, 34, 45),
  z = c(56, 67, 78))
format_time(x, time = 1:4, format = "dmyHMS")

respR documentation built on May 29, 2024, 7:14 a.m.