convertDate: Converts date columns formatted as characters to be of type...

In rmsharp/nprcmanager: Genetic Tools for Colony Management

Description

Part of Pedigree Curation

Usage

convertDate(ped, time.origin = as.Date("1970-01-01"), reportErrors = FALSE)

Arguments

ped	a dataframe of pedigree information that may contain birth, death, departure, or exit dates. The fields are optional, but will be used if present.(optional fields: birth, death, departure, and exit).
time.origin	date object used by as.Date to set origin.
reportErrors	logical value if TRUE will scan the entire file and make a list of all errors found. The errors will be returned in a list of list where each sublist is a type of error found.

Value

A dataframe with an updated table with date columns converted from character data type to Date data type. Values that do not conform to the format

Examples

library(lubridate)
set_seed(10)
someBirthDates <- paste0(sample(seq(0, 15, by = 3), 10,
                                replace = TRUE) + 2000, "-",
                         sample(1:12, 10, replace = TRUE), "-",
                         sample(1:28, 10, replace = TRUE))
someBadBirthDates <- paste0(sample(1:12, 10, replace = TRUE), "-",
                            sample(1:28, 10, replace = TRUE), "-",
                            sample(seq(0, 15, by = 3), 10,
                                   replace = TRUE) + 2000)
someDeathDates <- sample(someBirthDates, length(someBirthDates),
                         replace = FALSE)
someDepartureDates <- sample(someBirthDates, length(someBirthDates),
                             replace = FALSE)
ped1 <- data.frame(birth = someBadBirthDates, death = someDeathDates,
                   departure = someDepartureDates)
someDates <- ymd(someBirthDates)
ped2 <- data.frame(birth = someDates, death = someDeathDates,
                   departure = someDepartureDates)
ped3 <- data.frame(birth = someBirthDates, death = someDeathDates,
                   departure = someDepartureDates)
someNADeathDates <- someDeathDates
someNADeathDates[c(1, 3, 5)] <- ""
someNABirthDates <- someDates
someNABirthDates[c(2, 4, 6)] <- NA
ped4 <- data.frame(birth = someNABirthDates, death = someNADeathDates,
                   departure = someDepartureDates)

## convertDate identifies bad dates
result = tryCatch({
  convertDate(ped1)
}, warning = function(w) {
  print("Warning in date")
}, error = function(e) {
  print("Error in date")
})

## convertDate with error flag returns error list and not an error
convertDate(ped1, reportErrors = TRUE)

## convertDate recognizes good dates
all(is.Date(convertDate(ped2)$birth))
all(is.Date(convertDate(ped3)$birth))

## convertDate handles NA and empty character string values correctly
convertDate(ped4)

rmsharp/nprcmanager documentation built on April 24, 2021, 3:13 p.m.