tests/testthat/test_getPyramidAgeDist.R

In rmsharp/nprcmanager: Genetic Tools for Colony Management

#' Copyright(c) 2017-2020 R. Mark Sharp
#' This file is part of nprcgenekeepr
context("getPyramidAgeDist")
library(testthat)
library(lubridate)
library(stringi)

qcPed <- nprcgenekeepr::qcPed
ped <- qcPed[ , c("id", "sire", "dam", "sex", "birth", "exit")]
ped <- getPyramidAgeDist(ped)
test_that("getPyramidAgeDist classifies and ages animals correctly", {
  expect_equal(as.numeric(table(ped$status)[[1]]), 46)
  expect_true(ped$age[ped$id == "YIAD2N"] > 19.0 &
                ped$age[ped$id == "YIAD2N"] < 20.0)
})
ped <- getPyramidAgeDist()
test_that("getPyramidAgeDist gets qcPed by default", {
  expect_equal(as.numeric(table(ped$status)[[1]]), 46)
  expect_true(ped$age[ped$id == "YIAD2N"] > 19.0 &
                ped$age[ped$id == "YIAD2N"] < 20.0)
})
ped <- qcPed[ , c("id", "sire", "dam", "sex", "birth", "exit")]
charDatePed <- ped
charDatePed$birth <- format(charDatePed$birth, format = "%Y-%m-%d")
ped <- getPyramidAgeDist(charDatePed)
test_that("getPyramidAgeDist converts character based birth date", {
  expect_equal(as.numeric(table(ped$status)[[1]]), 46)
  expect_true(ped$age[ped$id == "YIAD2N"] > 19.0 &
                ped$age[ped$id == "YIAD2N"] < 20.0)
})
ped <- qcPed[ , c("id", "sire", "dam", "sex", "birth", "exit")]
charDatePed <- ped
charDatePed$exit <- format(charDatePed$exit, format = "%Y-%m-%d")
charDatePed$exit[176] <- "9999999999"
ped <- getPyramidAgeDist(charDatePed)
test_that(stri_c("getPyramidAgeDist converts 9999999999 exit_date to NA and ",
                 "makes status DECEASED"), {
  expect_equal(ped$status[ped$id == charDatePed$id[176]], "DECEASED")
  expect_true(is.na(ped$exit[ped$id == charDatePed$id[176]]))
})
pedOne <- data.frame(id = c("s1", "d1", "s2", "d2", "o1", "o2", "o3", "o4"),
                     sire = c(NA, NA, NA, NA, "s1", "s1", "s2", "s2"),
                     dam = c(NA, NA, NA, NA, "d1", "d2", "d2", "d2"),
                     sex = c("F", "M", "M", "F", "F", "F", "F", "M"),
                     birth = mdy(
                       paste0(sample(1:12, 8, replace = TRUE), "-",
                              sample(1:28, 8, replace = TRUE), "-",
                              sample(seq(0, 15, by = 3), 8, replace = TRUE) +
                                2000)),
                     stringsAsFactors = FALSE, check.names = FALSE)
pedOne$exit <- pedOne$birth + days(5000)
pedOne$age <- (now() - as.POSIXct(pedOne$birth)) / dyears(1)

ped <- pedOne
ped$birth <- rep(TRUE, nrow(ped))
test_that("getPyramidAgeDist detect birth column of wrong type ", {
  expect_error(getPyramidAgeDist(ped),
               stri_c("birth column must be of class 'Date', ",
                      "'POSIXct', or 'character'"))
})
ped <- pedOne
ped$exit <- rep(TRUE, nrow(ped))
test_that("getPyramidAgeDist detect exit column of wrong type ", {
  expect_error(getPyramidAgeDist(ped),
               stri_c("exit_date column must be of class 'Date', ",
                      "'POSIXct', or 'character'"))
})