Nothing
library(SimRVPedigree)
context("sim_RVped")
data("AgeSpecific_Hazards")
EXPed <- sim_RVped(hazard_rates = hazard(AgeSpecific_Hazards),
GRR = 35, carrier_prob = 0.002,
RVfounder = TRUE,
FamID = 1,
num_affected = 2,
recall_probs = c(1),
founder_byears = c(1900, 1910),
ascertain_span = c(1970, 2015))
test_that("returns a list containing two pedfiles", {
expect_true(is.list(EXPed))
expect_true(is.data.frame(EXPed[[1]]))
expect_true(is.data.frame(EXPed[[2]]))
})
test_that("pedigree always conatains more than 1 person", {
expect_gt(nrow(EXPed[[2]]), 1)
})
test_that("both pedigrees contains at least 2 affecteds when num_affected = 2", {
RVped1 <- EXPed[[1]]
RVped2 <- EXPed[[2]]
expect_gte(sum(RVped1$affected[which(RVped1$available == 1)]), 2)
expect_gte(sum(RVped2$affected[which(RVped2$available == 1)]), 2)
})
test_that("proband in trimmed pedigree had 1 affected relative before onset, when num_affected = 2", {
RVped <- sim_RVped(hazard_rates = hazard(AgeSpecific_Hazards),
GRR = 35, carrier_prob = 0.002,
RVfounder = TRUE,
FamID = 1,
num_affected = 2,
recall_probs = c(1),
founder_byears = c(1900, 1910),
ascertain_span = c(1970, 2015))[[2]]
Oyears <- RVped$onsetYr[which(RVped$affected == 1 &
RVped$available == 1 &
RVped$proband == 0)]
POyear <- RVped$onsetYr[RVped$proband == 1]
expect_gte(sum(Oyears <= POyear), 1)
})
test_that("there are n - 1 affected realtives NOT including any relatives affected before first_diagnosis", {
RVped <- sim_RVped(hazard_rates = hazard(AgeSpecific_Hazards),
GRR = 50, carrier_prob = 0.002,
RVfounder = TRUE,
FamID = 1,
num_affected = 2,
recall_probs = c(1),
founder_byears = c(1850, 1870),
ascertain_span = c(2000, 2015),
first_diagnosis = 1975)[[2]]
summary(RVped)
Oyears <- RVped$onsetYr[which(RVped$affected == 1
& RVped$available == 1
& RVped$proband == 0
& RVped$onsetYr >= 1975)]
expect_gte(length(Oyears), 1)
})
test_that("issues error when RR < 0", {
expect_error(sim_RVped(hazard_rates = hazard(AgeSpecific_Hazards),
GRR = -1, carrier_prob = 0.002, FamID = 1,
RVfounder = TRUE,
num_affected = 2,
founder_byears = c(1900, 1980),
ascertain_span = c(2000, 2015)))
})
test_that("issues error when ascertain_span not properly specified", {
expect_error(sim_RVped(hazard_rates = hazard(AgeSpecific_Hazards),
GRR = 35, carrier_prob = 0.002, FamID = 1,
RVfounder = TRUE,
num_affected = 2,
founder_byears = c(1900, 1980),
ascertain_span = c(2017, 2015)))
})
test_that("issues error when recall_probs not properly specified", {
expect_error(sim_RVped(hazard_rates = hazard(AgeSpecific_Hazards),
GRR = 35, carrier_prob = 0.002, FamID = 1,
RVfounder = TRUE,
num_affected = 2,
recall_probs = c(10, 5),
founder_byears = c(1900, 1980),
ascertain_span = c(2000, 2015)))
})
test_that("issues error when hazard_rates is not a hazard object", {
expect_error(sim_RVped(hazard_rates = list(AgeSpecific_Hazards, seq(0, 100, by = 1)),
GRR = 35, carrier_prob = 0.002, FamID = 1,
RVfounder = TRUE,
num_affected = 2,
founder_byears = c(1900, 1980),
ascertain_span = c(2000, 2015)))
})
# test_that("issues error when birth_range not properly specified", {
# expect_error(sim_RVped(hazard_rates = hazard(AgeSpecific_Hazards),
# GRR = 35, carrier_prob = 0.002, FamID = 1,
# RVfounder = TRUE,
# num_affected = 2,
# birth_range = c(10, 5),
# founder_byears = c(1900, 1980),
# ascertain_span = c(2000, 2015)))
# })
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.