Nothing
library(SimRVPedigree)
context("censor_ped")
data("AgeSpecific_Hazards")
test_that("censor_ped returns an error when expected", {
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, 1, 1, 0.5, 0.25),
founder_byears = c(1900, 1980),
ascertain_span = c(1980, 2015))[[2]]
#no proband and no censor_year
expect_error(censor_ped(RVped[, -which(colnames(RVped) %in% "proband")]))
#no censor_year, no onset data for proband, proabnd present
RVped$onsetYr <- NA
expect_error(censor_ped(RVped))
#muliple probands, no censor year
RVped$proband <- RVped$affected
expect_error(censor_ped(RVped))
#no date data
RVped$birthYr <- NA
RVped$deathYr <- NA
expect_error(censor_ped(RVped))
})
test_that("censor_ped returns a smaller or equally sized ped", {
RVped <- sim_RVped(hazard_rates = hazard(AgeSpecific_Hazards),
GRR = 50, carrier_prob = 0.002,
RVfounder = TRUE,
FamID = 1,
num_affected = 2,
recall_probs = c(1, 1, 1, 0.5, 0.25),
founder_byears = c(1900, 1980),
ascertain_span = c(1980, 2015))[[2]]
expect_gte(nrow(RVped), nrow(censor_ped(RVped)))
})
test_that("censor_ped does not return any info after the censor year", {
RVped <- sim_RVped(hazard_rates = hazard(AgeSpecific_Hazards),
GRR = 50, carrier_prob = 0.002,
RVfounder = TRUE,
FamID = 1,
num_affected = 2,
recall_probs = c(1, 1, 1, 0.5, 0.25),
founder_byears = c(1900, 1980),
ascertain_span = c(1980, 2015))[[2]]
my_Cyear <- RVped$onsetYr[which(RVped$proband == 1)]
C_ped <- censor_ped(ped_file = RVped, censor_year = my_Cyear)
expect_gte(my_Cyear, max(C_ped$birthYr, na.rm = T))
expect_gte(my_Cyear, max(C_ped$onsetYr, na.rm = T))
if(!all(is.na(C_ped$deathYr))){
expect_gte(my_Cyear, max(C_ped$deathYr, na.rm = T))
}
})
test_that("censor_ped issues a warnign if birthYr data missing", {
RVped <- sim_RVped(hazard_rates = hazard(AgeSpecific_Hazards),
GRR = 50, carrier_prob = 0.002,
RVfounder = TRUE,
FamID = 1,
num_affected = 2,
recall_probs = c(1, 1, 1, 0.5, 0.25),
founder_byears = c(1900, 1980),
ascertain_span = c(1980, 2015))[[2]]
RVped$birthYr <- NA
expect_warning(censor_ped(ped_file = RVped))
})
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