Nothing
library(ranger)
library(survival)
context("genabel")
test_that("classification gwaa rf is of class ranger with 14 elements", {
skip_if_not_installed("GenABEL")
skip_if_not_installed("MASS")
library(GenABEL)
dat.gwaa <- readRDS("../test_gwaa.rds")
rf <- ranger(CHD ~ ., data = dat.gwaa)
expect_is(rf, "ranger")
expect_equal(length(rf), 14)
})
test_that("GenABEL prediction works if no covariates and formula used", {
skip_if_not_installed("GenABEL")
skip_if_not_installed("MASS")
library(GenABEL)
dat <- readRDS("../test_gwaa.rds")
dat@phdata$Age <- NULL
rf <- ranger(CHD ~ .-Sex, data = dat, num.trees = 5)
expect_silent(predict(rf, dat))
})
test_that("SNP ordering working for binary classification", {
skip_if_not_installed("GenABEL")
skip_if_not_installed("MASS")
library(GenABEL)
dat.gwaa <- readRDS("../test_gwaa.rds")
rf <- ranger(CHD ~ ., data = dat.gwaa, num.trees = 5, respect.unordered.factors = "order")
expect_is(rf$forest$snp.order, "list")
expect_length(rf$forest$snp.order, nsnps(dat.gwaa))
})
test_that("SNP ordering working for regression", {
skip_if_not_installed("GenABEL")
skip_if_not_installed("MASS")
library(GenABEL)
dat.gwaa <- readRDS("../test_gwaa.rds")
rf <- ranger(Age ~ ., data = dat.gwaa, num.trees = 5, respect.unordered.factors = "order")
expect_is(rf$forest$snp.order, "list")
expect_length(rf$forest$snp.order, nsnps(dat.gwaa))
})
test_that("SNP ordering not working for multiclass", {
skip_if_not_installed("GenABEL")
skip_if_not_installed("MASS")
library(GenABEL)
dat <- readRDS("../test_gwaa.rds")
dat@phdata$mc <- factor(round(runif(nids(dat), 1, 5)))
expect_error(ranger(mc ~ ., data = dat, num.trees = 5, respect.unordered.factors = "order"),
"Error: Ordering of SNPs currently only implemented for regression and binary outcomes.")
})
test_that("SNP ordering not working for survival", {
skip_if_not_installed("GenABEL")
skip_if_not_installed("MASS")
library(GenABEL)
dat <- readRDS("../test_gwaa.rds")
dat@phdata$time <- runif(nids(dat), 1, 100)
dat@phdata$status <- rbinom(nids(dat), 1, 0.5)
expect_error(ranger(Surv(time, status) ~ ., data = dat, num.trees = 5, respect.unordered.factors = "order"),
"Error: Ordering of SNPs currently only implemented for regression and binary outcomes.")
})
test_that("SNP ordering working with corrected importance", {
skip_if_not_installed("GenABEL")
skip_if_not_installed("MASS")
library(GenABEL)
dat.gwaa <- readRDS("../test_gwaa.rds")
rf <- ranger(CHD ~ ., data = dat.gwaa, num.trees = 5, respect.unordered.factors = "order",
importance = "impurity_corrected")
expect_is(rf$forest$snp.order, "list")
expect_length(rf$forest$snp.order, nsnps(dat.gwaa))
rf <- ranger(CHD ~ 0, data = dat.gwaa, num.trees = 5, respect.unordered.factors = "order",
importance = "impurity_corrected")
expect_is(rf$forest$snp.order, "list")
expect_length(rf$forest$snp.order, nsnps(dat.gwaa))
})
test_that("SNP ordering not working with corrected importance for survival", {
skip_if_not_installed("GenABEL")
skip_if_not_installed("MASS")
library(GenABEL)
dat <- readRDS("../test_gwaa.rds")
dat@phdata$time <- runif(nids(dat), 1, 100)
dat@phdata$status <- rbinom(nids(dat), 1, 0.5)
expect_error(ranger(Surv(time, status) ~ 0, data = dat, num.trees = 5, respect.unordered.factors = "order",
importance = "impurity_corrected"),
"Error: Ordering of SNPs currently only implemented for regression and binary outcomes.")
})
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