Nothing
library(testthat)
library(Racmacs)
context("Test stress calculations")
map <- read.acmap(test_path("../testdata/testmap_h3subset.ace"))
test_that("point stresses", {
antigen_stresses <- agStress(map)
sera_stresses <- srStress(map)
map_stress <- mapStress(map)
expect_equal(
sum(antigen_stresses),
map_stress
)
expect_equal(
sum(sera_stresses),
map_stress
)
})
test_that("point stress per titer", {
ag_stress_per_titer <- agStressPerTiter(map)
sr_stress_per_titer <- srStressPerTiter(map)
expect_equal(nrow(ag_stress_per_titer), numAntigens(map))
expect_equal(nrow(sr_stress_per_titer), numSera(map))
})
test_that("point leverage", {
ag_leverage <- agLeverage(map)
sr_leverage <- srLeverage(map)
titer_leverage <- titerLeverage(map)
expect_equal(
length(ag_leverage),
numAntigens(map)
)
expect_equal(
length(sr_leverage),
numSera(map)
)
expect_equal(
dim(titer_leverage),
c(numAntigens(map), numSera(map))
)
})
test_that("Stress with NA coords", {
agCoords(map)[2,] <- NA
srCoords(map)[2,] <- NA
srCoords(map)[4,] <- NA
expect_equal(sum(is.na(agStress(map))), 1)
expect_equal(sum(is.na(srStress(map))), 2)
expect_equal(sum(!is.na(stressTable(map)[2,])), 0)
expect_equal(sum(!is.na(stressTable(map)[,2])), 0)
expect_equal(sum(!is.na(stressTable(map)[,4])), 0)
})
test_that("Stress with NA coords", {
set.seed(850909)
dat <- matrix(10*2^round(10*runif(100)), ncol=10)
dat[4,3:5] <- "*"
map <- make.acmap(dat)
expect_equal(
round(agStressPerTiter(map)[4, "nd_excluded"], 2),
1.67
)
})
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