Nothing
context("clusterInfectors Function")
library(nbTransmission)
#Creating a function with defaults equal to my simulated data
clusterInfWrapper <- function(nbResults,
indIDVar = "individualID",
pVar = "pScaled",
clustMethod = c("n", "kd", "hc_absolute", "hc_relative"),
cutoff = NA){
siData <- clusterInfectors(nbResults, indIDVar = indIDVar, pVar = pVar,
clustMethod = clustMethod, cutoff = cutoff)
return(siData)
}
clustKD1 <- clusterInfWrapper(nbResults, clustMethod = "kd", cutoff = 0.02)
clustKD2 <- clusterInfWrapper(nbResults, clustMethod = "kd", cutoff = 0.1)
clustHC1 <- clusterInfWrapper(nbResults, clustMethod = "hc_absolute", cutoff = 0.01)
clustHC2 <- clusterInfWrapper(nbResults, clustMethod = "hc_absolute", cutoff = 0.1)
clustHCR <- clusterInfWrapper(nbResults, clustMethod = "hc_relative", cutoff = 2)
clustN <- clusterInfWrapper(nbResults, clustMethod = "n", cutoff = 1)
test_that("clusterInf returns a dataframe with cluster column",{
expect_true(nrow(clustKD1) == nrow(nbResults))
expect_true(nrow(clustKD2) == nrow(nbResults))
expect_true(nrow(clustHC1) == nrow(nbResults))
expect_true(nrow(clustHC2) == nrow(nbResults))
expect_true(nrow(clustHCR) == nrow(nbResults))
expect_true(nrow(clustN) == nrow(nbResults))
expect_true("cluster" %in% names(clustKD1))
expect_true("cluster" %in% names(clustKD2))
expect_true("cluster" %in% names(clustHC1))
expect_true("cluster" %in% names(clustHC2))
expect_true("cluster" %in% names(clustHCR))
expect_true("cluster" %in% names(clustN))
})
test_that("Descriptive error messages returned",{
expect_error(clusterInfWrapper(nbResults, indIDVar = "garbage"),
"garbage.1 is not in the data frame.")
expect_error(clusterInfWrapper(nbResults, pVar = "garbage"),
"garbage is not in the data frame.")
#Removing individualID columns
nbResults2 <- nbResults[!names(nbResults) %in% c("individualID.1")]
expect_error(clusterInfWrapper(nbResults2, indIDVar = "individualID"),
"individualID.1 is not in the data frame.")
nbResults3 <- nbResults[!names(nbResults) %in% c("individualID.2")]
expect_error(clusterInfWrapper(nbResults3, indIDVar = "individualID"),
"individualID.2 is not in the data frame.")
#Testing that missing clustMethod gives an error
expect_error(clusterInfWrapper(nbResults),
"Please provide a clustering method")
#Providing an invalid clustering method
expect_error(clusterInfWrapper(nbResults, clustMethod = "garbage"),
"clustMethod must be one of: n, kd, hc_absolute, hc_relative")
})
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