Nothing
context("indToPair Function")
library(nbTransmission)
#Running on indData provided in package
pairU <- indToPair(indData = indData, indIDVar = "individualID", ordered = FALSE)
pairUD <- indToPair(indData = indData, indIDVar = "individualID",
dateVar = "infectionDate", units = "days", ordered = FALSE)
pairO <- indToPair(indData = indData, indIDVar = "individualID",
dateVar = "infectionDate", units = "hours", ordered = TRUE)
test_that("indToPair returns a dataframe of the correct length",{
expect_true(is.data.frame(pairU))
expect_true(is.data.frame(pairO))
expect_true(nrow(pairU) == choose(nrow(indData), 2) * 2)
expect_true(nrow(pairO) == choose(nrow(indData), 2))
})
test_that("indToPair with returns the right column names based on dateVar",{
expect_true("infectionDate.Diff" %in% names(pairUD))
expect_true("infectionDate.Diff" %in% names(pairO))
expect_false("infectionDate.Diff" %in% names(pairU))
})
test_that("Descriptive error messages returned",{
expect_error(indToPair(indData, indIDVar = "garbage"),
"garbage is not in the data frame.")
expect_error(indToPair(indData, indIDVar = "individualID", dateVar = "garbage"),
"garbage is not in the data frame.")
#Changing dates to character variables
indData$infectionDatec <- as.character(indData$infectionDate)
expect_error(indToPair(indData, indIDVar = "individualID", dateVar = "infectionDatec"),
"infectionDatec must be either a date or a date-time (POSIXt) object.",
fixed = TRUE)
#Testing error about having ordered = TRUE with no date
expect_error(indToPair(indData, indIDVar = "individualID", ordered = TRUE),
"If ordered = TRUE, then dateVar must be provided")
#Testing that missing units gives an error
expect_error(indToPair(indData, indIDVar = "individualID", dateVar = "infectionDate"),
"Please provide units for the time difference")
#Providing an invalid clustering method
expect_error(indToPair(indData, indIDVar = "individualID", dateVar = "infectionDate",
units = "garbage"),
"units must be one of: mins, hours, days, weeks")
})
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.