tests/testthat/test_calcProbabilities.R

In nbTransmission: Naive Bayes Transmission Analysis

context("nbProbabilities Function")
library(nbTransmission)

## Use the pairData dataset which represents a TB-like outbreak
# First create a dataset of ordered pairs
orderedPair <- pairData[pairData$infectionDiffY >= 0, ]

## Create a variable called snpClose that will define probable links
# (<3 SNPs) and nonlinks (>12 SNPs) all pairs with between 2-12 SNPs
# will not be used to train.
orderedPair$snpClose <- ifelse(orderedPair$snpDist < 3, TRUE,
                               ifelse(orderedPair$snpDist > 12, FALSE, NA))

## Running the algorithm

#Creating a function with defaults equal to my simulated data
nbProbWrapper <- function(orderedPair,
                          indIDVar = "individualID",
                          pairIDVar = "pairID",
                          goldStdVar = "snpClose",
                          covariates = c("Z1", "Z2", "Z3", "Z4", "timeCat"),
                          nReps = 1,
                          progressBar = FALSE){
  
  resGen <- nbProbabilities(orderedPair = orderedPair,
                            indIDVar = indIDVar,
                            pairIDVar = pairIDVar,
                            goldStdVar = goldStdVar,
                            covariates = covariates,
                            nReps = nReps,
                            progressBar = progressBar)
  return(resGen)
}


test_that("nbProbabilities returns a list of two data frames for valid input",{
  
  resGen <- nbProbWrapper(orderedPair)
  expect_true(is.data.frame(resGen[[1]]))
  expect_true(is.data.frame(resGen[[2]]))
  
  resGen2 <- nbProbWrapper(orderedPair, progressBar = TRUE)
  expect_true(is.data.frame(resGen2[[1]]))
  expect_true(is.data.frame(resGen2[[2]]))
})


test_that("Descriptive error messages returned",{

 expect_error(nbProbWrapper(orderedPair, indIDVar = "garbage"),
              "garbage.1 is not in the data frame.")
  
  expect_error(nbProbWrapper(orderedPair, pairIDVar = "garbage"),
               "garbage is not in the data frame.")
  
  expect_error(nbProbWrapper(orderedPair, goldStdVar = "garbage"),
               "garbage is not in the data frame.")
 
 #Removing individualID.1 column
 orderedPair2 <- orderedPair[!names(orderedPair) %in% c("individualID.1")]
 expect_error(nbProbWrapper(orderedPair2, indIDVar = "individualID"),
              "individualID.1 is not in the data frame.")
 
 #Removing individualID.1 column
 orderedPair3 <- orderedPair[!names(orderedPair) %in% c("individualID.2")]
 expect_error(nbProbWrapper(orderedPair3, indIDVar = "individualID"),
              "individualID.2 is not in the data frame.")

 #Using garbage covariates
 expect_error(nbProbWrapper(orderedPair, covariates = "garbage"),
              "At least one of the covariates is not in the data frame.")
 
 #Making some covariates factors
 orderedPair4 <- orderedPair
 orderedPair4$Z1 <- as.character(orderedPair4$Z1)
 expect_error(nbProbWrapper(orderedPair4),
              paste0("Z1 is not a factor"))
 
 orderedPair4$Z2 <- as.character(orderedPair4$Z2)
 expect_error(nbProbWrapper(orderedPair4),
              paste0("Z1, Z2 are not factors"))
 
})