tests/testthat/test-viralpreds.R

In viralmodels: Viral Load and CD4 Lymphocytes Regression Models

test_that("viralpreds() works", {
  library(dplyr)
  library(magrittr)
  library(baguette)
  library(kernlab)
  library(kknn)
  library(ranger)
  library(rules)
  library(glmnet)
  # Define the function to impute values in the undetectable range
  set.seed(123)
  impute_undetectable <- function(column) {
    ifelse(column <= 40,
           rexp(sum(column <= 40), rate = 1/13) + 1,
           column)
  }
  # Apply the function to all vl columns using purrr's map_dfc
  library(viraldomain)
  data("viral", package = "viraldomain")
  viral_imputed <- viral %>%
    mutate(across(starts_with("vl"), ~impute_undetectable(.x)))
  traindata <- viral_imputed
  target <- "cd_2022"
  viralvars <- c("vl_2019", "vl_2021", "vl_2022")
  logbase <- 10
  pliegues <- 5
  repeticiones <- 2
  rejilla <- 2
  semilla <- 123
  result <- viraltab(traindata, semilla, target, viralvars, logbase, pliegues,
                     repeticiones, rejilla, rank_output = FALSE) %>% 
    viralpreds(semilla, traindata, "full")
  # Snapshot the predictions and RMSE output
  expect_snapshot(result$predictions)
  expect_snapshot(result$RMSE)
})