tests/testthat/testwithanchoringdata.R

In DRomics: Dose Response for Omics

test_that("Test DRomics on anchoring data", {
  skip_on_cran()
  
  # importation and check of apical anchoring data
  # datafilename <- system.file("extdata", "apical_anchoring.txt", package="DRomics")
  # (o <- continuousanchoringdata(datafilename, backgrounddose = 0.1, check = TRUE))
  data("Scenedesmus_apical")
  (o <- continuousanchoringdata(Scenedesmus_apical, backgrounddose = 0.1, check = TRUE))
  
  
  # Use of only one endpoint
  #(o <- continuousanchoringdata(Scenedesmus_apical[c(1,2), ], 
  #  backgrounddose = 0.1,check = TRUE)) # growth
  # (o <- continuousanchoringdata(Scenedesmus_apical[c(1,3), ], 
  #   backgrounddose = 0.1, check = TRUE)) # photosynthesis
  plot(o)
  
  # item selection using the three methods
  (s_quad <- itemselect(o, select.method = "quadratic", FDR = 0.05))
  (s_lin <- itemselect(o, select.method = "linear", FDR = 0.05))
  (s_ANOVA <- itemselect(o, select.method = "ANOVA", FDR = 0.05))
  
  # fit
  (f <- drcfit(s_quad, progressbar = TRUE))
  f$fitres
  plot(f)
  plot(f, dose_log_transfo = FALSE)
  plot(f, plot.type = "dose_residuals")
  
  
  # calculation of benchmark doses
  # options in shiny : z (numerical positive value), x (numerical positive value : percentage)
  (r <- bmdcalc(f, z = 1, x = 10))
  r$res
  
  # plot of BMD with gradient
  bmdplotwithgradient(r$res, xmax = max(f$omicdata$dose))
  
  # various plot of fitted curves (without data)
  curvesplot(r$res, xmax = max(f$omicdata$dose), 
             facetby = "model", colorby = "model")
  curvesplot(r$res, xmax = max(f$omicdata$dose), 
             facetby = "typology")
  
  
  # Calculation of confidence intervals on BMDs by Bootstrap
  # niter <- 1000
  niter <- 10
  (b <- bmdboot(r, niter = niter)) # niter should be fixed at least at 1000 to get a reasonable precision
  plot(b)
}
)