tests/testthat/test_plot_AbanicoPlot.R

In R-Lum/Luminescence: Comprehensive Luminescence Dating Data Analysis

test_that("Test examples from the example page", {
  testthat::skip_on_cran()
  local_edition(3)

   ## load example data and recalculate to Gray
  data(ExampleData.DeValues, envir = environment())
  ExampleData.DeValues <- ExampleData.DeValues$CA1

  ## plot the example data straightforward
  expect_silent(plot_AbanicoPlot(data = ExampleData.DeValues))

  ## now with linear z-scale
  expect_silent(plot_AbanicoPlot(data = ExampleData.DeValues,
                   log.z = FALSE))

  ## now with output of the plot parameters
  expect_type(plot_AbanicoPlot(data = ExampleData.DeValues,
                            output = TRUE), "list")

  ## now with adjusted z-scale limits
  expect_silent(plot_AbanicoPlot(data = ExampleData.DeValues,
                   zlim = c(10, 200)))

  ## now with adjusted x-scale limits
  expect_silent(plot_AbanicoPlot(data = ExampleData.DeValues,
                   xlim = c(0, 20)))

  ## now with rug to indicate individual values in KDE part
  expect_silent(plot_AbanicoPlot(data = ExampleData.DeValues,
                   rug = TRUE))

  ## now with a smaller bandwidth for the KDE plot
  expect_silent(plot_AbanicoPlot(data = ExampleData.DeValues,
                   bw = 0.04))

  ## now with a histogram instead of the KDE plot
  expect_silent(plot_AbanicoPlot(data = ExampleData.DeValues,
                   hist = TRUE,
                   kde = FALSE))

  ## now with a KDE plot and histogram with manual number of bins
  expect_silent(plot_AbanicoPlot(data = ExampleData.DeValues,
                   hist = TRUE,
                   breaks = 20))

  ## now with a KDE plot and a dot plot
  expect_silent(plot_AbanicoPlot(data = ExampleData.DeValues,
                   dots = TRUE))

  ## now with user-defined plot ratio
  expect_silent(plot_AbanicoPlot(data = ExampleData.DeValues,
                   plot.ratio = 0.5))

  ## now with user-defined central value
  expect_silent(plot_AbanicoPlot(data = ExampleData.DeValues,
                   z.0 = 70))

  ## now with median as central value
  expect_silent(plot_AbanicoPlot(data = ExampleData.DeValues,
                   z.0 = "median"))

  ## now with the 17-83 percentile range as definition of scatter
  expect_silent(plot_AbanicoPlot(data = ExampleData.DeValues,
                   z.0 = "median",
                   dispersion = "p17"))

  ## now with user-defined green line for minimum age model
  CAM <- calc_CentralDose(ExampleData.DeValues,
                          plot = FALSE)

  expect_silent(plot_AbanicoPlot(data = ExampleData.DeValues,
                   line = CAM,
                   line.col = "darkgreen",
                   line.label = "CAM"))

  ## now create plot with legend, colour, different points and smaller scale
  expect_silent(plot_AbanicoPlot(data = ExampleData.DeValues,
                   legend = "Sample 1",
                   col = "tomato4",
                   bar.col = "peachpuff",
                   pch = "R",
                   cex = 0.8))

  ## now without 2-sigma bar, polygon, grid lines and central value line
  expect_silent(plot_AbanicoPlot(data = ExampleData.DeValues,
                   bar.col = FALSE,
                   polygon.col = FALSE,
                   grid.col = FALSE,
                   y.axis = FALSE,
                   lwd = 0))

  ## now with direct display of De errors, without 2-sigma bar
  expect_silent(plot_AbanicoPlot(data = ExampleData.DeValues,
                   bar.col = FALSE,
                   ylab = "",
                   y.axis = FALSE,
                   error.bars = TRUE))

  ## now with user-defined axes labels
  expect_silent(plot_AbanicoPlot(data = ExampleData.DeValues,
                   xlab = c("Data error (%)",
                            "Data precision"),
                   ylab = "Scatter",
                   zlab = "Equivalent dose [Gy]"))

  ## now with minimum, maximum and median value indicated
  expect_silent(plot_AbanicoPlot(data = ExampleData.DeValues,
                   stats = c("min", "max", "median")))

  ## now with a brief statistical summary as subheader
  expect_silent(plot_AbanicoPlot(data = ExampleData.DeValues,
                   summary = c("n", "in.2s")))

  ## now with another statistical summary
  expect_silent(plot_AbanicoPlot(data = ExampleData.DeValues,
                   summary = c("mean.weighted", "median"),
                   summary.pos = "topleft"))

  ## now a plot with two 2-sigma bars for one data set
  expect_silent(plot_AbanicoPlot(data = ExampleData.DeValues,
                   bar = c(30, 100)))

  ## now the data set is split into sub-groups, one is manipulated
  data.1 <- ExampleData.DeValues[1:30,]
  data.2 <- ExampleData.DeValues[31:62,] * 1.3
  data.3 <- list(data.1, data.2)

  ## now the two data sets are plotted in one plot
  expect_silent(plot_AbanicoPlot(data = data.3))

  ## now with some graphical modification
  expect_silent(plot_AbanicoPlot(data = data.3,
                   z.0 = "median",
                   col = c("steelblue4", "orange4"),
                   bar.col = c("steelblue3", "orange3"),
                   polygon.col = c("steelblue1", "orange1"),
                   pch = c(2, 6),
                   angle = c(30, 50),
                   summary = c("n", "in.2s", "median")))

  ## create Abanico plot with predefined layout definition
  expect_silent(plot_AbanicoPlot(data = ExampleData.DeValues,
                   layout = "journal"))

  ## now with predefined layout definition and further modifications
  expect_silent(plot_AbanicoPlot(data = data.3,
                   z.0 = "median",
                   layout = "journal",
                   col = c("steelblue4", "orange4"),
                   bar.col = adjustcolor(c("steelblue3", "orange3"),
                                         alpha.f = 0.5),
                   polygon.col = c("steelblue3", "orange3")))

  ## for further information on layout definitions see documentation
  ## of function get_Layout()

  ## now with manually added plot content
  ## create empty plot with numeric output
  expect_type(plot_AbanicoPlot(data = ExampleData.DeValues,
                         pch = NA,
                         output = TRUE), "list")


})

test_that("Cause full function stop", {
  testthat::skip_on_cran()
  local_edition(3)

  ##wrong input data
  expect_error(plot_AbanicoPlot(data = "Michael"),
               regexp = "Input data format is neither 'data.frame' nor 'RLum.Results'")


})