tests/testthat/test-ldnegbinomial.R

In jasp-stats/jaspDistributions: Distributions Module for JASP

context("Discover Distributions - Negative Binomial")

options <- jaspTools::analysisOptions("LDnegbinomial")
options$.meta <- list(newVariableName = list(containsColumn = TRUE), variable = list(
  containsColumn = TRUE))
options$chiSquare <- TRUE
options$ciInterval <- TRUE
options$ciIntervalInterval <- 0.95
options$ecdf <- TRUE
options$estCDF <- TRUE
options$estPMF <- TRUE
options$explanatoryText <- TRUE
options$highlightDensity <- TRUE
options$highlightProbability <- TRUE
options$histogram <- TRUE
options$methodMLE <- TRUE
options$min <- 2
options$moments <- TRUE
options$newVariableName <- ""
options$outputEstimates <- TRUE
options$outputSE <- TRUE
options$par <- 0.5
options$parsSupportMoments <- TRUE
options$plotCMF <- TRUE
options$ppplot <- TRUE
options$qqplot <- TRUE
options$summary <- TRUE
options$variable <- "NBinom100(nsuccess=1,p=0.5)"
set.seed(1)
results <- jaspTools::runAnalysis("LDnegbinomial", "Distributions.csv", options)


test_that("Empirical Cumulative Distribution plot matches", {
  plotName <- results[["results"]][["dataContainer"]][["collection"]][["dataContainer_ecdf"]][["data"]]
  testPlot <- results[["state"]][["figures"]][[plotName]][["obj"]]
  jaspTools::expect_equal_plots(testPlot, "empirical-cumulative-distribution")
})

test_that("Bar plot matches", {
  plotName <- results[["results"]][["dataContainer"]][["collection"]][["dataContainer_histogram"]][["data"]]
  testPlot <- results[["state"]][["figures"]][[plotName]][["obj"]]
  jaspTools::expect_equal_plots(testPlot, "bar-plot")
})

test_that("Observed Moments table results match", {
  table <- results[["results"]][["dataContainer"]][["collection"]][["dataContainer_moments"]][["data"]]
  jaspTools::expect_equal_tables(table,
                      list(0.79, 1, 0.79, 1.4059, 2, 2.03))
})

test_that("Descriptives table results match", {
  table <- results[["results"]][["dataContainer"]][["collection"]][["dataContainer_summary"]][["data"]]
  jaspTools::expect_equal_tables(table,
                      list(5, 0.79, 0, 0, 0, 1, 100, 1.19167991092449, 1.42010101010101,
                           "NBinom100(nsuccess=1,p=0.5)"))
})

test_that("Estimated Parameters table results match", {
  table <- results[["results"]][["mleContainer"]][["collection"]][["mleContainer_estParametersTable"]][["data"]]
  jaspTools::expect_equal_tables(table,
                      list(0.840421648116513, 0.206188804688018, "k", 0.323594131540805,
                           1.47465449154501, 0.515462577383601, 0.311965427262039, "p",
                           0.103826984437837, 0.718959727505163))
})

test_that("Empirical vs. Theoretical CDF plot matches", {
  plotName <- results[["results"]][["mleContainer"]][["collection"]][["mleContainer_mleFitAssessment"]][["collection"]][["mleContainer_mleFitAssessment_estCDF"]][["data"]]
  testPlot <- results[["state"]][["figures"]][[plotName]][["obj"]]
  jaspTools::expect_equal_plots(testPlot, "empirical-vs-theoretical-cdf")
})

test_that("Histogram vs. Theoretical PMF plot matches", {
  plotName <- results[["results"]][["mleContainer"]][["collection"]][["mleContainer_mleFitAssessment"]][["collection"]][["mleContainer_mleFitAssessment_estPMF"]][["data"]]
  testPlot <- results[["state"]][["figures"]][[plotName]][["obj"]]
  jaspTools::expect_equal_plots(testPlot, "histogram-vs-theoretical-pmf")
})

test_that("Fit Statistics table results match", {
  table <- results[["results"]][["mleContainer"]][["collection"]][["mleContainer_mleFitAssessment"]][["collection"]][["mleContainer_mleFitAssessment_fitStatisticsTable"]][["data"]]
  jaspTools::expect_equal_tables(table,
                      list(0.883474156794088, 1.74272206036203, "Chi-square"))
})

test_that("P-P plot matches", {
  plotName <- results[["results"]][["mleContainer"]][["collection"]][["mleContainer_mleFitAssessment"]][["collection"]][["mleContainer_mleFitAssessment_ppplot"]][["data"]]
  testPlot <- results[["state"]][["figures"]][[plotName]][["obj"]]
  jaspTools::expect_equal_plots(testPlot, "p-p-plot")
})

test_that("Q-Q plot matches", {
  plotName <- results[["results"]][["mleContainer"]][["collection"]][["mleContainer_mleFitAssessment"]][["collection"]][["mleContainer_mleFitAssessment_qqplot"]][["data"]]
  testPlot <- results[["state"]][["figures"]][[plotName]][["obj"]]
  jaspTools::expect_equal_plots(testPlot, "q-q-plot")
})

test_that("Cumulative Probability Plot matches", {
  plotName <- results[["results"]][["plotCMF"]][["collection"]][["plotCMF_cmfPlot"]][["data"]]
  testPlot <- results[["state"]][["figures"]][[plotName]][["obj"]]
  jaspTools::expect_equal_plots(testPlot, "cumulative-probability-plot")
})

test_that("Probability Mass Plot matches", {
  plotName <- results[["results"]][["plotPMF"]][["collection"]][["plotPMF_pmfPlot"]][["data"]]
  testPlot <- results[["state"]][["figures"]][[plotName]][["obj"]]
  jaspTools::expect_equal_plots(testPlot, "probability-mass-plot")
})