tests/testthat/test-convert_rate.R

In respR: Import, Process, Analyse, and Calculate Rates from Respirometry Data

# library(testthat)
# testthat::test_file("tests/testthat/test-convert_rate.R")
# covr::file_coverage("R/convert_rate.R", "tests/testthat/test-convert_rate.R")
# cvr <- covr::package_coverage()
# covr::report(cvr)

capture.output({  ## stops printing outputs on assigning

  if (!identical(Sys.getenv("NOT_CRAN"), "true")) return()
  skip_on_cran()

  test_that("convert_rate - works with default values", {
    expect_equal(suppressWarnings(convert_rate(10, volume = 1, time.unit = "s", oxy.unit = "mg/l")$rate.output),
                 36000)
  })

  test_that("convert_rate - accepts all allowed classes of 'x' input", {
    # numeric
    expect_error(suppressWarnings(convert_rate(10, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
                 NA)
    expect_message(suppressWarnings(convert_rate(10, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
                   "convert_rate: Numeric input detected. Converting all numeric rates.")

    # calc_rate
    cr_obj <- suppressWarnings(calc_rate(urchins.rd[,1:2], plot = F)) ## whole dataset
    expect_error(suppressWarnings(convert_rate(cr_obj, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
                 NA)
    expect_message(suppressWarnings(convert_rate(cr_obj, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
                   "convert_rate: Object of class 'calc_rate' detected. Converting all rates in '\\$rate'.")

    # calc_rate.int
    dt <- intermittent.rd %>%
      subset_data(from = 1) # removes first value at 0 time because of annoying messages during adjustments
    dt.insp <- inspect(dt, plot = F)
    sts <- c(1,2100,3899) # different from help file because first row removed above
    cr.int_obj <- calc_rate.int(dt.insp,
                                starts = sts,
                                plot = F)
    expect_error(suppressWarnings(convert_rate(cr.int_obj, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
                 NA)
    expect_message(suppressWarnings(convert_rate(cr.int_obj, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
                   "convert_rate: Object of class 'calc_rate.int' detected. Converting all rates in '\\$rate'.")

    # auto_rate
    ar_obj <- suppressWarnings(calc_rate(urchins.rd[,1:2], plot = F)) ## whole dataset
    expect_error(suppressWarnings(convert_rate(ar_obj, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
                 NA)
    expect_message(suppressWarnings(convert_rate(ar_obj, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
                   "convert_rate: Object of class 'calc_rate' detected. Converting all rates in '\\$rate'.")

    # auto_rate.int
    ar.int_obj <- auto_rate.int(dt.insp,
                                starts = sts,
                                width = 100,
                                measure = 600,
                                plot = F)
    expect_error(suppressWarnings(convert_rate(ar.int_obj, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
                 NA)
    expect_message(suppressWarnings(convert_rate(ar.int_obj, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
                   "convert_rate: Object of class 'auto_rate.int' detected. Converting all rates in '\\$rate'.")

    # adjust_rate - with numeric input
    adj_rt_num <- adjust_rate(-0.01, -0.001)
    expect_error(suppressWarnings(convert_rate(adj_rt_num, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
                 NA)
    expect_message(suppressWarnings(convert_rate(adj_rt_num, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
                   "convert_rate: Object of class 'adjust_rate' detected. Converting all adjusted rates in '\\$rate.adjusted'.")

    # adjust_rate - with calc_rate input
    adj_rt_cr <- adjust_rate(cr_obj, -0.005)
    expect_error(suppressWarnings(convert_rate(adj_rt_cr, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
                 NA)
    expect_message(suppressWarnings(convert_rate(adj_rt_cr, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
                   "convert_rate: Object of class 'adjust_rate' detected. Converting all adjusted rates in '\\$rate.adjusted'.")

    # adjust_rate - with calc_rate.int input
    adj_rt_cr.int <- adjust_rate(cr.int_obj, -0.0001)
    expect_error(suppressWarnings(convert_rate(adj_rt_cr.int, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
                 NA)
    expect_message(suppressWarnings(convert_rate(adj_rt_cr.int, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
                   "convert_rate: Object of class 'adjust_rate' detected. Converting all adjusted rates in '\\$rate.adjusted'.")

    # adjust_rate - with auto_rate input
    adj_rt_ar <- adjust_rate(ar_obj, -0.005)
    expect_error(suppressWarnings(convert_rate(adj_rt_ar, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
                 NA)
    expect_message(suppressWarnings(convert_rate(adj_rt_ar, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
                   "convert_rate: Object of class 'adjust_rate' detected. Converting all adjusted rates in '\\$rate.adjusted'.")

    # adjust_rate - with auto_rate.int input
    adj_rt_ar.int <- adjust_rate(ar.int_obj, -0.0001)
    expect_error(suppressWarnings(convert_rate(adj_rt_ar.int, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
                 NA)
    expect_message(suppressWarnings(convert_rate(adj_rt_ar.int, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
                   "convert_rate: Object of class 'adjust_rate' detected. Converting all adjusted rates in '\\$rate.adjusted'.")

    # calc_rate.bg (incl with mass/area even tho wrong)
    cr.bg.obj <- calc_rate.bg(urchins.rd, time = 1, oxygen = 18:19)
    expect_error(suppressWarnings(convert_rate(cr.bg.obj, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
                 NA)
    expect_message(suppressWarnings(convert_rate(cr.bg.obj, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
                   "convert_rate: Object of class 'calc_rate.bg' detected. Converting all background rates in '\\$rate.bg'.")
    expect_warning(convert_rate(cr.bg.obj, volume = 1, time.unit = "s", oxy.unit = "mg/l", mass = 1),
                   "convert_rate: A 'calc_rate.bg' \\(i.e. background) object is being converted, and a 'mass' or 'area' has been entered. Are you sure you want to do this?")
    expect_warning(convert_rate(cr.bg.obj, volume = 1, time.unit = "s", oxy.unit = "mg/l", area = 1),
                   "convert_rate: A 'calc_rate.bg' \\(i.e. background) object is being converted, and a 'mass' or 'area' has been entered. Are you sure you want to do this?")

    # calc_rate.ft - invalid input
    insp.ft.obj.outO2.1col.inO2.1col<- suppressWarnings(suppressMessages(inspect.ft(flowthrough_mult.rd, time = 1,
                                                                                    out.oxy = 2, in.oxy = 6, plot = F)))
    crft.obj.1rate <- calc_rate.ft(insp.ft.obj.outO2.1col.inO2.1col,
                                   from = 5, to = 900, by = "row",
                                   flowrate = 2, plot = F)
    expect_error(suppressWarnings(convert_rate(crft.obj.1rate, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
                 "convert_rate: Object of class 'calc_rate.ft' detected. \nPlease use 'convert_rate.ft' to convert the rate.")
    # none of the above - invalid input
    expect_error(suppressWarnings(convert_rate(urchins.rd, volume = 1, time.unit = "s", oxy.unit = "mg/l")),
                 "convert_rate: 'x' is not an accepted input.")

  })

  # use known warnings to do these checks
  # maybe make this more specific later
  test_that("convert_rate - falls back to default inputs properly", {
    expect_warning(convert_rate(10, volume = 1,  time.unit = "s", oxy.unit = "mg/l"),
                   "convert_rate: The 'output.unit' is not provided. Applying default: 'mg/h'")
    expect_equal(suppressWarnings(convert_rate(10, volume = 1,  time.unit = "s", oxy.unit = "mg/l")$output.unit),
                 "mgO2/hr")

    expect_warning(convert_rate(10, volume = 1,  time.unit = "s", oxy.unit = "mg/l", mass = 1),
                   "convert_rate: The 'output.unit' is not provided. Applying default: 'mg/h/kg'")
    expect_equal(suppressWarnings(convert_rate(10, volume = 1,  time.unit = "s", oxy.unit = "mg/l", mass = 1)$output.unit),
                 "mgO2/hr/kg")

    expect_warning(convert_rate(10, volume = 1,  time.unit = "s", oxy.unit = "mg/l", area = 1),
                   "convert_rate: The 'output.unit' is not provided. Applying default: 'mg/h/m2'")
    expect_equal(suppressWarnings(convert_rate(10, volume = 1,  time.unit = "s", oxy.unit = "mg/l", area = 1)$output.unit),
                 "mgO2/hr/m2")
  })

  #
  test_that("convert_rate - (adjust_scale) produces valid output", {
    expect_is(adjust_scale(10, "mg", "kg"), "numeric")
    expect_is(adjust_scale(10, "ml", "l"), "numeric")
  })

  ##
  test_that("convert_rate - stops if 'oxy.unit' or 'time.unit' are NULL or numeric", {
    expect_error(convert_rate(10, volume = 1, oxy.unit = "umol/l", time.unit = NULL),
                 "convert_rate: The 'time.unit' of the original data is required.")
    expect_error(convert_rate(10, volume = 1, oxy.unit = "umol/l", time.unit = 1.1),
                 "convert_rate: The 'time.unit' of the original data is required.")

    expect_error(convert_rate(10, volume = 1, oxy.unit = NULL, time.unit = "s"),
                 "convert_rate: The 'oxy.unit' of the original data is required.")
    expect_error(convert_rate(10, volume = 1, oxy.unit = 1.1, time.unit = "s"),
                 "convert_rate: The 'oxy.unit' of the original data is required.")
  })

  test_that("convert_rate - stops if 'volume' is NULL or NOT numeric", {
    expect_error(convert_rate(10, volume = NULL, oxy.unit = "umol/l", time.unit = "s", output.unit = "mg/h/g"),
                 "convert_rate: The 'volume' input is required.")
    expect_error(convert_rate(10, volume = "text", oxy.unit = "umol/l", time.unit = "s", output.unit = "mg/h/g"),
                 "convert_rate: The 'volume' input is required.")
  })

  test_that("convert_rate - stops if both 'mass' and 'area' inputs are entered", {
    expect_error(convert_rate(10, volume = 1, oxy.unit = "umol/l", time.unit = "s", output.unit = "mg/h/g",
                              mass = 1,
                              area = 1),
                 "convert_rate: Cannot have inputs for both 'mass' and 'area'.")
  })

  test_that("convert_rate - stops if 'output.unit' requires a 'mass' or 'area' input and neither is provided", {
    expect_error(convert_rate(10, volume = 1, oxy.unit = "mg/l", time.unit = "s", output.unit = "mg/h/g",
                              mass = NULL, area = NULL),
                 "convert_rate: 'output.unit' requires a value for 'mass' or 'area'")
    expect_error(convert_rate(10, volume = 1, oxy.unit = "mg/l", time.unit = "s", output.unit = "mg/h/cm2",
                              mass = NULL, area = NULL),
                 "convert_rate: 'output.unit' requires a value for 'mass' or 'area'")
  })

  test_that("convert_rate - stops if a 'mass' or 'area' input entered but output.unit is not mass- or area-specific", {
    expect_error(convert_rate(10, volume = 1, oxy.unit = "mg/l", time.unit = "s", output.unit = "mg/h",
                              mass = 1, area = NULL),
                 "convert_rate: A 'mass' has been entered, but a mass-specific unit has not been specified in 'output.unit'.")
    expect_error(convert_rate(10, volume = 1, oxy.unit = "mg/l", time.unit = "s", output.unit = "mg/h",
                              mass = NULL, area = 1),
                 "convert_rate: An 'area' has been entered, but an area-specific unit has not been specified in 'output.unit'.")
  })

  test_that("convert_rate - S3 generics work as expected", {
    res_abs <- convert_rate(-0.0001534657, oxy.unit = "mg/L", time.unit = "s", output.unit = "mg/h",
                            volume = 0.0032245)
    res_abs_mult <- convert_rate(c(-0.0001534657, -0.00015, -0.00016, -0.00017), oxy.unit = "mg/L", time.unit = "s", output.unit = "mg/h",
                                 volume = 0.0032245)
    res_ms <- convert_rate(-0.0001534657, oxy.unit = "mg/L", time.unit = "s", output.unit = "mg/h/g",
                           volume = 0.0032245, mass = 0.00534)
    res_as <- convert_rate(-0.0001534657, oxy.unit = "mg/L", time.unit = "s", output.unit = "mg/h/mm2",
                           volume = 0.0032245, area = 0.000001429)

    ## summary
    expect_output(summary(res_abs))
    expect_output(summary(res_ms))
    expect_output(summary(res_as))

    expect_error(summary(res_abs, pos = 2),
                 "summary.convert_rate: Invalid 'pos' rank: only 1 rates found.")
    expect_error(summary(res_abs, pos = 2:3),
                 "summary.convert_rate: Invalid 'pos' rank: only 1 rates found.")
    expect_output(summary(res_abs_mult))
    expect_output(summary(res_abs_mult, pos = 2:3))
    expect_output(summary(res_abs_mult, pos = 2:3),
                  "Summary of converted rates from entered 'pos' rank\\(s)")

    expect_is(summary(res_abs_mult, export = TRUE),
              "data.table")

    ## print
    expect_output(print(res_abs))
    expect_error(print(res_abs, pos = 2),
                 "print.convert_rate: Invalid 'pos' rank: only 1 rates found.")
    expect_error(print(res_abs, pos = 2:3),
                 "print.convert_rate: 'pos' must be a single value. To examine multiple results use summary().")
    expect_output(print(res_ms))
    expect_output(print(res_as))

    ## mean
    ## absolute
    expect_output(suppressWarnings(mean(res_abs)))
    expect_message(mean(res_abs),
                   "mean.convert_rate: Only 1 rate found or selected. Returning mean rate anyway...")
    expect_equal(suppressWarnings(mean(res_abs, export = TRUE)),
                 mean(res_abs$rate.output))
    ## mass-spec
    expect_output(suppressWarnings(mean(res_ms)))
    expect_message(mean(res_ms),
                   "mean.convert_rate: Only 1 rate found or selected. Returning mean rate anyway...")
    expect_equal(suppressWarnings(mean(res_ms, export = TRUE)),
                 mean(res_ms$rate.output))
    ## area-spec
    expect_output(suppressWarnings(mean(res_as)))
    expect_message(mean(res_as),
                   "mean.convert_rate: Only 1 rate found or selected. Returning mean rate anyway...")
    expect_equal(suppressWarnings(mean(res_as, export = TRUE)),
                 mean(res_as$rate.output))

    ## check multiple rates have correct mean
    rate <- suppressWarnings(inspect(urchins.rd[,1:2], plot = F)) %>%
      auto_rate(plot = F) %>%
      convert_rate(oxy.unit = "mg/L", time.unit = "s", output.unit = "mg/h/mm2",
                   volume = 0.0032245, area = 0.000001429)
    expect_output(suppressWarnings(mean(rate)))
    expect_equal(mean(rate, export = TRUE),
                 mean(rate$rate.output))

    # mean and pos
    expect_output(mean(rate, pos = 1:3),
                  "Mean of rate results from entered 'pos' ranks:")
    expect_error(mean(rate, pos = 5:6),
                 "mean.convert_rate: Invalid 'pos' rank: only 4 rates found.")

  })

  test_that("convert_rate - stops if units require S, t, and P", {

    expect_error(convert_rate(-0.0001534657, oxy.unit = "mL/L", time.unit = "s", output.unit = "mg/h/mm2",
                              volume = 0.0032245,
                              area = 0.000001429),
                 "convert_rate: Input or output units require Salinity input")

    expect_error(convert_rate(-0.0001534657, oxy.unit = "mL/L", time.unit = "s", output.unit = "mg/h/mm2",
                              volume = 0.0032245,
                              S = 35,
                              area = 0.000001429),
                 "convert_rate: Input or output units require Temperature input")

    expect_message(convert_rate(-0.0001534657, oxy.unit = "mL/L", time.unit = "s", output.unit = "mg/h/mm2",
                                volume = 0.0032245,
                                S = 35, t = 31, P = NULL,
                                area = 0.000001429),
                   "convert_rate: Input or output units require Atmospheric Pressure input")

  })

  test_that("convert_rate - stops if S, t, and P are vectors", {

    expect_error(convert_rate(-0.0001534657, oxy.unit = "mL/L", time.unit = "s", output.unit = "mg/h/mm2",
                              volume = 0.0032245,
                              area = 0.000001429,
                              S = 35:36,
                              t= 12,
                              P = 1.01),
                 "convert_rate: The 'S' input should be a single value.")
    expect_error(convert_rate(-0.0001534657, oxy.unit = "mL/L", time.unit = "s", output.unit = "mg/h/mm2",
                              volume = 0.0032245,
                              area = 0.000001429,
                              S = 35,
                              t= 12:13,
                              P = 1.01),
                 "convert_rate: The 't' input should be a single value.")
    expect_error(convert_rate(-0.0001534657, oxy.unit = "mL/L", time.unit = "s", output.unit = "mg/h/mm2",
                              volume = 0.0032245,
                              area = 0.000001429,
                              S = 35,
                              t= 12,
                              P = c(1,1.01)),
                 "convert_rate: The 'P' input should be a single value.")

  })

  test_that("convert_rate - correct S, t, and P values saved to summary", {

    # single rate value
    expect_equal(convert_rate(-0.0001534657, oxy.unit = "mL/L", time.unit = "s", output.unit = "mg/h/mm2",
                              volume = 0.0032245,
                              area = 0.000001429,
                              S = 35,
                              t= 12,
                              P = 1.01)$summary$S,
                 35)
    # multiple rate values
    expect_equal(convert_rate(c(-0.001, -0.002), oxy.unit = "mL/L", time.unit = "s", output.unit = "mg/h/mm2",
                              volume = 0.0032245,
                              area = 0.000001429,
                              S = 35,
                              t= 12,
                              P = 1.01)$summary$S,
                 c(35,35))
    # single rate value
    expect_equal(convert_rate(-0.0001534657, oxy.unit = "mL/L", time.unit = "s", output.unit = "mg/h/mm2",
                              volume = 0.0032245,
                              area = 0.000001429,
                              S = 35,
                              t= 12,
                              P = 1.01)$summary$t,
                 12)
    # multiple rate values
    expect_equal(convert_rate(c(-0.001, -0.002), oxy.unit = "mL/L", time.unit = "s", output.unit = "mg/h/mm2",
                              volume = 0.0032245,
                              area = 0.000001429,
                              S = 35,
                              t= 12,
                              P = 1.01)$summary$t,
                 c(12,12))
    # single rate value
    expect_equal(convert_rate(-0.0001534657, oxy.unit = "mL/L", time.unit = "s", output.unit = "mg/h/mm2",
                              volume = 0.0032245,
                              area = 0.000001429,
                              S = 35,
                              t= 12,
                              P = 1.01)$summary$P,
                 1.01)
    # multiple rate values
    expect_equal(convert_rate(c(-0.001, -0.002), oxy.unit = "mL/L", time.unit = "s", output.unit = "mg/h/mm2",
                              volume = 0.0032245,
                              area = 0.000001429,
                              S = 35,
                              t= 12,
                              P = 1.01)$summary$P,
                 c(1.01,1.01))
    # NA when NULL
    expect_equal(convert_rate(-0.0001534657, oxy.unit = "mg/L", time.unit = "s", output.unit = "mg/h/mm2",
                              volume = 0.0032245,
                              area = 0.000001429)$summary$S,
                 NA)
    expect_equal(convert_rate(-0.0001534657, oxy.unit = "mg/L", time.unit = "s", output.unit = "mg/h/mm2",
                              volume = 0.0032245,
                              area = 0.000001429)$summary$t,
                 NA)
    expect_equal(convert_rate(-0.0001534657, oxy.unit = "mg/L", time.unit = "s", output.unit = "mg/h/mm2",
                              volume = 0.0032245,
                              area = 0.000001429)$summary$P,
                 NA)
    # multiple rate values
    expect_equal(convert_rate(c(-0.001, -0.002), oxy.unit = "mg/L", time.unit = "s", output.unit = "mg/h/mm2",
                              volume = 0.0032245,
                              area = 0.000001429)$summary$S,
                 c(NA,NA))
  })


  ## Possibly update these in future with exact values we know are correct.
  ## For now, these just flag up if code changes cause output changes
  test_that("convert_rate - outputs correct conversion values - absolute rates", {

    res <- convert_rate(93.1, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h", volume = 1, S = 35, t = 25, P = 1.013253)
    expect_equal(res$rate.output, 22626.99, tolerance = 0.01) # exact value
    ## inputs and outputs are saved in object correctly
    expect_equal(res$rate.input, 93.1)
    expect_equal(res$inputs$oxy.unit, "%Air")
    expect_equal(res$inputs$time.unit, "sec")
    expect_equal(res$output.unit, "mgO2/hr")
    expect_equal(res$summary$rate.input, 93.1)
    expect_equal(res$summary$rate.output, 22626.99, tolerance = 0.01)
    expect_equal(res$summary$rate.abs, 22626.99, tolerance = 0.01)

    res <- convert_rate(4303, oxy.unit = "ug/l", time.unit = "hr", output.unit = "ml/minute", volume = 1, S = 35, t = 25, P = 1.013253)
    expect_equal(res$rate.output, 0.05477929, tolerance = 0.00001) # exact value
    ## inputs and outputs are saved in object correctly
    expect_equal(res$rate.input, 4303)
    expect_equal(res$inputs$oxy.unit, "ug/L")
    expect_equal(res$inputs$time.unit, "hr")
    expect_equal(res$output.unit, "mLO2/min")
    expect_equal(res$summary$rate.input, 4303)
    expect_equal(res$summary$rate.output, 0.05477929, tolerance = 0.00001)
    expect_equal(res$summary$rate.abs, 0.05477929, tolerance = 0.00001)

    res <- convert_rate(234, oxy.unit = "hPa", time.unit = "min", output.unit = "umol/min", volume = 1, S = 35, t = 25, P = 1.013253)
    expect_equal(res$rate.output, 236.739, tolerance = 0.001) # exact value
    ## inputs and outputs are saved in object correctly
    expect_equal(res$rate.input, 234)
    expect_equal(res$inputs$oxy.unit, "hPa")
    expect_equal(res$inputs$time.unit, "min")
    expect_equal(res$output.unit, "umolO2/min")
    expect_equal(res$summary$rate.input, 234)
    expect_equal(res$summary$rate.output, 236.739, tolerance = 0.001)
    expect_equal(res$summary$rate.abs, 236.739, tolerance = 0.001)

    # changing magnitude of inputs and outputs changes rate by right amount
    rate <- suppressWarnings(auto_rate(sardine.rd, plot = F))

    # sign of the rate
    expect_equal(
      convert_rate(-1*rate$rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output,
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output * -1
    )
    # time metric in output
    expect_equal(
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output,
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/m", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output*60
    )
    expect_equal(
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output,
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/s", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output*60*60
    )
    # time metric in input
    expect_equal(
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output,
      convert_rate(rate, oxy.unit = "%Air", time.unit = "m", output.unit = "mg/h", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output*60
    )
    expect_equal(
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output,
      convert_rate(rate, oxy.unit = "%Air", time.unit = "h", output.unit = "mg/h", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output*60*60
    )
    # volume
    expect_equal(
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h", volume = 10, S = 35, t = 14, P = 1.013253)$rate.output,
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h", volume = 1, S = 35, t = 14, P = 1.013253)$rate.output*10
    )

  })


  test_that("convert_rate - outputs correct conversion values - mass-specific rates", {

    res <- convert_rate(93.1, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 1, S = 35, t = 25, P = 1.013253,
                        mass = 0.012)
    expect_equal(res$rate.output, 1885.583, tolerance = 0.001) # exact value
    ## inputs and outputs are saved in object correctly
    expect_equal(res$rate.input, 93.1)
    expect_equal(res$inputs$oxy.unit, "%Air")
    expect_equal(res$inputs$time.unit, "sec")
    expect_equal(res$output.unit, "mgO2/hr/g")
    expect_equal(res$summary$rate.input, 93.1)
    expect_equal(res$summary$rate.output, 1885.583, tolerance = 0.01)
    expect_equal(res$summary$rate.abs, 22626.99, tolerance = 0.01)
    expect_equal(res$summary$rate.m.spec, 1885.583, tolerance = 0.001)

    res <- convert_rate(4303, oxy.unit = "ug/l", time.unit = "hr", output.unit = "ml/minute/kg", volume = 1, S = 35, t = 25, P = 1.013253,
                        mass = 0.012)
    expect_equal(res$rate.output, 4.564941, tolerance = 0.00001) # exact value
    ## inputs and outputs are saved in object correctly
    expect_equal(res$rate.input, 4303)
    expect_equal(res$inputs$oxy.unit, "ug/L")
    expect_equal(res$inputs$time.unit, "hr")
    expect_equal(res$output.unit, "mLO2/min/kg")
    expect_equal(res$summary$rate.input, 4303)
    expect_equal(res$summary$rate.output, 4.564941, tolerance = 0.00001)
    expect_equal(res$summary$rate.abs, 0.05477929, tolerance = 0.00001)
    expect_equal(res$summary$rate.m.spec, 4.564941, tolerance = 0.00001)

    res <- convert_rate(234, oxy.unit = "hPa", time.unit = "min", output.unit = "umol/min/ug", volume = 1, S = 35, t = 25, P = 1.013253,
                        mass = 0.012)
    expect_equal(res$rate.output, 0.00001972825, tolerance = 0.000001) # exact value
    ## inputs and outputs are saved in object correctly
    expect_equal(res$rate.input, 234)
    expect_equal(res$inputs$oxy.unit, "hPa")
    expect_equal(res$inputs$time.unit, "min")
    expect_equal(res$output.unit, "umolO2/min/ug")
    expect_equal(res$summary$rate.input, 234)
    expect_equal(res$summary$rate.output, 0.00001972825, tolerance = 0.000001)
    expect_equal(res$summary$rate.abs, 236.739, tolerance = 0.001)
    expect_equal(res$summary$rate.m.spec, 0.00001972825, tolerance = 0.000001)

    # changing magnitude of inputs and outputs changes rate by right amount
    rate <- suppressWarnings(auto_rate(sardine.rd, plot = F))

    # sign of the rate
    expect_equal(
      convert_rate(-1*rate$rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
                   mass = 0.012)$rate.output,
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
                   mass = 0.012)$rate.output * -1
    )
    # time metric in output
    expect_equal(
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
                   mass = 0.012)$rate.output,
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/m/g", volume = 10, S = 35, t = 14, P = 1.013253,
                   mass = 0.012)$rate.output*60
    )
    expect_equal(
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
                   mass = 0.012)$rate.output,
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/s/g", volume = 10, S = 35, t = 14, P = 1.013253,
                   mass = 0.012)$rate.output*60*60
    )
    # time metric in input
    expect_equal(
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
                   mass = 0.012)$rate.output,
      convert_rate(rate, oxy.unit = "%Air", time.unit = "m", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
                   mass = 0.012)$rate.output*60
    )
    expect_equal(
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
                   mass = 0.012)$rate.output,
      convert_rate(rate, oxy.unit = "%Air", time.unit = "h", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
                   mass = 0.012)$rate.output*60*60
    )
    # volume
    expect_equal(
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
                   mass = 0.012)$rate.output,
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 1, S = 35, t = 14, P = 1.013253,
                   mass = 0.012)$rate.output*10
    )
    # mass
    expect_equal(
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
                   mass = 0.012)$rate.output,
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/kg", volume = 10, S = 35, t = 14, P = 1.013253,
                   mass = 0.012)$rate.output/1000
    )
    expect_equal(
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
                   mass = 0.012)$rate.output,
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/mg", volume = 10, S = 35, t = 14, P = 1.013253,
                   mass = 0.012)$rate.output*1000
    )
    expect_equal(
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/g", volume = 10, S = 35, t = 14, P = 1.013253,
                   mass = 0.012)$rate.output,
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/ug", volume = 10, S = 35, t = 14, P = 1.013253,
                   mass = 0.012)$rate.output*1000000
    )

  })


  ## Kate Quigley data
  ## These values checked in Excel - first one is right

  test_that("convert_rate - outputs correct conversion values - area-specific rates", {

    res <- convert_rate(-0.0001534657, oxy.unit = "mg/L", time.unit = "s", output.unit = "mg/h/mm2",
                        volume = 0.0032245,
                        S = 35, t = 31, P = 1.013253,
                        area = 0.000001429)

    expect_equal(res$rate.output, -0.001246648) # exact value
    ## inputs and outputs are saved in object correctly
    expect_equal(res$rate.input, -0.0001534657)
    expect_equal(res$inputs$oxy.unit, "mg/L")
    expect_equal(res$inputs$time.unit, "sec")
    expect_equal(res$output.unit, "mgO2/hr/mm2")
    expect_equal(res$summary$rate.input, -0.0001534657)
    expect_equal(res$summary$rate.output, -0.001246648)
    expect_equal(res$summary$rate.abs, -0.001781461)
    expect_equal(res$summary$rate.a.spec, -0.001246648)

    ## these made up
    res <- convert_rate(4303, oxy.unit = "ug/l", time.unit = "hr", output.unit = "ml/minute/m2",
                        volume = 1, S = 35, t = 25, P = 1.013253,
                        area = 0.012)
    expect_equal(res$rate.output, 4.564941, tolerance = 0.00001) # exact value
    ## inputs and outputs are saved in object correctly
    expect_equal(res$rate.input, 4303)
    expect_equal(res$inputs$oxy.unit, "ug/L")
    expect_equal(res$inputs$time.unit, "hr")
    expect_equal(res$output.unit, "mLO2/min/m2")
    expect_equal(res$summary$rate.input, 4303)
    expect_equal(res$summary$rate.output, 4.564941, tolerance = 0.00001)
    expect_equal(res$summary$rate.abs, 0.05477929, tolerance = 0.00001)
    expect_equal(res$summary$rate.a.spec, 4.564941, tolerance = 0.00001)

    res <- convert_rate(234, oxy.unit = "hPa", time.unit = "min", output.unit = "umol/min/cm2",
                        volume = 1, S = 35, t = 25, P = 1.013253,
                        area = 0.012)
    expect_equal(res$rate.output, 1.972825, tolerance = 0.000001) # exact value
    ## inputs and outputs are saved in object correctly
    expect_equal(res$rate.input, 234)
    expect_equal(res$inputs$oxy.unit, "hPa")
    expect_equal(res$inputs$time.unit, "min")
    expect_equal(res$output.unit, "umolO2/min/cm2")
    expect_equal(res$summary$rate.input, 234)
    expect_equal(res$summary$rate.output, 1.972825, tolerance = 0.000001)
    expect_equal(res$summary$rate.abs, 236.739, tolerance = 0.001)
    expect_equal(res$summary$rate.a.spec, 1.972825, tolerance = 0.000001)

    # changing magnitude of inputs and outputs changes rate by right amount
    rate <- suppressWarnings(auto_rate(sardine.rd, plot = F))
    # time metric in output
    expect_equal(
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/cm2", volume = 10, S = 35, t = 14, P = 1.013253,
                   area = 0.012)$rate.output,
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/m/cm2", volume = 10, S = 35, t = 14, P = 1.013253,
                   area = 0.012)$rate.output*60
    )
    expect_equal(
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/cm2", volume = 10, S = 35, t = 14, P = 1.013253,
                   area = 0.012)$rate.output,
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/s/cm2", volume = 10, S = 35, t = 14, P = 1.013253,
                   area = 0.012)$rate.output*60*60
    )
    # time metric in input
    expect_equal(
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/cm2", volume = 10, S = 35, t = 14, P = 1.013253,
                   area = 0.012)$rate.output,
      convert_rate(rate, oxy.unit = "%Air", time.unit = "m", output.unit = "mg/h/cm2", volume = 10, S = 35, t = 14, P = 1.013253,
                   area = 0.012)$rate.output*60
    )
    expect_equal(
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/cm2", volume = 10, S = 35, t = 14, P = 1.013253,
                   area = 0.012)$rate.output,
      convert_rate(rate, oxy.unit = "%Air", time.unit = "h", output.unit = "mg/h/cm2", volume = 10, S = 35, t = 14, P = 1.013253,
                   area = 0.012)$rate.output*60*60
    )
    # volume
    expect_equal(
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/cm2", volume = 10, S = 35, t = 14, P = 1.013253,
                   area = 0.012)$rate.output,
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/cm2", volume = 1, S = 35, t = 14, P = 1.013253,
                   area = 0.012)$rate.output*10
    )
    # area
    # mm2 > cm2 > m2 > km2
    # 1 x 100 x 10000 x 1000000
    expect_equal(
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/mm2", volume = 10, S = 35, t = 14, P = 1.013253,
                   area = 0.012)$rate.output,
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/cm2", volume = 10, S = 35, t = 14, P = 1.013253,
                   area = 0.012)$rate.output/100
    )
    expect_equal(
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/mm2", volume = 10, S = 35, t = 14, P = 1.013253,
                   area = 0.012)$rate.output,
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/m2", volume = 10, S = 35, t = 14, P = 1.013253,
                   area = 0.012)$rate.output/100/10000
    )
    expect_equal(
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/mm2", volume = 10, S = 35, t = 14, P = 1.013253,
                   area = 0.012)$rate.output,
      convert_rate(rate, oxy.unit = "%Air", time.unit = "s", output.unit = "mg/h/km2", volume = 10, S = 35, t = 14, P = 1.013253,
                   area = 0.012)$rate.output/100/10000/1000000
    )

  })

  test_that("convert_rate - changing 'time' inputs changes rates by correct magnitude multiplier", {
    # Outputs
    # s to m
    expect_equal(
      convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mg/s/kg',
                   volume = 1.2, mass = 0.5)$rate.output * 60,
      convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mg/m/kg',
                   volume = 1.2, mass = 0.5)$rate.output)
    # s to h
    expect_equal(
      convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mg/s/kg',
                   volume = 1.2, mass = 0.5)$rate.output * 60 * 60,
      convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mg/h/kg',
                   volume = 1.2, mass = 0.5)$rate.output)
    # s to d
    expect_equal(
      convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mg/s/kg',
                   volume = 1.2, mass = 0.5)$rate.output * 60 * 60 * 24,
      convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mg/d/kg',
                   volume = 1.2, mass = 0.5)$rate.output)

    # If inut data was different time
    # d to s
    expect_equal(
      convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 'day', output.unit = 'mg/s/kg',
                   volume = 1.2, mass = 0.5)$rate.output * 60 * 60 * 24,
      convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 'day', output.unit = 'mg/d/kg',
                   volume = 1.2, mass = 0.5)$rate.output)
    # d to m
    expect_equal(
      convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 'day', output.unit = 'mg/m/kg',
                   volume = 1.2, mass = 0.5)$rate.output * 60 * 24,
      convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 'day', output.unit = 'mg/d/kg',
                   volume = 1.2, mass = 0.5)$rate.output)
    # d to h
    expect_equal(
      convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 'day', output.unit = 'mg/h/kg',
                   volume = 1.2, mass = 0.5)$rate.output * 24,
      convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 'day', output.unit = 'mg/d/kg',
                   volume = 1.2, mass = 0.5)$rate.output)
  })

  test_that("convert_rate - different magnitudes of umol/mmol/mol changes rates by correct magnitude multiplier", {

    expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mol/s/kg',
                              volume = 1.2, mass = 0.5)$rate.output,
                 convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mmol/s/kg',
                              volume = 1.2, mass = 0.5)$rate.output/1000)
    expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mol/s/kg',
                              volume = 1.2, mass = 0.5)$rate.output,
                 convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'umol/s/kg',
                              volume = 1.2, mass = 0.5)$rate.output/1000/1000)
    expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'umol/s/kg',
                              volume = 1.2, mass = 0.5)$rate.output,
                 convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mmol/s/kg',
                              volume = 1.2, mass = 0.5)$rate.output*1000)
    expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'umol/s/kg',
                              volume = 1.2, mass = 0.5)$rate.output,
                 convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'nmol/s/kg',
                              volume = 1.2, mass = 0.5)$rate.output/1000)
    expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mol/s/kg',
                              volume = 1.2, mass = 0.5)$rate.output,
                 convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'nmol/s/kg',
                              volume = 1.2, mass = 0.5)$rate.output/1000/1000/1000)
    expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'umol/s/kg',
                              volume = 1.2, mass = 0.5)$rate.output,
                 convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'pmol/s/kg',
                              volume = 1.2, mass = 0.5)$rate.output/1000000)
    expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mol/s/kg',
                              volume = 1.2, mass = 0.5)$rate.output,
                 convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'pmol/s/kg',
                              volume = 1.2, mass = 0.5)$rate.output/1000/1000/1000/1000)

    expect_equal(c(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mol/s/kg',
                                volume = 1.2, mass = 0.5)$rate.output,
                   convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mmol/s/kg',
                                volume = 1.2, mass = 0.5)$rate.output/1000,
                   convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'umol/s/kg',
                                volume = 1.2, mass = 0.5)$rate.output/1000/1000,
                   convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'nmol/s/kg',
                                volume = 1.2, mass = 0.5)$rate.output/1000/1000/1000,
                   convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'pmol/s/kg',
                                volume = 1.2, mass = 0.5)$rate.output/1000/1000/1000/1000),
                 rep(6.750253e-05, 5))
  })

  test_that("convert_rate - ml & ul oxygen output unit correct values ", {
    # should be ml times 1000
    expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'ml/h/kg',
                              volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output * 1000,
                 convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'ul/h/kg',
                              volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output)
  })

  test_that("convert_rate - mg & ug oxygen output unit correct values ", {
    # should be mg times 1000
    expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mg/h/kg',
                              volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output * 1000,
                 convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'ug/h/kg',
                              volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output)
  })

  test_that("convert_rate - mm3 & cm3 (cc) oxygen output unit correct values ", {
    # these are equivalent to ul and ml
    expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'cm3/h/kg',
                              volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output * 1000,
                 convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mm3/h/kg',
                              volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output)
    expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'cm3/h/kg',
                              volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output,
                 convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'ml/h/kg',
                              volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output)
    expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'cc/h/kg',
                              volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output,
                 convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'ml/h/kg',
                              volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output)
    expect_equal(convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'mm3/h/kg',
                              volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output,
                 convert_rate(0.9, oxy.unit = 'mg/l', time.unit = 's', output.unit = 'ul/h/kg',
                              volume = 1.2, mass = 0.5, S = 35, t = 12, P = 1)$rate.output)
  })

  # Plotting ----------------------------------------------------------------

  test_that("convert_rate - plot is produced with converted auto_rate objects", {

    ar_mult <-
      suppressWarnings(
        urchins.rd %>%
          inspect(1,2, plot = FALSE) %>%
          auto_rate(width = 0.2, plot = FALSE) %>%
          convert_rate(oxy.unit = "mg/l",
                       time.unit = "min",
                       output.unit = "mg/h/g",
                       volume = 1.09,
                       mass = 0.005)
      )

    expect_output(plot(ar_mult))
    expect_output(plot(ar_mult, pos = 1:2))
    expect_output(plot(ar_mult, pos = 1:2, type = "full"))
    expect_output(plot(ar_mult, pos = 1:2, type = "full", highlight = 2))
    expect_output(plot(ar_mult, pos = 1:2, type = "overlap"))
    expect_output(plot(ar_mult, pos = 1:2, type = "overlap", highlight = 2))
    expect_output(plot(ar_mult, pos = 1:2, type = "rate"))
    expect_output(plot(ar_mult, pos = 1:2, type = "rate", highlight = 2))
    expect_output(plot(ar_mult, type = "overlap", highlight = 2))

    # adjusted
    ar_mult_adj <-
      suppressWarnings(
        urchins.rd %>%
          inspect(1,2, plot = FALSE) %>%
          auto_rate(width = 0.2, plot = FALSE) %>%
          adjust_rate(by = -0.005) %>%
          convert_rate(oxy.unit = "mg/l",
                       time.unit = "min",
                       output.unit = "mg/h/g",
                       volume = 1.09,
                       mass = 0.005))
    expect_output(plot(ar_mult_adj))

  })

  test_that("convert_rate - plot is produced with converted calc_rate objects", {
    cr <-
      suppressWarnings(
        urchins.rd %>%
          inspect(1,2, plot = FALSE) %>%
          calc_rate(plot = FALSE) %>%
          convert_rate(oxy.unit = "mg/l",
                       time.unit = "min",
                       output.unit = "mg/h",
                       volume = 1.09))
    expect_output(plot(cr))
  })

  test_that("convert_rate - plot pos and highlight correct messages", {
    cr <-
      suppressWarnings(
        urchins.rd %>%
          inspect(1,2, plot = FALSE) %>%
          calc_rate(plot = FALSE) %>%
          convert_rate(oxy.unit = "mg/l",
                       time.unit = "min",
                       output.unit = "mg/h",
                       volume = 1.09))
    expect_message(plot(cr, pos = 50),
                   "convert_rate: One or more 'pos' inputs higher than number of rows in '\\$summary'. Applying default of all rows.")
    expect_message(plot(cr, pos = 50, type = "overlap"),
                   "convert_rate: One or more 'pos' inputs higher than number of rows in '\\$summary'. Applying default of all rows.")
    expect_message(plot(cr, highlight = 50, type = "overlap"),
                   "convert_rate: 'highlight' not within 'pos' input. Applying default of first 'pos' entry.")
  })

  test_that("convert_rate - plot errors with various disallowed inputs", {
    num <- c(1,2,3) %>%
      convert_rate(oxy.unit = "mg/l",
                   time.unit = "min",
                   output.unit = "mg/h",
                   volume = 1.09)
    expect_error(plot(num),
                 "plot.convert_rate: Plot is not available for 'convert_rate' objects containing rates converted from numeric values.")

    crbg <- suppressWarnings(urchins.rd %>%
                               inspect(1,2, plot = FALSE) %>%
                               calc_rate.bg(plot = FALSE) %>%
                               convert_rate(oxy.unit = "mg/l",
                                            time.unit = "min",
                                            output.unit = "mg/h",
                                            volume = 1.09))
    expect_error(plot(crbg),
                 "plot.convert_rate: Plot is not available for converted 'calc_rate.bg' objects because rates may come from different columns of the dataframe.")

    cr <- suppressWarnings(urchins.rd %>%
                             inspect(1,2, plot = FALSE) %>%
                             calc_rate(plot = FALSE) %>%
                             convert_rate(oxy.unit = "mg/l",
                                          time.unit = "min",
                                          output.unit = "mg/h",
                                          volume = 1.09))
    expect_error(plot(cr, type = "text"),
                 "plot.convert_rate: 'type' input not recognised.")
  })

  test_that("overlap.p - errors with various disallowed inputs", {
    crbg <-
      calc_rate.bg(urchins.rd[,1:2]) %>%
      convert_rate(oxy.unit = "mg/l",
                   time.unit = "min",
                   output.unit = "mg/h",
                   volume = 1.09)
    expect_error(overlap.p(crbg),
                 "overlap.p: Plot is not available for converted 'calc_rate.bg' objects because rates may come from different columns of the dataframe.")
    crbg <-
      calc_rate.bg(urchins.rd[,1:2])
    expect_error(overlap.p(crbg),
                 "overlap.p: 'x' should be an 'auto_rate' or 'convert_rate' object.")
    num <-
      c(1,2,3) %>%
      convert_rate(oxy.unit = "mg/l",
                   time.unit = "min",
                   output.unit = "mg/h",
                   volume = 1.09)
    expect_error(overlap.p(num),
                 "overlap.p: Plot is not available for 'convert_rate' objects containing rates converted from numeric values.")
  })

  test_that("convert_rate - correct message when plot is called on objects with zero rates", {

    # message with zero rates for both methods
    ar_mult_no_rts <-
      suppressWarnings(
        urchins.rd %>%
          inspect(1,2, plot = FALSE) %>%
          auto_rate(width = 0.2, plot = FALSE) %>%
          convert_rate(oxy.unit = "mg/l",
                       time.unit = "min",
                       output.unit = "mg/h/g",
                       volume = 1.09,
                       mass = 0.005) %>%
          select_rate("rate", c(-0.05, -0.06)))
    expect_message(plot(ar_mult_no_rts),
                   "convert_rate: Nothing to plot! No rates found in object.")
    expect_message(plot(ar_mult_no_rts, type = "overlap"),
                   "convert_rate: Nothing to plot! No rates found in object.")
  })


  test_that("convert_rate - plot defaults are correctly restored", {

    # reset plotting first
    dev.off()
    # save par before
    parb4 <- par(no.readonly = TRUE)
    # now use a fn with plot
    suppressWarnings(urchins.rd %>%
                       inspect(1,2, plot = FALSE) %>%
                       auto_rate(width = 0.2, plot = FALSE) %>%
                       convert_rate(oxy.unit = "mg/l",
                                    time.unit = "min",
                                    output.unit = "mg/h/g",
                                    volume = 1.09,
                                    mass = 0.005,
                                    plot = TRUE))
    # save after
    paraft <- par(no.readonly = TRUE)
    # mai is something changed from the default,
    # so if par settings not restored properly this should fail
    expect_identical(parb4$mai,
                     paraft$mai)

  })


}) ## end capture.output