flux_plot.md
In fluxible: Ecosystem Gas Fluxes Calculations for Closed Loop Chamber Setup

plot for exponential fit

Code
  suppressMessages(flux_plot(slopes0_flag, conc, datetime, f_plotname = "test_exp_plot",
    print_plot = FALSE, output = "pdfpages"))

plot for linear fit

Code
  vdiffr::expect_doppelganger("plot for linear fit", flux_plot(slopes30lin_flag,
    conc, datetime))
Message
  Plotting in progress

plot for linear fit with jpg extension works

Code
  suppressMessages(flux_plot(slopes30lin_flag, conc, datetime, f_plotname = "test_lin_plot",
    print_plot = FALSE, output = "ggsave", ggsave_args = list(device = "jpg")))

plot for exp_tz fit

Code
  vdiffr::expect_doppelganger("plot for exp_tz fit", flux_plot(flux_quality(
    flux_fitting(co2_conc, conc, datetime, fit_type = "exp_tz", end_cut = 60,
      t_zero = 20), conc), conc, datetime))
Message
  Cutting measurements...
  Estimating starting parameters for optimization...
  Optimizing fitting parameters...
  Calculating fits and slopes...
  Done.

   Total number of measurements: 6

   ok    5   83 %
   discard   1   17 %
   zero      0   0 %
   force_discard     0   0 %
   start_error   0   0 %
   no_data   0   0 %
   force_ok      0   0 %
   force_zero    0   0 %
   force_lm      0   0 %
   no_slope      0   0 %
  Plotting in progress

plot for exp_tz fit with mid missing data

Code
  vdiffr::expect_doppelganger("plot for exp_tz fit with mid missing data",
    flux_plot(flux_quality(flux_fitting(co2_conc_mid_missing, conc, datetime,
      fit_type = "exp_tz", end_cut = 60, t_zero = 20), conc), conc, datetime))
Message
  Cutting measurements...
  Estimating starting parameters for optimization...
  Optimizing fitting parameters...
  Calculating fits and slopes...
  Done.
Condition
  Warning in `flux_fitting()`:

   fluxID 1 : slope was estimated on 139 points out of 150 seconds
   fluxID 2 : slope was estimated on 114 points out of 150 seconds
   fluxID 4 : slope was estimated on 103 points out of 150 seconds
Message

   Total number of measurements: 6

   ok    5   83 %
   discard   1   17 %
   zero      0   0 %
   force_discard     0   0 %
   start_error   0   0 %
   no_data   0   0 %
   force_ok      0   0 %
   force_zero    0   0 %
   force_lm      0   0 %
   no_slope      0   0 %
  Plotting in progress

plot for exp_zhao18 fit with mid missing data

Code
  vdiffr::expect_doppelganger("plot for exp_zhao18 fit with mid missing data",
    flux_plot(flux_quality(flux_fitting(co2_conc_mid_missing, conc, datetime,
      fit_type = "exp_zhao18", end_cut = 60, t_zero = 20), conc), conc, datetime))
Message
  Cutting measurements...
  Estimating starting parameters for optimization...
  Optimizing fitting parameters...
  Calculating fits and slopes...
  Done.
Condition
  Warning in `flux_fitting()`:

   fluxID 1 : slope was estimated on 139 points out of 150 seconds
   fluxID 2 : slope was estimated on 114 points out of 150 seconds
   fluxID 4 : slope was estimated on 103 points out of 150 seconds
Message

   Total number of measurements: 6

   ok    6   100 %
   discard   0   0 %
   zero      0   0 %
   force_discard     0   0 %
   start_error   0   0 %
   no_data   0   0 %
   force_ok      0   0 %
   force_zero    0   0 %
   force_lm      0   0 %
   no_slope      0   0 %
  Part of the fit will not be displayed
      because f_ylim_lower is too high.
  Plotting in progress

plot for quadratic fit with mid missing data

Code
  vdiffr::expect_doppelganger("plot for quadratic fit with mid missing data",
    flux_plot(flux_quality(flux_fitting(co2_conc_mid_missing, conc, datetime,
      fit_type = "quadratic", end_cut = 60, t_zero = 20), conc), conc, datetime))
Condition
  Warning in `flux_fitting()`:

   fluxID 1 : slope was estimated on 139 points out of 150 seconds
   fluxID 2 : slope was estimated on 114 points out of 150 seconds
   fluxID 4 : slope was estimated on 103 points out of 150 seconds
Message

   Total number of measurements: 6

   ok    6   100 %
   discard   0   0 %
   zero      0   0 %
   force_discard     0   0 %
   start_error   0   0 %
   no_data   0   0 %
   force_ok      0   0 %
   force_zero    0   0 %
   force_lm      0   0 %
   no_slope      0   0 %
  Plotting in progress

plot for exp_hm fit

Code
  vdiffr::expect_doppelganger("plot for exp_hm fit", flux_plot(flux_quality(
    flux_fitting(co2_conc, conc, datetime, fit_type = "exp_hm", end_cut = 60,
      t_zero = 20), conc), conc, datetime))
Message
  Cutting measurements...
  Optimizing fitting parameters...
  Calculating fits and slopes...
  Done.

   Total number of measurements: 6

   ok    6   100 %
   discard   0   0 %
   zero      0   0 %
   force_discard     0   0 %
   start_error   0   0 %
   no_data   0   0 %
   force_ok      0   0 %
   force_zero    0   0 %
   force_lm      0   0 %
   no_slope      0   0 %
  Plotting in progress

plot for kappamax fit

Code
  vdiffr::expect_doppelganger("plot for kappamax fit", flux_plot(flux_quality(
    flux_fitting(co2_conc, conc, datetime, fit_type = "exp_hm", end_cut = 30,
      t_zero = 10), conc, f_pvalue = f_pvalue_lm, f_rsquared = f_rsquared_lm,
    kappamax = TRUE), conc, datetime))
Message
  Cutting measurements...
  Optimizing fitting parameters...
  Calculating fits and slopes...
  Done.
Condition
  Warning in `flux_fitting()`:

   fluxID 5 : slope is NA, most likely an issue with the model optimization.
          Check your data or use a different model.
Message

   Number of measurements with linear fit: 1

   Total number of measurements: 6

   ok    5   83 %
   zero      1   17 %
   discard   0   0 %
   force_discard     0   0 %
   start_error   0   0 %
   no_data   0   0 %
   force_ok      0   0 %
   force_zero    0   0 %
   force_lm      0   0 %
   no_slope      0   0 %
  Plotting in progress