flux_plot: Plotting fluxes for visual evaluation

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

Plotting fluxes for visual evaluation

Description

Plots the fluxes, fit and slope in facets with color code indicating quality flags This function takes time to run and is optional in the workflow, but it is still highly recommended to use it to visually check the measurements. Note that 'flux_plot' is specific to the fluxible package and will work best with datasets produced following a fluxible workflow.

Usage

flux_plot(
  slopes_df,
  f_conc = f_conc,
  f_datetime = f_datetime,
  color_discard = "#D55E00",
  color_cut = "#D55E00",
  color_ok = "#009E73",
  color_zero = "#CC79A7",
  scale_x_datetime_args = list(date_breaks = "1 min", minor_breaks = "10 sec",
    date_labels = "%e/%m \n %H:%M"),
  f_ylim_upper = 800,
  f_ylim_lower = 400,
  f_plotname = "",
  facet_wrap_args = list(ncol = 4, nrow = 3, scales = "free"),
  y_text_position = 500,
  print_plot = "FALSE",
  output = "print_only",
  ggsave_args = list()
)

Arguments

slopes_df	dataset containing slopes, with flags produced by flux_quality
f_conc	column with gas concentration
f_datetime	column with datetime of each data point
color_discard	color for fits with a discard quality flag
color_cut	color for the part of the flux that is cut
color_ok	color for fits with an ok quality flag
color_zero	color for fits with a zero quality flag
scale_x_datetime_args	list of arguments for scale_x_datetime
f_ylim_upper	y axis upper limit
f_ylim_lower	y axis lower limit
f_plotname	filename for the extracted pdf file; if empty, the name of slopes_df will be used
facet_wrap_args	list of arguments for facet_wrap_paginate
y_text_position	position of the text box
print_plot	logical, if TRUE it prints the plot as a ggplot object but will take time depending on the size of the dataset
output	pdfpages, the plots are saved as A4 landscape pdf pages; ggsave, the plots can be saved with the ggsave function; print_only (default) prints the plot without creating a file (independently from print_plot being TRUE or FALSE)
ggsave_args	list of arguments for ggsave (in case output = "ggsave")

Value

plots of fluxes, with raw concentration data points, fit, slope, and color code indicating quality flags and cuts. The plots are organized in facets according to flux ID, and a text box display the quality flag and diagnostics of each measurement. The plots are returned as a ggplot object if print_plot = TRUE; if print_plot = FALSE it will not return anything but will produce a file according to the output argument.

Examples

data(co2_conc)
slopes <- flux_fitting(co2_conc, conc, datetime, fit_type = "exp_zhao18")
slopes_flag <- flux_quality(slopes, conc)
flux_plot(slopes_flag, conc, datetime)

fluxible documentation built on June 25, 2025, 1:08 a.m.