oxygen_evol: oxygen_evol.

In chrisjw18/OxygenEvol: Calculates oxygen evolution (FireSting optode) matched to FL3500 PSI data

Description

extract and match firesting oxygen data to FL3500 PSI fluorescence data.

Usage

oxygen_evol(fluorwin_filename, firesting_filename, no_light_steps,
  time_step = 60, calibration_file = NA, data_output = F,
  end_respiration = F)

Arguments

fluorwin_filename	name of the fluorwin .txt file to process.
firesting_filename	name of the firesting oxygen data file to process.
no_light_steps	the number of light steps in the curve.
time_step	length of the window (in seconds) of oxygen data to extract per light step.
calibration_file	flashlet calibration file used to calculate PAR from voltages for FL3500 data. Generic calibration file is built into package so leave as NA if no specific calibration available.
data_output	logical (default FALSE), if TRUE dataframes produced are written to CSV and plots written to single .pdf file (see Values below)
end_respiration	logical (default FALSE), if TRUE function will perform an end respiration calculation using oxygen data from immediately after the final light step of the light curve over the duration set by time_step

Value

oxy_results list containing the following two dataframes: 1. raw_oxygen dataframe containing the tidy outputs from the Firesting optode (i.e. complete oxygen trace with formatted time columns). 2. matched_oxygen dataframe containing the FL3500 light step with matched calculated rate of oxygen evolution (units of umol s-1), with columns showing voltage and PAR levels per light step

If data_output = TRUE: x2 CSV files of raw_oxygen and matched_oxygen datasets appended with oxygen datafile name

AND

.pdf document appended with oxygen datafile name showing: 1. complete oxygen trace with grey areas highlighting which sections have been clipped and matched to fluorescence data (As determined by the time_step selected) 2. individual plots of each linear regression for oxygen evolution calculations 3. calculated oxygen evolution ~ light step over the course of the light curve with PAR levels shown in blue trace in brackground 4. scatter plot of oxygen evolution ~ PAR

Examples

To import example data, run the following code:

example_fluorwin_data<-system.file("extdata", "example_fluorwin_data.txt", package = "OxygenEvol")
example_oxygen_data<-system.file("extdata", "example_oxygen_data.txt", package = "OxygenEvol")
oxygen_evol(example_fluorwin_data, example_oxygen_data, no_light_steps=11, time_step=60, calibration_file=NA, data_output=F, end_respiration = T)

chrisjw18/OxygenEvol documentation built on May 12, 2019, 5:23 p.m.