extract_picarro: Data extraction from Lehmann lab Picarro isotope analyzer

Description Usage Arguments Details Value Author(s) Examples

View source: R/extract_picarro_data.r

Description

Function to convert raw data from picarro analyzer to respiration data

Usage

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extract_picarro(data_path = NA, use_dodgy_fudge_factor, lambda = 1e-04,
  raw.data = FALSE)

Arguments

data_path

Directory containing all raw data from picarro analyzer within nested subdirectories. If not provided, user will be asked for path interactively.

use_dodgy_fudge_factor

Required parameter indicting whether to correct headspace concentrations using the factors in fractional_volume.txt file. Note that these correction factors were introduced by Silene deCiuces to correct for observed differences between a standard calibration gas and Picarro measurements. These discrepancies may or may not have been caused by mixing with gas in the pipework or by exchanges with ambient air through leaks.Depending on the current setup of the instrument, these corrections may or may not be required. If you are not sure, then please run a calibration standard to find out.

lambda

Optional smoothing parameter (positive real numeric). Higher values give greater smoothing. Smaller values follow data more closely. See help(regSmooth) for more details.

raw.data

Optional logical value for whether to return raw data tables in addition to the processed one. Useful for diagnostics and trouble shooting.

Details

This function returns a data.table with respired CO2 and CH4 concentrations and delta-13C values for each jar at each samping time

The data path must contain the following three things:

  1. All raw Picarro data files for this experiment. Can be in nested subdirectories. NB picarro files are assumed to end in .dat – No other files in the data path should have this ending

  2. fractional_volume.txt = provides fraction of head space gas divided by total volume including residal gas in the analyzer and pipework. Only required if the parameter use_dodgy_fudge_factor is set to TRUE

  3. logfile (filename must start with the characters "logfile"), which contains epoch time, sample ID, and step ID ("Step 2" = sample analysis; "Step 3" = end of step 2; "Step 5" = purge analysis; "Step 6" = end of step 5).

The returned data.table columns, and their descriptions are:

Value

Provides a data.table with respired CO2 and CH4 concentrations and delta-13C values for each jar at each samping time. See details. If called with raw.data = TRUE, then function returns a named list containing short.data = the above table; long.data = the same data in long format; and pic.data = the raw Picarro data, with columns added for sample number, step, cycle, and smoothed data.

Author(s)

Dominic Woolf. d.woolf@cornell.edu

Examples

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short.data = extract_picarro()
library(ggplot2)
ggplot(short.data[-1], aes(day, respired.co2)) +
  geom_line() +
  facet_wrap(~ jar)

ggplot(short.data[-1], aes(day, evolved.ch4)) +
  geom_line() +
  facet_wrap(~ jar)

domwoolf/picarro documentation built on Aug. 26, 2020, 8:44 p.m.