analyzer: Gas analyzer setup

In tekknosol/glimmr: Gas Fluxes and Dynamic Chamber Measurements

Description

Analyzer mappings describe how columns of meta file are mapped to properties of the gas analyzer

Usage

analyzer(time_stamp = "timestamp", conc_columns = NULL,
  pressure = NULL, pressure_factor = 1, temperature = NULL,
  manual_temperature = NULL, offset = "offset",
  duration_count = FALSE, plot = "plot", date = "date",
  start = "start", end = "end", trimmer = NULL, V = 0.01461,
  A = 0.098)

Arguments

time_stamp	Timestamp
conc_columns	A named vector declaring the columns containing the actual mixing rations. E.g. 'c(CO2 = "CO2")'.
pressure	Column containing the atmospheric preasure in mbar.
pressure_factor	If preasure is provided in a different unit than mbar, a conversion factor can be specified.
temperature	Column containing the temperature in °C.
manual_temperature	Column conatining an additional measured temperature. If specified, the 'temperature' value is ommited.
offset	(Default = '0:0'). Colon separated value for offsetting the datasets. First value offsets the first, second value offsets the last datapoint. Positive values shrinken the dataset i.e '2:3' skips two datapoints at the beginning and truncates three datapoints at the end of the dataset. Negative values expand the dataset i.e. '-2:-3' add two datapoints at the beginning and three datapoints at the end of the dataset.
duration_count	If TRUE, 'end' is determined by the number of datapoints within each measurement. If FALSE, 'end' is treated as duration or point in time.
plot	(Default = "plot"). Column containing the ID of the measurement location.
date	(Default = "date"). Column containing the day of measurement. Format: "YYYY-MM-DD".
start	(Default = "start"). Column containing the start of measurement. Format: "HH:MM" or "HH:MM:SS".
end	(Default = "end"). Column containing the end of measurement. There are several options: Point in Time. Format: "HH:MM" or "HH:MM:SS" (e.g. '"13:43"'). Duration in minutes (e.g. '5'). Number of Datapoints regardless of the effectively elapsed time (e.g. '10'). This behaviour is controlled by 'duration_count'. Alternatively a single number treated as Duration or Number of Datapoints for all measurements (e.g. '5', behaviour is again controlled by 'duration_count').
trimmer	A function to trim the intervall between 'start' and 'end'. See 'trim_time()' for details.
V	Volume of the chamber.
A	Area of the chamber.

Value

An object of clas lyzr.

Examples

# setup analyzer
custom_analyzer <- analyzer(
  #define datastructure
  time_stamp = "Time",
  conc_columns = c(CH4 = "[CH4]_ppm", CO2 = "[CO2]_ppm"),
  pressure = "GasP_torr",
  pressure_factor = 1.33322,
  temperature = "AmbT_C",
  trimmer = trim_time,
  # define metadata structure
  plot = "plot",
  date = "date",
  start = "start",
  end = "end",
  #define chamber dimensions
  V = 0.01461,
  A = 0.098
)

tekknosol/glimmr documentation built on Oct. 17, 2020, 1:39 a.m.