Type: Package
Title: Parsing, Computation, and Diagnostics for Greenhouse Gas Measurements
Version: 1.1.0
Description: Parse static-chamber greenhouse gas measurement files generated by a variety of instruments; compute flux rates using multi-observation metadata; and generate diagnostic metrics and plots. Designed to be easy to integrate into reproducible scientific workflows.
URL: https://github.com/COMPASS-DOE/fluxfinder
License: MIT + file LICENSE
Encoding: UTF-8
Imports: broom (≥ 1.0), jsonlite (≥ 1.8), lubridate (≥ 1.0), MASS (≥ 7.0)
Suggests: gasfluxes, ggplot2, knitr, rmarkdown, testthat (≥ 3.0.0), withr (≥ 2.0)
Config/testthat/edition: 3
RoxygenNote: 7.3.2
VignetteBuilder: knitr
BugReports: https://github.com/COMPASS-DOE/fluxfinder/issues
NeedsCompilation: no
Packaged: 2025-06-21 14:51:05 UTC; wilsonsj
Author: Stephanie Wilson ORCID iD [cre], Ben Bond-Lamberty ORCID iD [aut], Genevieve Noyce ORCID iD [ctb], Roberta Bittencourt Peixoto ORCID iD [ctb], Patrick Megonigal ORCID iD [ctb], Smithsonian Institution [cph, fnd]
Maintainer: Stephanie Wilson <sjw22120@gmail.com>
Repository: CRAN
Date/Publication: 2025-06-21 16:00:02 UTC

Compute fluxes for multiple groups (measurements)

Description

Compute fluxes for multiple groups (measurements)

Usage

ffi_compute_fluxes(
  data,
  group_column,
  time_column,
  gas_column,
  dead_band = 0,
  normalize_time = TRUE,
  fit_function = ffi_fit_models,
  ...
)

Arguments

data

A data.frame (or tibble or data.table)

group_column

Name of the grouping column in data, character; pass NULL to run with no grouping

time_column

Name of the time column in data, character

gas_column

Name of the gas (concentration or quantity) column in data, character

dead_band

Length of the dead band in seconds (numeric), the equilibration period whose data is dropped. This can be either a single number OR the name of the dead band column in data

normalize_time

Normalize the values so that first is zero? Logical

fit_function

Optional flux-fit function; default is ffi_fit_models

...

Other parameters passed to fit_function

Value

A data.frame with one row per group_column value. It will always include the mean, minimum, and maximum values of time_column for that group, but other columns depend on what is returned by the fit_function.

See Also

ffi_fit_models

Examples

# No grouping
ffi_compute_fluxes(cars, group_column = NULL, "speed", "dist")
# With grouping
cars$Plot <- c("A", "B")
ffi_compute_fluxes(cars, "Plot", "speed", "dist")
# See the introductory vignette for a fully-worked example with real data

Fit various models to gas concentration data

Description

Fit various models to gas concentration data

Usage

ffi_fit_models(time, conc, area, volume)

Arguments

time

Relative time of observation (typically seconds), numeric

conc

Greenhouse gas concentration (typically ppm or ppb), numeric

area

Area covered by the measurement chamber (typically cm2), numeric

volume

Volume of the system (chamber + tubing + analyzer, typically cm3), numeric

Details

If a linear model cannot be fit, NULL is returned. If the robust linear and/or polynomial models cannot be fit, then NA is returned for their particular statistics. The HM1981 approach is only valid for saturating (exponential) data and NA is returned otherwise.

Value

A wide-form data.frame with fit statistics for linear ("lin", lm), robust linear ("rob", rlm), polynomial ("poly"), and H&M1981 ("HM81", ffi_hm1981) models. The latter is based on an exponential model drawn from one-dimensional diffusion theory; see Hutchinson and Mosier (1981) and Nakano et al. (2004).

For each model type, the following columns are returned:

Note

Normally this is not called directly by users, but instead via ffi_compute_fluxes.

References

Nakano, T., Sawamoto, T., Morishita, T., Inoue, G., and Hatano, R.: A comparison of regression methods for estimating soil–atmosphere diffusion gas fluxes by a closed-chamber technique, Soil Biol. Biochem., 36, 107–113, 2004. doi:10.1016/j.soilbio.2003.07.005

Hutchinson, G. L. and Mosier, A. R.: Improved soil cover method for field measurement of nitrous oxide fluxes, Soil Sci. Soc. Am. J., 45, 311-316, 1981. doi:10.2136/sssaj1981.03615995004500020017x

Examples

# Toy data - linear
ffi_fit_models(cars$speed, cars$dist)

# Toy data - nonlinear
ffi_fit_models(Puromycin$conc, Puromycin$rate)

# Real data
f <- system.file("extdata/TG10-01087.data", package = "fluxfinder")
dat <- ffi_read_LI7810(f)[1:75,] # isolate first observation
dat$SECONDS <- dat$SECONDS - min(dat$SECONDS) # normalize time to start at 0
plot(dat$SECONDS, dat$CO2)
ffi_fit_models(dat$SECONDS, dat$CO2)

Compute flux using nonlinear Hutchinson and Mosier (1981) model

Description

Compute flux using nonlinear Hutchinson and Mosier (1981) model

Usage

ffi_hm1981(time, conc, h = 1)

Arguments

time

Time values, numeric

conc

Gas concentration values, numeric

h

Effective chamber height

Value

Flux estimate; see references for more information.

References

Hutchinson, G. L. and Mosier, A. R.: Improved soil cover method for field measurement of nitrous oxide fluxes, Soil Sci. Soc. Am. J., 45, 311-316, 1981. doi:10.2136/sssaj1981.03615995004500020017x

Examples

# If data are approximately linear, then NA is returned
ffi_hm1981(cars$speed, cars$dist)
# If data are nonlinear (saturating) then flux based on gas diffusion theory
ffi_hm1981(Puromycin$conc, Puromycin$rate)

Check if fluxfinder.quiet option is TRUE

Description

Check if fluxfinder.quiet option is TRUE

Usage

ffi_isquiet()

Value

TRUE or FALSE

Match metadata info with a vector of data timestamps

Description

Match metadata info with a vector of data timestamps

Usage

ffi_metadata_match(data_timestamps, start_dates, start_times, obs_lengths)

Arguments

data_timestamps

Data timestamps, either character (YYYY-MM-DD HH:MM:SS) or POSIXct

start_dates

Metadata measurement dates, either character (YYYY-MM-DD) or POSIXct

start_times

Metadata measurement start time entries, either character (HH:MM:SS) or period

obs_lengths

Observation lengths in seconds, numeric; must be same length as start_dates. This should include both the intended measurement period as well as any dead band time at the beginning

Value

A numeric vector equal in length to data_timestamps, with each entry indicating the metadata entry that should be used for that observation. NA is returned if a timestamp has no match in the metadata (i.e., does not fall within any window defined by the start_dates, start_times, and observation length parameters).

Note

If data_timestamps or start_dates cannot be parsed as YYYY-MM-DD, the preferred format, then MM/DD/YYYY (used by U.S. versions of Microsoft Excel when saving CSV files, for example) will be tried.

Examples

# Data timestamps
d_t <- c("2024-01-01 13:00:05", "2024-01-01 13:00:10",
"2024-01-01 13:05:05", "2024-01-01 13:10:00")
# Metadata start dates and times: two measurements, starting 5 minutes apart
s_d <- c("2024-01-01", "2024-01-01")
s_t <- c("13:00:00", "13:05:00")
ol <- c(60, 60) # Observation lengths
ffi_metadata_match(d_t, s_d, s_t, ol)
# Returns {1, 1, 2, NA} indicating that the first and second data timestamps
# correspond to metadata entry 1, the third to entry 2, and the fourth
# has no match

# This generates an error because of overlapping timestamps:
## Not run: 
s_t <- c("13:00:00", "13:01:00")
ffi_metadata_match(d_t, s_d, s_t, ol)

## End(Not run)

Normalize a vector of times

Description

Normalize a vector of times

Usage

ffi_normalize_time(time, normalize = TRUE)

Arguments

time

A vector of time values, either POSIXct or numeric

normalize

Normalize the values so that first is zero? Logical

Value

A numeric vector of normalized values (if normalize_time is TRUE) or the original vector if not.

Generate a QA/QC document

Description

Generate a QA/QC document

Usage

ffi_qaqc(
  flux_data,
  group_column,
  output_file = "qaqc.html",
  output_dir = getwd(),
  open_output = TRUE
)

Arguments

flux_data

A data frame from ffi_compute_fluxes or similar

group_column

Name of the grouping label column in flux_data, character; pass NULL to run with no grouping

output_file

Name of the output file

output_dir

Name of the output directory; default is current working directory

open_output

Automatically open the output HTML file?

Value

The path of the output file.

Examples

# Toy data
cars$Plot <- c("A", "B")
fd <- ffi_compute_fluxes(cars, "Plot", "speed", "dist")
x <- ffi_qaqc(fd, group_column = "Plot", output_dir = tempdir())
file.remove(x) # clean up
# See the introductory vignette for a fully-worked example with real data

Read an EGM-4 data file

Description

Read an EGM-4 data file

Usage

ffi_read_EGM4(file, year, tz = "UTC")

Arguments

file

Filename to read, character

year

Four-digit year of the data (EGM-4 output files have month, day, hour, and minute, but not year), numeric or character

tz

Time zone of the file's time data, character (optional)

Value

A data.frame with the parsed data.

Examples

f <- system.file("extdata/EGM4-data.dat", package = "fluxfinder")
dat <- ffi_read_EGM4(f, 2023)
dat <- ffi_read_EGM4(f, 2023, tz = "EST") # specify time zone

Read a LGR 915-0011 data file

Description

Read a LGR 915-0011 data file

Usage

ffi_read_LGR915(file, date_format = "DMY", tz = "UTC")

Arguments

file

Filename to read, character

date_format

Date format, character: "MDY" (month-day-year) "DMY" (day-month-year), or "YMD" (year-month-day)

tz

Time zone of the file's time data, character (optional)

Details

The LGR 915-0011 was an Ultra-Portable Greenhouse Gas Analyzer made by Los Gatos Research. The date in its output files can appear in different formats, which is why the date_format parameter is needed.

Value

A data.frame with the parsed data.

Note

Some LGR 915 files can have a PGP block at the end; this is ignored.

Examples

f <- system.file("extdata/LGR-data.csv", package = "fluxfinder")
dat <- ffi_read_LGR915(f, date_format = "MDY")
dat <- ffi_read_LGR915(f, date_format = "MDY", tz = "EST") # specify time zone

Read a LI-7810 data file

Description

Read a LI-7810 data file

Usage

ffi_read_LI7810(file)

Arguments

file

Filename to read, character

Details

Currently LI-7810 and LI-7820 files are handled identically.

Value

A data.frame with the parsed data.

Examples

f <- system.file("extdata/TG10-01087.data", package = "fluxfinder")
dat <- ffi_read_LI7810(f)

Read a LI-7820 data file

Description

Read a LI-7820 data file

Usage

ffi_read_LI7820(file)

Arguments

file

Filename to read, character

Details

Currently LI-7810 and LI-7820 files are handled identically.

Value

A data.frame with the parsed data.

Examples

f <- system.file("extdata/TG20-01182.data", package = "fluxfinder")
dat <- ffi_read_LI7820(f)

Internal utility function to read LI-78x0 files

Description

Internal utility function to read LI-78x0 files

Usage

ffi_read_LI78x0(file, model)

Arguments

file

Filename to read, character

model

Instrument model name, string

Details

The is an internal function used by ffi_read_LI7810 and ffi_read_LI7820, and not normally called by users.

Value

A data.frame with the parsed data.

Read a LI-850 data file

Description

Read a LI-850 data file

Usage

ffi_read_LI850(file, tz = "UTC")

Arguments

file

Filename to read, character

tz

Time zone of the file's time data, character (optional)

Value

A data.frame with the parsed data, including a TIMESTAMP column.

Examples

f <- system.file("extdata/LI850.txt", package = "fluxfinder")
dat <- ffi_read_LI850(f)
dat <- ffi_read_LI850(f, tz = "EST") # specify time zone

Read a LI-8200-01S (smart chamber) data file

Description

Read a LI-8200-01S (smart chamber) data file

Usage

ffi_read_LIsmartchamber(file, concentrations = TRUE)

Arguments

file

Filename to read, character

concentrations

Return concentration data (the default), or just summary information? Logical

Value

A data.frame with the parsed data.

Note

These files are in JSON format. See also https://www.licor.com/env/products/soil-flux/smart-chamber.

Author(s)

Ben Bond-Lamberty

Examples

f <- system.file("extdata/LI8200-01S.json", package = "fluxfinder")
dat <- ffi_read_LIsmartchamber(f) # returns 240 rows
ffi_read_LIsmartchamber(f, concentrations = FALSE) # only 4 rows

Read a Picarro G2301 data file

Description

Read a Picarro G2301 data file

Usage

ffi_read_PicarroG2301(file, tz = "UTC")

Arguments

file

Filename to read, character

tz

Time zone of the file's time data, character (optional)

Value

A data.frame with the parsed data.

References

https://www.picarro.com/environmental/products/g2301_gas_concentration_analyzer

Examples

f <- system.file("extdata/PicarroG2301-data.dat", package = "fluxfinder")
dat <- ffi_read_PicarroG2301(f)
dat <- ffi_read_PicarroG2301(f, tz = "EST") # specify time zone

Convert gas concentration to quantity using the Ideal Gas Law

Description

Convert gas concentration to quantity using the Ideal Gas Law

Usage

ffi_ppm_to_umol(ppm, volume, temp, atm)

ffi_ppb_to_nmol(ppb, volume, temp, atm)

Arguments

ppm

Gas concentration (ppmv), numeric

volume

System volume (chamber + tubing + analyzer, m3), numeric

temp

Optional chamber temperature (degrees C), numeric

atm

Optional atmospheric pressure (Pa), numeric

ppb

Gas concentration (ppbv), numeric

Value

The quantity value, in micromoles (for ffi_ppm_to_umol) or nanomoles (for ffi_ppb_to_nmol).

Note

If temp and/or atm are not provided, the defaults are NIST normal temperature and pressure.

References

Steduto et al.: Automated closed-system canopy-chamber for continuous field-crop monitoring of CO2 and H2O fluxes, Agric. For. Meteorol., 111:171-186, 2002. doi:10.1016/S0168-1923(02)00023-0

Examples

ffi_ppm_to_umol(400, 0.1)
ffi_ppb_to_nmol(400, 0.1)