README.md

In bgctw/RespChamberProc: Processing Data from Respiration Chambers

Overview

RespChamberProc package supports deriving gas fluxes from a time series of gas concentrations in a chamber.

Installation

install.packages( # dependencies from CRAN
  c("rlang", "changepoint", "nlme", "segmented", "tibble",  "dplyr", "purrr"))
# install.packages("devtools")
devtools::install_github("bgctw/RespChamberProc")

Usage

See the package vignettes for an introduction.

A simple example estimates photosynthesis (negative CO2 flux into the light chamber) in units micromol/second from CO2 concentration data in ppm.

library(RespChamberProc)
#?RespChamberProc

ds <- chamberLoggerEx1s               # example data with the package
ds$Pa <- chamberLoggerEx1s$Pa * 1000  # convert kPa to Pa
ds$CO2_dry <- corrConcDilution(ds)    # correct for water vapour
resFit <- calcClosedChamberFlux(
  ds
  , colConc = "CO2_dry", colTime = "TIMESTAMP"  
  , colTemp = "TA_Avg", colPressure = "Pa"  # Temperature in K, Pressure in Pa
  , volume = 1, area = 1                    # chamber dimensions m3 and m2
)
dplyr::select(resFit ,c("flux","sdFlux"))
#> # A tibble: 1 x 2
#>        flux    sdFlux
#>       <dbl>     <dbl>
#> 1 -3.534767 0.7084692
plotResp(ds, resFit, label = "Example Series")

bgctw/RespChamberProc documentation built on Jan. 4, 2024, 6:12 a.m.