readosense

The readosense R package provides an easy way to import raw files from Eosense ecosystem gas flux chambers as dataframes that can be used with the fluxible package.

Installation

You can install the development version of readosense from GitHub with:

# install.packages("pak")
pak::pak("jogaudard/readosense")

Workflow

Importing the log files

library(readosense)

# this step is not needed if you know where your data are
path_logs <- system.file("extdata/ex_logs", package = "readosense")

logs <- eo_import_logs(path_logs)

chamber_log <- eo_logs(logs)

env_variables <- eo_env(logs)

Doing so, the function eo_import_logs is run only once, which is faster.

Importing the data files

# this step is not needed if you know where your data are
path_data <- system.file("extdata/ex_data", package = "readosense")

data <- eo_data(path_data)


# it is more practical to join the environmental data here

data <- data |>
  dplyr::left_join(env_variables, by = dplyr::join_by(f_datetime == datetime))

Using fluxible

The first step of the fluxible workflow would then look like this:

library(fluxible)

conc <- flux_match(
  raw_conc = data,
  field_record = chamber_log,
  f_datetime = f_datetime,
  start_col = closing,
  end_col = opening
)