Introduction
Hello and welcome to ConFluxPro - a toolkit for soil gas analysis.
This package implements the Flux-Gradient Method (FGM) to model soil gas fluxes from concentration profiles. It provides a range of functions that cover the complete process from raw data to modeling fluxes and beyond. “ConFluxPro” stands for Concentration, Flux and Production - the three levels of integration of gases in the soil. This vignette provides an overview over the package structure, including the most important functions and general workflow.
Workflow
Modeling gas fluxes in ConFluxPro is modular and
straightforward. Starting with data preparation, we collect all
necessary data in a compatible way and combine them into a single model
frame cfp_dat(). From this, calculating flux rates is as
simple as calling a single function. fg_flux() implements
different ‘forward’ methods to derive flux rates, while
pro_flux() calls an inverse model. From the returned model
result, we can then extract the efflux() or
production() rates within the soil or perform different
post-hoc analyses such as calibrating the model with
alternate() or deriving an estimate of model uncertainty
with bootstrap_error().
Each aspect of the workflow is explained in more detail in the other articles of this documentation.
- Create a
cfp_dat()data set:vignette("data_preparation", package = "ConFluxPro") - Basic modeling with
fg_flux()andpro_flux():vignette("flux", package = "ConFluxPro") - Parameter variation and calibration with
alternate():vignette("calibration", package = "ConFluxPro") - Uncertainty estimation with
bootstrap_error():vignette("uncertainty", package = "ConFluxPro")
Package structure and classes
A focus of this package is to promote reproducibility and ease of use. We implemented a class and method system to enable easy and consistent data handling. The basic philosophy behind that was that at any point in the process, every aspect of a model should be contained in a single object, including the original data.
To this end, we implemented a central S3-class
cfp_dat(). If you are new to R or not familiar with S3,
that’s no problem. Basically, S3-classes just enforces a certain data
structure and tells the functions in this package how to interact with
it, so you don’t have to. A cfp_dat() object contains all
data you need to model soil gas fluxes. All other classes are either
components of a cfp_dat() object or build on it to add
specific settings for the models used.
Learn more about the classes in ConFluxPro in TODO
Conveniance functions
Much of data analysis and modeling is trial-and-error. To enable a
hands-on approach in modeling soil gas fluxes, we added some
functionality to facilitate easy data handling and exploration. Most
importantly, we implemented methods for the dplyr::filter()
function for most classes in this package. This makes it easy to subset
a model result for only one site or to look into one date in more
detail. This especially handy in combination with a simple plotting
function plot_profile() that shows many information of
measured and derived parameters within the soil per distinct profile.
This helps to better understand the data and the modeled results.
Finally, the reverse is also possible with combine_models()
that automatically joins different datasets if they are compatible.