What it does

The rsofun R package provides functions for all the routine steps of running the P-model within R.

  • Setup of the model environment
  • Preparation of input files
  • Calibrating model parameters
  • Running the model
  • Reading outputs into R
  • Evaluating outputs (benchmarking)

It also provides a generic function (pmodel()) to run alternative implementations of the P-model in different languages (Fortran using the SOFUN modelling framework, Python not implemeted yet), wrapped within R, and an impementation in R itself.

Installation

To install and load the rsofun package run the following command in your R terminal:

if(!require(devtools)){install.packages(devtools)}
devtools::install_github( "stineb/rsofun", dependencies = NA, build_vignettes = FALSE )
library(rsofun)

The vignettes need to be built in a separate step after manually specifying the path of where SOFUN is located locally. This is done by defining the option rsofun.dor.sofun. Change the paths in the vignettes vignettes/overview.Rmd and vignettes/test_implementations.Rmd from "string_path_where_sofun_is" to wherever you put it by hand. Then build the vignettes in R:

options( list( rsofun.dir.sofun="string_path_where_sofun_is" ) )
devtools::build_vignettes()

Display the rsofun overview vignette for a comprehensive documentation of the package:

vignette("overview", "rsofun")

Dependencies

The rsofun package requires a large number of other R-packages (dependencies). Required dependencies are essential for rsofun functions and are:

  • dplyr, ggplot2, lubridate, Metrics, mgcv, ncdf4, optimr, purrr, readr, rlang, stringr, tidyr, LSD, and GenSA,

Suggested dependencies are required only for certain optional tasks and are:

  • BayesianTools, caret, gplots, hydroGOF, maps, maptools, neuralnet, nnet, raster, sp, and testthat

To install locally unavailable packages, run

install_dependencies_rsofun()

To load dependencies, run

load_dependencies_rsofun()

Suggested dependencies are only used optionally:

  • GenSA: used by calib_sofun(), if settings_calib$method=="gensa", see calib_sofun.R
  • BayesianTools: used by calib_sofun(), if settings_calib$method=="BayesianTools", see calib_sofun.R
  • caret: used by gapfill_nn(), see gapfill_nn.R and prepare_input_sofun.R
  • neuralnet: used by gapfill_nn() and eval_response_neuralnet(), see eval_response_neuralnet.R and gapfill_nn.R
  • nnet: used by gapfill_nn() and eval_response_neuralnet(), see eval_response_neuralnet.R and gapfill_nn.R
  • hydroGOF: used by analyse_modobs() to calculate the Nash-Sutcliffe model efficiency, see analyse_modobs.R

External environment

Several functions require external programs called by system() calls from within R. Required programs need to be installed beforehand, as follows (Note: These are not required for the “Simple usage”, described below):

  • NCO. Is used by get_pointdata_() functions (executing the Bash script "./extract_pointdata_byfil.sh" with NCO command ncks). Before using rsofun, install NCO on a Mac by

    brew tap homebrew/science
brew install nco

  • CDO. Is used by the proc_ncout_sofun_bysite() function (executing Bash script "./proc_output_sofun.sh" with CDO command cdo mergetime). Before using rsofun, install CDO on a Mac by

    brew install cdo

    Apparently, CDO is no longer available as a Homebrew formula (right?). Unse MacPorts instead:

    sudo port install cdo

Acknowledgements

The main author (B. Stocker) was funded by Marie Sklodowska-Curie fellowship H2020-MSCA-IF-2015, project FIBER, grant number 701329.