This repository contains the code for the R-package that provides functions for all the routine steps in running the SOFUN model:

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

Get this R-package by

install_github("stineb/rsofun")

Note that the package rsofun requires a large number of other R-packages (dependencies). Some are required only for specific tasks (e.g. creating certain plots or applying certain calibration methods). These are loaded optionally (XXX TODO XXX). Others are essential as the source code is generally implemented adopting tidyverse syntax. Essential dependencies need to be installed beforehand and are loaded with the library(rsofun) call. These are:

• dplyr
• tidyr
• purrr
• readr
• rlang
• stringr
• ggplot2
• lubridate
• Metrics
• mgcv
• ncdf4
• optimr

Suggested dependencies are:

• 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

Install required dependencies by:

list_of_packages <- c( "dplyr", "tidyr", "purrr", "readr", "rlang", "stringr", 
                       "ggplot2", "lubridate", "Metrics", "mgcv", "ncdf4", "optimr" 
                       )
new_packages <- list_of_packages[!(list.of.packages %in% installed.packages()[,"Package"])]
if( length(new_packages)>0 ) install.packages(new_packages)

Several functions require external programs called by system() calls from within R. Required programs need to be installed beforehand, as follows:

• 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

Examples are given in several vignettes, also available here.