README.md

In aemon-j/SimstratR: Work with Simstrat in R

SimstratR

R package for basic Simstrat model running. SimstratR holds the version compiled or downloaded from the website on 2021-04-23 (version 3.0.1) and should run virtually on any Windows, Linux and macOS system. This package does not contain the source code for the model, only the executable. This package was inspired by GLMr.

Installation

You can install SimstratR from Github with:

```{r gh-installation, eval = FALSE}

install.packages("devtools")

devtools::install_github("aemon-j/SimstratR")

## Usage
Compatible with Windows, Linux (tested on Ubuntu 18.04.3 LTS) and macOS X.

### Run

```{r example, eval=FALSE}
library(SimstratR)
sim_folder <- system.file('extdata', package = 'SimstratR')
run_simstrat(sim_folder, par_file = 'simstrat.par')

Output

```{r example, eval = FALSE} library(LakeEnsemblR) par_file <- file.path(sim_folder, 'simstrat.par')

out_file <- file.path(sim_folder, 'Results', 'T_out.dat')

Extract output

sim_out <- read.table(out_file, header = T, sep=",", check.names = F)

Convert decimal days to yyyy-mm-dd HH:MM:SS

timestep <- get_json_value(par_file, "Simulation", "Timestep s") reference_year <- get_json_value(par_file, "Simulation", "Start year")

Convert date

sim_out[,1] <- as.POSIXct(sim_out[,1] * 3600 * 24, origin = paste0(reference_year, "-01-01"))

In case sub-hourly time steps are used, rounding might be necessary

sim_out[,1] <- lubridate::round_date(sim_out[,1], unit = lubridate::seconds_to_period(timestep))

First column datetime, then depth from shallow to deep

sim_out <- sim_out[,c(1,ncol(sim_out):2)]

Remove columns without any value

sim_out <- sim_out[,colSums(is.na(sim_out))<nrow(sim_out)]

Extract depths for colnames

depths <- abs(as.numeric(colnames(sim_out)[-1])) colnames(sim_out) <- c("datetime", paste0('wtr_',abs(depths)))

Plot heatmap

rLakeAnalyzer::wtr.heat.map(sim_out)

```

aemon-j/SimstratR documentation built on March 29, 2022, 5:33 p.m.