README.md

In aemon-j/MyLakeR: Work with MyLake in R

MyLakeR

My Lake initial implementation in R

Installation

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

install.packages("devtools")

devtools::install_github("aemon-j/MyLakeR") library(MyLakeR)

## Example:  Lake Vansjø (Norway)
```{r gh-installation, eval = FALSE}
mylake_path <- system.file(package="MyLakeR")

# configure some lake parameters from .yaml file into format required by MyLake
config_mylake(config_file="Vansjo_master_config.yaml",
              folder=file.path(mylake_path,"extdata","example"))

# create meteorological file from standardized met input into format required by MyLake
meteo_mylake(meteo_file="LakeEnsemblR_meteo_standard.csv",
             folder=file.path(mylake_path,"extdata","example"))

# config file already created for Vansjø in correct format
# located in ".../extdata/example/MyLake/mylake.Rdata"

# create initial profile file from standardized initial conditions into format required by MyLake
init_mylake(wtemp_file="LakeEnsemblR_wtemp_profile_standard.csv",
            date="2002-03-02 0:00",
            folder=file.path(mylake_path,"extdata","example"))

# run MyLake model from 2002-03-02 to 2002-12-31
run_mylake(sim_folder=file.path(mylake_path,"extdata","example"))

Post-Processing: Modelled Water Temperature

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

load libraries for processing

library(tidyverse) library(lubridate)

load output file with model results

load(file.path(mylake_path,"extdata","example","MyLake","output","output.RData"))

extract depth, water temperature, and dates (daily) from model output

depths <- res$zz temps <- res$Tzt dates <- mdy(res$tt) colnames(temps) <- dates

combine into single data frame for ggplot

temp_data <- as.data.frame(temps) %>% mutate(depths=depths) %>% gather(key=date, value=temp_C, 1:(ncol(.)-1)) %>% mutate(date=as.Date(as.numeric(date),origin="1970-01-01"))

heat-map plot of modelled water temperature

ggplot() + geom_tile(data=temp_data,aes(x=date,y=depths,fill=temp_C)) + scale_y_reverse(expand=c(0,0)) + scale_x_date(expand=c(0,0), limits=c(ymd("2002-01-01"),ymd("2002-12-31")), date_labels="%b\n%Y") + scale_fill_distiller(palette="Spectral",name="degC") + labs(x=NULL,y="Depth (m)",title="MyLake_watertemp: Vansjø") + theme_bw() ```

aemon-j/MyLakeR documentation built on March 8, 2024, 3:50 p.m.