glmtools

Tools for interacting with the General Lake Model (GLM) in R. glmtools includes some basic functions for calculating physical derivatives and thermal properties of model output, and some plotting functionality (see example image below).

glmtools Functions (as of v0.2.5.2)

Package	Topic	Title
glmtools	calibrate_sim	Calibrates GLM-AED2 variables to improve fit between observed and simulated data
glmtools	compare_to_field	compare metric for GLM vs field observations
glmtools	convert_sim_var	convert an existing simulation variable into a different one
glmtools	epi.temperature	Get volumetrically averaged epilimnion temp
glmtools	get_calib_init_validation	Get last values from a calibration period to be used for the validation
glmtools	get_calib_periods	Splits time period into calibration and validation period
glmtools	get_calib_setup	Creates an example setup for a calibration run
glmtools	get_evaporation	get evaporation from GLM simulation
glmtools	get_hypsography	retrieve hypsography information
glmtools	get_ice	get ice depth from GLM simulation
glmtools	get_nml_value	gets a nml value according to an arg_name
glmtools	get_raw	get raw data from GLM simulation
glmtools	get_surface_height	get surface height from GLM simulation
glmtools	get_temp	get water temperatures from a GLM simulation
glmtools	get_var	get variable from a GLM simulation
glmtools	get_wind	get wind speed from GLM simulation
glmtools	hypo.temperature	Get volumetrically averaged hypolimnion temp
glmtools	plot_compare_stage	Plot simulated and observed stage data
glmtools	plot_meteo	Plot meterological drivers from a csv file
glmtools	plot_temp	Deprecated. Plot water temperatures from a GLM simulation
glmtools	plot_temp_compare	Deprecated. Plot matching heatmaps for modeled and observed temp
glmtools	plot_validate_profiles	Plot validation and model temperature profiles for all unique dates
glmtools	plot_var_compare	Plot matching heatmaps for modeled and observed temp
glmtools	plot_var_df	Plot variables from a data frame
glmtools	plot_var_nc	Plot variables from a .nc file
glmtools	read_field_obs	Read in field data into a data.frame
glmtools	read_field_stage	Read in a field stage file
glmtools	read_nml	read in a GLM simulation *.nml file
glmtools	resample_sim	get subset of time from a generic timeseries data.frame
glmtools	resample_to_field	Match GLM water temperatures with field observations
glmtools	run_example_sim	Run example simulation
glmtools	set_nml	sets values in nml object
glmtools	sim_metrics	get possible metrics for comparing GLM outputs to field
glmtools	sim_var_longname	Get long name of variable from a GLM simulation
glmtools	sim_var_units	Get units of variable from a GLM simulation
glmtools	sim_vars	Get list of variables from a GLM simulation
glmtools	summarize_sim	Creates GLM simulation summary outputs
glmtools	validate_sim	Run diagnostics on model results vs observations
glmtools	water.temperature	Mimic rLakeAnalyzer function
glmtools	whole.lake.temperature	Get volumetrically averaged whole lake temperature
glmtools	write_nml	write GLM .nml for a GLM simulation

FAQ

How do I install glmtools? It isn’t on CRAN!

glmtools can be installed from the USGS GRAN repository. To install glmtools and all dependencies, follow the appropriate instructions below:

1. Setup R to add GRAN using the instructions on the USGS R page.

2. After GRAN is setup (usually requires a restart of R), then use the following command in R:

   install.packages("glmtools")

What libraries does glmtools need?

This version requires the NetCDF version R library (called ncdf4), and rLakeAnalyzer, and tools if you would like to run all examples.

package	version
R	>= 3.0
GLM3r	*
rLakeAnalyzer	*
akima	*
adagio	*
dplyr	*
ggplot2	*
lazyeval	*
methods	*
patchwork	*
ncdf4	*
readr	*
reshape2	*
tidyr	*
tools	*

How do I contribute new code back to the glmtools project?

In order to contribute to this code, we recommend the following workflow:

1. “fork” this repository to your own personal github account

2. clone the github repository to your computer:

   $git clone https://github.com/{username}/glmtools.git

3. modify code or add new functionality, save the code

4. add the repository master to a remote master called “upstream”

   $cd glmtools

   $git remote add upstream https://github.com/USGS-R/glmtools.git

5. before pushing your changes to your repository, pull in the current version of the GLEON master:

   $git fetch upstream

6. merge these differences with your own “master” version:

   $git merge upstream/master

7. push your changes to your github repository, in addition to changes made by pulling in the GLEON master:

   $git push

8. submit a pull request to GLEON master using your account at github.com