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, as of v0.2.5, can also call GLM using the GLMr package. Shown here running GLM from R with example driver data that is part of the package:

glmtools Functions (as of v0.2.5.2)

Function	Title
compare_to_field	compare metric for GLM vs field observations
get_evaporation	get evaporation from GLM simulation
get_hypsography	retrieve hypsography information
get_ice	get ice depth from GLM simulation
get_nml_value	gets a nml value according to an arg_name
get_surface_height	get surface height from GLM simulation
get_temp	get water temperatures from a GLM simulation
get_wind	get wind speed from GLM simulation
model_diagnostics	run diagnostics on model results
plot_temp	plot water temperatures from a GLM simulation
read_field_obs	read in field data into a data.frame
read_nml	read in a GLM simulation *.nml file
resample_sim	get subset of time from a generic timeseries data.frame
resample_to_field	match GLM water temperatures with field observations
set_nml	sets values in nml object
sim_metrics	get possible metrics for comparing GLM outputs to field
summarize_sim	creates GLM simulation summary outputs
validate_sim	run diagnostics on model results vs observations
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 ncdf), and rLakeAnalyzer, and tools if you would like to run all examples.

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