Difference between revisions of "Document RGLM tools"

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[[Category:Task]]
 
[[Category:Task]]
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= Overview =
 
= Overview =
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:rGLM is a package in the [http://www.r-project.org/ R statistical language] designed to support scripted interactions with [[GLM_Software]]. rGLM Includes some basic functions for calculating physical derivatives and thermal properties of model output.
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GLEON and CIDA (center for data analytics) at the USGS have developed two software packages written in the R statistical language to interact with GLM
 +
*GLM: lake model
 +
*GLMr: package designed to support scripted interactions with [[GLM_Software]].  
 +
*glmtools: tools to reproducible model results, adjust parameter files, and plot visualizations
 +
 
 +
== Why R? ==
 +
*Performace: stable, light and fast
 +
*Support network
 +
**documentation, community, developers
 +
*Reproducibility
 +
**anyone anywhere can reproduce results
 +
**enables dissemination - this presentation is a .Rmd file!
 +
*Versatility: unified solution to almost any numerical problem, graphical capabilities
 +
*Testing: integrated “R package” testing limits bugs
 +
 
 +
== Package Downloads ==
 +
Download R packages from GRAN (Geological Survey R Archive Network)
 +
*[http://owi.usgs.gov/R/gran.html GRAN]
 +
 
 +
== glmtools Functions (as of v0.2.5.2) ==
 +
Maintainer: Jordan S Read <br>
 +
Authors: Jordan S Read, Luke A Winslow<br>
 +
{| {{table}}
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| align="center" style="background:#f0f0f0;"|'''Function'''
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| align="center" style="background:#f0f0f0;"|'''Title'''
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|-
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| compare_to_field||compare metric for GLM vs field observations
 +
|-
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| get_evaporation||get evaporation from GLM simulation
 +
|-
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| get_hypsography||retrieve hypsography information
 +
|-
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| get_ice||get ice depth from GLM simulation
 +
|-
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| get_nml_value||gets a nml value according to an arg_name
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|-
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| get_surface_height||get surface height from GLM simulation
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|-
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| get_temp||get water temperatures from a GLM simulation
 +
|-
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| get_wind||get wind speed from GLM simulation
 +
|-
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| model_diagnostics||run diagnostics on model results
 +
|-
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| plot_temp||plot water temperatures from a GLM simulation
 +
|-
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| read_field_obs||read in field data into a data.frame
 +
|-
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| read_nml||read in a GLM simulation *.nml file
 +
|-
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| resample_sim||get subset of time from a generic timeseries data.frame
 +
|-
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| resample_to_field||match GLM water temperatures with field observations
 +
|-
 +
| set_nml||sets values in nml object
 +
|-
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| sim_metrics||get possible metrics for comparing GLM outputs to field
 +
|-
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| summarize_sim||creates GLM simulation summary outputs
 +
|-
 +
| validate_sim||run diagnostics on model results vs observations
 +
|-
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| write_nml||write GLM *.nml for a GLM simulation
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|}
  
 
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{{#set:|
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{{#set:
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Owner=Paul_Hanson}}
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Expertise=Physical_limnology|
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Github=https://github.com/GLEON/rGLM|
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Owner=Hilary_Dugan|
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Participants=Jordan_Read|
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Progress=100|
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StartDate=2015-04-19|
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TargetDate=2015-04-23|
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Type=Low}}

Latest revision as of 18:17, 23 April 2015

Overview

GLEON and CIDA (center for data analytics) at the USGS have developed two software packages written in the R statistical language to interact with GLM

  • GLM: lake model
  • GLMr: package designed to support scripted interactions with GLM_Software.
  • glmtools: tools to reproducible model results, adjust parameter files, and plot visualizations

Why R?

  • Performace: stable, light and fast
  • Support network
    • documentation, community, developers
  • Reproducibility
    • anyone anywhere can reproduce results
    • enables dissemination - this presentation is a .Rmd file!
  • Versatility: unified solution to almost any numerical problem, graphical capabilities
  • Testing: integrated “R package” testing limits bugs

Package Downloads

Download R packages from GRAN (Geological Survey R Archive Network)

glmtools Functions (as of v0.2.5.2)

Maintainer: Jordan S Read
Authors: Jordan S Read, Luke A Winslow

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


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