Predicting and Visualizing Thermal Habitat: thermopic

The thermopic R package provides functionality for predicting and visualizing the seasonal availability of thermal habitat in lakes.

Installation

Installation is easiest from an R commandline using the devtools package.

devtools::install_github('stevencarlislewalker/thermopic')

It might be necessary to preceed this first step by installing devtools.

install.packages('devtools')

Once the package is installed, it may be loaded using the library function.

library(thermopic)

Quick tour

The thermopic package runs within a project directory, which we create using the optional temporary_thermopic_directory function.

root = temporary_thermopic_directory()

We now use thermopic's setup_directory function to create the required directory structure for our project. For this quick tour we use sample input data contained within the package, which is the default behaviour of setup_directory.

setup_directory(root, overwrite = TRUE)

To inspect the resulting directory structure one may use thermopics print_directory_tree function.

print_directory_tree(root)

## thermopic_project           
##  ¦--DataIn                  
##  ¦   ¦--0_User_Options.csv  
##  ¦   ¦--1_Lake.csv          
##  ¦   °--2_Climate.csv       
##  ¦--DataOut                 
##  ¦   °--ThermoPics          
##  ¦--ThermoPic_Dictionary.csv
##  ¦--ThermoPic_Guide.pdf     
##  °--ThermoPic_TechReport.pdf

Now that the structure is in place one may fit the thermopic model.

fitted_thermopic_model = thermopic_model(
  path = root,
  Lake = '1_Lake.csv',
  Climate = '2_Climate.csv'
)

And create the report as well as the thermopic images themselves.

thermopic_report_data = thermopic_report(
  path = root,
  STM_Parameters = '4_STM_Parameters.csv',
  Nlakes_test = 5,
  show_progress_bar = FALSE
)

Here we see the resulting outputs including the images in jpeg format files.

## thermopic_project                                          
##  ¦--DataIn                                                 
##  ¦   ¦--0_User_Options.csv                                 
##  ¦   ¦--1_Lake.csv                                         
##  ¦   °--2_Climate.csv                                      
##  ¦--DataOut                                                
##  ¦   ¦--3_Model_Inputs.csv                                 
##  ¦   ¦--4_STM_Parameters.csv                               
##  ¦   ¦--5_ThermalSpace4D.csv                               
##  ¦   ¦--ThermoPics                                         
##  ¦   ¦   ¦--4_Wingiskus Lake_15-3543-56122_P2001-2010.jpeg 
##  ¦   ¦   ¦--5_Cygnet Lake_15-3653-55394_P2001-2010.jpeg    
##  ¦   ¦   ¦--5_Malachi Lake_15-3559-55281_P2001-2010.jpeg   
##  ¦   ¦   ¦--5_South Scot Lake_15-3523-55336_P2001-2010.jpeg
##  ¦   ¦   °--5_Whitefish Lake_15-3532-55170_P2001-2010.jpeg 
##  ¦   ¦--tmp_ClimMetrics.csv                                
##  ¦   °--tmp_IceClimMetrics.csv                             
##  ¦--ThermoPic_Dictionary.csv                               
##  ¦--ThermoPic_Guide.pdf                                    
##  °--ThermoPic_TechReport.pdf

Further information

For a more detailed introduction see this tutorial.