
# Commands for running Python and C++ LAGRANGE examples
# These are all examples from the published literature or LAGRANGE practice examples
# (HawaRee & Smith 2008



#######################################################
# Hawaiian Psychotria (shrubs) (Ree & Smith 2008; http://www.reelab.net/lagrange/configurator/index)
# M0 -- unconstrained
#######################################################

# Python Lagrange, 2012 version

# Python Lagrange, 2012 version
cd /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M0/LGpy_2012/
python psychotria_M0.lagrange.py

# Python Lagrange, 2013 version
cd /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M0/LGpy_2013/
python psychotria_M0.lagrange.py

# C++ Lagrange, 2013 version
cd /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M0/LGcpp 
./lagrange_cpp /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M0/LGcpp/Psychotria_M0.lg | tee /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M0/LGcpp/Psychotria_M0_lgcpp_out.txt



#######################################################
# Hawaiian Psychotria (shrubs) (Ree & Smith 2008; http://www.reelab.net/lagrange/configurator/index)
# M0 -- unconstrained, but stratified as a double-check
#######################################################

# Python Lagrange, 2012 version
cd /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M0strat/LGpy_2012/
python psychotria_M0_strat.lagrange.py

# Python Lagrange, 2013 version
cd /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M0strat/LGpy_2013/
python psychotria_M0_strat.lagrange.py

# C++ Lagrange, 2013 version
cd /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M0strat/LGcpp/
./lagrange_cpp /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M0strat/LGcpp/Psychotria_M0strat.lg | tee /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M0strat/LGcpp/Psychotria_M0strat_lgcpp_out.txt





#######################################################
# Hawaiian Psychotria (shrubs) (Ree & Smith 2008; http://www.reelab.net/lagrange/configurator/index)
# M1 -- constrained to 2 areas only
#######################################################

# Python Lagrange, 2012 version

# Python Lagrange, 2012 version
cd /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M1/LGpy_2012/
python psychotria_M1.lagrange.py

# Python Lagrange, 2013 version
cd /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M1/LGpy_2013/
python psychotria_M1.lagrange.py

# C++ Lagrange, 2013 version
cd /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M1/LGcpp 
./lagrange_cpp /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M1/LGcpp/Psychotria_M1.lg | tee /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M1/LGcpp/Psychotria_M1_lgcpp_out.txt



#######################################################
# Hawaiian Psychotria (shrubs) (Ree & Smith 2008; http://www.reelab.net/lagrange/configurator/index)
# M1 -- constrained to 2 areas only, but stratified as a double-check
#######################################################

# Python Lagrange, 2012 version
cd /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M1strat/LGpy_2012/
python psychotria_M1_strat.lagrange.py

# Python Lagrange, 2013 version
cd /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M1strat/LGpy_2013/
python psychotria_M1_strat.lagrange.py

# C++ Lagrange, 2013 version
cd /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M1strat/LGcpp/
./lagrange_cpp /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M1strat/LGcpp/Psychotria_M1strat.lg | tee /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M1strat/LGcpp/Psychotria_M1strat_lgcpp_out.txt






#######################################################
# Hawaiian Psychotria (shrubs) (Ree & Smith 2008; http://www.reelab.net/lagrange/configurator/index)
# M2 -- constrained to 2 areas only
#######################################################

# Python Lagrange, 2012 version

# Python Lagrange, 2012 version
cd /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M2/LGpy_2012/
python psychotria_M2.lagrange.py

# Python Lagrange, 2013 version
cd /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M2/LGpy_2013/
python psychotria_M2.lagrange.py

# C++ Lagrange, 2013 version
cd /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M2/LGcpp 
./lagrange_cpp /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M2/LGcpp/Psychotria_M2.lg | tee /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M2/LGcpp/Psychotria_M2_lgcpp_out.txt



#######################################################
# Hawaiian Psychotria (shrubs) (Ree & Smith 2008; http://www.reelab.net/lagrange/configurator/index)
# M2 -- constrained to 2 areas only, but stratified as a double-check
#######################################################

# Python Lagrange, 2012 version
cd /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M2strat/LGpy_2012/
python psychotria_M2_strat.lagrange.py

# Python Lagrange, 2013 version
cd /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M2strat/LGpy_2013/
python psychotria_M2_strat.lagrange.py

# C++ Lagrange, 2013 version
cd /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M2strat/LGcpp/
./lagrange_cpp /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M2strat/LGcpp/Psychotria_M2strat.lg | tee /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M2strat/LGcpp/Psychotria_M2strat_lgcpp_out.txt







#######################################################
# Hawaiian Psychotria (shrubs) (Ree & Smith 2008; http://www.reelab.net/lagrange/configurator/index)
# M3 -- stratified by time
#######################################################

# Python Lagrange, 2012 version
cd /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M3strat/LGpy_2012/
python psychotria_M3_strat.lagrange.py

# Python Lagrange, 2013 version
cd /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M3strat/LGpy_2013/
python psychotria_M3_strat.lagrange.py

# C++ Lagrange, 2013 version
cd /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M3strat/LGcpp/
./lagrange_cpp /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_M3strat.lg | tee /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_M3strat_lgcpp_out.txt


# C++ Lagrange, 2013 version, input version 2 (calctype = 0)
cd /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/
./lagrange_cpp /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_M3strat.lg | tee /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_M3strat_lgcpp_out.txt













#######################################################
# Pacific Cyrtandra shrubs (Smith & Donoghue 2010)
# M0 -- unconstrained, but stratified as a double-check
#######################################################

# Python Lagrange, 2012 version
cd /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Cyrtandra_M0/LGpy_2012/
python Cyrtandra_M0.lagrange.py

# Python Lagrange, 2013 version
cd /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Cyrtandra_M0/LGpy_2013/
python Cyrtandra_M0.lagrange.py

# C++ Lagrange, 2013 version
cd /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Cyrtandra_M0/LGcpp/
./lagrange_cpp /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Cyrtandra_M0/LGcpp/Cyrtandra_M0.lg | tee /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Cyrtandra_M0/LGcpp/Cyrtandra_M0_lgcpp_out.txt 










#######################################################
# Pacific Lonicera shrubs (Smith & Donoghue 2010)
# M0 -- unconstrained, but stratified as a double-check
#######################################################

# Python Lagrange, 2012 version
cd /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Lonicera_M0/LGpy_2012/
python Lonicera_M0.lagrange.py

# Python Lagrange, 2013 version
cd /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Lonicera_M0/LGpy_2013/
python Lonicera_M0.lagrange.py

# C++ Lagrange, 2013 version
cd /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Lonicera_M0/LGcpp/
./lagrange_cpp /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Lonicera_M0/LGcpp/Lonicera_M0.lg | tee /Dropbox/_njm/__packages/BioGeoBEARS_setup/inst/extdata/examples/Lonicera_M0/LGcpp/Lonicera_M0_lgcpp_out.txt 


