Author: Colleen Roy
Last Edited: 2021-10-29
The software and associated files uploaded in this repository were used to generate the results published in:
Schmolke A, Bartell SM, Roy C, Green N, Galic N, Brain R. 2019. Species-specific population dynamics and their link to an aquatic food web: a hybrid modeling approach. Ecological Modelling. 405:1-14
Schmolke A, Bartell SM, Roy C, Desmarteau D, Moore A, Cox MJ, Maples-Reynolds NL, Galic N, Brain R. 2021. Applying a hybrid modeling approach to evaluate potential pesticide effects and mitigation effectiveness for an endangered fish in simulated oxbow habitats. Environmental Toxicology and Chemistry. 40:9:2615-2628.
Galic N, Schmolke A, Bartell SM, Roy C, Brain R. Applying a hybrid model to support management of the endangered Topeka shiner in oxbow habitats. Submitted.
This software and associated files are provided "as is" with the sole purpose to allow the reproduction of the published results without any warranties of performance or fitness for any other purpose.
CASM: TRACE_documentation_CASM-OC_Jun2021.pdf
TS-IBM: TRACE_documentation_TS-IBM_Jun2021.pdf
All files associated with this publication are in the folder "Schmolke_2019". This how to documents how to run CASM, the TS-IBM, and the linked CASM + TS-IBM in R.
In order to run either the TS-IBM or the Linked CASM + TS-IBM you must:
- Have NetLogo 6 installed (for runs in this study, NetLogo 6.0.2 was used)
- Have the R package "RNetLogo" installed
- Run CASM first (see below for instructions)
File: 1_CASM.R
Initial Folder Locations/Names:
Line 9: Directory of project (must already exist)
Line 10: Name of scenario (note: this will become a folder in the project directory)
CASM Files:
Line 13: CASM executable file (ex. casm_ibm_tsv42.exe)
Line 14: CASM control file (ex. casm_IBM_TS_control.dat)
Line 15: CASM habitat parameters (ex. casm_TS_bio_parms_RSK_WithTS_08Oct2018.txt)
Line 16: CASM food web parameters (ex. web_casmTS_HRM_20Jun2018.dat)
Line 17: CASM environmental time series (ex. env_casmTS_2010_08May2018.prn)
Line 18: CASM contaminant time series (ex. ATZ_exp_zero_test.dat)
Line 19: CASM toxicity parameters (ex. TS_toxicity_atrazine_tri_base.dat)
(note: toxicity scenarios are not considered in this study BUT these files
need to be present for CASM to run correctly)
Note: Lines 13-19 refer to file paths relative to the project directory (defined in line 9). If these files are not located in the project directory, full file paths must be provided instead of just the file names
Model Parameters:
Line 22: Years to Run CASM (numeric)
Run the R script.
Run CASM: Run the CASM executable located in the scenario folder (named in line 10 and created by the R script)
The output file containing daily biomasses is named IBM_TS_master_ref.out and is located in the scenario folder
File: 2_IBMOnly.R
Initial Folder Locations/Names:
Line 9: Directory of project (must already exist)
Line 10: Name of scenario (note: this will become a folder in the project directory)
NetLogo Location/Files:
Line 13: NetLogo app folder (ex. C:/Program Files/NetLogo 6.0.2/app)
Line 14: NetLogo jar file (in NetLogo app folder) (ex. netlogo-6.0.2.jar)
IBM Files:
Line 17: TS-IBM NetLogo Model (ex. TS_IBM_March2019.nlogo)
Line 18: TS-IBM Input Parameter Files (ex. InputParameters_20Jun2018.txt)
Note: Lines 17-18 refer to file paths relative to the project directory (defined in line 9). If these files are not located in the project directory, full file paths must be provided instead of just the file names
CASM Files:
Line 21: Name of CASM scenario created/ran previously (same value as line 9 from 1_CASM.R)
Line 22: CASM environmental time series used in CASM scenario (ex. env_casmTS_2010_08May2018.prn)
Note: Line 22 refers to a file within the CASM scenario folder named in line 21
CASM Model Parameters:
Line 25: CASM simulation year to use in TS-IBM (numeric)
IBM Model Parameters:
Line 28: TS-IBM RandomNumberSeed input, numeric
Line 29: TS-IBM pondArea input, numeric
Line 30: TS-IBM CASM_pool_area input, numeric
Line 31: TS-IBM Sunfish input, logical
Line 32: TS-IBM Predation input, logical
Line 33: TS-IBM DD_egg_larva input, logical
Line 34: TS-IBM AverageKmin input, numeric
Line 35: TS-IBM ScalingSearchArea input, numeric
Line 36: TS-IBM MaxDetritusDepth input, numeric
Line 37: TS-IBM YearsToRun input, numeric
Run the R script.
The output file containing daily biomasses is named TS-IBM_output.txt and is located in the scenario folder
File: 3_Linked.R
Initial Folder Locations/Names:
Line 9: Directory of project (must already exist)
Line 10: Name of scenario (note: this will become a folder in the project directory)
NetLogo Location/Files:
Line 13: NetLogo app folder (ex. C:/Program Files/NetLogo 6.0.2/app)
Line 14: NetLogo jar file (in NetLogo app folder) (ex. netlogo-6.0.2.jar)
IBM Files:
Line 17: TS-IBM NetLogo Model (ex. TS_IBM_March2019.nlogo)
Line 18: TS-IBM Input Parameter Files (ex. InputParameters_20Jun2018.txt)
Note: Lines 17-18 refer to file paths relative to the project directory (defined in line 9). If these files are not located in the project directory, full file paths must be provided instead of just the file names
CASM Files:
Line 21: Name of CASM scenario created/ran previously (same value as line 9 from 1_CASM.R)
Line 22: CASM executable file (ex. casm_ibm_tsv42.exe)
Line 23: CASM control file (ex. casm_IBM_TS_control.dat)
Line 24: CASM habitat parameters (ex. casm_TS_bio_parms_RSK_WithTS_08Oct2018.txt)
Line 25: CASM food web parameters (ex. web_casmTS_HRM_20Jun2018.dat)
Line 26: CASM environmental time series (ex. env_casmTS_2010_08May2018.prn)
Line 27: CASM contaminant time series (ex. ATZ_exp_zero_test.dat)
Line 28: CASM toxicity parameters (ex. TS_toxicity_atrazine_tri_base.dat)
(note: toxicity scenarios are not considered in this study BUT these files
need to be present for CASM to run correctly)
Note: Line 22-28 refers to files within the CASM scenario folder named in line 21
CASM Model Parameters:
Line 31: CASM simulation year to use as day 1 numbers in CASM + TS-IBM (numeric)
IBM Model Parameters:
Line 34: TS-IBM RandomNumberSeed input, numeric
Line 35: TS-IBM pondArea input, numeric, units: m2
Line 36: TS-IBM CASM_pool_area input, numeric, units: m2
Line 37: TS-IBM Sunfish input, logical
Line 38: TS-IBM Predation input, logical
Line 39: TS-IBM DD_egg_larva input, logical
Line 40: TS-IBM AverageKmin input, numeric
Line 41: TS-IBM ScalingSearchArea input, numeric
Line 42: TS-IBM MaxDetritusDepth input, numeric, units: cm
Run the R script. for the linked scenario, R automatically runs CASM, no other steps are needed
The output file containing daily biomasses is named TS-IBM_output.txt and is located in the scenario folder
All files associated with this publication are in the folder "Schmolke_2021". This how to documents how to run CASM and the TS-IBM in R.
In order to run either the TS-IBM you must:
- Have NetLogo 6 installed (for runs in this study, NetLogo 6.0.2 was used)
- Have the R package "RNetLogo" installed
- Run CASM first (see below for instructions)
File: 1_CASM.R
Line 8: Directory of project (must already exist)
Line 9: Exposure Profile Name (Control, 0VFS, 15VFS, Pond18, or Pond19)
Line 10: Multiplication Factor for Exposure Profile
Run the R script.
The output files containing daily biomasses are named IBM_TS_master_ref.out for the unexposed scenario and IBM_TS_master_eff.out for the exposure scenario and is located in the scenario folder
File: 2_IBMOnly.R
Line 8: Directory of project (must already exist)
Line 9: Exposure Profile Name (Control, 0VFS, 15VFS, or Pond)
Line 10: Multiplication Factor for Exposure Profile
Line 11: IBM Effects module to use (GUTS-IT, GUTS-SD, GUTS-IT + Sublethal, GUTS-SD + Sublethal, or Sublethal)
Run the R script.
The output file containing daily biomasses is named [#]_output.txt where the number represents the random number seed used for the run and is located in the scenario folder
All files associated with this publication are in the folder "Galic_2021". This how to documents how to run the One At A Time and Latin Hyper Cube analyses in R.
In order to run either script you must:
- Have NetLogo 6 installed (for runs in this study, NetLogo 6.0.3 was used)
- Have the R package "RNetLogo" installed
- Have the R package "lhs" installed (Latin Hyper Cube only)
File: OneAtATime.R
Initial Folder Locations/Names:
Line 8: Directory of project (must already exist)
Line 9: Name of scenario (note: this will become a folder in the project directory)
IBM Parameters:
Line 10: Number of years to run IBM (numeric)
Line 11: Initial Topeka Shiner Biomass (if NA, the CASM value will be used) (numeric)
Line 12: Random Number Seeds (numeric list)
One At A Time Parameters:
Line 13: Variable to Change (character: 'Te_Th', 'N', 'P', 'TIS', 'depth', 'I0')
Line 14: Changes to the Variable (numeric list)
Run the R script.
File: LatinHyperCube.R
Initial Folder Locations/Names:
Line 8: Directory of project (must already exist)
Line 9: Name of scenario (note: this will become a folder in the project directory)
IBM Parameters:
Line 10: Number of years to run IBM (numeric)
Line 11: Initial Topeka Shiner Biomass (if NA, the CASM value will be used) (numeric)
One At A Time Parameters:
Line 12: Number of Latin Hyper Cube Simulations (numeric) OR filepath to a csv with an already created LHC (character)
Run the R script.