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Data Types:

- Software/Code

Plasma Vortex Theory is the engineered application of known sciences to create efficient velocity during spaceflight using electricity and propellant gas. **Oscillation** of granulate and liquid reagents using simple harmonic motion has been shown to excite particles to form geometric patterns when using calibrated **frequencies** discovered by the late Dr. Hans Jenny. Calibration methods will be used to attain vortex formations in the reagents Lycopodium, Sulfur Hexafluoride, CO2 and Xenon. **Frequencies** which form vortex patterns in Lycopodium powder using known methods will be used to excite Sulfur Hexafluoride (density 6.17 kg/m3), at incremental partial pressures. Air-filled mass objects will be used to observe acceleration, force and velocity data for a dense gas during **oscillation** and vortex formation. Xenon gas (density 5.761 kg/m3) will be ionized by external electrode field before, during and after vortex formations are created using acoustic measures.

Data Types:

- Software/Code

Plasma Vortex Theory is the engineered application of known sciences to create efficient velocity during spaceflight using electricity and propellant gas. **Oscillation** of granulate and liquid reagents using simple harmonic motion has been shown to excite particles to form geometric patterns when using calibrated **frequencies** discovered by the late Dr. Hans Jenny. Calibration methods will be used to attain vortex formations in the reagents Lycopodium, Sulfur Hexafluoride, CO2 and Xenon. **Frequencies** which form vortex patterns in Lycopodium powder using known methods will be used to excite Sulfur Hexafluoride (density 6.17 kg/m3), at incremental partial pressures. Air-filled mass objects will be used to observe acceleration, force and velocity data for a dense gas during **oscillation** and vortex formation. Xenon gas (density 5.761 kg/m3) will be ionized by external electrode field before, during and after vortex formations are created using acoustic measures.

Data Types:

- Software/Code

Note: This application is currently designed to run on Windows and requires the 2016 LabVIEW runtime engine. It is available free to download in the references.
Brachistochrone- An example of how a cycloid is the solution to the shortest path between two points in a particular potential.2-D Membrane Modes- The first few normal modes of a 2-D membrane.Coupled Harmonic **Oscillators**- Select up to 10 masses (and 11 springs) and examine their normal modes of **oscillation** ordered in ascending **frequency** with various spring constants.

Data Types:

- Software/Code

Supplementary material for the paper:
Taylor, M.H., Mildenberger, T.K., 2017. Extending electronic length **frequency** analysis in R. Fisheries Management and Ecology. https://doi.org/10.1111/fme.12232
Description:
The R scripts demonstrate use of a recent implementation of extending electronic length **frequency** analysis (ELEFAN) (Pauly and David 1980, 1981) for estimating growth function parameters in the R package "TropFishR" (Mildenberger et al., 2017). In addition to the traditional ELEFAN methodology, TropFishR also includes two optimization approaches for growth curve fitting: 1. Generalized Simulated Annealing ('ELEFAN_SA'), and 2. Genetic Algorithm ('ELEFAN_GA').
The scripts contain a demonstration of both optimization methods using a generated length-**frequency** data set with known seasonally-**oscillating** von Bertalanffy growth function (soVBGF) parameters.
References:
Mildenberger, T.K., Taylor, M.H., Wolff, M., 2017. TropFishR: Tropical Fisheries Analysis with R. R package version 1.1.3, https://github.com/tokami/TropFishR.
Pauly, D., David, N., 1980. An objective method for determining fish growth from length-**frequency** data. ICLARM Newsl. 3, 13–15.
Pauly, D., David, N., 1981. ELEFAN I, a basic program for the objective extraction of growth parameters from length-**frequency** data. Berichte Dtsch. Wiss. Kommissuib Für Meeresforsch. 28, 205–211.
Contents:
Supplement_Taylor_Mildenberger.Rproj - RStudio project file. When opened in RStudio, script file paths should remain compatible across platforms.
/figures - Graphical outputs.
/results - Results of scripts (e.g. .Rdata and .csv files)
/scripts - Scripts used in the analysis. Script names begin with a number indicating the required order:
/scripts/01_create_LFQ_data.R - Not required, but shows the settings for LFQ data generation ("synLFQ4" data in TropFishR package)
/scripts/02_basic_demonstration.R - Shows the basic setup of ELEFAN_GA and ELEFAN_SA fitting procedures.
/scripts//03_sensitivity_analysis.R - Runs analyses used in the work. Warning: requires sufficient computation time (ca. 12 hours on modern personal computer with 4 processing cores).
/scripts/04_stats_and_figures - Reproduces figures and statistical analysis using results objects.
/scripts/05_make_supplementary_figures_doc.R - Runs the R Markdown document "supplementary_figures.Rmd" to create "supplementary_figures.pdf"

Data Types:

- Software/Code

Supplementary material for the paper:
Taylor, M.H., Mildenberger, T.K., 2017. Extending electronic length **frequency** analysis in R. Fisheries Management and Ecology. https://doi.org/10.1111/fme.12232
Description:
The R scripts demonstrate use of a recent implementation of ELEFAN I (Pauly and David 1980, 1981) in the R package TropFishR (Mildenberger et al., 2017). In addition to the traditional methodology, TropFishR also includes two optimization approaches for growth curve fitting: 1. Generalized Simulated Annealing ('ELEFAN_SA'), and 2. Genetic Algorithm ('ELEFAN_GA').
The scripts contain a demonstration of both optimization methods using a generated length-**frequency** data set with known seasonally-**oscillating** von Bertalanffy growth function (soVBGF) parameters.
A more detailed test of parameter estimation performance is conducted using the ELEFAN_GA approach under variable settings.
References:
Mildenberger, T.K., Taylor, M.H., Wolff, M., 2017. TropFishR: Tropical Fisheries Analysis with R. R package version 1.1.3, https://github.com/tokami/TropFishR.
Pauly, D., David, N., 1980. An objective method for determining fish growth from length-**frequency** data. ICLARM Newsl. 3, 13–15.
Pauly, D., David, N., 1981. ELEFAN I, a basic program for the objective extraction of growth parameters from length-**frequency** data. Berichte Dtsch. Wiss. Kommissuib Für Meeresforsch. 28, 205–211.
Contents:
Supplement_Taylor_Mildenberger.Rproj - RStudio project file. When opened in RStudio, script file paths should remain compatible across platforms.
/figures - Graphical outputs.
/packages - R package versions used at the time of the study.
/results - Results of scripts (e.g. .Rdata and .csv files)
/scripts - Scripts used in the analysis. Script names begin with a number indicating the required order:
/01_create_LFQ_data.R - Not required, but shows the settings for LFQ data generation ("synLFQ4" data in TropFishR package)
/02_basic_demonstration.R - Shows the basic setup of ELEFAN_GA and ELEFAN_SA fitting procedures.
/03_sensitivity_analysis.R - Runs analyses used in the work. Warning: requires sufficient computation time (ca. 12 hours on modern personal computer with 4 processing cores).
/04_stats_and_figures - Reproduces figures and statistical analysis using results objects.
/05_make_supplementary_figures_doc.R - Runs the R Markdown document "supplementary_figures.Rmd" to create "supplementary_figures.pdf"

Data Types:

- Software/Code

Supplementary material for the paper:
Taylor, M.H., Mildenberger, T.K., 2017. Extending electronic length **frequency** analysis in R. Fisheries Management and Ecology. https://doi.org/10.1111/fme.12232
Description:
The R scripts demonstrate use of a recent implementation of extending electronic length **frequency** analysis (ELEFAN) (Pauly and David 1980, 1981) for estimating growth function parameters in the R package "TropFishR" (Mildenberger et al., 2017). In addition to the traditional ELEFAN methodology, TropFishR also includes two optimization approaches for growth curve fitting: 1. Generalized Simulated Annealing ('ELEFAN_SA'), and 2. Genetic Algorithm ('ELEFAN_GA').
The scripts contain a demonstration of both optimization methods using a generated length-**frequency** data set with known seasonally-**oscillating** von Bertalanffy growth function (soVBGF) parameters.
References:
Mildenberger, T.K., Taylor, M.H., Wolff, M., 2017. TropFishR: Tropical Fisheries Analysis with R. R package version 1.1.3, https://github.com/tokami/TropFishR.
Pauly, D., David, N., 1980. An objective method for determining fish growth from length-**frequency** data. ICLARM Newsl. 3, 13–15.
Pauly, D., David, N., 1981. ELEFAN I, a basic program for the objective extraction of growth parameters from length-**frequency** data. Berichte Dtsch. Wiss. Kommissuib Für Meeresforsch. 28, 205–211.
Contents:
Supplement_Taylor_Mildenberger.Rproj - RStudio project file. When opened in RStudio, script file paths should remain compatible across platforms.
/figures - Graphical outputs.
/results - Results of scripts (e.g. .Rdata and .csv files)
/scripts - Scripts used in the analysis. Script names begin with a number indicating the required order:
/scripts/01_create_LFQ_data.R - Not required, but shows the settings for LFQ data generation ("synLFQ4" data in TropFishR package)
/scripts/02_basic_demonstration.R - Shows the basic setup of ELEFAN_GA and ELEFAN_SA fitting procedures.
/scripts//03_sensitivity_analysis.R - Runs analyses used in the work. Warning: requires sufficient computation time (ca. 12 hours on modern personal computer with 4 processing cores).
/scripts/04_stats_and_figures - Reproduces figures and statistical analysis using results objects.
/scripts/05_make_supplementary_figures_doc.R - Runs the R Markdown document "supplementary_figures.Rmd" to create "supplementary_figures.pdf"

Data Types:

- Software/Code

Supplementary material for the paper:
Taylor, M.H., Mildenberger, T.K., 2016. Extending ELEFAN in R. https://dx.doi.org/10.6084/m9.figshare.4206561
Description:
The R scripts demonstrate use of a recent implementation of ELEFAN I (Pauly and David 1980, 1981) in the R package TropFishR (Mildenberger et al., 2016). In addition to the traditional methodology, TropFishR also includes two optimization approaches for growth curve fitting: 1. Generalized Simulated Annealing ('ELEFAN_SA'), and 2. Genetic Algorithm ('ELEFAN_GA').
The scripts contain a demonstration of both optimization methods using a generated length-**frequency** data set with known seasonally-**oscillating** von Bertalanffy growth function (soVBGF) parameters.
A more detailed test of parameter estimation performance is conducted using the ELEFAN_GA approach under variable settings.
References:
Mildenberger, T.K., Taylor, M.H., Wolff, M., 2017. TropFishR: Tropical Fisheries Analysis with R. R package version 1.1.2, https://github.com/tokami/TropFishR.
Pauly, D., David, N., 1980. An objective method for determining fish growth from length-**frequency** data. ICLARM Newsl. 3, 13–15.
Pauly, D., David, N., 1981. ELEFAN I, a basic program for the objective extraction of growth parameters from length-**frequency** data. Berichte Dtsch. Wiss. Kommissuib Für Meeresforsch. 28, 205–211.
Contents:
Supplement_Taylor_Mildenberger.Rproj - RStudio project file. When opened in RStudio, script file paths should remain compatible across platforms.
/figures - Graphical outputs.
/packages - R package versions used at the time of the study.
/results - Results of scripts (e.g. .Rdata and .csv files)
/scripts - Scripts used in the analysis. Script names begin with a number indicating the required order:
/01_create_LFQ_data.R - Not required, but shows the settings for LFQ data generation ("synLFQ4" data in TropFishR package)
/02_basic_demonstration.R - Shows the basic setup of ELEFAN_GA and ELEFAN_SA fitting procedures.
/03_sensitivity_analysis.R - Runs analyses used in the work. Warning: requires sufficient computation time (ca. 12 hours on modern personal computer with 4 processing cores).
/04_stats_and_figures - Reproduces figures and statistical analysis using results objects.
/05_make_supplementary_figures_doc.R - Runs the R Markdown document "supplementary_figures.Rmd" to create "supplementary_figures.pdf"

Data Types:

- Software/Code

Supplementary material for the paper:
Taylor, M.H., Mildenberger, T.K., 2016. Extending ELEFAN in R. doi:10.6084/m9.figshare.4206561
Description:
The R scripts demonstrate use of a recent implementation of ELEFAN I (Pauly and David 1980, 1981) in the R package TropFishR (Mildenberger et al., 2016). In addition to the traditional methodology, TropFishR also includes two optimization approaches for growth curve fitting: 1. Generalized Simulated Annealing ('ELEFAN_SA'), and 2. Genetic Algorithm ('ELEFAN_GA').
The scripts contain a demonstration of both optimization methods using a generated length-**frequency** data set with known seasonally-**oscillating** von Bertalanffy growth function (soVBGF) parameters.
A more detailed test of parameter estimation performance is conducted using the ELEFAN_GA approach under variable settings.
References:
Mildenberger, T.K., Taylor, M.H., Wolff, M., 2016. TropFishR: Tropical Fisheries Analysis with R. R package version 1.0.0, https://github.com/tokami/TropFishR.
Pauly, D., David, N., 1980. An objective method for determining fish growth from length-**frequency** data. ICLARM Newsl. 3, 13–15.
Pauly, D., David, N., 1981. ELEFAN I, a basic program for the objective extraction of growth parameters from length-**frequency** data. Berichte Dtsch. Wiss. Kommissuib Für Meeresforsch. 28, 205–211.
Contents:
Supplement_Taylor_Mildenberger.Rproj - RStudio project file. When opened in RStudio, script file paths should remain compatible across platforms.
/figures - Graphical outputs.
/packages - R package versions used at the time of the study.
/results - Results of scripts (e.g. .Rdata and .csv files)
/scripts - Scripts used in the analysis. Script names begin with a number indicating the required order:
/01_create_LFQ_data.R - Not required, but shows the settings for LFQ data generation ("synLFQ4" data in TropFishR package)
/02_analysis.R - Runs analyses used in the work. Warning: the section titled "GA and sensitivity of ELEFAN" requires sufficient computation time (ca. 12 hours on modern personal computer with 4 processing cores).
/03_stats_and_figures - Reproduces figures and statistical analysis using results objects.

Data Types:

- Software/Code