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Code for reproducing results presented in the paper "Total replacement of fish meal with black soldier fly (Hermetia illucens) larvae meal does not compromise the gut health of Atlantic salmon (Salmo salar)".
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AqFl2_GutHealth.Rproj
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README.md

README.md

Launch Rstudio Binder

AquaFly-SeawaterGutHealth-Aquaculture-2019

This repository contains the data and code to reproduce the results presented in the paper Total replacement of fish meal with black soldier fly (Hermetia illucens) larvae meal does not compromise the gut health of Atlantic salmon (Salmo salar).

Run codes online

To run the analyses online, simply click on the launch binder badge above to start an RStudio instance. Note that multi-core parallel computing won't be availbe for the RStudio stance we use here. Thus, delete the codes for running parallel parametric bootstraps if you run the analyses via binder.

Run codes locally

To run the analyses locally, download this repository as a zipped file. After decompression, open the R project file (AqFl2_GutHealth.Rproj) in the RStudio and run the R codes directly from the project root directory. Versions of R packages for each anaylsis can be found in the session information (*_sessionInfo.txt) under the same folder of R codes.

File organization

Below is an overview of the file organization descending to level-3 directories.

root
├── AqFl2_GutHealth.Rproj
├── DESCRIPTION
├── LICENSE
├── README.md
├── analysis
│   ├── code
│   │   ├── histology.R
│   │   ├── histology_sessionInfo.txt
│   │   ├── organosomatic_index.R
│   │   ├── organosomatic_index_sessionInfo.txt
│   │   ├── qPCR_ref_DI.R
│   │   ├── qPCR_ref_DI_sessionInfo.txt
│   │   ├── qPCR_ref_PI.R
│   │   ├── qPCR_ref_PI_sessionInfo.txt
│   │   ├── qPCR_target_DI.R
│   │   ├── qPCR_target_DI_sessionInfo.txt
│   │   ├── qPCR_target_PI.R
│   │   └── qPCR_target_PI_sessionInfo.txt
│   ├── exploratory_analysis
│   │   ├── OSI_boxPlot.pdf
│   │   ├── OSI_violin.pdf
│   │   ├── histology_histogram.pdf
│   │   ├── qPCR_ref_DI_barPlot.pdf
│   │   ├── qPCR_ref_DI_boxPlot.pdf
│   │   ├── qPCR_ref_DI_pointDiagram.pdf
│   │   ├── qPCR_ref_PI_barPlot.pdf
│   │   ├── qPCR_ref_PI_boxPlot.pdf
│   │   ├── qPCR_ref_PI_pointDiagram.pdf
│   │   ├── qPCR_target_DI_boxPlot.pdf
│   │   ├── qPCR_target_DI_heatmap.pdf
│   │   ├── qPCR_target_DI_violin.pdf
│   │   ├── qPCR_target_PI_boxPlot.pdf
│   │   ├── qPCR_target_PI_heatmap.pdf
│   │   └── qPCR_target_PI_violin.pdf
│   └── model_diagnostics
│       ├── OSI_LMMs_residual.pdf
│       ├── OSI_welch-t_qqplot.pdf
│       ├── qPCR_DI_LMMs_residual.pdf
│       ├── qPCR_DI_welch-t_qqplot.pdf
│       ├── qPCR_PI_LMMs_residual.pdf
│       └── qPCR_PI_welch-t_qqplot.pdf
├── data
│   ├── README.md
│   ├── clean_data
│   │   ├── AqFl2_qPCR_ref_DI.csv
│   │   ├── AqFl2_qPCR_ref_PI.csv
│   │   ├── AqFl2_qPCR_target_DI.csv
│   │   ├── AqFl2_qPCR_target_PI.csv
│   │   └── Interplate_calibration.xlsx
│   └── raw_data
│       ├── AqFl2_LightCycler_files
│       ├── AqFl2_histology.csv
│       └── AqFl2_organosomatic_index.csv
└── results
    ├── figures
    │   ├── Figure 1.tiff
    │   ├── Figure 2.tiff
    │   ├── Figure 3.tiff
    │   ├── Figure 4.tiff
    │   ├── Figure S1.tiff
    │   └── Figure S2.tiff
    └── reference_gene_ranks
        ├── ref_gene_rank_DI.pdf
        └── ref_gene_rank_PI.pdf

Acknowledgements

The R package holepunch was used to make the present R project binder-ready. Thanks are due to the holepunch developer Karthik Ram, who kindly helped to configure the Docker file and get the binder up and running.

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