Skip to content

Commit

Permalink
Finalise GitHub Page functionality
Browse files Browse the repository at this point in the history 
Merge branch 'main' of https://github.com/valentinitnelav/Saldur-ROR-analysis into main

# Conflicts:
#	index.Rmd
  • Loading branch information
@valentinitnelav
valentinitnelav committed Jun 22, 2022
2 parents 3b23a51 + 5d677d8 commit 78aac69
Show file tree
Hide file tree
Showing 5 changed files with 92 additions and 122 deletions.
30 changes: 30 additions & 0 deletions LICENSE
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,30 @@
License: MIT + file LICENSE

Based on suggestions at https://www.r-project.org/Licenses
License text based on http://opensource.org/licenses/MIT

YEAR: 2022
COPYRIGHT HOLDER: Alberto Scotti, Dean Jacobsen, Valentin Ștefan, Ulrike Tappeiner, and Roberta Bottarin1

************************************************************************

Copyright (c) 2022, Alberto Scotti, Dean Jacobsen, Valentin Ștefan, Ulrike Tappeiner, and Roberta Bottarin1

Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:

The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
88 changes: 27 additions & 61 deletions README.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,85 +2,51 @@

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6642841.svg)](https://doi.org/10.5281/zenodo.6642841)

This repository contains the R scripts and data used for performing the analysis in:
"Small hydropower – small ecological footprint? A multi-annual environmental impact analysis using aquatic macroinvertebrates as bioindicators. Part 1: effects on community structure"
Here we provide the analysis of the environmental impact of a "run-of-river" hydropower plant on the riverine ecosystem of the Saldur stream, a glacier-fed stream located in the Italian Central-Eastern Alps.

Here we provide the analysis of the environmental impact of a "run-of-river" hydropower plant on the riverine ecosystem of the Saldur stream, a glacier-fed stream located in the Italian Central-Eastern Alps.
This analysis is associated with the paper: [Small hydropower – small ecological footprint? A multi-annual environmental impact analysis using aquatic macroinvertebrates as bioindicators. Part 1: effects on community structure][1].

## License

Upon acceptance we will release a permisible license.
[1]: https://www.frontiersin.org/articles/10.3389/fenvs.2022.902603/abstract

## How to use this repository

You can [download][1] or clone the repository then run the scripts using the *Saldur-ROR-analysis.Rproj* file ([R][2] and [R Studio][3] are needed).
You can view the analysis HTML reports at [this GitHub Pages link][2].

Alternatively, you can [download][3] or clone the repository then run the scripts using the *Saldur-ROR-analysis.Rproj* file ([R][4] and [R Studio][5] are needed).

For cloning, run this in a terminal (git should be [installed][4]):
For cloning, run the following command in a terminal (first, git should be [installed][6]):

```
git clone https://github.com/valentinitnelav/Saldur-ROR-analysis.git
git clone https://github.com/valentinitnelav/Saldur-ROR-analysis
```

Check also the readme file in the *analysis* folder with details about the scripts.

[1]: https://github.com/valentinitnelav/Saldur-ROR-analysis/archive/main.zip
[2]: https://www.r-project.org/
[3]: https://www.rstudio.com/products/rstudio/download/
[4]: https://git-scm.com/downloads
[2]: https://valentinitnelav.github.io/Saldur-ROR-analysis/
[3]: https://github.com/valentinitnelav/Saldur-ROR-analysis/archive/main.zip
[4]: https://www.r-project.org/
[5]: https://www.rstudio.com/products/rstudio/download/
[6]: https://git-scm.com/downloads

## Data

The original data are hosted by "PANGAEA - Data Publisher for Earth & Environmental Science".
Data repository at this permanent address: https://doi.pangaea.de/10.1594/PANGAEA.922524

From this original file we derived all the pre-prepared files included and stored in this repository in the "data" folder, which can be used as input files or templates for faster analyses.

## Scripts/Analysis
The original data are hosted by "PANGAEA - Data Publisher for Earth & Environmental Science". The data repository is located [here][7].

The analysis of similarities, spatial and temporal beta-diversity calculations, and indicator taxa analysis are presented in the script `analysis/anosim_beta_multipatt.R`.
From this original file we derived all the data files included and stored in our GitHub repository in the `./data` folder.

The Before-After-Control-Impact (BACI) analysis using the GLMM framework is documented in the directory `analysis/baci_glmm`. The reader is encouraged to follow the html reports. Each report corresponds to the following variables of interest:
[7]: https://doi.pangaea.de/10.1594/PANGAEA.922524

- taxonomic richness (N0) -- baci-n0.html (generated from baci-n0.Rmd);
- density (individuals/m2) -- baci-density.html (generated from baci-density.Rmd);
- % Ephemeroptera–Plecoptera–Tricoptera (% EPT) -- baci-ept.html (generated from baci-ept.Rmd);
- Shannon evenness (Hill’s ratio, E10) -- baci-e10.html (generated from baci-e10.Rmd);
- Simpson evenness (Hill’s ratio, E20) -- baci-e20.html (generated from baci-e20.Rmd).
## Analysis

## Information About the R Session
You can either read the analysis at [this GitHub Pages link][2], or if you prefer to download or clone the repository, then:

Information About the Current R Session at the time of running the BACI analysis:
- the analysis of similarities, spatial and temporal beta-diversity calculations, and indicator taxa analysis are presented in the script `analysis/anosim_beta_multipatt.R`.
- the Before-After-Control-Impact (BACI) analysis using the GLMM framework is documented in the directory `analysis/baci_glmm`. You can open and read the html reports in your browser. Each report corresponds to the following variables of interest:

```r
> sessionInfo()
R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS
- taxonomic richness (N0) -- baci-n0.html (generated from baci-n0.Rmd);
- density (individuals/m2) -- baci-density.html (generated from baci-density.Rmd);
- % Ephemeroptera–Plecoptera–Tricoptera (% EPT) -- baci-ept.html (generated from baci-ept.Rmd);
- Shannon evenness (Hill’s ratio, E10) -- baci-e10.html (generated from baci-e10.Rmd);
- Simpson evenness (Hill’s ratio, E20) -- baci-e20.html (generated from baci-e20.Rmd).

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
## License - MIT

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=de_DE.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=de_DE.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base

other attached packages:
[1] directlabels_2021.1.13 ggplot2_3.3.3 magrittr_2.0.1 data.table_1.13.6 DHARMa_0.3.3.0 lsmeans_2.30-0
[7] emmeans_1.5.4 AICcmodavg_2.3-1 glmmTMB_1.0.2.1

loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 mvtnorm_1.1-1 lattice_0.20-41 zoo_1.8-8 assertthat_0.2.1 digest_0.6.27 unmarked_1.0.1
[8] foreach_1.5.1 R6_2.5.0 plyr_1.8.6 stats4_4.0.4 evaluate_0.14 coda_0.19-4 pillar_1.4.7
[15] rlang_0.4.10 multcomp_1.4-16 minqa_1.2.4 raster_3.4-5 nloptr_1.2.2.2 Matrix_1.3-2 rmarkdown_2.7
[22] splines_4.0.4 lme4_1.1-26 statmod_1.4.35 TMB_1.7.19 munsell_0.5.0 compiler_4.0.4 xfun_0.21
[29] pkgconfig_2.0.3 htmltools_0.5.1.1 tidyselect_1.1.0 tibble_3.0.6 quadprog_1.5-8 codetools_0.2-18 crayon_1.4.1
[36] dplyr_1.0.4 withr_2.4.1 MASS_7.3-53.1 grid_4.0.4 nlme_3.1-152 xtable_1.8-4 gtable_0.3.0
[43] lifecycle_1.0.0 DBI_1.1.1 scales_1.1.1 estimability_1.3 sp_1.4-5 ellipsis_0.3.1 vctrs_0.3.6
[50] generics_0.1.0 boot_1.3-27 sandwich_3.0-0 TH.data_1.0-10 iterators_1.0.13 tools_4.0.4 glue_1.4.2
[57] purrr_0.3.4 survival_3.2-7 yaml_2.2.1 colorspace_2.0-0 VGAM_1.1-5 knitr_1.31
```
See LICENSE file in this repository.
0 analysis/baci_glmm/baci-n0.html → docs/baci-n0.html
View file
File renamed without changes.
36 changes: 12 additions & 24 deletions docs/index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -354,35 +354,23 @@

<div id="overview" class="section level1">
<h1>Overview</h1>
<p><a href="https://doi.org/10.5281/zenodo.6642841"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.6642841.svg" alt="DOI" /></a></p>
<p>This repository contains the R scripts and data used for performing the analysis in: “Small hydropower – small ecological footprint? A multi-annual environmental impact analysis using aquatic macroinvertebrates as bioindicators. Part 1: effects on community structure”</p>
<p>Here we provide the analysis of the environmental impact of a “run-of-river” hydropower plant on the riverine ecosystem of the Saldur stream, a glacier-fed stream located in the Italian Central-Eastern Alps.</p>
<div id="license" class="section level2">
<h2>License</h2>
<p>Upon acceptance we will release a permisible license.</p>
</div>
<div id="how-to-use-this-repository" class="section level2">
<h2>How to use this repository</h2>
<p>You can <a href="https://github.com/valentinitnelav/Saldur-ROR-analysis/archive/main.zip">download</a> or clone the repository then run the scripts using the <em>Saldur-ROR-analysis.Rproj</em> file (<a href="https://www.r-project.org/">R</a> and <a href="https://www.rstudio.com/products/rstudio/download/">R Studio</a> are needed).</p>
<p>For cloning, run this in a terminal (git should be <a href="https://git-scm.com/downloads">installed</a>):</p>
<pre><code>git clone https://github.com/valentinitnelav/Saldur-ROR-analysis.git</code></pre>
<p>Check also the readme file in the <em>analysis</em> folder with details about the scripts.</p>
</div>
<p>This analysis is associated with the paper: <a href="https://www.frontiersin.org/articles/10.3389/fenvs.2022.902603/abstract">Small hydropower – small ecological footprint? A multi-annual environmental impact analysis using aquatic macroinvertebrates as bioindicators. Part 1: effects on community structure</a>.</p>
<div id="data" class="section level2">
<h2>Data</h2>
<p>The original data are hosted by “PANGAEA - Data Publisher for Earth &amp; Environmental Science”. Data repository at this permanent address: <a href="https://doi.pangaea.de/10.1594/PANGAEA.922524" class="uri">https://doi.pangaea.de/10.1594/PANGAEA.922524</a></p>
<p>From this original file we derived all the pre-prepared files included and stored in this repository in the “data” folder, which can be used as input files or templates for faster analyses.</p>
<p>The original data are hosted by “PANGAEA - Data Publisher for Earth &amp; Environmental Science”. The data repository is located <a href="https://doi.pangaea.de/10.1594/PANGAEA.922524">here</a>.</p>
<p>From this original file we derived all the data files included and stored in our GitHub repository in the <a href="https://github.com/valentinitnelav/Saldur-ROR-analysis/tree/main/data">data</a> folder, which were used for the analyses mentioned below.</p>
</div>
<div id="scriptsanalysis" class="section level2">
<h2>Scripts/Analysis</h2>
<p>The analysis of similarities, spatial and temporal beta-diversity calculations, and indicator taxa analysis are presented in the script <code>analysis/anosim_beta_multipatt.R</code>.</p>
<p>The Before-After-Control-Impact (BACI) analysis using the GLMM framework is documented in the directory <code>analysis/baci_glmm</code>. The reader is encouraged to follow the html reports. Each report corresponds to the following variables of interest:</p>
<div id="analysis" class="section level2">
<h2>Analysis</h2>
<p>The analysis of similarities, spatial and temporal beta-diversity calculations, and indicator taxa analysis are presented in the script <a href="https://github.com/valentinitnelav/Saldur-ROR-analysis/blob/main/analysis/anosim_beta_multipatt.R">analysis/anosim_beta_multipatt.R</a>.</p>
<p>Below you find HTML reports for the Before-After-Control-Impact (BACI) analysis using the GLMM framework for the following variables:</p>
<ul>
<li>taxonomic richness (N0) – <a href="baci-n0.html">baci-n0.html</a> (generated from baci-n0.Rmd);</li>
<li>density (individuals/m2) – baci-density.html (generated from baci-density.Rmd);</li>
<li>% Ephemeroptera–Plecoptera–Tricoptera (% EPT) – baci-ept.html (generated from baci-ept.Rmd);</li>
<li>Shannon evenness (Hill’s ratio, E10) – baci-e10.html (generated from baci-e10.Rmd);</li>
<li>Simpson evenness (Hill’s ratio, E20) – baci-e20.html (generated from baci-e20.Rmd).</li>
<li><a href="baci-n0.html">taxonomic richness (N0)</a>, generated from <a href="https://github.com/valentinitnelav/Saldur-ROR-analysis/blob/main/analysis/baci_glmm/baci-n0.Rmd">baci-n0.Rmd</a>;</li>
<li><a href="baci-density.html">density (individuals/m2)</a>, generated from <a href="https://github.com/valentinitnelav/Saldur-ROR-analysis/blob/main/analysis/baci_glmm/baci-density.Rmd">baci-density.Rmd</a>;</li>
<li><a href="baci-ept.html">% Ephemeroptera–Plecoptera–Tricoptera (% EPT)</a>, generated from <a href="https://github.com/valentinitnelav/Saldur-ROR-analysis/blob/main/analysis/baci_glmm/baci-ept.Rmd">baci-ept.Rmd</a>;</li>
<li><a href="baci-e10.html">Shannon evenness (Hill’s ratio, E10)</a>, generated from <a href="https://github.com/valentinitnelav/Saldur-ROR-analysis/blob/main/analysis/baci_glmm/baci-e10.Rmd">baci-e10.Rmd</a>;</li>
<li><a href="baci-e20.html">Simpson evenness (Hill’s ratio, E20)</a>, generated from <a href="https://github.com/valentinitnelav/Saldur-ROR-analysis/blob/main/analysis/baci_glmm/baci-e20.Rmd">baci-e20.Rmd</a>;</li>
</ul>
</div>
<div id="information-about-the-r-session" class="section level2">
Expand Down
60 changes: 23 additions & 37 deletions index.Rmd
View file
Original file line number Diff line number Diff line change
@@ -1,51 +1,38 @@
# Overview

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6642841.svg)](https://doi.org/10.5281/zenodo.6642841)
Here we provide the analysis of the environmental impact of a "run-of-river" hydropower plant on the riverine ecosystem of the Saldur stream, a glacier-fed stream located in the Italian Central-Eastern Alps.

This repository contains the R scripts and data used for performing the analysis in:
"Small hydropower – small ecological footprint? A multi-annual environmental impact analysis using aquatic macroinvertebrates as bioindicators. Part 1: effects on community structure"
This analysis is associated with the paper: [Small hydropower – small ecological footprint? A multi-annual environmental impact analysis using aquatic macroinvertebrates as bioindicators. Part 1: effects on community structure][1].

Here we provide the analysis of the environmental impact of a "run-of-river" hydropower plant on the riverine ecosystem of the Saldur stream, a glacier-fed stream located in the Italian Central-Eastern Alps.
[1]: https://www.frontiersin.org/articles/10.3389/fenvs.2022.902603/abstract

## License

Upon acceptance we will release a permisible license.

## How to use this repository

You can [download][1] or clone the repository then run the scripts using the *Saldur-ROR-analysis.Rproj* file ([R][2] and [R Studio][3] are needed).

For cloning, run this in a terminal (git should be [installed][4]):

```
git clone https://github.com/valentinitnelav/Saldur-ROR-analysis.git
```

Check also the readme file in the *analysis* folder with details about the scripts.
## Data

[1]: https://github.com/valentinitnelav/Saldur-ROR-analysis/archive/main.zip
[2]: https://www.r-project.org/
[3]: https://www.rstudio.com/products/rstudio/download/
[4]: https://git-scm.com/downloads
The original data are hosted by "PANGAEA - Data Publisher for Earth & Environmental Science". The data repository is located [here][2].

## Data
From this original file we derived all the data files included and stored in our GitHub repository in the [data][3] folder, which were used for the analyses mentioned below.

The original data are hosted by "PANGAEA - Data Publisher for Earth & Environmental Science".
Data repository at this permanent address: https://doi.pangaea.de/10.1594/PANGAEA.922524
[2]: https://doi.pangaea.de/10.1594/PANGAEA.922524
[3]: https://github.com/valentinitnelav/Saldur-ROR-analysis/tree/main/data

From this original file we derived all the pre-prepared files included and stored in this repository in the "data" folder, which can be used as input files or templates for faster analyses.
## Analysis

## Scripts/Analysis
The analysis of similarities, spatial and temporal beta-diversity calculations, and indicator taxa analysis are presented in the script [analysis/anosim_beta_multipatt.R][4].

The analysis of similarities, spatial and temporal beta-diversity calculations, and indicator taxa analysis are presented in the script `analysis/anosim_beta_multipatt.R`.
Below you find HTML reports for the Before-After-Control-Impact (BACI) analysis using the GLMM framework for the following variables:

The Before-After-Control-Impact (BACI) analysis using the GLMM framework is documented in the directory `analysis/baci_glmm`. The reader is encouraged to follow the html reports. Each report corresponds to the following variables of interest:
- <a href="baci-n0.html">taxonomic richness (N0)</a>, generated from [baci-n0.Rmd][5];
- <a href="baci-density.html">density (individuals/m2)</a>, generated from [baci-density.Rmd][6];
- <a href="baci-ept.html">% Ephemeroptera–Plecoptera–Tricoptera (% EPT)</a>, generated from [baci-ept.Rmd][7];
- <a href="baci-e10.html">Shannon evenness (Hill’s ratio, E10)</a>, generated from [baci-e10.Rmd][8];
- <a href="baci-e20.html">Simpson evenness (Hill’s ratio, E20)</a>, generated from [baci-e20.Rmd][9];

- taxonomic richness (N0) -- <a href="./analysis/baci_glmm/baci-n0.html">baci-n0.html</a> (generated from baci-n0.Rmd);
- density (individuals/m2) -- baci-density.html (generated from baci-density.Rmd);
- % Ephemeroptera–Plecoptera–Tricoptera (% EPT) -- baci-ept.html (generated from baci-ept.Rmd);
- Shannon evenness (Hill’s ratio, E10) -- baci-e10.html (generated from baci-e10.Rmd);
- Simpson evenness (Hill’s ratio, E20) -- baci-e20.html (generated from baci-e20.Rmd).
[4]: https://github.com/valentinitnelav/Saldur-ROR-analysis/blob/main/analysis/anosim_beta_multipatt.R
[5]: https://github.com/valentinitnelav/Saldur-ROR-analysis/blob/main/analysis/baci_glmm/baci-n0.Rmd
[6]: https://github.com/valentinitnelav/Saldur-ROR-analysis/blob/main/analysis/baci_glmm/baci-density.Rmd
[7]: https://github.com/valentinitnelav/Saldur-ROR-analysis/blob/main/analysis/baci_glmm/baci-ept.Rmd
[8]: https://github.com/valentinitnelav/Saldur-ROR-analysis/blob/main/analysis/baci_glmm/baci-e10.Rmd
[9]: https://github.com/valentinitnelav/Saldur-ROR-analysis/blob/main/analysis/baci_glmm/baci-e20.Rmd

## Information About the R Session

Expand Down Expand Up @@ -83,5 +70,4 @@ loaded via a namespace (and not attached):
[43] lifecycle_1.0.0 DBI_1.1.1 scales_1.1.1 estimability_1.3 sp_1.4-5 ellipsis_0.3.1 vctrs_0.3.6
[50] generics_0.1.0 boot_1.3-27 sandwich_3.0-0 TH.data_1.0-10 iterators_1.0.13 tools_4.0.4 glue_1.4.2
[57] purrr_0.3.4 survival_3.2-7 yaml_2.2.1 colorspace_2.0-0 VGAM_1.1-5 knitr_1.31
```

```

0 comments on commit 78aac69

Please sign in to comment.