diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..6228912 --- /dev/null +++ b/LICENSE @@ -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. diff --git a/README.md b/README.md index e6bd80e..303199f 100644 --- a/README.md +++ b/README.md @@ -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. diff --git a/analysis/baci_glmm/baci-n0.html b/docs/baci-n0.html similarity index 100% rename from analysis/baci_glmm/baci-n0.html rename to docs/baci-n0.html diff --git a/docs/index.html b/docs/index.html index 1acb2d8..266f40e 100644 --- a/docs/index.html +++ b/docs/index.html @@ -354,35 +354,23 @@

Overview

-

DOI

-

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.

-
-

License

-

Upon acceptance we will release a permisible license.

-
-
-

How to use this repository

-

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

-

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

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

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

-
+

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.

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.

+

The original data are hosted by “PANGAEA - Data Publisher for Earth & Environmental Science”. The data repository is located here.

+

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

-
-

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.

-

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:

+
+

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.

+

Below you find HTML reports for the Before-After-Control-Impact (BACI) analysis using the GLMM framework for the following variables:

diff --git a/index.Rmd b/index.Rmd index 39515c5..4b49475 100644 --- a/index.Rmd +++ b/index.Rmd @@ -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: +- taxonomic richness (N0), generated from [baci-n0.Rmd][5]; +- density (individuals/m2), generated from [baci-density.Rmd][6]; +- % Ephemeroptera–Plecoptera–Tricoptera (% EPT), generated from [baci-ept.Rmd][7]; +- Shannon evenness (Hill’s ratio, E10), generated from [baci-e10.Rmd][8]; +- Simpson evenness (Hill’s ratio, E20), generated from [baci-e20.Rmd][9]; -- 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). +[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 @@ -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 -``` - +``` \ No newline at end of file