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and Restoration","monthly_downloads":350,"total_dependent_repos":3,"total_dependent_packages":1,"readme":"\n\u003c!-- badges: start --\u003e\n[![Coverage\nstatus](https://codecov.io/gh/spatial-ews/spatialwarnings/branch/master/graph/badge.svg)](https://codecov.io/github/spatial-ews/spatialwarnings?branch=master)\n[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/spatialwarnings)](https://cran.r-project.org/package=spatialwarnings)\n[![CRAN_downloads](https://cranlogs.r-pkg.org/badges/last-week/spatialwarnings)](https://cran.r-project.org/package=spatialwarnings)\n[![R-CMD-check](https://github.com/spatial-ews/spatialwarnings/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/spatial-ews/spatialwarnings/actions/workflows/R-CMD-check.yaml)\n\u003c!-- badges: end --\u003e\n\nSpatial early warning signs - R package\n=======================================\n\nThis package helps computing spatial early warning signals of critical\ntransitions, and metrics commonly-used in the related literature. This has been \ninitiated by a collaborative project between [Sonia Kefi's group](http://sonia.kefi.fr/) \n(Institut de Sciences d'Evolution, CNRS, IRD, Université Montpellier, France) and \n[Vishwesha Guttal's](https://teelabiisc.wordpress.com/) (Center for Ecological Sciences,\nIndian Institute of Science, Bangalore, India).\n\nThe R package provides several sets of functions related to the computation of\nearly warning signals of ecosystem tipping points and irreversible\ntransitions (also known as *catastrophic shifts*). In particular, it\nfacilitates computing those indicators, assess their significance and plot\ntheir trends.\n\nTo understand the context behind those indicators, and see how they\ncan be computed, the best way is to have a look at our paper about the package:\n\n[Génin, A. , Majumder, S. , Sankaran, S. , Danet, A. , Guttal, V. , Schneider, F. D. and Kéfi, S. (2018), Monitoring ecosystem degradation using spatial data and the R package\n'spatialwarnings'. Methods in Ecology and Evolution.](https://dx.doi.org/10.1111/2041-210X.13058)\n\nFor more advanced users and/or technical questions that may arise,\na FAQ is also available [there](https://alex.lecairn.org/spatialwarnings-faq.html).\n\n## Contributors\n\nAlain Danet, [Alexandre Génin (Maintainer)](mailto:alexandre.genin@sete.cnrs.fr),\nVishwesha Guttal, Sonia Kefi, Sabiha Majumder, Sumithra Sankaran, Florian Schneider\n\n`spatialwarnings` has also benefited from contributions from Angeles Garcia-Mayor, Vasilis Dakos and Koen Siteur\n\n## Installation\n\n`spatialwarnings` is available on CRAN and can be installed through:\n\n```r\ninstall.packages('spatialwarnings')\n```\n\nThe development version of this package can be installed using the\n`devtools` package in R:\n\n```\nif ( ! require(devtools) ) {\n  install.packages(\"devtools\")\n}\ndevtools::install_github(\"spatial-ews/spatialwarnings\")\n```\n\n## The spatial indicators\n\nEcological systems can suffer drastic transitions such as desertification or\neutrophication, sometimes even after a slight change in one or more external\nparameters, such as aridity or nutrient input. These qualitative changes in the\nbehavior of a system at a threshold represents a critical or bifurcation point,\nand can give rise to *catastrophic shifts* when associated with irreversibility.\nA growing body of litterature suggests that a dynamical system should exhibit\ncertain measurable properties around those critical points.\n\nThis package aims at providing a practical set of tools for the detection of\nthese upcoming critical points in spatial datasets, by using indicators based on\nthose properties. Some of those indicators fall within broad families around \nwhich the package is centered, such as \"generic\" spatial indicators or \nindicators based on patch-size distributions. Significance of patterns \ncan be assessed using permutation-based tests and results can be displayed \nusing familiar summary/plot methods. \n\nIn total, spatialwarnings provides the following spatial indicators published \nin the literature: \n  \n  - lag-1 autocorrelation (Moran's I, Dakos et al. 2010)\n  - Variance (Guttal et al. 2008)\n  - Skewness (Guttal et al. 2008)\n  - SDR Ratio (Kéfi et al. 2014)\n  - Patch-size distribution shape (Kéfi et al. 2011)\n  - Power-law range (Berdugo et al. 2017)\n  - Flowlength (Rodriguez et al. 2017)\n  - Kolmogorov complexity (Dakos et al. 2017)\n  - Variogram-based indicators (Nijp et al. 2019)\n  - Clustering of pairs (Schneider et al. 2016)\n\nIn addition, this package provides a straightforward way to implement and test \nnew indicators, so you can design your favorite spatial metric for your \necosystem of interest. \n\n## Code sample\n\nA simple analysis with `spatialwarnings` can fit in a few lines of code: \n\n```r\n\u003e library(ggplot2)\n\u003e library(spatialwarnings)\n\u003e\n\u003e # Compute indicators\n\u003e serengeti.ic \u003c- generic_sews(serengeti,\n\u003e                              subsize = 5,\n\u003e                              moranI_coarse_grain = TRUE)\n\u003e serengeti.test \u003c- indictest(serengeti.ic)\n\n```\n\n```r\n\u003e # Textual summary of trends\n\u003e summary(serengeti.test)\nGeneric Spatial Early-Warnings\n\n Mat. # Mean Moran's I P\u003cnull     Skewness P\u003cnull     Variance P\u003cnull\n      1 0.98      0.58 \u003c1e-03 ***    -6.94  0.999        0.011 \u003c1e-03 ***\n      2 0.98      0.62 \u003c1e-03 ***    -6.17  0.999        0.012 \u003c1e-03 ***\n      3 0.97      0.51 \u003c1e-03 ***    -5.59  0.999        0.015 \u003c1e-03 ***\n      4 0.96      0.68 \u003c1e-03 ***    -4.56  0.999        0.022 \u003c1e-03 ***\n      5 0.96      0.66 \u003c1e-03 ***    -4.37  0.999        0.024 \u003c1e-03 ***\n      6 0.95      0.62 \u003c1e-03 ***    -3.84  0.999        0.031 \u003c1e-03 ***\n      7 0.95      0.79 \u003c1e-03 ***    -3.96  0.999        0.034 \u003c1e-03 ***\n      8 0.94      0.75 \u003c1e-03 ***    -3.40  0.999        0.041 \u003c1e-03 ***\n      9 0.93      0.66 \u003c1e-03 ***    -3.26  0.999        0.040 \u003c1e-03 ***\n     10 0.93      0.58 \u003c1e-03 ***    -3.02  0.999        0.040 \u003c1e-03 ***\n     11 0.89      0.58 \u003c1e-03 ***    -2.29  0.999        0.054 \u003c1e-03 ***\n     12 0.85      0.62 \u003c1e-03 ***    -1.75  0.999        0.074 \u003c1e-03 ***\n     13 0.71      0.72 \u003c1e-03 ***    -0.87  0.999        0.131 \u003c1e-03 ***\n\n Significance tested against 999 randomly shuffled matrices\n Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1\n\n```\n\n```r\n\u003e # Plot trends\n\u003e plot(serengeti.test, along = serengeti.rain) +\n\u003e  geom_vline(xintercept = 593, color = \"red\", linetype = \"dashed\") +\n\u003e  labs(x = \"Annual rainfall\",\n\u003e       y = \"Mean cover/indicator value\",\n\u003e       title = \"Early warning signals of a shift in tree cover in Serengeti, Tanzania (Eby et al. 2016)\",\n\u003e       subtitle = \"Grey ribbons indicate the 5-95% quantiles of the null distribution\")\n```\n\n![Example result](./tools/imgs/serengeti_example.png)\n\n## Getting help \n\nThere is also a quite thorough user guide with tutorials, answers to technical \nproblems and examples of analyses at this address: \n\n[https://alex.lecairn.org/spatialwarnings-faq.html](https://alex.lecairn.org/spatialwarnings-faq.html)\n\nWe also welcome any question or constructive criticism! Please feel free to \nopen an issue or send us an email if you have any question about the package, or \nwould like to see improvements. \n\n## Original authors and License\n\nThis package is derived from the [Dakos et al.'s work](https://github.com/earlywarningtoolbox/spatial_warnings) on early warnings signals (see also the\nreference website for the [early-warnings signals toolbox](http://www.early-warning-signals.org/)).\n\nThis work is licensed under an MIT license. Some code included in unit tests has\nbeen written by Cosma Rohilla Shalizi [http://bactra.org/](http://bactra.org/)\nand is redistributed in its entirety with the source of this R package as\nper the recommandations in its README file.\n\nThe MIT License (MIT)\n\nCopyright (c) 2015 the authors\n\nPermission is hereby granted, free of charge, to any person obtaining a copy\nof this software and associated documentation files (the \"Software\"), to deal\nin the Software without restriction, including without limitation the rights\nto use, copy, modify, merge, publish, distribute, sublicense, and/or sell\ncopies of the Software, and to permit persons to whom the Software is\nfurnished to do so, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in\nall copies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\nIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\nFITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\nAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\nLIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\nOUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\nTHE SOFTWARE.\n\n## References\n\n[Génin, A., Majumder, S., Sankaran, S., Danet, A., Guttal, V.,\nSchneider, F. D. and Kéfi, S. (2018),\nMonitoring ecosystem degradation using spatial data and the R package\n'spatialwarnings'. Methods in Ecology and Evolution.](https://dx.doi.org/10.1111/2041-210X.13058)\n\n[Kéfi S., Guttal V., Brock W.A., Carpenter S.R., Ellison A.M., et al. (2014)\nEarly Warning Signals of Ecological Transitions: Methods for Spatial Patterns.\nPLoS ONE 9(3): e92097.](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0092097)\n\nEcologists interested in this package will also probably like the \nfollowing review: \n\n[Nijp, J. J., Temme, A. J.A.M., van Voorn, George A.K., Kooistra, L., \nHengeveld, G.M., Soons, M.B., Teuling, A.J. and Wallinga, J. (2019) \nSpatial early warning signals for impending regime shifts: A\npractical framework for application in real‐world landscapes](https://onlinelibrary.wiley.com/doi/full/10.1111/gcb.14591)\n\n","funding_links":[],"readme_doi_urls":["https://dx.doi.org/10.1111/2041-210X.13058"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://ost.ecosyste.ms/api/v1/projects/11982","html_url":"https://ost.ecosyste.ms/projects/11982"}