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Life and Fishery","monthly_downloads":0,"total_dependent_repos":0,"total_dependent_packages":0,"readme":"\n# RSP\u003cimg src=\"vignettes/RSP_logo.png\" align=\"right\" width=\"120\" /\u003e\n\n[![R-CMD-check](https://github.com/YuriNiella/RSP/workflows/R-CMD-check/badge.svg)](https://github.com/YuriNiella/RSP/actions)\n[![codecov](https://codecov.io/github/YuriNiella/RSP/branch/master/graphs/badge.svg)](https://codecov.io/github/YuriNiella/RSP)\n[![DOI](https://zenodo.org/badge/200786116.svg)](https://zenodo.org/badge/latestdoi/200786116)\n\nRefining the Shortest Paths (RSP) of animals tracked with acoustic\ntransmitters \n\n## Overview\n\nThe RSP toolkit is a method for analyzing the fine scale movements of\naquatic animals tracked with passive acoustic telemetry in estuarine\nenvironments, that accounts for the surrounding land masses. The animal\nmovements between detections are recreated to have occurred exclusively\nin water and the utilization distribution areas are limited by the land\ncontours, providing realistic estimations of space use. The method can\nbe divided into the following three main steps:\n\n1)  Refining the shortest paths in water between consecutive acoustic detections\n2)  Calculating utilization distribution areas using dynamic Brownian\n    Bridge Movement Models (dBBMM)\n3)\tCalculating the overlaps between different biological groups monitored\n\nDepending on the research questions being addressed, the utilization\ndistribution areas can be calculated for the entire monitoring periods,\nor in fine-scale according to fixed temporal intervals in hours\n(timeframes). Tracked animals are assigned to specific biological groups\n(different species, different sexes from a same species, etc.) prior to\nanalysis, and RSP can be used for calculating the amounts of inter-group overlap in\nspace and time between all groups monitored. This approach allows\nspatial ecologists to use the outputs from such fine-scale space use\nmodels (areas of use, or the between-group overlaps) as input for\nfurther statistical analysis.\n\nHere is an example of the same animal movements animated both using\n**only the receiver locations** and the **receiver and RSP positions\ncombined**:\n\n![](vignettes/animationRSP.gif)\n\n## Main RSP functions\n\n### Running the analysis\n\n**runRSP()**\n\nUsed to estimate the shortest in-water paths. Each\nanimal monitored is analysed individually and all detections are\nassigned to separate **tracks**: a sequence of detections with\nintervals shorter than 24 hours (by default, max.time = 24). When the animal is not detected for\na period of time longer than the maximum.time argument, a new track is created.\n\n**dynBBMM()**\n\nAfter the shortest in-water paths are estimated, the utilization distribution areas can be calculated with\n**dynamic Brownian Bridge Movement Models** (dBBMM). Models can be either calculated for the entire monitoring, or during a particular interval of interest. \n\n**getDistances()**\n\nCalculates the distances travelled (in meters) during each RSP track, both using only the receiver locations and also the exclusively in-water tracks. \n\n**getAreas()**\n\nObtains the in-water areas (in squared meters) for the tracked animals, either at monitored group or track levels. The contour levels of interest from the dBBMMs can be set, and by default areas are calculated for the **50%** and **95%** contours.\n\n**getOverlaps()**\n\nCalculates the amounts of overlap among different biological groups monitored, at the same contour levels as defined in getAreas(). Overlaps are returned as **only in space** for group dBBMM, and if a timeframe is set (in hours), overlaps are **simultaneously in space and time** for timeslot dBBMM.  \n\n\n### Plotting the results\n\n**plotTracks()**\n\nThis function can be used to visualize the tracks created using **runRSP()**:\n\n\u003cimg src=\"vignettes/plotTrack4.png\" width=\"700\"  /\u003e\n\n**plotContours()**\n\nPlots the dBBMM utilization distribution areas calculated for each animal using **dynBBMM()**:\n\n\u003cimg src=\"vignettes/plotContours_readme.png\" width=\"700\"  /\u003e\n \n**plotAreas()**\n\nThis plot shows the space use areas from a particular group of animals:\n\n\u003cimg src=\"vignettes/plotAreas1.png\" width=\"650\"  /\u003e\n\n**plotOverlap()**\n\nThis function shows where in the study area the overlaps between **different\nbiological groups** occurred:\n\n\u003cimg src=\"vignettes/plotOverlaps2.png\" width=\"850\"  /\u003e\n\n\n**animateTracks()**\n\nThis function can be used to create an **animation** of the **RSP tracks**:\n\n![](vignettes/Sydney_anim.gif)\n\n## Installation\n\nCurrent version: **1.0.5**\n\nYou will need the **remotes** package **to install RSP**:\n``` \ninstall.packages(\"remotes\")\nlibrary(\"remotes\")     \n```\n\nNow you can install RSP using:\n```\ninstall_github(\"YuriNiella/RSP\", build_opts = c(\"--no-resave-data\", \"--no-manual\"), build_vignettes = TRUE)\n```\n\nAll the information you need on how to perform the RSP analysis can be\nfound in the package vignettes:\n```\nbrowseVignettes(\"RSP\")\n```\n","funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://ost.ecosyste.ms/api/v1/projects/95559","html_url":"https://ost.ecosyste.ms/projects/95559"}