{"Package":"rbison","Title":"Interface to the 'USGS' 'BISON' API","Description":"Interface to the 'USGS' 'BISON' ()\nAPI, a 'database' for species occurrence data. Data comes from\nspecies in the United States from participating data providers. You can get\ndata via 'taxonomic' and location based queries. A simple function\nis provided to help visualize data.","Version":"0.7.0","License":"MIT + file LICENSE","URL":"https://github.com/ropensci/rbison","BugReports":"https://github.com/ropensci/rbison/issues","Authors@R":"c(person(\"Scott\", \"Chamberlain\",\nrole = c(\"aut\", \"cre\"),\nemail = \"myrmecocystus@gmail.com\",\ncomment = c(ORCID = \"0000-0003-1444-9135\")))","LazyData":"true","VignetteBuilder":"knitr","Encoding":"UTF-8","Imports":"plyr, crul (>= 0.3.4), ggplot2, mapproj, grid, sp, dplyr (>=\n0.5.0), jsonlite (>= 1.1), data.table","Suggests":"roxygen2 (>= 6.1.0), knitr, testthat, taxize, vcr","RoxygenNote":"6.1.0","X-schema.org-applicationCategory":"DataAccess","X-schema.org-keywords":"species, occurrences, biodiversity, maps, USGS,\nBISON","X-schema.org-isPartOf":"\"https://ropensci.org\"","NeedsCompilation":"no","Packaged":"2018-10-25 16:03:48 UTC; sckott","Author":"Scott Chamberlain [aut, cre] ()","Maintainer":"Scott Chamberlain ","Repository":"CRAN","Date/Publication":"2018-10-25 16:30:03 UTC","repoType":"cran","tarballUrl":"ftp://cran.r-project.org/pub/R/src/contrib/rbison_0.7.0.tar.gz","jsonAuthors":[{"name":"Scott Chamberlain","email":"myrmecocystus@gmail.com","maintainer":true}],"readme":"rbison\n======\n\n\n\n[![cran checks](https://cranchecks.info/badges/worst/rbison)](https://cranchecks.info/pkgs/rbison)\n[![Build Status](https://api.travis-ci.org/ropensci/rbison.png)](https://travis-ci.org/ropensci/rbison)\n[![Build status](https://ci.appveyor.com/api/projects/status/cba5mqg33hakour1?svg=true)](https://ci.appveyor.com/project/sckott/rbison)\n[![codecov.io](https://codecov.io/github/ropensci/rbison/coverage.svg?branch=master)](https://codecov.io/github/ropensci/rbison?branch=master)\n[![rstudio mirror downloads](http://cranlogs.r-pkg.org/badges/rbison?color=E664A4)](https://github.com/metacran/cranlogs.app)\n[![cran version](http://www.r-pkg.org/badges/version/rbison)](https://cran.r-project.org/package=rbison)\n\nWrapper for the [USGS Bison](https://bison.usgs.gov) API\n\n## Description\n\nUSGS Biodiversity Information Serving Our Nation (BISON) is a web-based federal mapping resource that provides access to georeferenced (those with latitude and longitude coordinates) and non-georeferenced data describing the occurrence or presence of terrestrial and aquatic species recorded or collected by a person (or instrument) at a specific time in the United States, U.S. Territories, U.S. Marine Exclusive Economic Zones (EEZs), and Canada. Each record in a species occurrence dataset available in BISON will typically consist of a scientific name (genus and specific epithet), a date, and one or more geographic references such as a state name, county name, and/or decimal latitude and longitude coordinates. In addition to these typical data fields, species occurrence datasets often include many other data fields that describe each species occurrence event in more detail.\n\n`rbison` allows one to pull species occurrence data from these datasets, inspect species occurance summaries, and then map species occurance within the US, within the contiguous 48 states, and/or at county or state level.\n\nCurrent data providers for BISON can be found at \n\nSee for API docs for the BISON API.\n\n\n## Installation\n\nFrom CRAN\n\n\n```r\ninstall.packages(\"rbison\")\n```\n\nOr the development version from Github\n\n\n```r\ninstall.packages(\"devtools\")\ndevtools::install_github(\"ropensci/rbison\")\nlibrary('rbison')\n```\n\nLoad package\n\n\n```r\nlibrary(\"rbison\")\n```\n\nNotice that the function `bisonmap` automagically selects the map extent to plot for you, being one of the contiguous lower 48 states, or the lower 48 plus AK and HI, or a global map. If some or all points outside the US, a global map is drawn, and throws a warning. . You may want to make sure the occurrence lat/long coordinates are correct.\n\n## get data\n\n\n```r\nout <- bison(species = \"Phocoenoides dalli dalli\", count = 10)\n```\n\n\n### inspect summary\n\n\n```r\nout$summary\n#> $specimen\n#> [1] 7\n```\n\n### map occurrences\n\n\n```r\nbisonmap(out)\n```\n\n![plot of chunk unnamed-chunk-7](tools/unnamed-chunk-7-1.png)\n\n## All points within the US (including AK and HI)\n\n### get data\n\n\n```r\nout <- bison(species = \"Cyanocitta stelleri\", count = 500)\n```\n\n\n### inspect summary\n\n\n```r\nout$summary\n#> $fossil\n#> [1] 2\n#> \n#> $observation\n#> [1] 566346\n#> \n#> $centroid\n#> [1] 1\n#> \n#> $specimen\n#> [1] 3294\n#> \n#> $unknown\n#> [1] 208\n```\n\n### map occurrences\n\n\n```r\nbisonmap(out)\n```\n\n![plot of chunk unnamed-chunk-10](tools/unnamed-chunk-10-1.png)\n\n## All points within the contiguous 48 states\n\n### get data\n\n\n```r\nout <- bison(species = \"Aquila chrysaetos\", count = 300)\n```\n\n\n### inspect summary\n\n\n```r\nout$summary\n#> $literature\n#> [1] 1641\n#> \n#> $fossil\n#> [1] 642\n#> \n#> $observation\n#> [1] 128811\n#> \n#> $centroid\n#> [1] 1\n#> \n#> $unknown\n#> [1] 9734\n#> \n#> $specimen\n#> [1] 1899\n```\n\n\n### map occurrences\n\n\n```r\nbisonmap(out)\n```\n\n![plot of chunk unnamed-chunk-13](tools/unnamed-chunk-13-1.png)\n\n\n## Map county or state level data\n\n### Counties - using last data call for Aquila\n\n\n```r\nbisonmap(out, tomap = \"county\")\n```\n\n![plot of chunk unnamed-chunk-14](tools/unnamed-chunk-14-1.png)\n\n### States - using last data call for Aquila\n\n\n```r\nbisonmap(out, tomap = \"state\")\n```\n\n![plot of chunk unnamed-chunk-15](tools/unnamed-chunk-15-1.png)\n\n\n## BISON SOLR interface\n\n### taxa\n\nThe taxa service searches for and gives back taxonomic names\n\n\n```r\nbison_tax(query = \"*bear\")\n#> $numFound\n#> [1] 48\n#> \n#> $names\n#> lc_vernacularName vernacularName\n#> 1 Louisiana black bear Louisiana black bear\n#> 2 Sloth Bear Sloth Bear\n#> 3 grizzly bear grizzly bear\n#> 4 bear oak bear oak\n#> 5 yellow woollybear yellow woollybear\n#> 6 bear daisy bear daisy\n#> 7 banded woollybear banded woollybear\n#> 8 Asiatic black bear Asiatic black bear\n#> 9 Kodiak bear Kodiak bear\n#> 10 black-ended bear black-ended bear\n#> \n#> $highlight\n#> NULL\n#> \n#> $facets\n#> NULL\n```\n\nAnd you can search by scientific name\n\n\n```r\nbison_tax(query = \"Helianthus*\", method = \"scientificName\")\n#> $numFound\n#> [1] 212\n#> \n#> $names\n#> scientificName\n#> 1 Discoaster helianthus\n#> 2 Helianthus divaricatus latifolius\n#> 3 Helianthus decapetalus\n#> 4 Helianthus ambiguus\n#> 5 Helianthus dowellianus\n#> 6 Helianthus luxurians\n#> 7 Helianthus arenicola\n#> 8 Helianthus atrorubens\n#> 9 Helianthus frondosus\n#> 10 Helianthus nuttallii canadensis\n#> \n#> $highlight\n#> NULL\n#> \n#> $facets\n#> NULL\n```\n\n### occurrence search\n\nThe occurrence service searches by scientific names and gives back occurrence \ndata similar to data given back by the `bison()` function\n\nSearching for data and looking at output\n\n\n```r\nx <- bison_solr(scientificName = \"Aquila chrysaetos\", rows = 10, \n fl = \"scientificName,decimalLongitude,decimalLatitude\")\nx$points\n#> decimalLongitude scientificName decimalLatitude\n#> 1 -117.6185 Aquila chrysaetos 33.71447\n#> 2 -117.6185 Aquila chrysaetos 33.71447\n#> 3 -117.6185 Aquila chrysaetos 33.71447\n#> 4 -117.6185 Aquila chrysaetos 33.70987\n#> 5 -117.6014 Aquila chrysaetos 33.65099\n#> 6 -117.4997 Aquila chrysaetos 33.68344\n#> 7 -117.4544 Aquila chrysaetos 33.65246\n#> 8 -117.4544 Aquila chrysaetos 33.65246\n#> 9 -117.4543 Aquila chrysaetos 34.02910\n#> 10 -117.4543 Aquila chrysaetos 34.02910\n```\n\nMapping the data\n\n\n```r\nout <- bison_solr(scientificName = \"Aquila chrysaetos\", rows = 1000)\nbisonmap(out)\n```\n\n![plot of chunk unnamed-chunk-19](tools/unnamed-chunk-19-1.png)\n\n## Meta\n\n* Please [report any issues or bugs](https://github.com/ropensci/rbison/issues).\n* License: MIT\n* Get citation information for `rbison` in R doing `citation(package = 'rbison')`\n* Please note that this project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). By participating in this project you agree to abide by its terms.\n\nThis package is part of a richer suite called [SPOCC Species Occurrence Data](https://github.com/ropensci/spocc), along with several other packages, that provide access to occurrence records from multiple databases. We recommend using SPOCC as the primary R interface to rbison unless your needs are limited to this single source.\n\n[![ropensci_footer](https://ropensci.org/public_images/github_footer.png)](https://ropensci.org)","jobInfo":{"package":"rbison","version":"0.7.0","parsingStatus":"success","parserVersion":1,"parsedAt":"2019-05-03T23:29:50+0000"}}

Description

Arguments