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Please edit that file --\u003e\n\n```{r setup, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"100%\"\n)\n```\n# naturecounts\n\n\u003c!-- badges: start --\u003e\n[![lifecycle](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)\n[![R-CMD-check](https://github.com/BirdsCanada/naturecounts/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/BirdsCanada/naturecounts/actions/workflows/R-CMD-check.yaml)\n![r-universe](https://birdscanada.r-universe.dev/badges/naturecounts)\n\u003c!-- badges: end --\u003e\n\nAccess and download data on plant and animal populations from various databases through NatureCounts, a service managed by Birds Canada.\n\nSee tutorials, documentation and articles on the [naturecounts package Website](https://birdscanada.github.io/naturecounts)\n\n## Installation\n\nYou can install the main version of `naturecounts` from our R-Universe\n\n```{r eval = FALSE}\ninstall.packages(\"naturecounts\", \n                 repos = c(birdscanada = 'https://birdscanada.r-universe.dev',\n                           CRAN = 'https://cloud.r-project.org'))\n```\n\n## Usage\n\n```{r}\nlibrary(naturecounts)\n```\n\n### Fetching counts\n\nUse the `nc_count()` function to return collections and the number of observations in each for which you have access (here returns all collections associated with username **sample**).\n\n```{r}\nnc_count(username = \"sample\")\n```\n\nUse the `show = \"all\"` argument to show counts for all collections available (public or otherwise).\n\n```{r}\nnc_count(show = \"all\") %\u003e%\n  head()\n```\n\n### Fetching data\n\nFetch all observations of bittern which are available to user **sample** into a local data frame.\n\nFirst find the species id\n```{r}\nsearch_species(\"American Bittern\")\n```\n\nUse this id with `nc_data_dl()`. The `info` parameter is a short description of what the data is being downloaded for.\n```{r}\nbittern \u003c- nc_data_dl(species = 2490, username = \"sample\", \n                    info = \"readme_example\")\n```\n\nAlternatively, save the downloaded data as a SQLite database (`bittern`).\n```{r}\nbittern \u003c- nc_data_dl(species = 2490, sql_db = \"bittern\", username = \"sample\", \n                    info = \"readme_example\")\n```\n\n```{r cleanup, include = FALSE}\nfile.remove(\"bittern.nc\")\n```\n\n### Authorizations\n\nTo access private/semi-public projects/collections you must [sign up](https://www.birdscanada.org/birdmon/default/profile.jsp) for a free NatureCounts account and [register](https://www.birdscanada.org/birdmon/default/projects.jsp) for the projects you'd like to access. Once registered, you can use the `username` argument (you will be prompted for a password) for both `nc_count()` and `nc_data_dl()`, which will then return a different set of records.\n\n```{r, eval = FALSE}\nnc_count(username = \"my_user_name\")\nbittern \u003c- nc_data_dl(species = 2490, username = \"my_user_name\", info = \"readme_example\")\n```\n\n### More advanced options\n\n`nc_count()` and `nc_data_dl()` have a variety of arguments that allow you to filter the counts/data prior to downloading. These options include `collections`, `species`, `years`, `doy` (day-of-year), `region`, and `site_type` (users can specify up to 3 of these). For `nc_data_dl()` you have the additional arguments `fields_set` and `fields` with which you can customize which fields/columns to include in your download.\n\nSee the function examples ([`nc_count()`](https://birdscanada.github.io/naturecounts/reference/nc_count.html), [`nc_data_dl()`](https://birdscanada.github.io/naturecounts/reference/nc_data_dl.html)) the following articles for more information on these filters:\n\n- Collections\n- [Species Codes](https://birdscanada.github.io/naturecounts/articles/species-codes.html)\n- [Regional Codes](https://birdscanada.github.io/naturecounts/articles/region-codes.html)\n- [IBAs and BCRs (regions)](https://birdscanada.github.io/naturecounts/articles/region-areas.html)\n- [Using spatial data to filter observations](https://birdscanada.github.io/naturecounts/articles/region-spatial.html)\n\nWe also have an [article on post-filtering your data](https://birdscanada.github.io/naturecounts/articles/filtering-data.html)\n\n### Metadata\n\nNatureCounts includes a great deal of metadata which can be accessed through the functions with the `meta_` prefix. See the [Meta Documentation](https://birdscanada.github.io/naturecounts/reference/meta.html) for specifics.\n","funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["optimize","archiving","measur","transforms","bird","generic","compose","observation","conversion","animals"],"project_url":"https://ost.ecosyste.ms/api/v1/projects/301869","html_url":"https://ost.ecosyste.ms/projects/301869"}