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Update README and DESCRIPTION
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mccrea-cobb committed Oct 4, 2023
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Expand Up @@ -16,7 +16,7 @@ Description: Functions to query multiple biodiversity databases (e.g., GBIF,
from the outstanding work of the rOpenSci community (https://ropensci.org).
License: CC0
Depends:
R (>= 3.5.0)
R (>= 4.3.1)
Imports:
curl (>= 3.0),
dplyr (>= 0.7.3),
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19 changes: 11 additions & 8 deletions README.Rmd
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Expand Up @@ -7,8 +7,11 @@ knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "README-",
message = FALSE)
message = FALSE,
warning = FALSE)
```

``` {r, echo = FALSE, eval = TRUE}
library(fwspp)
```

Expand All @@ -24,7 +27,7 @@ library(fwspp)

## Overview

This packages contains functions to perform geographic query of several biodiversity databases based on U.S. Fish and Wildlife Service (USFWS) administrative or acquisition property boundaries (plus optional buffers). At present, the package queries the [Global Biodiversity Information Facility (GBIF)](http://www.gbif.org/), [Biodiversity Information Serving Our Nation (BISON)](https://bison.usgs.gov/#home), [Integrated Digitized Biocollections (iDigBio)](https://www.idigbio.org/), [VertNet](http://vertnet.org/), the [Berkeley Ecoinformatics Engine](https://ecoengine.berkeley.edu/), and [AntWeb](http://www.antweb.org/). It draws heavily from the outstanding work by the [ROpenScience group](https://ropensci.org/) and their suite of species occurrence packages.
This packages contains functions to perform geographic query of several biodiversity databases based on U.S. Fish and Wildlife Service (USFWS) administrative or acquisition property boundaries (plus optional buffers). At present, the package queries the [Global Biodiversity Information Facility (GBIF)](http://www.gbif.org/), [Integrated Digitized Biocollections (iDigBio)](https://www.idigbio.org/), [VertNet](http://vertnet.org/), the [Berkeley Ecoinformatics Engine](https://ecoengine.berkeley.edu/), and [AntWeb](http://www.antweb.org/). It draws heavily from the outstanding work by the [ROpenScience group](https://ropensci.org/) and their suite of species occurrence packages.

We provide options to:

Expand All @@ -33,7 +36,7 @@ We provide options to:

## Installation

The `fwspp` package requires [R](https://www.r-project.org/) (>= 3.4) and [Rtools](https://cran.r-project.org/bin/windows/Rtools/). Both will require administrative privileges but the subsequent installation of packages will not.
The `fwspp` package requires [R](https://www.r-project.org/) (>= 3.4) and [Rtools](https://cran.r-project.org/bin/windows/Rtools/). Both will require administrative privileges but the subsequent installation of packages will not.

With R and Rtools installed, it's relatively painless to install and load the `fwspp` package. If you receive an SSL or CA Certificate error, take the extra steps documented below.

Expand All @@ -48,7 +51,7 @@ devtools::install_github("[email protected]:USFWS/fwspp.git", ref = "main")
library("fwspp")
```

Prior to your first use of `fwspp`, you'll need to install the USFWS Cadastral Geodatabase. You can do this now, using the `install_fws_cadastral` function
Prior to your first use of `fwspp`, you'll need to install the USFWS Cadastral Geodatabase. You can do this now, using the `install_fws_cadastral` function:

```
install_fws_cadastral()
Expand Down Expand Up @@ -114,13 +117,13 @@ r6_all <- find_fws(ptype = c("NWR", "WPA"), region = 6)

#### USFWS property types

The `find_fws` function gives you a `ptype` argument to search for several USFWS property types. The most common and default property type is the National Wildlife Refuge (NWR), but other options include Waterfowl Production Areas (WPA), Wildlife Management Areas (WMA), National Fish Hatcheries (NFH), Wildlife Management Areas (WMA), and Farm Service Agency indices (FSA). You can specify multiple options as illustrated in the last example above.
The `find_fws` function gives you a `ptype` argument to search for several USFWS property types. The most common and default property type is the National Wildlife Refuge (NWR), but other options include Waterfowl Production Areas (WPA), Wildlife Management Areas (WMA), National Fish Hatcheries (NFH), Wildlife Management Areas (WMA), and Farm Service Agency indices (FSA). You can specify multiple options as illustrated in the last example above.

### Step 2 - Boundary, scrubbing, and taxonomic decisions

#### Boundary options

We offer two options for querying the boundaries of refuges and other USFWS properties via the `bnd` argument to the `fws_occ` function. The default `bnd = "admin"` queries those lands and waters **administered** by the USFWS in North America, U.S. Trust Territories and Possessions. It may also include inholdings that are not administered by the USFWS. The primary source for this information is the USFWS Realty program. See https://ecos.fws.gov/ServCat/Reference/Profile/82894 for more information. Using `bnd = "acq"` queries the external boundaries of lands and waters that are **approved for acquisition** by the USFWS in North America, U.S. Trust Territories and Possessions. See https://ecos.fws.gov/ServCat/Reference/Profile/82893 for more information.
We offer two options for querying the boundaries of refuges and other USFWS properties via the `bnd` argument to the `fws_occ` function. The default `bnd = "admin"` queries those lands and waters **administered** by the USFWS in North America, U.S. Trust Territories and Possessions. It may also include inholdings that are not administered by the USFWS. The primary source for this information is the USFWS Realty program. See https://ecos.fws.gov/ServCat/Reference/Profile/82894 for more information. Using `bnd = "acq"` queries the external boundaries of lands and waters that are **approved for acquisition** by the USFWS in North America, U.S. Trust Territories and Possessions. See https://ecos.fws.gov/ServCat/Reference/Profile/82893 for more information.

#### Scrubbing options

Expand Down Expand Up @@ -161,8 +164,8 @@ Querying many properties can take hours, particularly if they are relatively lar

## Getting help

Contact the project maintainer for help with this repository template.
Contact the project maintainer for help with this repository.

## Contribute

Contact the project maintainer for information about contributing to this repository template. Submit a [GitHub Issue](https://github.com/USFWS/fwspp/issues/new) to report a bug or request a feature or enhancement.
Contact the project maintainer for information about contributing to this repository. Submit a [GitHub Issue](https://github.com/USFWS/fwspp/issues/new) to report a bug or request a feature or enhancement.
37 changes: 9 additions & 28 deletions README.md
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Expand Up @@ -15,14 +15,13 @@ This packages contains functions to perform geographic query of several
biodiversity databases based on U.S. Fish and Wildlife Service (USFWS)
administrative or acquisition property boundaries (plus optional
buffers). At present, the package queries the [Global Biodiversity
Information Facility (GBIF)](http://www.gbif.org/), [Biodiversity
Information Serving Our Nation (BISON)](https://bison.usgs.gov/#home),
[Integrated Digitized Biocollections
(iDigBio)](https://www.idigbio.org/), [VertNet](http://vertnet.org/),
the [Berkeley Ecoinformatics Engine](https://ecoengine.berkeley.edu/),
and [AntWeb](http://www.antweb.org/). It draws heavily from the
outstanding work by the [ROpenScience group](https://ropensci.org/) and
their suite of species occurrence packages.
Information Facility (GBIF)](http://www.gbif.org/), [Integrated
Digitized Biocollections (iDigBio)](https://www.idigbio.org/),
[VertNet](http://vertnet.org/), the [Berkeley Ecoinformatics
Engine](https://ecoengine.berkeley.edu/), and
[AntWeb](http://www.antweb.org/). It draws heavily from the outstanding
work by the [ROpenScience group](https://ropensci.org/) and their suite
of species occurrence packages.

We provide options to:

Expand Down Expand Up @@ -54,7 +53,7 @@ take the extra steps documented below.

Prior to your first use of `fwspp`, you’ll need to install the USFWS
Cadastral Geodatabase. You can do this now, using the
`install_fws_cadastral` function
`install_fws_cadastral` function:

install_fws_cadastral()

Expand Down Expand Up @@ -98,10 +97,6 @@ strict as necessary. Here are a few examples:
# Get all National Wildlife Refuges (527 as of 2017-11-10)
# Issues a warning because of two identically-named, but distinct, refuges
all_refs <- find_fws()
#> Warning: Your search returned multiple USFWS properties with the same name.
#> * BUFFALO LAKE NATIONAL WILDLIFE REFUGE
#> To avoid querying an unwanted property, check the output and perhaps
#> specify the `region` argument to avoid unintended behavior.

# Search across all refuges with a partial name match
# Only 1 refuge contains 'longleaf'; Mountain Longleaf NWR
Expand Down Expand Up @@ -174,7 +169,7 @@ National Fish Hatcheries (NFH), Wildlife Management Areas (WMA), and
Farm Service Agency indices (FSA). You can specify multiple options as
illustrated in the last example above.

### Step 2 - Boundary, scrubbing, taxonomic decisions, and start date
### Step 2 - Boundary, scrubbing, and taxonomic decisions

#### Boundary options

Expand Down Expand Up @@ -226,17 +221,6 @@ Number, common names, NPS-specific taxon code, and a general taxa
returned. Modifications to observation taxonomy can be suppressed with
`taxonomy = FALSE`.

#### Start Date

Some databases allow us to subset by a range of dates. Specifically,
GBIF, iDigBio, VertNet, and ServCat and be queried by the 'last interpreted',
'last modified', 'last indexed', and 'last issued' attributes respectively. By
default, the start date is January 1st, 1776. If we would like to specify a more
recent start date to reduce the records already retrieved in a previous
query, we can specify the start date. It must be noted that the start date does
not necessarily represent the date the record was added. Often it represents
the date the record was most recently modified or updated.

#### Other options

By default, the `fws_occ` function makes the query using the actual
Expand Down Expand Up @@ -274,9 +258,6 @@ Some examples:
kw <- find_fws("key west")
kw_occ <- fws_occ(kw, buffer = 10, taxonomy = FALSE)

# Query Key West NWR using a start date of September 5th, 2023
kw_occ <- fws_occ(kw,start_day = 05,start_month= 9, start_year = 2023)

### Step 4 - Wait…

Querying many properties can take hours, particularly if they are
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