SitesReport {lifeR} | R Documentation |
Create report for sites with most unseen species
Description
Create report for sites with most unseen species
Usage
SitesReport(
centers,
ebird_key,
species_seen,
center_names = NULL,
report_filename = "Goals-Report",
report_dir = getwd(),
report_format = c("html", "pdf"),
max_sites = 5,
dist = 50,
back = 4,
hotspot = TRUE,
include_provisional = FALSE,
max_tries = 5,
timeout_sec = 30,
messages = c("minimal", "none", "verbose"),
drop_patterns = c("sp\\.", "\\/", "Domestic type", "hybrid"),
include_maps = TRUE
)
Arguments
centers |
Numeric vector or matrix of latitude and longitude
coordinates; vector should be of length 2, e.g.
|
ebird_key |
Character vector with eBird API key. |
species_seen |
Character vector of species that have already been seen. |
center_names |
Character vector of names to use for each pair of
latitude and longitude coordinates in |
report_filename |
Name of output file without file extension (see
|
report_dir |
Destination folder for the output file; if |
report_format |
File format for report; takes one of two values: "html" or "pdf". |
max_sites |
Maximum number of sites to return for each pair of
coordinates defined in |
dist |
Numeric radius in kilometers of distance from each geographic
center point defined by coordinates in |
back |
Number of days back to search for observations. |
hotspot |
Logical indicating whether or not to restrict results to hotspot locations. |
include_provisional |
Logical indicating whether not to include observations which have not yet been reviewed. |
max_tries |
Maximum number of query attempts to try (only for expert use). |
timeout_sec |
Integer time to allow before query is aborted (only for expert use). |
messages |
Character indicating the degree to which messages are printed during the report assembly process. Options are "minimal", "none", or "verbose". |
drop_patterns |
Character vector of patterns in species' names to
exclude certain species from consideration, such as domesticated species,
hybrids, and observations not identified to species level (e.g.
"Toxostoma sp."). The function uses |
include_maps |
Logical vector indicating whether or not to draw maps
of identified sites; should be length 1 or the number of centers (i.e. same
length as |
Details
The function uses the eBird API (see https://documenter.getpostman.com/view/664302/S1ENwy59/) to build the report. Queries to the eBird API require a user key; you can request an eBird API key by logging into your eBird account and navigating to https://ebird.org/api/keygen/. See examples and vignette for using your eBird API key.
Value
Silently returns a list with two named elements:
- results_list
A list where each element is a list of the results of queries for a center. Each element is a list with two named elements:
- center_info
A list with latitude (
lat
), longitude (longitude
), and namename
of the geographic center.- results
A tibble of observations from the top sites (with a maximum number of sites defined by
max_sites
).
- report_details
A list containing the settings used to build this report, such as days back and distances.
Examples
## Not run:
# Read in data downloaded from eBird
list_file <- system.file("extdata", "example-list.csv", package = "lifeR")
user_list <- read.csv(file = list_file)
# Only common names are required
my_species <- user_list$Common.Name
# Read in eBird API key from a text file
key <- scan(file = "ebird-key.txt", what = "character")
# A single center requires vector of coordinates
locs <- c(45, -109)
SitesReport(centers = locs, ebird_key = key,
species_seen = my_species)
# For multiple centers, pass a matrix to centers argument
loc_mat <- matrix(data = c(33, -109, 39, -119.1), nrow = 2, byrow = TRUE)
loc_names <- c("Brushy Mountain", "Yerington")
SitesReport(centers = loc_mat, ebird_key = key,
species_seen = my_species, center_names = loc_names)
## End(Not run)