tabulAve: Build report-ready table with all known bird occurrences for...

In pecard/tabuleia: Collect biodiversity from different sources for a region of interest.

Build report-ready table with all known bird occurrences for a region of interest.

Description

The tabulAve function will create a reference table considering all bird species occurring in a roi, joining all relevant information (taxonomic, conservation, occurrence status and legal framework). It will also summarize roi status (ratios for protected and threatened species).

Usage

tabulAve(
  utm_ae = utm_ae,
  utm_q = utm_contig,
  fielddata = NULL,
  atlas = atlas_aves,
  ebird = NULL,
  gbif = NULL
)

Arguments

utm_ae	character vector of utm grid cells touching roi.
utm_q	character vector of utm grid cells around roi
fielddata	a data.frame with bid data obtained for the roi. Typically a table with species utm reference.
atlas	data.frame with Mammal and Bat Atlas data with references to the UTM 10x10 grid cell.
ebird	data.frame with eBird Dataset from 2005 to 2019.
gbif	data.frame with GBIF Dataset from 2005 to 2019.
ae	any spatial (sp, spatialdataframe) or coordinates vector indicating a region of interest.

Details

ensure that field datasheet follow the standardized formatting.

Value

an data.frame file with a complete and pre-formatted table, ready for use on reports.

Author(s)

Paulo E. Cardoso

Examples

## Not run: 
# read roi from shapefile
ae <- sf::read_sf(here::here("sig", "ae_buffer250m.shp"),
  stringsAsFactors = F
) %>%
  st_set_crs(3763)
# Cast multipolygon geometry to single parts
aeu <- st_cast(ae, "POLYGON")
# Add an UID to each
aeu$id <- c(1:2)
# get UTM codes for your roi
utm_all <- utm_id(grid = utm10k, roi = aeu %>% filter(id == 2), buff = NULL,
                  contiguity = "queen")
utm_ae <- utm_all$ae
utm_contig <- utm_all$contig
# tabulate species occurence and status in the area
tave <- tabulEIA::tabulAve(utm_ae = utm_ae, utm_q = utm_contig,
                           fielddata = NULL,
atlas = atlas_aves, ebird = ebird, gbif = gbif)
# export to csv
write_excel_csv(tave,
                path = here::here("output", "tabela_avifauna_agolada.csv"))

## End(Not run)

pecard/tabuleia documentation built on June 16, 2022, 3:32 a.m.