inst/doc/occurrences-example.R

In galaxias: Describe, Package, and Share Biodiversity Data

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## -----------------------------------------------------------------------------
library(galaxias)
library(dplyr)
library(readr)

obs <- read_csv("dummy-dataset-sb.csv",
                show_col_types = FALSE) |>
  janitor::clean_names()

obs |> 
  gt::gt() |>
  gt::opt_interactive(page_size_default = 5)

## -----------------------------------------------------------------------------
obs |>
  suggest_workflow()

## -----------------------------------------------------------------------------
obs_dwc <- obs |>
  set_scientific_name(scientificName = species) |>
  set_coordinates(decimalLatitude = lat,
                  decimalLongitude = lon) |>
  set_datetime(eventDate = lubridate::ymd(date)) # specify year-month-day format

## -----------------------------------------------------------------------------
obs_dwc |>
  suggest_workflow()

## -----------------------------------------------------------------------------
obs_dwc <- obs_dwc |>
  set_occurrences(
    occurrenceID = composite_id(sequential_id(), site, landscape),
    basisOfRecord = "humanObservation"
    ) |>
  set_coordinates(
    geodeticDatum = "WGS84",
    coordinateUncertaintyInMeters = 30
    # coordinateUncertaintyInMeters = with_uncertainty(method = "phone")
    ) |>
  set_individual_traits()

## -----------------------------------------------------------------------------
obs_dwc |>
  suggest_workflow()

## -----------------------------------------------------------------------------
obs_dwc <- obs_dwc |>
  select(any_of(occurrence_terms())) # select any matching terms

obs_dwc |>
  gt::gt() |>
  gt::opt_interactive(page_size_default = 5)

## -----------------------------------------------------------------------------
# # Save in ./data-processed
# use_data_occurrences(obs_dwc)