read_ebd: Read an EBD file

In mstrimas/auk: eBird Data Processing with AWK

Description

Read an eBird Basic Dataset file using data.table::fread(), readr::read_delim(), or read.delim depending on which packages are installed. read_ebd() reads the EBD itself, while read_sampling()' reads a sampling event data file.

Usage

read_ebd(x, reader, sep, unique, setclass)

## S3 method for class 'character'
read_ebd(x, reader, sep = "\t", unique = TRUE,
  setclass = c("tbl", "data.frame", "data.table"))

## S3 method for class 'auk_ebd'
read_ebd(x, reader, sep = "\t", unique = TRUE,
  setclass = c("tbl", "data.frame", "data.table"))

read_sampling(x, reader, sep, unique, setclass)

## S3 method for class 'character'
read_sampling(x, reader, sep = "\t", unique = TRUE,
  setclass = c("tbl", "data.frame", "data.table"))

## S3 method for class 'auk_ebd'
read_sampling(x, reader, sep = "\t", unique = TRUE,
  setclass = c("tbl", "data.frame", "data.table"))

Arguments

x	filename or auk_ebd object with associated output files as created by auk_filter().
reader	character; the function to use for reading the input file, options are "fread", "readr", or "base", for data.table::fread(), readr::read_delim(), or read.delim, respectively. This argument should typically be left empty to have the function choose the best reader based on the installed packages.
sep	character; single character used to separate fields within a row.
unique	logical; should duplicate grouped checklists be removed. If unique = TRUE, auk_unique() is called on the EBD before returning.
setclass	tbl, data.frame, or data.table; optionally set additional classes to set on the output data. All return objects are data frames, but may additionally be tbl (for use with dplyr and the tidyverse) or data.table (for use with data.table). The default is to return a tibble.

Details

This functions performs the following processing steps:

• Data types for columns are manually set based on column names used in the February 2017 EBD. If variables are added or names are changed in later releases, any new variables will have data types inferred by the import function used.

• Variables names are converted to snake_case.

• Duplicate observations resulting from group checklists are removed using auk_unique(), unless unique = FALSE.

Value

A data.frame with additional class tbl unless setclass is used, in which case a standard data.frame or data.table can be returned. An additional column, checklist_id, is added to output files if unique = TRUE, that uniquely identifies the checklist from which the observation came. This field is equal to sampling_event_identifier for non-group checklists, and group_identifier for group checklists.

Methods (by class)

• character: Filename of EBD.

• auk_ebd: auk_ebd object output from auk_filter()

• character: Filename of sampling event data file

• auk_ebd: auk_ebd object output from auk_filter(). Must have had a sampling event data file set in the original call to auk_ebd().

Examples

ebd <- system.file("extdata/ebd-sample.txt", package = "auk") %>%
  read_ebd()
# optionally return a plain data.frame
ebd_df <- system.file("extdata/ebd-sample.txt", package = "auk") %>%
  read_ebd(setclass = "data.frame")
# read a sampling event data file
x <- system.file("extdata/zerofill-ex_sampling.txt", package = "auk") %>%
  read_sampling()

mstrimas/auk documentation built on May 20, 2019, 5:26 p.m.