read_beqi2 {benthos}

Read and Validate BEQI2 Input Files

Description

This function reads and checks BEQI2 input files. The format has been specified in Van Loon (2013) and is described in the vignette of the BENMMI-package.

Usage

read_beqi2(filename)

validate_beqi2(.data)

Arguments

filename

name of BEQI2 input file (character)

.data

table in BEQI2-format

Details

The function performs the following tasks:

• checks the existence of filename;

• checks availablitity of required columns (case insensitive);

• make column names with aggregation data case-insensitive;

• removes redundant spaces;

• checks if DATE-field adheres to ISO 8601 (YYYY-mm-dd);

• constructs a unique identifier ID by concatenating columns OBJECTID and DATE;

• checks that each ID has a unique AREA;

• checks azoic samples for VALUE=0;

• removes records with VALUE=0, not belonging to azoic samples;

• checks VALUE-field on missing values;

• checks if VALUE-field is an integer;

Functions

• validate_beqi2(): validator for BEQI2-format

References

Willem van Loon, 2013. BEQI2 INPUT FORMAT. See the package-vignette of the BENMMI-package.