3.1 Create a new project

The easiest way to start working with litteR is to create an empty project directory. This directory can be filled with example and reference files by running:

create_litter_project("d:/work/litter-projects/beach-litter")

in the RStudio-console. For more information on how to obtain and use RStudio, consult its website or read our installation guide.

The argument of function create_litter_project (i.e., the quoted part in parentheses) is an existing work directory on your computer. This can be any valid directory name with sufficient user privileges. Note for MS-Windows users: R requires forward slashes!

It is also possible to run create_litter_project() without an argument. In that case, a simple graphical user interface pops up for interactive directory selection.

3.2 Perform litter analysis

litteR can be started typing litter() in the RStudio console (see the figure below).

After entering litter(), a simple graphical user interface pops up for file selection. An example of a file selection dialogue is given below.

4.1 Type file

The type file contains a list of all litter types that are allowed to use in the data file. It also indicates to which litter group each litter type belongs. Two example files, named ‘types-ospar.csv’ and ‘types-ospar-tc-sup-fish-plastic.csv’ are automatically generated when using the create_litter_project-function, a described earlier in this tutorial. A type file assigns each litter type (type_name) to one or more litter groups. The first 10 rows of ’types-ospar-tc-sup-fish-plastic.csv are given in the table below.

The following columns are in this table:

• type_name. This column is required and gives all litter types that are allowed in the data file. Litter types given in this column need to be unique;
• included: This column indicates whether a type specified in column type_name will be used in the analysis or not. Only type_names that are included in the analysis will contribute to the total litter count (TC).
• SUP, FISH, PLASTIC, etc.: these columns give the definition of each litter group. In the example above three groups are given: ‘single use plastics’ (SUP), ‘fisheries related litter’ (FISH), and ‘plastics’ (PLASTIC). A cross (x) indicates that a litter type in type_name is a member of a litter group or not. A cross (x) means ‘a member’, an empty cell means ‘not a member’.

The user may use one of the provided type files as a template for his own type file. litteR will use the type file that has been specified in the settings-file.

4.2 Data file

litteR supports a simple and flexible data format. It is similar to the OSPAR-format. The data are stored in so called wide format: each row refers to a single survey, each column to a single litter type or metadata. The table below gives an example of (a small) part of a data file.

The columns spatial_code and date are required. The remaning codes are either litter types or optional metadata. Each litter type should also be available in the litter type file. Only litter types in the litter type file are valid. Column names that are neither valid litter types nor spatial_code or date are considered as optional metadata columns. These columns do not affect the results. In the example above, country codes have been added as metadata.

The column spatial_code gives the spatial aggregation level. All analysis results will be presented on this spatial aggregation level. In the example above, the spatial aggregation level is the beach where the litter surveys took place. However, higher spatial aggregation levels such as the country level, or regional levels can also be used. The date column gives the monitoring date in ISO format, i.e., YYYY-mm-dd (for example 2020-07-03, to indicate 3 July 2020). For convenience, also the OSPAR-format (dd/mm/YYYY) is currently supported (for example 03/07/2020, to indicate 3 July 2020).

The third column country_code, in the type file given above, is not required and will not be used in the analysis. The remaining columns Plastic: Bags [2], Plastic: Small_bags [3], etc. contain the counts for each litter type that are selected in the litter type file.

4.3 Settings file

The settings file contains all settings needed to run litteR. An example of the contents of a settings file is given in the figure below.

# litteR settings file

# Period to analyse (YYYY-mm-dd)
date_min: 2012-01-01
date_max: 2017-12-31

# Percentage of total count to analyse (0 < percentage_total_count <= 100)
percentage_total_count: 80

# Data file. Note: the datafile must be in the same path as the settings file
file_data: beach-litter-nl-2012-2017.csv

# Type file. Defines the types and their groups
file_types: types-ospar.csv

# Select trend figures to plot in the report
spatial_code: ["Noordwijk", "Terschelling"]
group_code: ["TC", "SUP", "FISH"]
type_name: ["Plastic: Bags [2]"]
figure_quality: low

The settings-file contains the following entries:

• date_min and date_max, the first and final date of the period to analyze. Dates should be given in ISO format, i.e., YYYY-mm-dd (for example 2020-07-03, to indicate 3 July 2020);
• percentage_total_count: the percentage of the total count used to estimate statistics. See the section on descriptive statistics for more information;
• file_data: name of the data file (including its path, e.g., c:/my-litter-directory/my-litter-data.csv);
• file_types: name of the type file (including its path, e.g., c:/my-litter-directory/types-ospar.csv);
• spatial_code: name(s) of location(s) to plot. Spatial codes should be available in column spatial_code in the data file;
• group_code: name(s) of group(s) to plot. Litter groups should be available as column names in the type file;
• type_name: name(s) of type(s) to plot; Type names should be available in the type file and data file;
• figure_quality: quality of the plots in the report, either high or low.

4.4 Data Quality Control

All input files are validated by litteR. The following validation rules apply:

1. all required columns (see above) should be available;
2. the date format should be valid, i.e. preferably YYYY-mm-dd (ISO). For convenience, the OSPAR-date format (dd/mm/YYYY) is currently also supported;
3. litter type names should be specified in the type file;
4. litter counts in the data file are natural numbers (ISO 80000-2). However, in some cases data files contain real numbers due to preprocessing. Think about normalizing survey lengths to a common length. Although litteR prefers natural numbers, real numbers are also allowed for convenience. In case non-natural numbers are found, litteR will give a warning but will continue the analysis.;
5. all records should be unique, duplicated records will be removed with a warning;
6. all cells should be filled with the appropriate data type (numbers, text or dates).
7. the data file should be a comma-separated values file (CSV), i.e., a text file where the columns are separated by commas (,) and not by spaces, semicolons (;) or tabs.

5.1 Report

litteR produces an HTML-report that can best be viewed with modern web browsers like Mozilla FireFox, Google Chrome, or Safari. These browsers are freely available from the internet.

The filename of each report starts with ‘litter-results’, followed by a timestamp: YYYYmmddTHHMMSS and the extension html. For example: litteR-results-20200602T141829.html

This section briefly describes each section in the HTML-report

5.2 Statistical summary file

In addition to a report, a CSV-file with descriptive statistics for each spatial code is produced. An example of such a table is given below. See Section descriptive statistics for more details.

5.3 Log-file

litteR’s log-file is very helpful to understand warnings and error messages. The log-file stores the description of all data analysis steps in chronological order. Part of a log-file is given below.

2020-06-02 14:18:29 [INFO] Starting a new litteR session
2020-06-02 14:18:29 [INFO] litteR version: 0.8.0
2020-06-02 14:18:29 [INFO] litteR release date: 2020-01-31
2020-06-02 14:18:29 [INFO] Reading settings file ‘settings.yaml’
2020-06-02 14:18:29 [INFO] Check optional settings...
2020-06-02 14:18:29 [INFO] Check existence of required settings...
2020-06-02 14:18:29 [INFO] All required settings are available
2020-06-02 14:18:29 [INFO] Checking settings 'date_min' and 'date_max'
2020-06-02 14:18:29 [INFO] Settings 'date_min' and 'date_max' are valid
2020-06-02 14:18:29 [INFO] Checking setting 'percentage_total_count'
2020-06-02 14:18:29 [INFO] Setting 'percentage_total_count' is valid
2020-06-02 14:18:29 [INFO] Checking setting 'figure_quality'
2020-06-02 14:18:29 [INFO] Setting 'figure_quality' is valid
2020-06-02 14:18:29 [INFO] Settings file has been read
2020-06-02 14:18:29 [INFO] Constructing filename for report
2020-06-02 14:18:29 [INFO] Filename ‘litteR-results-20200602T141829.html’ created
2020-06-02 14:18:29 [INFO] Construct filename for storing statistics
2020-06-02 14:18:29 [INFO] Filename ‘litteR-results-20200602T141829.csv’ created
2020-06-02 14:18:29 [INFO] Starting litter analysis
2020-06-02 14:18:29 [INFO] Checking parameters in settings file 

Each line contains a single log-event and always has the following format:

1. timestamp;
2. type of log event: INFO for informative messages, WARN for warnings, ERROR for errors;
3. a log message.