Earthcape in the field with metapopulation survey

(A guest post by Metapopulation Research Centre @metapopulation about their use of EarthCape)image description

Introduction

The core of our research has been the long-term study of the Glanville fritillary butterfly (Melitaea cinxia) that has been conducted since 1991 in a large network of 4,000 habitat patches (dry meadows) within a study area of 50 by 70 km in the Åland Islands in Finland. Since 2010, we have implemented EarthCape as our database management system, into which we have integrated data collection in the field as well as subsequent tasks related to the management of samples collected during the survey and various tasks related to data analysis. EarthCape is also used to streamline the planning of the field surveys, recording measurements in the laboratory based on material collected from the field work as well as in data exploration and visualization. The web version of the program is used to provide an easy access to the data for our researchers after it has been imported into a main database.

Current EarthCape setup in our research group. All the data is stored in the main database and copied, usually only a part of the data, to local / temporary databases (black arrows) when needed for e.g. in the field experiments. New data is generated in the field and in the laboratory and sometimes also from other sources and copied into the main database (grey arrows).

workflow nettisivulle

Field survey

Recently our field survey has employed up to 70 field assistants and the rearing facilities up to 15 assistants simultaneously. The number of computers and thus local database copies has therefore been considerable and demand for program capable of keeping record of data and being able to convey it from facility to another has been required. Flexibility of program interface and data types that can be stored in the program have further encouraged other teams in our research group to start utilizing the program in their own experiments. These experiments include other field surveys in Åland islands, elsewhere in Finland and abroad. The best thing is that customizing the user interface can be done per project by ourselves, it only requires a minimum amount of practice and can greatly facilitate the workflow in the field.

 

Customized program for the field

Before each field survey, we extract data from the main database to plan the amount of resources needed for the field work. Map files and current habitat patch outlines are transferred to field computers with a customized copy of the database. During the years we have successfully used several types and models of netbook, notebook and tablet computers with EarthCape. To speeden up data recording in the field, templates for the samples are pregenerated and barcode stickers printed out to be used to mark the samples collected in the field. The same physical stickers move further down the pipeline with samples in the laboratory.

Patch outlines are stored as WKT text and visualized in the GIS editor

map_wkt

In our system each habitat patch is stored as a geographic object in EarthCape. Patch geometry is stored in OGC WKT format as polygons and is fully editable using the built-in GIS editor (see figure above). Thus our field assistants (FA) are able to make corrections to patch outlines in the field if necessary.

The default views of localities, units and map in EarthCape

Locality_default units_default map_default

For the purposes of the survey, the EarthCape interface is modified using built-in utilities to better fit the workflow of field assistants. By carefully planning the view, even the rather small netbook computer screen can be used to show all the necessary information without making it too crowded for efficient use in the field. Custom parameters (measurements or ”fields”) are defined by the survey coordinator during the construction of the field copy of the database. These allow introduction of per project based parameters without changing the database structure, thus keeping all projects compatible with each other and stored in the same database.

Modified view of localities, units and map used in the field survey. The most significant modifications include the combination of three different data types into a single view, adding custom parameters for the survey, adding tools for the GIS editor including a GPS option (build in) and overall rearranging the elements for the easy access for the current needs.

locality_modified

We can also have all other patch-specific information available, such as the patch categorizations, records of previous locations of larval groups and past information on host plants for use by field assistants or by the survey coordinator if needed e.g. in solving some more complex (data integrity or mistyped data) problems that inevitably arise in large scale field survey. That information can either be put under additional tabs (out of the immediate view) or hidden from the field assistants by modifying the user access rights in the program and allowing its use for the survey coordinator only.

The data from each computer into a single database (from several database engine possibilities we have used Microsoft SQL Server and SQLite) every evening to construct preliminary pivot tables that enable spotting missing data, obvious outliers, areas still to be surveyed, and so forth. The ability to see and explore the data on the topographic map or preview in Google Earth makes a big difference when cleaning up the data. Data are synchronized using EarthCape import/export mechanism, which also serves a backup purpose, but could be also done by utilizing the current SQL provider tools.

 

Further down the line (laboratory)

After the field work is done and data copied into a single database it is copied into our main database and also relayed to laboratory facilities along with the samples collected (up to 30 000 samples / year). The laboratory uses EarthCape program that is customized for their use and enter additional data for the samples when it is accumulated.

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