Data Management using NEON Small Mammal Data

Authors: 
Jim McNeil, Megan A. Jones

Teaching Module Overview

Undergraduate STEM students are graduating into professions that require them to manage and work with data at many points of a data management life cycle. Within ecology, students are presented not only with many opportunities to collect data themselves, but increasingly to access and use public data collected by others. This activity introduces the basic concept of data management from the field through to data analysis. The accompanying presentation materials mention the importance of considering long-term data storage and data analysis using public data.

This data set is a subset of small mammal trapping data from the National Ecological Observatory Network (NEON). The accompanying activity introduces students to proper data management practices including how data moves from collection to analysis. Students perform basic spreadsheet tasks to complete a Lincoln-Peterson mark-recapture calculation to estimate population size for a species of small mammal. Pairs of students will work on different sections of the datasets allowing for comparison between seasons or, if instructors download additional data, between sites and years. Data from six months at NEON’s Smithsonian Conservation Biology Institute (SCBI) field site are included in the materials download. Data from other years or locations can be downloaded directly from the NEON data portal to tailor the activity to a specific location or ecological topic.

Learning objectives are achieved through a variety of tactics. By the end of this activity, students will be able to:

  • explain the importance of data management in the scientific process. This is accomplished through discussion with faculty/class. Presentation slides are provided to guide this discussion.
  • identify elements of a useful, organized data sheet. This is accomplished through inspection of the provided NEON data sheet and how the different data collected are entered into the data collection sheet.
  • create a spreadsheet data table for transcription of field collected data. Students will accomplish this by creating and revising a spreadsheet data table and by comparing their version to the provided standardized spreadsheet data table. Faculty are provided with the example Excel workbook and presentation slides to facilitate this learning.
  • explain how NEON small mammal data are collected and understand the format that the data are provided.  To accomplish this students will read through the provided data collection protocol, view the .csv file containing NEON small mammal data, and view the variables data file to understand what data are contained in the data files.  The NEON small mammal data set, protocols, and metadata are included.
  • manipulate data in a spreadsheet program (example provided is Microsoft Excel). An example workbook and student handout are provided to show the steps.  
  • calculate plot-level species population abundance using the Lincoln-Peterson Mark-Recapture model.  Presentation slides are provided to introduce the model, and an example workbook and student instructions are provided to show the analysis steps.   
  • interpret results in plot level species abundance based on temporal variation, geographic locations, or by species. Faculty are provided with notes to help guide this discussion.   

This activity was developed while the NEON project was still in construction. There may be future changes to the format of collected and downloaded data. If using data directly from the NEON Data Portal instead of using the data sets accompanying this activity, we recommend testing out the data each year prior to implementing this activity in the classroom.

This module was originally taught starting with a field component where students accompanied NEON technicians during the small mammal trapping. The rest of the activity was implemented in a classroom with students using personal computers. As a field component is not a possibility for most courses, the initial part of the activity has been modified to include optional videos that instructors can use to show how small mammal trapping is conducted. Instructors are also encouraged to bring small mammal traps and small mammal specimens into the classroom when available. Students will need access to computer to complete this activity, however, we recommend they complete the activity in pairs.  This could be presented in a computer lab or in a classroom where student have access to personal computers. 

Crosslistings

This teaching module was originally published as Jim McNeil and Megan A. Jones. April 2018, posting date. Data Management using National Ecological Observatory Network’s (NEON) Small Mammal Data with Accompanying Lesson on Mark Recapture Analysis. Teaching Issues and Experiments in Ecology, Vol. 13: Practice #9 [online]. http://tiee.esa.org/vol/v13/issues/data_sets/mcneil/abstract.html

This teaching module, along with modifications of it by other faculty, can also be found on QUBESHub: Data Management using National Ecological Observatory Network's (NEON) Small Mammal Data with Accompanying Lesson on Mark Recapture Analysis.


Estimated Duration: 50 minutes

Themes: Data Management, Organismal Data

Audience: Undergraduate courses

Class size: Any (adapt the Q&A/Discussion questions to small group discussions or instructor-led introductions as needed)

Technology Needed

  • Instructor:
    • Internet access: if presenting, live from the website or accessing videos.
    • Computer & projector: if presenting, live from the website or accessing videos.
    • Optional: audio capabilities for videos
  • Student:
    • Computer with a spreadsheet program (Excel, Google Sheets)
    • Internet access for downloading data sets (or have them pre-downloaded)

Materials Needed

  • Instructor:
    • Optional: small mammal specimen/small mammal trapping equipment
  • Student:
    • Handout with instructions & questions

Learning Objectives

This lesson introduces the basic concept of data management from the field through to data analysis while teaching students about a core ecological field data practice of small mammal trapping. 

Science Content Objectives

After the lesson, students will be able to: 

  • Explain a basic process of data management from collection through analysis and archiving
  • Calculate population size estimates using the Lincoln-Peterson Method

Data Skills Objectives

After the lesson, students will be able to: 

  • Create a well layed out spreadsheet
  • Describe data management practices for 

Components

All Teaching Module components are available for download under the Detailed Lesson Plan tab in the sidebar menu.  

The Data Sets

The National Ecological Observatory Network is a program sponsored by the National Science Foundation and operated under cooperative agreement by Battelle Memorial Institute. This material is based in part upon work supported by the National Science Foundation through the NEON Program. The associated datasets are posted for educational purposes only. Data for research purposes should be obtained directly from the National Ecological Observatory Network.

Data Citation: National Ecological Observatory Network. 2017. Data Product: NEON.DP1.10072.001. Provisional data downloaded from http://data.neonscience.org. Battelle, Boulder, CO, USA

Instructional Materials

The materials for this lesson are presented as both a single webpage with the primary content and as downloadable materials that can be used in the classroom. 


Use of NEON Teaching Modules 

All lessons developed for the National Ecological Observatory Network data are open-access (CC-BY) and designed as a resource for the greater community. General feedback on the lesson is welcomed in the comments section on each page. If you develop additional materials related to or supporting this lesson, and are willing to share them, we provide the opportunity for you 

to share them with other instructors. Please contact NEON Data Skills or, if familiar with GitHub, submit an issue or pull request with new materials in the NEON Data Skills repo (tutorials are on master branch). All materials will be reviewed by staff prior to inclusion in or linking from the NEON Data Skills materials. 


This teaching module has had several revisions.  To preview all versions by McNeil and Jones and to see adaptations by other faculty, please view the teaching module posted on QUBESHub (no log in needed).  Version 2 of this teaching module was also published in Teaching Issues and Experiments in Ecology and can be viewed there — McNeil and Jones 2018.  The materials from version 1 are available for download below.  Version 1 and 2 have minor changes to the faculty and student instruction text but not substantial changes to the activity. 

Activity Data Sets

The following datasets are posted for educational purposes only. Data for research purposes should be obtained directly from the National Ecological Observatory Network (www.neonscience.org).

Data Citation: National Ecological Observatory Network. 2017. Data Product: NEON.DP1.10072.001. Provisional data downloaded from  NEON Data Portal . Battelle, Boulder, CO, USA

  • NEON.D02.SCBI.DP1.10072.001.mam_pertrapnight.072014to052015.csv – Small mammal trapping data from NEON’s Smithsonian Conservation Biology Institute (SCBI) field site for July 2014 to May 2015 (seven months total as no trapping was conducted November to March). This .csv contains combined months from the combined small mammal trapping data from September and October 2014. This data are a combined table based on the individual site-month tables available from the NEON Data Portal. This file should be used with a group of student to implement their skills and allow different partners to estimate abundance for different plots and seasons to allow for larger patterns to be examined in the classroom.
  • NEON.D02.SCBI.DP1.10072.001_variables.csv – Metadata file for NEON small mammal data (DP1.10072.001) describing the variable names.
  • NEON.DP1.10072.001_readme.txt – Metadata file for the NEON small mammal data (DP1.1072.001) providing more information on the data product.
  • NEON.D02.SCBI.DP1.10072.001.20140917-20140924.xml – Example XML file for the September 2014 data that is provided with this lesson. 
  • Abbreviated NEON Small Mammal Trapping Protocols.pdf – This document is adapted from NEON Document NEON.DOC.000481 in May 2017. It describes the layout of NEON small mammal sampling grids and is only intended for use with the educational teaching module outlined in this article.
  • NEONSmallMammal_SCBI_BlankDataSheet.pdf – This document shows how a NEON field data sheet is formatted and is provided to show a potential format for recording this type of data. This document is limited to D02 data sheets, all NEON Small Mammal trapping data sheet can be found in document NEON.DOC.001585 Datasheets for TOS Protocol and Procedure: Small Mammal Sampling

Download a .zip file (759 KB) with all the teaching data files below. 

Activity Workbooks & Materials

The following materials are provided to complete the teaching module. 

  • NEONTeachingModule_Teacher_DataManagementWithNEONSmallMammalDataAndMarkRecapture.doc – The document provides instructors with additional information for presenting the materials. 
  • NEONTeachingModule_Student_DataManagementWithNEONSmallMammalDataAndMarkRecapture.doc – This document can be used as a student handout (instructors much make a few changes to decide on preferred instructions) to guide the work through the data activity. 
  • NEONSmallMammalDataAbundanceWorkbook.xlsx – This workbook contains only the September and October data from the NEON.D02.SCBI.DP1.10072.001.mam_pertrapnight.072014to052015.csv file. Each worksheet lays out one step needed to conduct that Lincoln-Peterson species population abundance analysis.
  • NEONTeachingModule_DataManagement_Slides.ppt –  This presentation accompanies the student activity and provides visuals to support the steps of the activity.

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