This lesson is still being designed and assembled (Pre-Alpha version)

Data Carpentry for Camera Traps:

Lesson Authors: Eve Bohnett

The episodes in this lesson cover how to open, work with, and model camera trapping data in R. Additional topics include Whiskerbook for individual identification and Spatial Capture Recapture Modeling Data Preparation

Interested in teaching these materials? Please contact evebohnett@yahoo.com so that we can discuss a workshop. The workshop materials are available in video format.

Getting Started

Data Carpentry’s teaching is hands-on, so participants are encouraged to use their own computers to ensure the proper setup of tools for an efficient workflow. To most effectively use these materials, please make sure to download the data and install everything before working through this lesson.

To get started, follow the directions in the Setup tab to get access to the required software and data for this workshop.

Data

The data and lessons in this workshop were originally collected by WCS Afghanistan for a field project located inthe Wakhan Corridor. for snow leopard detections: There is one data set included, which are available on figshare that is shared by request

  • Wakhan Corridor Snow Leopard Data () under a CC-BY-04 license. You can download all of the data used in this workshop by clicking Clicking the download link will download all of the files as a single compressed (.zip) file. To expand this file, double click the folder icon in your file navigator application (for Macs, this is the Finder application).

These data files represent teaching version of the data, with sufficient complexity to teach many aspects of data analysis and camera trapping, without providing such a large dataset that the processing takes a long time.

Dataset File name Description
Camera trap images 2012_CTdata.zip Raw camera trap data for 294 images of a subset of data
Camera Trap Metadata Metadata_CT_2012.csv Metadata that accompanys the camera trap images only
Whiskerbook export Whiskerbook_export.csv A subset of raw data downloaded from the Wildbook interface after the data have been individually identified and labeled by side (left, right, back, front) and quality (high, medium, and low)
Camera Trap Metadata Metadata_CT_2012_2.csv Metadata that accompanys the Whiskerbook export file
Geospatial Data Files GeospatialData.zip Rasters including elevation, roughness, and topographical position index, and the shapefile of the park boundary for the study area
Wildbook Template WildbookStandardFormat.csv and .xlsx Whiskerbook template file

Schedule

Setup Download files required for the lesson
00:00 1. Organizing Camera Trap Data How can we use program R and package camTrapR to organize camera trap data?
01:30 2. Organizing Whiskerbook How can we properly organize the data for batch import into Whiskerbook?
03:00 3. Wildbook Data Portal Tutorial How do I bulk import data into the interface?
How can I run hotspotter on my images?
How do I use the visual matcher?
How can I report an encounter?
04:30 4. Whiskerbook Post-Export How to manipulate data for descriptive information
How can we organize data using dplyr?
How can we organize data for input into oSCR?
06:00 5. Whiskerbook Data Manipulation How to manipulate data for descriptive information
07:30 6. Spatial-Capture Recapture Data Preparation How to setup single 3 month season oSCR data?
How to setup our oSCR data that exclude areas of high elevation?
What is a buffer mask and how to parameterize it?
09:00 7. Spatial-Capture Recapture Modeling How to setup and run oSCR models?
How to interpret the model outputs?
10:30 Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.