Code, data, and exploration on GitHub.
Code, data, and exploration on GitHub.
Seven magical steps into a dataframe.
By Nargol Ghazian
This is a summary of the protocol I have been using for that past few months to process all the amazing camera trap photos from the Mojave National Preserve and the Carrizo National Monument. After reading a few papers on cam trap processing and exploring the CamtrapR package, the best approach would be to create your datasets manually as no other program is able to automatically detect animals for you. This method also ensures that you obtain the best dataset for the statistical analysis you wish to perform. This seven step guide should give you a quick rundown on how to get started with processing and maintaining a good workflow.
|1.Year||We are working on the 2017 images|
|2.Region||MNP is Mojave and CNM is Carrizo|
|3.Site||Mojave or Carrizo|
|4.Calendar date||The date the picture was taken in dd-mm-yr. I like to do the pictures belonging to the same date for each photo rep in order. If the date is wrong, don’t worry too much, just do it all as one for the last date of the particular week you are working on|
|5.Microsite||Carrizo is shrub or open, 3 weeks for each. Mojave is Buckhorn or Larea, also 3 weeks for each.|
|6.Day||This goes in a 1,2,3..n order|
|7.Rep||This refers to the camera trap station. There are 10 stations per microsite. For example you might have four pictures for the same day in station #2 of open, so you would write 2 four times: 2,2,2,2 each corresponding to an image|
|8.Photo Rep||A continuous number starting at 1 and continuing until you’ve finished processing all your pictures for the particular site|
|9.Animal||The animal in a hit photo. The most common are rat, rabbit, squirrel, fox, lizard and sometimes bird. There are times where you might have to guess. If it’s really hard then write ‘unidentifiable’. If it’s a false hit leave it blank.|
|10.Animal. Capture||binary 0 = false hit, 1 = animal present|
|11.Time block||Look at the timestamp. Is the photo taken at night, noon, afternoon or in the morning. If the timestamp is wrong, guess based on the darkness or lightness.|
|12.Night. Day||Based on whether it’s dark or light.|
|13.Actual time||Actual time written on the photo. Let’s hope it’s the correct timestamp J|
|14.Observations||If you see absolutely anything interesting in the photo, note it! Otherwise leave this column blank. I usually write ‘x2’ or ‘x3’ if there is more than one animal in the photo. Sometimes I write ‘eyes visible’ if it’s dark and you can only tell the presence of the animal from its shining eyes (rats usually)|
|15.Temp of positive||This is noted on the picture in Fahrenheit or Celsius. Whatever unit is shown, note it in your meta-data. If you’ve been working with one unit, and a certain photo rep has a different one, just use a converter to convert to the units you’ve been using for that particular photo rep.|
|16.Week||This is either 1, 2 or 3 since there are only 3 weeks per microsite. This column is super important because sometimes the datestamps are wrong but at least the week of sampling is correct|
*Note: The only time we actually fill in anything for columns 9 and 11-15 is when we have a “hit” and there is an actual animal.
The first micronet study is now complete. Cuyama Valley was instrumented using Onset micro-stations with temperature and soil moisture sensors for two full seasons. I made some very important discoveries in wrapping it up this autumn.
Here is hoping the data recovered are just as fascinating. Honestly, I am tempted to do a wire-addition experiment. Observation suggests that there is a very real magnet effect of wires.
Full details are provided here.
The purpose of this workshop is to provide tools for a new/novice analyst to more effectively and efficiently analyse their data in R. This hands-on workshop will introduce the basic concepts of R and use of generalized linear models in R to describe patterns. Participants will be encouraged to help one another and to apply what they have learned to their own problems.
Who: The course is aimed at R beginners and novice to intermediate analysts. You do not need to have any previous knowledge of the tools that will be presented at the workshop.
Where: 88 Pond Road, York University. Room 2114 DB (TEL). Google maps
Requirements: Participants should bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) with administrative privileges. If you want to work along during tutorial, you must have R studio installed on your own computer. However, you are still welcome to attend because all examples will be presented via a projector in the classroom. Coffees and cookies provided for free.