Project 4 KMA353 Data handling and Statistics 3 (2021)

Project 4
Effect of top carnivore declines on carcass discovery times in Tasmania
Due date: 10am Monday, May 3rd, 2021

Introduction Weight Weight of the pademelon carcass (kg).

Habitat The habitat where the carcass was placed: Wet =

This assignment involves analysing a data set from a recently
wet eucalypt/rainforest habitat, and Dry = dry euca-
published manuscript that was authored by University of Tas-
lypt/coastal scrub habitat.
mania researchers:
Disease The disease status of the site: Healthy, and
Cunningham CX, Johnson CN, Barmuta LA, Hollings T,
Diseased (these two levels are defined above).
Woehler EJ, Jones ME. (2018) Top carnivore decline has
cascading effects on scavengers and carrion persistence. Site Abbreviated name of the study site.
Proc. R. Soc. B, 285: 20181582.
This assignment focusses on identifying the factors that in-
Tasmania’s top carnivore, the Tasmanian devil (Sarcophilus
fluence carcass discovery time. Note that Cunningham et al.
harrisii), has suffered severe population declines due to devil
(2018) also investigated carcass persistence times. Your sta-
facial tumour disease (DFTD). The researchers conducted
tistical analysis will be very different to the one adopted by
a scavenging experiment to investigate the effects of Tas-
these authors.
manian devil population declines on community-wide carrion
consumption.

Tasmania was split into two regions based on the timing Part 1 [3 marks]
of DFTD arrival: a healthy region in the northwest of the
state, where DFTD had not caused population declines, and
Your first task is to produce an informative figure (or two if
a diseased region, where DFTD arrived 3 – 19 years prior
you like) of the data that clearly indicates if carcass discovery
to the study. Tasmanian pademelon (Thylogale billardierii)
time (irrespective of the species that discovered it) is related
carcasses were experimentally placed at 96 locations among
to whether or not the carcass was placed in a diseased or
twelve independent study sites; 5 sites were located in the
healthy site. This figure should also include information on
healthy region and 7 were in the diseased region. Remote
carcass weight and other potentially informative environmen-
cameras were then used to identify when scavengers were at
tal variables. Make sure that your figure is accompanied by
each carcass.
an informative figure legend. This legend should be written
The carcass data for this study can be found in the file: in the R Markdown text section that is immediately below
CarcassTas.csv. This file contains information taken from the displayed figure.
95 carcasses (a camera failed to operate on one of the car-
casses). The columns of the data file are:

DaysDis Number of days after placement it took any carni-
vore species to first discover the carcass.
DisSp Carnivore species that first discovered the carcass.
DisDev Whether or not a Tasmanian devil discovered the
carcass (0 = No, 1 = Yes).
Part 2 [2 marks]
Using the figure(s) created in Part 1 briefly describe the pat-
terns displayed (2–3 sentences). Your description should pro-
vide a preliminary conclusion regarding the apparent influence
of the disease status of a site on discovery time.

1
Project 4 KMA353 Data handling and Statistics 3 (2021)

Part 3 [6 marks] your findings (or you can refer to figures produced in earlier
Parts).
Perform a statistical analysis that allows you to draw a con-
clusion regarding the statistical significance of disease status
on carcass discovery time. Include enough comments in your Hints and important information
R code so that your methodology is clear. Add newlines where
necessary so that all of your code is displayed when converted There is no need to perform any data wrangling for this as-
to a PDF. signment beyond specifying which columns are factors.

It should be clear that the response variable is DaysDis. It is

Part 4 [3 marks] up to you to decide which environmental predictor variables
to include when fitting your models.
Produce a figure that gives you confidence that your final
fitted model has adequately described the observations. For Do not include random factors or AIC values in your
example, you could place predicted discovery times on the x- statistical analysis. Your analysis should be performed us-
axis and observed discovery times on the y-axis, and use the ing the glm function. Do not use the function glmer. For
color and shape options in ggplot to depict important pre- completeness you have been provided the name of the site
dictor variables. Make sure you include a figure legend below where the carcass was located (Site). A complete analysis
the figure as you did in Part 1. would incorporate this information in your fitted model; how-
ever, including Site is best dealt with using a random factor.
For this assignment you should not include the variable
Part 5 [2 marks] Site in your model fits.

Write a brief description of your statistical approach that Feel free to discuss ideas about the project with others, how-
would be appropriate for the Methods section of a report ever the writing up of the assignment must be your own
(3–5 sentences). work. Very similar chunks of writing observed across multiple
assignments will be considered as plagiarism.

Part 6 [4 marks] Try to submit to MyLO a PDF generated by knitting your R

Markdown document in RStudio; however, if you cannot gen-
Write a brief summary of your findings that would be appro- erate a PDF, then submit a working R Markdown document
priate for the Results section of a report (3–6 sentences). You instead. Or, you might be able to knit to a word document
can include a table or figure if you think it helps you explain and then convert the word document into a PDF.