BIO2POS: DA Computer Lab 1 Solutions
Topic 1: Descriptive Statistics and Graphs in jamovi
These are the solutions for DA Computer Lab 1.
Please make sure to go over these after the lab session, and finish off any questions you may have missed during the lab.
1 jamovi š±
No answer required.
2 Red Crab Data š±
No answer required.
In this question we assessed data on red crabs from Christmas island (Green, 1997).
The red crab data set contains recorded values for variables including:
- CW: The carapace width (mm)
- LEG: The leg length (mm)
- CLAW: Claw length (mm)
- WEIGHT: Weight (grams)
- SEX: The crabās sex (M/F)
2.1
This red crab data is available in this weekās tile on the LMS, in the file crab_data.omv.
2.2
No answer required.
2.3
No answer required.
2.4
- CW: The carapace width (mm) is a continuous numerical variable
- LEG: The leg length (mm) is a continuous numerical variable
- CLAW: Claw length (mm) is a continuous numerical variable
- WEIGHT: Weight (grams) is a continuous numerical variable
- SEX: The crabās sex (M/F) is a nominal categorical variable
2.5 Descriptives
No answer required.
2.5.1
The CW mean, median, and standard deviation are 70.757, 73.050 and 23.404 mm respectively.
2.5.2
Example output is shown below:
2.5.3
Example output is shown below:
2.5.4
We note that the male crabs have a larger mean CW value of 73.872 mm compared to 67.967 mm for female crabs.
2.6 Statistics
No answer required.
2.6.1
Example output is shown below:
2.6.2
The 95% confidence interval for the CW of male crabs is \((69.391, 78.353)\).
The 95% confidence interval for the CW of female crabs is \((64.539, 71.395)\)
If we compare these intervals, we notice that while the male crabs typically have a larger CW, the two confidence intervals overlap. Therefore we do not have sufficient evidence to conclude that the average carapace width is different between male and female red crabs.
2.7 Plots
No answer required.
2.7.1
The distribution of the data appears to be reasonably symmetric and bell-shaped, although we observe more CW observations of approximately 25-30mm than we might expect, if the data were normally distributed.
2.7.2
2.7.3
2.7.4
2.8
No answer required.
2.8.1
No answer required.
2.9
Splitting the data by SEX has been somewhat useful as it has highlighted that the CW distributions differ slightly between male and female crabs. For example, the female crabs have a shorter range of observed CW values.
3 Shore Crab Data š±
No answer required.
In this question we assessed data onshore crabs from the southwest UK (Stevens et al., 2014).
The shore crab data set contains recorded values for variables including:
- Site: The location the recording was made
- Maturity: The maturity of the crab (i.e.Ā adult, not adult)
- Carapace width: The carapace width of the crab
3.1
This shore crab data is available in this weekās tile on the LMS, in the file shore_crabs.omv.
3.2
No answer required.
3.2.1
The carapace width of the shore crabs appears to be clearly right-skewed. This suggests we should use the median rather than the mean when discussing ātypicalā carapace width values.
3.2.2
Shore crabs at the Godrevy site exhibit the greatest variability in carapace width, while shore crabs at St Mawes exhibit the least variability in carapace width. Shore crabs at the Falmouth and Helford sites appear to have similar carapace width spreads.
All four sites have large outliers skewing the distributions of carapace width to the right.
3.2.3
As we would expect, the mature crabs have much larger carapace widths. Interestingly, the immature crabsā carapace width distributions appear to be approximately symmetrical across all four sites, whereas the distributions for the mature crabs are all clearly skewed.
3.2.4
3.2.5
Only the alternate bar plot is shown here, for conciseness.
3.2.6
The summary below is an example only, and focuses on the differences between immature and mature crabs.
A data set on \(N=677\) shore crabs in the southwest of the UK was assessed, and descriptive statistics were computed regarding the carapace widths of the crabs. We split crabs into two categories, with each crab classified as being either immature (489 crabs) or mature (188 crabs).
Immature crabs had a mean and median carapace width of 14.659 and 14.852 mm respectively. Mature crabs had much larger carapace widths typically, with mean and median values of 35.995 and 32.545 mm respectively. Mature crabs also exhibited greater variability in carapace width, with a standard deviation of 12.42 mm, compared to 5.457 mm for immature crabs.
4 Pea Plant Data š³
No answer required.
Background Information
Figure 4.1 below contains pea plant seedling height recordings, across three groups:
- C: a control group, were sprayed with water
- TA: a treatment group, were sprayed with a 25mg/L solution of gibberellic acid (GA)
- TB: a treatment group, were sprayed with a 50mg/L solution of GA
Figure 4.1: Pea Plant Raw Data
4.1
No answer required.
4.2
No answer required.
4.3
No answer required.
4.3.1
Note that depending on which messy observations you chose to include/not include, the results shown below may differ slightly to your own.
4.3.2
There were 32.9% of seedlings in the control group, 37.6% in the treatment A group, and 29.4% in the treatment B group.
4.3.3
4.3.4
The overall sample size for this data is 85.
4.3.5
The mean seedling height overall is 296.618 mm.
The mean seedling heights for each treatment group are:
- C: 179.161 mm
- TA: 358.313 mm
- TB: 349.200 mm
The TA treatment group has the highest mean height.
4.3.6
The 95% confidence intervals for the true mean heights of the seedlings exposed to the three treatment types are:
- C: (162.948, 195.373)
- TA: (328.460, 388.165)
- TB: (321.586, 376.814)
These intervals suggest we are unlikely to observe the true mean heights of seedlings exposed to these treatments being outside these ranges.
Since there is some overlap between the TA and TB intervals, this suggests that there may be no difference between these treatmentsā effects, on average. However, the 95% confidence interval for the control group does not overlap the other intervals, suggesting that the treatments do lead to faster growth of seedlings, on average.
4.3.7
No answer required.
4.3.8
No answer required.
5 Lyrebird Paper Review š³
No answer required.
This question discussed the paper by Nugent et al.Ā (2014) on the interactions between lyrebirds and fire in south-eastern Australia.
5.1
No answer required.
5.1.1
No answer required.
You should be able to identify the mean and standard deviation (sd) values in the tables. Note that some tables list standard error (s.e.) instead of standard deviation.
References
Green, P. T. (1997). Red crabs in rain forest on Christmas Island, Indian Ocean: activity patterns, density and biomass. Journal of Tropical Ecology, 13(1), 17-38
Nugent, D. T., Leonard, S. W. J. and Clarke, M. F. (2014). Interactions between the superb lyrebird (Menura novaehollandiae) and fire in south-eastern Australia. Wildlife Research, 41(3), 203-211
Stevens, M, Lown, A. E. and Wood, L. E. (2014). Camouflage and Individual Variation in Shore Crabs (Carcinus maenas) from Different Habitats. PLOS ONE 9(12): e115586. https://doi.org/10.1371/journal.pone.0115586
These notes have been prepared by Rupert Kuveke. The copyright for the material in these notes resides with the author named above, with the Department of Mathematical and Physical Sciences and with the Department of Environment and Genetics and with La Trobe University. Copyright in this work is vested in La Trobe University including all La Trobe University branding and naming. Unless otherwise stated, material within this work is licensed under a Creative Commons Attribution-Non Commercial-Non Derivatives License BY-NC-ND.