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ENVS222 assignment

创建日期：2024-07-29 15:29:37

所属分类：计算机computer science

标签： ENVS222

assignment

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ENVS222 assignment 1: root growthin
mustard seeds
You should produce a report of approximately 3 pages (including figures, but excluding your R code,
which should be added as an appendix as described below).
Background
Wewant to know whether the roots of germinating mustard seeds typically grow longer in the dark
or in the light, and whether any difference is consistent across replication attempts. We will use data
collected this year and from the 2011/12 academic year, when the experiment was set up in a
similar way.
Data
The tab-separated text file rootlengths.txt (available on the Assignment 1 page on Canvas)

contains the data. Download this file. Each row contains the data from a single dish in a single year.

There are three variables: treatment (either light or dark), meanrootlengthmm (the

mean length of the roots produced by the 10 seeds in a dish, in millimetres) and year (the year in
which the experiment was done: either 2011/12 or 2022/23). Note that mean root length was
calculated from all seeds in each dish, including those that did not germinate (which were counted
as having root length 0 mm).
2Analysis and report
You should use R for analysis. Everything needed has been covered in the workshops from weeks 1
to 4, and you are welcome to base your R script on scripts that were provided for these workshops.
Your report should be written up individually. Because you have not yet had much practice at data
analysis, we have broken down the report into sections, and explained what we want in each.
Sections 1-5 contain material that would typically appear in the methods of a scientific paper,
sections 6-9 contain results material. Modern scientific papers will often include code in an appendix
or supporting information section, as in section 10. Within each section, where writing is involved
you should write proper sentences rather than bullet points. You do not need to write anything that
is not asked for below. The report will be marked out of 40, with marks as listed below. See the mark
scheme on Canvas for more information about how the marks are broken down within each step.
1. Explain briefly what we did to avoid bias in the design of the experiment, and why this is
important (2 marks).
2. Explain briefly why it is appropriate to work with mean root lengths from each dish rather
than the 10 individual root length measurements from the dish. You should use appropriate
terminology, for which you may find it helpful to refer to the external reading from week 4
(2 marks).
3. Based on what you saw in your own dishes, what difference might it have made if we had
included only those seeds that germinated when calculating mean root length for each dish?
How might we decide which approach is most appropriate? (3marks).
4. Suggest a statistical test to investigate the scientific hypothesis that mustard seed roots will
typically grow longer in the dark than in the light, and to investigate whether this difference
is consistent across years, with a brief (one-sentence) justification (3marks).
5. List the assumptions of this test. Check these assumptions, explain how you checked, and
what the outcome was. If necessary, choose and carry out an appropriate transformation to
address any problems. Remember that the importance of some assumptions may change as
sample size increases. Also note that violations of assumptions should suggest cautious
interpretation, which will matter less if there is very strong evidence for an effect (8marks).
6. Provide a graphical comparison of the distributions of mean root lengths (transformed as
appropriate) in dark and light dishes in each year, including appropriate axis labels, with
units where appropriate, and an informative, numbered legend underneath (4marks).
7. Carry out the test and provide a table that summarizes the results. Add a numbered legend
above the table. Remember to use an appropriate level of precision and (if relevant) choose
an appropriate way to express very small numbers (5 marks).
8. Produce an interaction plot showing how the predicted mean root length (transformed as
appropriate) depends on year and treatment. Include this figure in your report, with a
numbered legend below (4 marks).
9. Write two to three sentences summarizing what we can say about the difference in mean
root length (transformed as appropriate) between dark and light treatments, whether mean
root length depends on year, and whether the effect of treatment depends on year,
referring by number to the table from step 7 and the figures from steps 6 and 8 (8marks).
10. Include your R script as an appendix. This means I can see exactly what you did, and in the
steps above, may allow me to award partial marks even if you did not get exactly the right
answer (1 mark).

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