2023-11-27 PSYC3900 Lab Exam 2

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Memorial University of Newfoundland *

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3900

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Psychology

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Dec 6, 2023

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PSYC3900 Bitton Fall 2023 Lab Exam 2 PSYC3900 Lab Exam 2 Fall 2023 - Memorial University of Newfoundland Total out of 50 This is a ‘take home exam’. You have ~28 hours to complete the assignment with three of those hours overlapping with your regular lab section, and one hour overlapping with regular class time. The exam was released at 900 on Wednesday November 29 th ; you have until 11:59 a.m. (noon) on Thursday November 30 th to submit your work. Through this process, you can ask questions at pbitton@mun.ca . Realize that if you contact me in the middle of the night I will not answer immediately. You can look at your notes and other resources but I ask you not to contact your peers. Note: Each student is receiving a completely different dataset for each Part. These datasets have known properties from which we can extract exact test values, and each dataset will have different answers and different analytical pathways (e.g., different assumptions violated ). As such, you cannot rely on someone else’s pathway, never mind their specific answers. To complete this exam, you need 2 documents: A This questionnaire (so far so good!), B A single ‘csv’ file with the complete data. This csv file was included in the email sent to you. PLEASE CONFIRM THAT YOU HAVE THE ‘CSV’ FILE WITH YOUR NAME BEFORE STARTING . The value of answers is indicated at the end of each question. I provided a decision tree at the end of the document to guide you through the assumptions I require you to verify before running a test, and the pathway if assumptions are violated. You will not need to manipulate data in Excel, but you may need to modify variable information in jamovi (e.g., variable type, coding of levels). All statistical and assumption tests should use analyses under the ‘Regression’ tab in jamovi, no others (i.e., do not use the GAMLj tab). For clean figures, use Flexplot . Submit your answers to the following questions in a PDF document in the Brightspace folder called E xam 2’. Your file name should be informative , a n example would be ‘YYYY_MM_DD LastName StudentID PSYC3900 E xam 2’. Also, submit the omv file. Delay in submitting the exam will lead to a penalty of 10% for the first 2 hours and file submission will not be accepted after 1500 on Thursday. Online rooms will be open for questions on Wednesday between 1400 1500, and 1800 1900. I will also open a room on Thursday from 900-1015.
PSYC3900 Bitton Fall 2023 Lab Exam 2 The following is a fictional scenario. Names, characters, businesses, places, events, locales, and incidents are either the products of the author's imagination or used in a fictitious manner. Any resemblance to actual persons, living or dead, or actual events is purely coincidental. Do omega-3 fatty acids influence the cognitive development of young New Caledonian Crows? Background information For your honour’s thesis, you hit gold! You have been invited to travel to New Caledonia and study the local wild crows. These amazing birds have been shown to modify twigs and leaves to make tools, which they then use to extract insects from holes in tree trunks. These skills are socially passed on from parents to offspring making the New Caledonian Crow the only bird with evidence of cumulative cultural evolution in tool manufacturing (I told you this was gold!). Lately, because of human encroachment on their habitat, some of the crows have been visiting landfills. The consequence is that some of the crows are now consuming, and feeding their offspring, processed food that is high in saturated fats, rather than their regular diet of nuts and insects, which provide them with omega-3 fatty acids and no saturated fats. Omega-3 fatty acids have been shown to play a critical role in early brain development. Specifically, it is associated with neurogenesis and size of the forebrain in several species of mammals, including humans. In other animals such as rats (of course!), omega-3 fatty acids are correlated with cognitive abilities. The question you have been asked to address for your thesis is: ‘Does proximity and use of landfills influence brain development and cognitive abilities o f young New Caledonian crows?’ Experimental design Your research group has identified several nests across the island, all of which hold a single young crow. Each nest is found either in an urban area (coded as ‘0’), or a rural setting (coded as ‘1’). The distance of each nest to the nearest landfill was measured in kilometers using an accurate map and GPS locations of the nests and landfills. All nests are distant enough that pseudo-replication is not a problem. Since this is an established study site, all adults had been captured as young crows, and the nests are constantly monitored. Therefore, you also have data on the age of the mother (in years), and her recently measured cognitive abilities, on a continuous scale, based on observed tool use. For your thesis work, you visit each nest once when the young crow is around 50 days old (with some variance). During that visit you collect a blood sample from which omega-3 fatty acids are quantified (in μ g per liter), determine their ability to solve a simple puzzle box (fail coded as ‘0’, pass coded as ‘1’), and use a small portable x-ray machine to take pictures of the birds from which you determine brain volume in cm 3 (by imaging the brain case and extrapolating the cavity size).
PSYC3900 Bitton Fall 2023 Lab Exam 2 Statistical Analyses Q1 Before determining the impact of omega-3 levels on the cognitive abilities of young birds, you should confirm that their access to landfills indeed influences fatty acids level in their blood. Using the most complete model, determine if omega-3 fatty acids are influenced by the distance of nests from landfills, and their location (urban vs rural). A) Evaluate the assumptions you can with analyses under the ‘Regression’ tab in jamovi (no need to evaluate outliers for this question). If a statistical test for the assumption is available, reproduce the output AND report its result in a complete sentence. If only a figure can be produced to evaluate the assumption, reproduce that figure AND report its result in (a) complete sentence(s). B) Do not reduce the model, report the results from the omnibus test using (a) complete sentence(s). In this sentence, report the proportion of variance explained by the complete model, and include the test statistic (with appropriate degrees of freedom) and p-value for each term. Reproduce (copy/paste) your omnibus table. C) Produce the figure that best demonstrates the relationships between omega-3 fatty acids as a function of distance and location. D) What inferences can you make from your statistical results based on the trends observed in the figure? /14 Q2 Your next step is to investigate if various measures can predict if the young crows succeeded in solving the puzzle box. Specifically, you are interested in determining if the mother ’s age and cognitive abilities, in addition to the young crow’s age and omega -3 fatty acid blood levels can predict success at solving the puzzle box. You decide to use the appropriate test, without interactions. A) Before you look at your model, evaluate the relationships between the independent measures. Report the results in (a) full sentence(s) that includes the appropriate test statistics and p-values. Reproduce the appropriate table(s) of results and the associated figure(s). B) Build the model to predict puzzle box solving success, and test the assumptions you can (using only statistics) within the test menu. No need to evaluate outliers for this question. Report your evaluation of the assumptions in a complete sentence with appropriate test statistic(s). Reproduce the appropriate table(s). C) Reduce the model until only significant terms are included. Report the results using a complete sentence. In this sentence, report the proportion of variance explained by the final model, and include the test statistic(s) (with appropriate degrees of freedom) and p-value for each term. Reproduce the table with model fit and coefficients. D) Produce the figure that best demonstrates the relationships between the puzzle box solving success and the terms included in the final model. E) Discuss in a sentence or two how good the final model is at classifying (predicting) the puzzle solving abilities of the young crows. Reproduce the appropriate table(s). F) What kind of inferences regarding the impact of landfills on cognitive ability can you draw from these results? Discuss in one or two sentences. /22 Q3 Finally, you are interested in determining what influences the size of the young crow’s frontal cortex. As predictors, you are interested in the distance from a landfill, the location (rural or urban areas), the age of the young crow, and the blood concentration of omega-3 fatty acids. The model you are interested in testing does not include any interaction. A) Evaluate the assumptions you can with analyses under the ‘Regression’ tab in jamovi (no need to evaluate outliers for this question). If a statistical test for the assumption is available, reproduce the output AND report its result in a complete sentence. If only a figure can be produced to evaluate the assumption, reproduce that figure AND report its result in (a) complete sentence(s). B) Reduce the model until only significant terms are included, and
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PSYC3900 Bitton Fall 2023 Lab Exam 2 verify the assumptions again (no need to evaluate outliers for this question). If a statistical test for the assumption is available, reproduce the output AND report its result in a complete sentence. If only a figure can be produced to evaluate the assumption, reproduce that figure AND report its result in (a) complete sentence(s). If one of the assumptions is violated, explain in a sentence how you would fix it. C) If needed and possible within your current test menu, fix the violation of assumption. Report the results of the omnibus test using a complete sentence. In this sentence, report the proportion of variance explained by the complete model, and include the test statistic (with appropriate degrees of freedom) and p-value for each term. Reproduce the table with model fit and coefficient. /14 Decision tree For this exam 1) Correlations a. Linear relationship i. Use Spearman’s if monotonic b. Continuous traits i. Use Kendall if categorical ordinal 2) Logistic regression a. Multicollinearity i. Remove one of highly correlated trait if needed 3) Multiple regression a. Linear relationship between dependent and all independent b. Multicollinearity i. Remove one of highly correlated trait if needed c. Homogeneity of variance i. Violation would require Generalized linear model not covered in class Just indicate so and proceed as without assumptions d. Normality of residuals i. Violation would require Generalized linear model not covered in class Just indicate so and proceed as without assumptions