Homework 12

Due: 2022-12-04, 11:59pm

All homework must be submitted via Blackboard. Your answers must be in a MS Word (DOCX) or PDF format. Your submitted document should have sections corresponding to those in this homework.

Please make sure that you have watched the videos and have done the readings. Everyone should do this independently; you can discuss the process, but the answers are expected to be different.

Include graphs as images in your document. Make sure you comment on the Stata output, figures and tables. Include all code used to complete the homework so that your results can be reproduced (you may edit out irrelevant portions). Use the lecture notes as a guide.

1. Frog abnormalities data (100%)

We are going to use the frog abnormalities dataset collected by Reeves et. al. (2010). We are going to use a subset of the data they collected which gives details of over 9000 frogs sampled in Alaska by the researchers. Their objective was to study potentical causes of amphibian abnormalities. See the file FrogAbnormalities.csv More details about the data are in the file README.

We will focus on just four variables, the snout to vent length (SVL), the Gosner (developmental) stage of the animal (GOSNER_STAGE), whether or not the frog had an abnormality (ABNORMAL), and whether or not the animal showed signs of a protozoan infection (Perkensus).

Our main goal is to examine if the snout to vent length is associated with abnormalities, accounting for the Gosner developmental stage and possible protozoan infection.

  • Perform a descriptive analysis of the four variables of interest. Calculate appropriate summary statistics for each variable.
  • Are there any missing data, if so how many and for which variables?
  • Use graphical summaries to examine association of the snout to vent length with the other variables. Which variable appears to show strongest association?
  • Use linear regression to examine association between snout to vent length and Gosner stage. What is the meaning of the slope and intercept of the line fitted?
  • How much of the variation in snout to vent length is explained by variation in Gosner stage?
  • Use a t-test comparing snout to vent length in animals with and without an abnormality.
  • Use linear regression of to explain snout to vent length using whether or not a frog had an abnormality as a predictor. Compare the results of linear regression to the t-test.
  • Build a linear regression model for snout to vent length and whether or not the animal was abnormal adjusting for Gosner stage and protozoan infection status. Interpret the output of the regression model.
  • Check model fit using a residual vs fitted plot. Does it look satisfactory?
  • What is your overall conclusion regarding the relationship between snout to vent length and frog abnormalities?

2. Acknowledgements

Please acknowledge individuals who helped you or resources thay were helpful in completing the homework.