Assignment 5

S1 - 7.5 points

Basic requirements

Q1 - 1 point

Can you open the pdf and it’s not blank?

  • No
  • Yes

Q2 - 1 point

Is the report anonymous?

  • No
  • Yes

S2 - 42.5 points

Metropolis

Q3 - 1 point

Is the brief description of Metropolis algorithm included (and it’s not complete nonsense)? Provide also a brief comment on how clear you think that description is (and potentially mention errors if you see them).

  • No
  • Yes

Q4 - 1 point

In 1 a), is the implementation of the density_ratio function included?

  • No
  • Yes

Q5 - 1 point

In 1 b), is the implementation of the metropolis_bioassay function included?

  • No
  • Yes

Q6 - 1 point

2 a) Is the proposal/jumping distribution reported ?

  • No
  • Yes

Q7 - 1 point

2 b) Are the starting points or the mechanism how they are generated reported?

  • No
  • Yes

Q8 - 1 point

2 c) Is the number of draws per chain reported?

  • No
  • Yes

Q9 - 1 point

2 d) Is the warm-up length reported?

  • No
  • Yes

Q10 - 1 point

2 e) Is the number of chains reported?

  • No
  • Yes

Q11 - 1 point

2 f) and 2 g) Are line plots of the chains included? (Separate plots for alpha and beta)

  • No plots are included
  • Yes, but both plots are in a single figure, or the plots are scatter plots (scatter plots aren’t useful for visual convergence evaluation).
  • Yes, but only a plot for alpha or beta is included.
  • Yes, separate line plots for both alpha and beta are included.

Q12 - 1 point

Is there a discussion on the convergence of the chains?

  • No discussion on convergence.
  • Yes, but the discussion is not convincing.
  • Yes, discussed in the report.

Q13 - 1 point

Is it mentioned which implementation of Rhat is used ? (Possible answers mentioned in peergrade)

  • No
  • Yes

Q14 - 1 point

Is the brief description of Rhat included (and it’s not complete nonsense)? Provide also a brief comment on how clear you think that description is (and potentially mention errors if you see them).

Q15 - 1 point

Are the Rhat-values for alpha and beta reported?

  • No
  • Yes, but incorrectly computed.
  • Yes, but computed separately for each chain
  • Yes, but only for alpha or beta
  • Yes, single values both for alpha and beta

Q16 - 1 point

Is the interpretation of Rhat values correct (correct interpretation will be given in peergrade)?

  • No interpretation or discussion about the Rhat-values, or conclusions clearly wrong
  • Somewhat correct
  • Interpretation correct

Q17 - 1 point

Does the report contain a scatter plot of the draws of alpha and beta? Do the results look reasonable, that is, roughly like in the Figure below (figure attached in peergrade)?

  • No plot included
  • Plot included, but the results do not look like in the figure above
  • Plot included, and the results look roughly like in the figure above

S3 - 7.5 points

Overall quality of the report

Q18 - 1 point

Does the report follow the formatting instructions?

  • Not at all
  • Little
  • Mostly
  • Yes

Q19 -

In case the report doesn’t fully follow the formatting instructions, specify the formatting instruction that is not followed. If applicable, specify the page of the report, where this difference in formatting is visible.

Q20 -

Please provide also feedback on the presentation (e.g. text, layout, flow of the responses, figures, figure captions). Part of the course is practicing making data analysis reports. By providing feedback on the report presentation and other students can learn what they can improve or what they already did well. You should be able to provide constructive or positive feedback for all non-empty reports, even if there is nothing to say about the technical correctness of the answers. You can also provide feedback on code.