Important modifications to be applied to Workshop 9

[estebangongora]

Before developing and modifying this workshop, please read through the presenter and developer protocol carefully and refer back to it regularly as you work.

General issues to be addressed

Specific to adapting workshops to a remote framework:

• Fit this workshop to a 3-hour format. The duration of this workshop should be ~3 hours (including exercises and one or two breaks of 5 minutes; excluding longer breaks). To fit this format, please add, edit, or hide slides from existing workshops. You can begin by hiding repetitive examples, non-essential slides, or some of the additional advanced slides that are included at the end of some workshops. Some workshops will be more difficult to shorten than others, due to their subject matter. It is not a problem to let these workshops run slightly over 3 hours to guarantee accurate and complete information. (Use your judgment). DO NOT delete slides. Use the instruction: hidden_remote tag. See an example below:

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exclude: true

# Slide title: I love statistics!

### Content: Amazing!
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• Develop new or adapt current exercises to better suit the remote workshop format and the use of breakout rooms. Exercises should be informative and engaging. Remember to leave time for students to work through exercises and ask questions. Refer to these guidelines to find suggestions of exercises promoting active learning. You may use additional resources to create the exercises.

Specific to slide structure, grammar and style

• Ensure code is working correctly and that code matches workshop presentation. Continue to check this as you make changes.

• Proofread correcting spelling, grammar, or punctuation errors (for example, ).

• Look for and correct the content of slides that overflow the screen (for example, slides 56, 61, 69, 70, 75, 95).

• Look for and correct prose that mentions function names, object names, package names and code chunks that do not use backticks.

• Look for and correct unnecessary abbreviations (e.g. use do not instead of don’t).

• Correct unnecessary long sentences.

• Ensure that the slides are written in a consistent style, which helps with the flow of workshops and student understanding. This is especially important when working collaboratively with other developers.

• Include presenter notes to the slides you modify. You can write notes for yourself to read in the presenter mode (press the keyboard shortcut p). These notes are written under three question marks ???. See the example below:

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The content of this workshop is essential for your graduate studies.

???

Note: _The presenter should sing this slide to the participants_.
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Specific to the translation of this workshop

• Add and translate the new modified content to the French version of the workshop.

• Proofread and correct spelling, grammar and punctuation errors.

• Correct unnecessary long sentences.

Specific to this workshop

• Where possible, console output should be generated from code chunks within the .Rmd, rather than screenshots (e.g. slides 63-68, 96, 103-104, etc.)
• Similarly, there are several figures that could be generated from code chunks, but are inserted as images. Where possible, code these figures (e.g. slide 54, 56 (fix sizing to avoid overspill), 81, 125-126, etc.)
• Slide 45: Wording (and content) to be improved
• Slide 51: Some definitions would benefit from a visual support. For example, showing orthogonality, score, and dispersion. (There is also a typo in the Eigenvalues definition: Proportion*).
• Slide 90: Horseshoe plot is described in a warning, but in a way that is a bit hard to understand. This point would be more intuitive with a plot showing what such a problem would look like.
• Mention of ggbiplot package somewhere (near the end?) could be good, since it is a convenient way to visualize ordination results

Format details

• Slide 4: Learning objectives are different sizes.
• Slide 90: The sentence "multinormal distribution of the data (only if you wish to make inferences)" changes sizes during the transition.

Only close this issue after all cases have been ticked and verified.

[pedrohbraga]

Other important general modifications to be added

• Include learning objectives;
• If possible, generate figures using R code, so they are reproducible;
• Slide 11 is a 'no-go': ignoring algebra does not help with understanding and appropriately using ordination techniques;
• Slide 12 seems to be unnecessary;
• Slide 15: the removal of rows with no data through data.x[-8, ] may cause confusion. A version appropriately dealing with that should be prioritized (e.g., which(is.na(data.x), arr.ind=TRUE), etc.)
• Slide 23 has two h1 headers. Change Examples to just bold.
• Change correlation plots to GGally::ggpairs() to improve visualization;
• Slide 28: Use LaTeX instead of the figure to create the matrix;
• Slide 31: Add equations for the distances and a short explanation;
• Slides 32, 33 and 34: Combine slides into an incremental one, replace the figure by real code output (no need to display all associations);
• Slide 36 (Challenge first slide edits #1): Correct neighbor to neighbour and make the question clearer;
• Slide 38: Transform into a diagram using DiagrammeR;
• Slide 39: Generate figure using R;
• Slide 40: Add acronyms to help the association between R options and the ones also available within books. Make the three first bullet points as a number list;
• Slides 41 and 42: If possible, combine slides and improve the explanation. Figures should be displayed by code output;
• Slide 43: Explanation must be improved. Figures should be generated by code;
• Slides 44 and 45: Figures should be generated by code. Code showing how to generate the complete linkage clustering figure should be displayed;
• Slide 46: Explanation must be improved.
• Slides 47 and 48: Explanation must be improved. If possible, combine both slides;
• Slide 52: Typo ç;
• Section on PCA, PCoA, CA and NMDS: This part needs more detailed content. It needs a lot of improvement in its visuals and in the theoretical explanation of the analyses. Most figures can and should be generated by code.

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• Solve issue The section on hierarchical clustering needs improvement #3 .