[Review]: High-dimensional Statistics

[gperu]

Lesson Title

High-dimensional Statistics with R

Lesson Repository URL

https://github.com/carpentries-incubator/high-dimensional-stats-r

Lesson Website URL

https://carpentries-incubator.github.io/high-dimensional-stats-r/

Lesson Description

This course is intended for those who have a working knowledge of statistics and linear models with R and wish to learn high-dimensional statistical methods with R.

This is a short course aimed at familiarising learners with statistical and computational methods for the extremely high-dimensional data commonly found in biomedical and health sciences (e.g., gene expression, DNA methylation, health records). These datasets can be challenging to approach, as they often contain many more features than observations, and it can be difficult to distinguish meaningful patterns from natural underlying variability. To this end, we will introduce and explain a range of methods and approaches to disentangle these patterns from natural variability. After completion of this course, learners will be able to understand, apply, and critically analyse a broad range of statistical methods. In particular, we focus on providing a strong grounding in high-dimensional regression, dimensionality reduction, and clustering.

Author Usernames

@alanocallaghan
@catavallejos
@ailithewing

Zenodo DOI

No response

Differences From Existing Lessons

No response

Confirmation of Lesson Requirements

• is the original work of the author(s), or that any content derived from another source is reused with permission and appropriate attribution
• aligns with The Carpentries Code of Conduct
• is published under a CC-BY or CC0 license
• uses The Carpentries lesson template or Carpentries Workbench without significant customisation/adaptation.

JOSE Submission Requirements

• the lesson repository includes paper.md and paper.bib files as described in the JOSE submission guide for learning modules

Potential Reviewers

No response

[tobyhodges]

Thank you for submitting this lesson for review, @gperu.

My capacity for managing lesson reviews is quite limited at the moment and I will not be able to handle reviews of all of your submitted lessons simultaneously. If you have a preference for which lesson(s) you would like us to prioritise for review, please let me know and I will do my best to focus on that/those first.

[catavallejos]

Thanks @tobyhodges and @gperu. Probably good to keep this course towards the end. @hannesbecher and I are working on some final changes to incorporate some of the feedback we have received during delivery. I will add a note here when ready.

[catavallejos]

@gperu could you please add @hannesbecher as an author? I can't edit the issue.

[catavallejos]

Hi @tobyhodges and @gperu. @hannesbecher and I completed our last round of planned changes so these materials are now ready to be reviewed. Please let me know what do we need to do to get the process started.

Best
Cata

[catavallejos]

Note that I cannot edit the original post in this thread to add additional authors or suggest reviewers

[mallewellyn]

Hi @tobyhodges, following further community reviews and changes, we would like to re-submit the lesson for review if at all possible. We totally understand that your capacity for reviews is limited. In case this helps, we have documented our community reviews, changes made in response to these reviews, and how we conform to The Carpentries' requirements here.

[Fgazzelloni]

Editor checks are complete. 👇

Editor Checklist - High-dimensional Statistics

Accessibility

• All figures are also described in image alternative text or elsewhere in the lesson body.

• The lesson uses appropriate heading levels:

  • h2 is used for sections within a page.
  • no "jumps" are present between heading levels e.g. h2->h4.
  • no page contains more than one h1 element i.e. none of the source files include first-level headings.

• The contrast ratio of text in all figures is at least 4.5:1.

• Comments:

• The lesson doesn't use appropriate heading levels

  • h1 is used for sections within a page (page contains more than one h1 element)
  • h2 is used for challenges

• The ALT txt could be longer for some of the figures throughout the lesson, for example:

  • Ch1 first table ALT txt could be: "Table displaying a high-dimensional data set with many features in individual columns relating to health data such as blood pressure, heart rate and respiratory rate. Each row contains the data for individual patients."
  • Ch7 A nearby image has the same alternative text for the heat-maps in the Using different distance methods section.

• Suggested ALT text for 04-principal-component-analysis - pairsplot(pc) - "An upper triangular grid of scatter plots of each principal component versus the others."

• Empty table header: Ch2: Adjusting for multiple tests section

Content

• The lesson teaches data and/or computational skills that could promote efficient, open, and reproducible research.
• All exercises have solutions.
• Opportunities for formative assessments are included and distributed throughout the lesson sufficiently to track learner progress. (We aim for at least one formative assessment every 10-15 minutes.)
• Any data sets used in the lesson are published under a permissive open license i.e. CC0 or equivalent.

Design

• Learning objectives are defined for the lesson and every episode.
• The target audience of the lesson is identified specifically and in sufficient detail.

Repository

The lesson repository includes:

• a CC-BY or CC0 license.
• a CODE_OF_CONDUCT.md file that links to The Carpentries Code of Conduct.
• a list of lesson maintainers.
• tabs to display Issues and Pull Requests for the project.

Structure

• Estimated times are included in every episode for teaching and completing exercises.

• Episodes lengths are appropriate for the management of cognitive load throughout the lesson.

• Comments: Not sure about the episodes lengths, if they are appropriate for the management of cognitive load throughout the lesson.

Supporting information

The lesson includes:

• a list of required prior skills and/or knowledge.
• setup and installation instructions.
• a glossary of key terms or links out to definitions in an external glossary e.g. Glosario.

General

• Very well done, this lesson requires just little adjustments for assuring appropriate heading levels and some extra explanation on the ALT txt of the figures.

[Fgazzelloni]

Checks are completed-General Very well done, this lesson requires just little adjustments for assuring appropriate heading levels and some extra explanation on the ALT txt of the figures.

[alanocallaghan]

Many thanks for the review! I've checked over the feedback from your review and hope I've responded to everything here, do let me know if anything else needs to be addressed before we update the lesson:

The lesson uses appropriate heading levels:

Changed here (all heading level issues are changed here): carpentries-incubator/high-dimensional-stats-r#183

The ALT txt could be longer for some of the figures throughout the lesson, for example:
Ch1 first table ALT txt could be: "Table displaying a high-dimensional data set with many features in individual columns relating to health data such as blood pressure, heart rate and respiratory rate. Each row contains the data for individual patients."
Suggested ALT text for 04-principal-component-analysis - pairsplot(pc) - "An upper triangular grid of scatter plots of each principal component versus the others."

I'm not sure I understand these comments, as these are the alt-text values already present. Should we make these longer and more informative? If so, I have attempted to improve these alt text values in carpentries-incubator/high-dimensional-stats-r#183

Ch7 A nearby image has the same alternative text for the heat-maps in the Using different distance methods section.

I couldn't identify a duplicated alt text value in this section. I have anyway made the alt text slightly clearer in carpentries-incubator/high-dimensional-stats-r#183

Empty table header: Ch2: Adjusting for multiple tests section

Addressed here: carpentries-incubator/high-dimensional-stats-r#183

a CODE_OF_CONDUCT.md file that links to The Carpentries Code of Conduct.

We have this here: https://github.com/carpentries-incubator/high-dimensional-stats-r/blob/main/CODE_OF_CONDUCT.md?plain=1

a list of lesson maintainers.

We have this here: https://github.com/carpentries-incubator/high-dimensional-stats-r/blob/9012bd21ed2dfcd2703df8d78afccfa4766602b0/README.md?plain=1#L35-L42

tabs to display Issues and Pull Requests for the project.

These are enabled for the repo

Episodes lengths are appropriate for the management of cognitive load throughout the lesson.

That is a difficulty in this style of lesson; we hope that learners have an appropriate level of programming knowledge and foundational statistical knowledge going in such that cognitive load can be managed. Generally, cohorts have gotten through the content and had positive feedback, but we imagine that in some cases later content might need to be omitted for a normal 2 day FTE course. I have added a note explaining this to the instructor notes here: carpentries-incubator/high-dimensional-stats-r#183

[Fgazzelloni]

Thanks! All checked.