Content from Preparation and installation

Last updated on 2023-01-05 | Edit this page

Estimated time: 12 minutes

Code of Conduct

To make clear what is expected, everyone participating in The Carpentries activities is required to abide by our Code of Conduct. Any form of behaviour to exclude, intimidate, or cause discomfort is a violation of the Code of Conduct. In order to foster a positive and professional learning environment we encourage you to:

  • Use welcoming and inclusive language
  • Be respectful of different viewpoints and experiences
  • Gracefully accept constructive criticism
  • Focus on what is best for the community
  • Show courtesy and respect towards other community members

If you believe someone is violating the Code of Conduct, we ask that you report it to The Carpentries Code of Conduct Committee by completing this form.

Zotero, Zotero Connector, Zutilo, Better Bibtex for Zotero, Better notes for Zotero and text editing in R Cloud

Go to Zotero.org and download the relevant Zotero desktop version and connector for your PC, Mac or Linux machine. We are going to use Zutillo add-on to Zotero and SR Accelerator in order to get an overview of our field of research.

Download the zutilo. xpi file from Zutilo’s GitHub releases page. Then go to Tools-> Add-ons in Zotero. Click on the gear button in the upper right area of the Add-ons Manager window and install the Add-on from the file. Then select the downloaded zutilo. Note that this should not be done in Mozilla. Most other web browsers should work. Do same procedure with Better notes for Zotero and Better bibtex for zotero.

You will need a google account, or a GitHub account in order to be able to use the cloud service of RStudio called Posit. If you need digital privacy, you may download R and R Studio to your desktop instead. In this case, you do not have to make a user id for login.

Academic preparation In this course we have an academic problem that is used for learning the method: “Water scarcity or floods are increasingly a problem during the anthropocene. How is this problem solved in varouis regions, and what has the scientific community suggested in previous research?”

However, feel free to limit the scope of the problem, or use your own academic problem in episode 2. You must be able to easily find at least 500 references treating the chosen subject. We do this in order to simulate how to easily get an overview over a relatively good search on the literature on the chosen subject.

Check the functionality After the installation. Check your usual text editor. For Word users: Do you see the tab for Zotero functionality somewhere to the right? If not, you may use googles solution:

Zotero tab does not appear in the Word Ribbon Open the Templates and Add-ins window by going to File → Options → Add-ins, selecting “Word Add-ins” in the Manage drop-down at the bottom, and clicking “Go…”. Then, make sure Zotero.dotm is present and ticked.

Zotero supports the text editors Google Docs, Microsoft Word and Libre Office.

Installing the Zotero Word Processor Plugins Vitit this site: https://www.zotero.org/support/word_processor_plugin_installation

Overview

Questions

  • How do you write a lesson using Markdown and sandpaper?

Objectives

  • Have all the installations ready on your PC/ Mac
  • Be technically ready to start working with Zotero

Introduction

This is a lesson created via The Carpentries Workbench. It is written in Pandoc-flavored Markdown for static files and R Markdown for dynamic files that can render code into output. Please refer to the Introduction to The Carpentries Workbench for full documentation.

What you need to know is that there are three sections required for a valid Carpentries lesson:

  1. questions are displayed at the beginning of the episode to prime the learner for the content.
  2. objectives are the learning objectives for an episode displayed with the questions.
  3. keypoints are displayed at the end of the episode to reinforce the objectives.

Inline instructor notes can help inform instructors of timing challenges associated with the lessons. They appear in the “Instructor View”

Challenge 1: Can you do it?

How did you organize your references the last time you wrote an assignment?

  1. Endnote

  2. I did it manually

  3. Zotero

the right answer should be c) Zotero

Challenge 2: how do you nest solutions within challenge blocks?

You can add a line with at least three colons and a solution tag.

Figures

You can use standard markdown for static figures with the following syntax:

![optional caption that appears below the figure](figure url){alt='alt text for accessibility purposes'}

Blue Carpentries hex person logo with no text.
You belong in The Carpentries!

Math

One of our episodes contains \(\LaTeX\) equations when describing how to create dynamic reports with {knitr}, so we now use mathjax to describe this:

$\alpha = \dfrac{1}{(1 - \beta)^2}$ becomes: \(\alpha = \dfrac{1}{(1 - \beta)^2}\)

Cool, right?

Key Points

  • Use .md files for episodes when you want static content
  • Use .Rmd files for episodes when you need to generate output
  • Run sandpaper::check_lesson() to identify any issues with your lesson
  • Run sandpaper::build_lesson() to preview your lesson locally

Content from Making the first manual reference and the first library

Last updated on 2023-01-23 | Edit this page

Estimated time: 12 minutes

Making a manual reference In zotero desktop, choose file –> New item –> Book

Insert the data for this book:

Title: Behave: The Biology of Humans at Our Best and Worst Format: Hardcover – Illustrated, May 2, 2017 by Robert M. Sapolsky (Author)

Making a Library Go to Zotero desktop and choose File –> New collection –> Name the collection

Make a “New library” New library–> This will send you to the Zotero cloud solution. Make your own username and password. Find an adeqate group name. Choose group type and settings, and save the settings. Go back to the desktop to see how it now looks. If you cannot see the group right away, try the sync option.

Download single articles Download the following references to Zotero. Check that everything is downloaded correctly in the Zotero app, and then cite the source in the text editor. Make the bibliography. Note that the last one is a an open access book. Click on the PDF icon where Zotero icon normally are. Check the item in the zotero app. Dod you manage to get all of these into your library?

Downloading references from research databases There are various for profit databases held in subscriptions by the University Libraries. We reccomend those who has the privilege to try these. Carpentry is about open databases and open access. We have therefore chosen the databases below. Feel free to use other databases.

If you do not have your own academic problem, you may use this one: “Many people in the world live with water scarcity. How is this problem solved in varouis regions, and what has the scientific community suggested in previous research?”

Try to downlowd at least 500 references directly to your new group. Find the export solution for the relevant database. We recommend the RIS format for Zotero. Open/ import the file in Zotero. Put the references in the group you made.

Look at your references, mark 20 of them, and use the function “find pdf”. You may use “fn lock” to mark several references, –> right click –> find available pdfs. This solution will work better it you are on a university campus with subscriptions to academic journals. If using it from the home office, it will import open access resources.

Overview

Questions

  • How do you write a lesson using Markdown and sandpaper?

Objectives

  • Have all the installations ready on your PC/ Mac
  • Be technically ready to start working with Zotero

Introduction

This is a lesson created via The Carpentries Workbench. It is written in Pandoc-flavored Markdown for static files and R Markdown for dynamic files that can render code into output. Please refer to the Introduction to The Carpentries Workbench for full documentation.

What you need to know is that there are three sections required for a valid Carpentries lesson:

  1. questions are displayed at the beginning of the episode to prime the learner for the content.
  2. objectives are the learning objectives for an episode displayed with the questions.
  3. keypoints are displayed at the end of the episode to reinforce the objectives.

Inline instructor notes can help inform instructors of timing challenges associated with the lessons. They appear in the “Instructor View”

Challenge 1: Can you do it?

How did you organize your references the last time you wrote an assignment.

  1. Endnore

  2. I did it manually

  3. Zotero

the right answer should be c) Zotero

Challenge 2: how do you nest solutions within challenge blocks?

You can add a line with at least three colons and a solution tag.

Figures

You can use standard markdown for static figures with the following syntax:

![optional caption that appears below the figure](figure url){alt='alt text for accessibility purposes'}

Blue Carpentries hex person logo with no text.
You belong in The Carpentries!

Math

One of our episodes contains \(\LaTeX\) equations when describing how to create dynamic reports with {knitr}, so we now use mathjax to describe this:

$\alpha = \dfrac{1}{(1 - \beta)^2}$ becomes: \(\alpha = \dfrac{1}{(1 - \beta)^2}\)

Cool, right?

Key Points

  • Use .md files for episodes when you want static content
  • Use .Rmd files for episodes when you need to generate output
  • Run sandpaper::check_lesson() to identify any issues with your lesson
  • Run sandpaper::build_lesson() to preview your lesson locally

Content from 03 The academic writing process - Zotero and text editors

Last updated on 2022-08-16 | Edit this page

Estimated time: 12 minutes

Using Zotero with a text editor Open R-cloud when Zotero run. Log into Zotero to generate Zotero Web API https://www.zotero.org/settings/keys/new . Name this key for example Rmarkdown and generate key. Go to R-markdown an click on Tools, Rmarkdown, Citations, paste in the citation key from Zotero. Then go to Tools, Project options, Rmarkdown, select zotero libraries.

Then copy and paste an example text from the Lorem ipsum generator. url: https://www.lipsum.com/

Save your file somewhere so that you know where to find it.

Storing your data in a good way When working with text and files, it is important to know how and where to store them. Most universities offer protected storage drives at their networks. This makes students and reaearchers able to store their data in an adequate way. Often these storage places come with high quality backup. Familiarize yourself with the recommendations of your home institution. Check out the available platforms of storage. You should know the difference between these storage platforms - Private OneDrive - Institutional OneDrive - Office 365 - local harddrive (C:) - personal network storage on campus (M:)

There are other storage places too, but the above are the most important.

File structure and file names Your data should be organizes with folders and sub folders that make it easy to fing your data, even in the future, when you have stopped working with the project. Store versions and backup in an appropriate and orderly way. Use the right kind of filenames, where you avoid space bar and special characters. Rememver the dot means the file ending is coming, and avoid the wrong use of period in the file name.

Save your document Save your document in a way that takes the above mentioned into account. Check that you have both Zotero and your text editor open. Experiment with taking in text references. Put in several text references. Make the bibliography. How do you take in page numbers to your references?

Overview

Questions

  • How do you write a lesson using Markdown and sandpaper?

Objectives

  • Know how to integrate zotero into your own usual workflow, with your favourite text editor
  • Importing bibliographic data
  • Placing text references
  • Backup

Introduction

This is a lesson created via The Carpentries Workbench. It is written in Pandoc-flavored Markdown for static files and R Markdown for dynamic files that can render code into output. Please refer to the Introduction to The Carpentries Workbench for full documentation.

What you need to know is that there are three sections required for a valid Carpentries lesson:

  1. questions are displayed at the beginning of the episode to prime the learner for the content.
  2. objectives are the learning objectives for an episode displayed with the questions.
  3. keypoints are displayed at the end of the episode to reinforce the objectives.

Inline instructor notes can help inform instructors of timing challenges associated with the lessons. They appear in the “Instructor View”

Challenge 1: Can you do it?

You want to send your manuscript to a journal that tell you to follow these style: Referansene skal følge Harvard Style of Referencing. Referansene i teksten skal være som følger ved henholdsvis en, to og flere forfattere: «…Meland (2010), Bårdsen og Nymoen (2011), Finstad mfl. (2002)…». Referanser i parentes skrives som følger: «… (Finstad mfl., 2002; Meland, 2010)…». g. Referanselisten skal ha overskriften REFERANSER og ha følgende format: Melberg, H. O. (2010). Animal spirit: Fargerik tomhet? Samfunnsøkonomen 64 (2), 4–10. Bårdsen, G. og R. Nymoen (2011). Innføring i økonometri. Fakbokforlaget, Bergen. Finstad, A., G. Haakonsen og K. Rypdal (2002). Utslipp til luft av dioksiner i Norge – Dokumentasjon av metode og resultater. Rapporter 2002/7, Statistisk sentralbyrå.

How can you do that?

R 

paste("This", "new", "lesson", "looks", "good")

Take a copy of the document, in the copy go to “Unlink citations” in the Zotero menu, use the Find and Replace function in the text editor and replace the et al. with mfl., then correct the paranthesis, and fill in the Place of publication. It depend if you have used the APA style or Cite Them Right.Try different styles in Zotero “Document preferences”.

Output

OUTPUT 

[1] "This new lesson looks good"

Challenge 2: how do you nest solutions within challenge blocks?

You can add a line with at least three colons and a solution tag.

Figures

You can use standard markdown for static figures with the following syntax:

![optional caption that appears below the figure](figure url){alt='alt text for accessibility purposes'}

Blue Carpentries hex person logo with no text.
You belong in The Carpentries!

Math

One of our episodes contains \(\LaTeX\) equations when describing how to create dynamic reports with {knitr}, so we now use mathjax to describe this:

$\alpha = \dfrac{1}{(1 - \beta)^2}$ becomes: \(\alpha = \dfrac{1}{(1 - \beta)^2}\)

Cool, right?

Key Points

  • Use .md files for episodes when you want static content
  • Use .Rmd files for episodes when you need to generate output
  • Run sandpaper::check_lesson() to identify any issues with your lesson
  • Run sandpaper::build_lesson() to preview your lesson locally

Content from 04 Mapping your archive

Last updated on 2022-08-16 | Edit this page

Estimated time: 12 minutes

Creating the overview through SR Accelerator Now that we already have a big archive with literature on a specific research area, it will be useful to apply some tools for getting a qiuck overview of the material. Go to the Zotero folder where you have the literature on the water management question, or the research question you chose. Export the collection in an .ris file and put it somewhere in your folder locations so that you know how to find it again. Go to the web page SR Accelerator and choose WordFreq from the left hand menu. Upload the .ris file that you made. Do you see any unexpected terms in your data? Are there any terms that you would expect to have a greater frequency?

Making the folders talk You may now go back to your archive and look for the possibility of making

Right click “my library” to the left, and make –> new saved search. Make a folder with 000 and the term as a name, like this 000Drought. See that the folder takes up all of the literature with the relevant term. then check the number and rename the folder so that the number before the term is right. The name of the folder should look something like this 040Drought, and current number of references containing the terms.

Overview

Questions

  • What is characteristic with open digital science?

Objectives

  • organizing and mapping a large amount of references
  • knowing how Zotero can ease cooperation in study groups or research groups

Introduction

This is a lesson created via The Carpentries Workbench. It is written in Pandoc-flavored Markdown for static files and R Markdown for dynamic files that can render code into output. Please refer to the [Zotero]([https://www.zotero.org/support/] for full documentation.

What you need to know is that there are three sections required for a valid Carpentries lesson:

  1. questions are displayed at the beginning of the episode to prime the learner for the content.
  2. objectives are the learning objectives for an episode displayed with the questions.
  3. keypoints are displayed at the end of the episode to reinforce the objectives.

Inline instructor notes can help inform instructors of timing challenges associated with the lessons. They appear in the “Instructor View”

Challenge 1: Can you do it?

Did you ever use a reference manager integrated into a text editor

  1. no, I used only the reference manager itself

  2. I Use Word and Zotero. I am an advanced user

R 

paste("This", "new", "lesson", "looks", "good")

OUTPUT 

[1] The answer will soon be: b) I Use Word and Zotero. I am an advanced user

Challenge 2: how do you nest solutions within challenge blocks?

You can add a line with at least three colons and a solution tag.

Figures

You can use standard markdown for static figures with the following syntax:

![optional caption that appears below the figure](figure url){alt='alt text for accessibility purposes'}

Blue Carpentries hex person logo with no text.
You belong in The Carpentries!

Math

One of our episodes contains \(\LaTeX\) equations when describing how to create dynamic reports with {knitr}, so we now use mathjax to describe this:

$\alpha = \dfrac{1}{(1 - \beta)^2}$ becomes: \(\alpha = \dfrac{1}{(1 - \beta)^2}\)

Cool, right?

Key Points

  • Use .md files for episodes when you want static content
  • Use .Rmd files for episodes when you need to generate output
  • Run sandpaper::check_lesson() to identify any issues with your lesson
  • Run sandpaper::build_lesson() to preview your lesson locally

Content from Zotero and markdown

Last updated on 2022-08-04 | Edit this page

Estimated time: 0 minutes

Overview

Questions

  • TODO

Objectives

  • TODO

Introduction

This is a lesson created via The Carpentries Workbench. It is written in Pandoc-flavored Markdown for static files and R Markdown for dynamic files that can render code into output. Please refer to the Introduction to The Carpentries Workbench for full documentation.

What you need to know is that there are three sections required for a valid Carpentries lesson:

  1. questions are displayed at the beginning of the episode to prime the learner for the content.
  2. objectives are the learning objectives for an episode displayed with the questions.
  3. keypoints are displayed at the end of the episode to reinforce the objectives.

Inline instructor notes can help inform instructors of timing challenges associated with the lessons. They appear in the “Instructor View”

Challenge 1: Can you do it?

What is the output of this command?

R 

paste("This", "new", "lesson", "looks", "good")

OUTPUT 

[1] "This new lesson looks good"

Challenge 2: how do you nest solutions within challenge blocks?

You can add a line with at least three colons and a solution tag.

Figures

You can use standard markdown for static figures with the following syntax:

![optional caption that appears below the figure](figure url){alt='alt text for accessibility purposes'}

Blue Carpentries hex person logo with no text.
You belong in The Carpentries!

Math

One of our episodes contains \(\LaTeX\) equations when describing how to create dynamic reports with {knitr}, so we now use mathjax to describe this:

$\alpha = \dfrac{1}{(1 - \beta)^2}$ becomes: \(\alpha = \dfrac{1}{(1 - \beta)^2}\)

Cool, right?

Key Points

  • Use .md files for episodes when you want static content
  • Use .Rmd files for episodes when you need to generate output
  • Run sandpaper::check_lesson() to identify any issues with your lesson
  • Run sandpaper::build_lesson() to preview your lesson locally

Content from Using Markdown

Last updated on 2022-11-10 | Edit this page

Estimated time: 12 minutes

Overview

Questions

  • How do you write a lesson using Markdown and sandpaper?

Objectives

  • Explain how to use markdown with The Carpentries Workbench
  • Demonstrate how to include pieces of code, figures, and nested challenge blocks

Introduction

From e-mail

Structure Zotero with Master- and PhD students:

  • Refresher on academic referencing, why it’s important to cite correctly, and basic citation formats
  • Information on reference management software in general (what it can do and why you should use it)
  • Choice of reference management software (i.e. the advantages of zotero, comparison to others)
  • Using Zotero:

SH 

*	Basic workflow (browser button and word plugin)
*	Other outputs (citation styles, copy to clipboard, adjust in word, export formats, …)
*	Other inputs - single items (eg from doi, from file, manual, …)
*	Other inputs - multiple items (eg from database, drag and drop, …)
*	Organizing your library (notes, tags, folders, …)
*	Getting the most out of zotero (shared libraries, proxy settings, retraction watch, sync & storage, addons,  …)

Suggest to put most of these except maybe the last point into the ‘basics’ for the first 3 hours, then we would need some structure for the afternoon part as well. Maybe we can merge that somehow with P‘s ideas to organize by activities, e.g. writing, reading, literature searches, etc.

This is a lesson created via The Carpentries Workbench. It is written in Pandoc-flavored Markdown for static files and R Markdown for dynamic files that can render code into output. Please refer to the Introduction to The Carpentries Workbench for full documentation.

What you need to know is that there are three sections required for a valid Carpentries lesson:

  1. questions are displayed at the beginning of the episode to prime the learner for the content.
  2. objectives are the learning objectives for an episode displayed with the questions.
  3. keypoints are displayed at the end of the episode to reinforce the objectives.

Inline instructor notes can help inform instructors of timing challenges associated with the lessons. They appear in the “Instructor View”

Challenge 1: Can you do it?

What is the output of this command?

R 

paste("This", "new", "lesson", "looks", "good")

OUTPUT 

[1] "This new lesson looks good"

Challenge 2: how do you nest solutions within challenge blocks?

You can add a line with at least three colons and a solution tag.

Figures

You can use standard markdown for static figures with the following syntax:

![optional caption that appears below the figure](figure url){alt='alt text for accessibility purposes'}

Blue Carpentries hex person logo with no text.
You belong in The Carpentries!

Math

One of our episodes contains \(\LaTeX\) equations when describing how to create dynamic reports with {knitr}, so we now use mathjax to describe this:

$\alpha = \dfrac{1}{(1 - \beta)^2}$ becomes: \(\alpha = \dfrac{1}{(1 - \beta)^2}\)

Cool, right?

Key Points

  • Use .md files for episodes when you want static content
  • Use .Rmd files for episodes when you need to generate output
  • Run sandpaper::check_lesson() to identify any issues with your lesson
  • Run sandpaper::build_lesson() to preview your lesson locally

Content from Using Markdown

Last updated on 2022-06-14 | Edit this page

Estimated time: 12 minutes

Overview

Questions

  • How do you write a lesson using Markdown and sandpaper?

Objectives

  • Explain how to use markdown with The Carpentries Workbench
  • Demonstrate how to include pieces of code, figures, and nested challenge blocks

Introduction

This is a lesson created via The Carpentries Workbench. It is written in Pandoc-flavored Markdown for static files and R Markdown for dynamic files that can render code into output. Please refer to the Introduction to The Carpentries Workbench for full documentation.

What you need to know is that there are three sections required for a valid Carpentries lesson:

  1. questions are displayed at the beginning of the episode to prime the learner for the content.
  2. objectives are the learning objectives for an episode displayed with the questions.
  3. keypoints are displayed at the end of the episode to reinforce the objectives.

Inline instructor notes can help inform instructors of timing challenges associated with the lessons. They appear in the “Instructor View”

Challenge 1: Can you do it?

What is the output of this command?

R 

paste("This", "new", "lesson", "looks", "good")

OUTPUT 

[1] "This new lesson looks good"

Challenge 2: how do you nest solutions within challenge blocks?

You can add a line with at least three colons and a solution tag.

Figures

You can use standard markdown for static figures with the following syntax:

![optional caption that appears below the figure](figure url){alt='alt text for accessibility purposes'}

Blue Carpentries hex person logo with no text.
You belong in The Carpentries!

Math

One of our episodes contains \(\LaTeX\) equations when describing how to create dynamic reports with {knitr}, so we now use mathjax to describe this:

$\alpha = \dfrac{1}{(1 - \beta)^2}$ becomes: \(\alpha = \dfrac{1}{(1 - \beta)^2}\)

Cool, right?

Key Points

  • Use .md files for episodes when you want static content
  • Use .Rmd files for episodes when you need to generate output
  • Run sandpaper::check_lesson() to identify any issues with your lesson
  • Run sandpaper::build_lesson() to preview your lesson locally

Content from Using Markdown

Last updated on 2022-06-14 | Edit this page

Estimated time: 12 minutes

Overview

Questions

  • How do you write a lesson using Markdown and sandpaper?

Objectives

  • Explain how to use markdown with The Carpentries Workbench
  • Demonstrate how to include pieces of code, figures, and nested challenge blocks

Introduction

This is a lesson created via The Carpentries Workbench. It is written in Pandoc-flavored Markdown for static files and R Markdown for dynamic files that can render code into output. Please refer to the Introduction to The Carpentries Workbench for full documentation.

What you need to know is that there are three sections required for a valid Carpentries lesson:

  1. questions are displayed at the beginning of the episode to prime the learner for the content.
  2. objectives are the learning objectives for an episode displayed with the questions.
  3. keypoints are displayed at the end of the episode to reinforce the objectives.

Inline instructor notes can help inform instructors of timing challenges associated with the lessons. They appear in the “Instructor View”

Challenge 1: Can you do it?

What is the output of this command?

R 

paste("This", "new", "lesson", "looks", "good")

OUTPUT 

[1] "This new lesson looks good"

Challenge 2: how do you nest solutions within challenge blocks?

You can add a line with at least three colons and a solution tag.

Figures

You can use standard markdown for static figures with the following syntax:

![optional caption that appears below the figure](figure url){alt='alt text for accessibility purposes'}

Blue Carpentries hex person logo with no text.
You belong in The Carpentries!

Math

One of our episodes contains \(\LaTeX\) equations when describing how to create dynamic reports with {knitr}, so we now use mathjax to describe this:

$\alpha = \dfrac{1}{(1 - \beta)^2}$ becomes: \(\alpha = \dfrac{1}{(1 - \beta)^2}\)

Cool, right?

Key Points

  • Use .md files for episodes when you want static content
  • Use .Rmd files for episodes when you need to generate output
  • Run sandpaper::check_lesson() to identify any issues with your lesson
  • Run sandpaper::build_lesson() to preview your lesson locally