<commit_before># Organization 1

## People

-  <NAME>: [@jennybc]
-  <NAME>: [@hlapp]
-  **<NAME>** [@iamciera]
-  <NAME> <EMAIL>
-  <NAME> <EMAIL>
-  <NAME> <EMAIL>

## Overview and learning objectives

Students will learn the benefits of project and folder organization,
and how these enable reproducibility and reusability. They will then
complete an activity highlighting the structure of data files,
emphasizing the importance of documenting any changes made. Finally,
they will bring these two activities together in the context of a
reproducible project workflow centered around using `knitr` in
RStudio.

At the begining of the session, students should be able

- to use a spreadsheet program to generate a plot
- to use a text editor (Word, Google Docs, etc.) to communicate
- be familiar with Rstudio: Rstudio layout, running R commands, knitr,
  and basic ggplot syntax (from Intro section)

At the end of the session students will be able to

- Evaluate folder and file structure of a project.
- Recognize common problems that occur in file organization.
- Be able to identify what plain text is.
- Demonstrate the benefits of using plain text.
- Distinguish between input and output files.
- Integrate file naming standards to projects.
- Distinguish between a spreadsheet formatted properly for later
  analysis in R and one formatted improperly
- Be able to recognize common data entry errors and how to handle them
- Be able to describe the concept of 'raw data' and why it is important
- Differentiate between manual and programmatic file manipulation and
  know the pros and cons of each

##01-file-naming

### Activity - Forensic Science

[Link to forensic science lesson](https://github.com/Reproducible-Science-Curriculum/rr-organization1/blob/master/01-file-organization.md)

This section starts with an activity to get the students thinking
about "excavating" a folder in the future.  It is meant to get the
students thinking about what file names, file organization, and file
content and what these can tell us about a project.

### Lecture - File Naming 

TO-DO (@jennybc): Create mini lecture on file naming.  Lecture drafts housed here: [https://github.com/jennybc/organization-and-naming](https://github.com/jennybc/organization-and-naming) 

##02-programatic-modification

### Activity 2 - Cleaning up data in Excel

[Link to programatic modification lesson](https://github.com/Reproducible-Science-Curriculum/rr-organization1/blob/master/02-programatic-modification.md)

In this section, the students will explore why it is beneficial to do
programmatic modification by exploring what it takes to clean up a
data file in Excel.

##Coffee Break

## 03-literate-programming - R via RStudio 

### Activity 

**Note: could overlap in part with Intro, Activity 2; may require
  on-the-fly adjustments in response to that.**

Students "knit" and modify. Using
[countryPick4.Rmd](files/03-literate-programming-activity/countryPick4.Rmd)
as a template, students learn how to import data, filter to one
country, make a plot, write it to file, and comment data choices.
Then the activity will illustrate what happens when you knit:
- Preview/Knit HTML, note what sorts of outputs are left behind.
- Discuss input and output files.
- Which files can we delete and reproduce? Which files are inputs,
outputs, converters of inputs to outputs?

This section is meant for students to explore the power of writing
reports in R.

TO-DO: Create Lesson guide and instructor guide. 

###Lecture

Wrap up lecuture: [Organizaing Files into Directories Draft](https://github.com/jennybc/organization-and-naming/tree/master/organization)

## Links relevant to items above

#### UBC Library Research Data Management has good resources

- File Naming Conventions & Best Practices <http://researchdata.library.ubc.ca/organize/>
- File Format Considerations <http://researchdata.library.ubc.ca/format/>Links from Jenny relevant to our outline

#### Naming practices

- ISO 8601 standard for dates <http://en.wikipedia.org/wiki/ISO_8601>
- File naming guides and suggestions
    - http://www.exadox.com/en/articles/file-naming-convention-ten-rules-best-practice
    - http://www.mnhs.org/preserve/records/electronicrecords/erfnaming.php
    - http://www.recordsmanagement.ed.ac.uk/InfoStaff/RMstaff/RMprojects/PP/FileNameRules/FileNameRules.htm
    - http://www.recordsmanagement.ed.ac.uk/InfoStaff/RMstaff/RMprojects/PP/FileNameRules/Rules.htm
- Filename extension conventions <http://en.wikipedia.org/wiki/List_of_file_formats>
<commit_msg>Cleans up headings and lesson links.<commit_after># Organization 1

## People

-  <NAME>: [@jennybc]
-  <NAME>: [@hlapp]
-  **<NAME>** [@iamciera]
-  <NAME> <EMAIL>
-  <NAME>berg <EMAIL>
-  <NAME> <EMAIL>

## Overview and learning objectives

Students will learn the benefits of project and folder organization,
and how these enable reproducibility and reusability. They will then
complete an activity highlighting the structure of data files,
emphasizing the importance of documenting any changes made. Finally,
they will bring these two activities together in the context of a
reproducible project workflow centered around using `knitr` in
RStudio.

At the begining of the session, students should be able

- to use a spreadsheet program to generate a plot
- to use a text editor (Word, Google Docs, etc.) to communicate
- be familiar with Rstudio: Rstudio layout, running R commands, knitr,
  and basic ggplot syntax (from Intro section)

At the end of the session students will be able to

- Evaluate folder and file structure of a project.
- Recognize common problems that occur in file organization.
- Be able to identify what plain text is.
- Demonstrate the benefits of using plain text.
- Distinguish between input and output files.
- Integrate file naming standards to projects.
- Distinguish between a spreadsheet formatted properly for later
  analysis in R and one formatted improperly
- Be able to recognize common data entry errors and how to handle them
- Be able to describe the concept of 'raw data' and why it is important
- Differentiate between manual and programmatic file manipulation and
  know the pros and cons of each

## File organization

### Activity - Forensic Science

Lesson: [01-file-organization](01-file-organization.md)

This section starts with an activity to get the students thinking
about "excavating" a folder in the future.  It is meant to get the
students thinking about what file names, file organization, and file
content and what these can tell us about a project.

### Lecture - File Naming 

TO-DO (@jennybc): Create mini lecture on file naming.  Lecture drafts housed here: [https://github.com/jennybc/organization-and-naming](https://github.com/jennybc/organization-and-naming) 

## Documenting data modifications

Lesson: [02-programatic-modification](02-programatic-modification.md)

### Activity 2 - Cleaning up data in Excel

In this section, the students will explore why it is beneficial to do
programmatic modification by exploring what it takes to clean up a
data file in Excel.

## Literate programming - R via RStudio 

Lesson: [03-literate-programming](03-literate-programming.md)

### Activity 

**Note: could overlap in part with Intro, Activity 2; may require
  on-the-fly adjustments in response to that.**

Students "knit" and modify. Using
[countryPick4.Rmd](files/03-literate-programming-activity/countryPick4.Rmd)
as a template, students learn how to import data, filter to one
country, make a plot, write it to file, and comment data choices.
Then the activity will illustrate what happens when you knit:
- Preview/Knit HTML, note what sorts of outputs are left behind.
- Discuss input and output files.
- Which files can we delete and reproduce? Which files are inputs,
outputs, converters of inputs to outputs?

This section is meant for students to explore the power of writing
reports in R.

TO-DO: Create Lesson guide and instructor guide. 

### Lecture

Wrap up lecuture: [Organizaing Files into Directories Draft](https://github.com/jennybc/organization-and-naming/tree/master/organization)

## Links relevant to items above

#### UBC Library Research Data Management has good resources

- File Naming Conventions & Best Practices <http://researchdata.library.ubc.ca/organize/>
- File Format Considerations <http://researchdata.library.ubc.ca/format/>Links from Jenny relevant to our outline

#### Naming practices

- ISO 8601 standard for dates <http://en.wikipedia.org/wiki/ISO_8601>
- File naming guides and suggestions
    - http://www.exadox.com/en/articles/file-naming-convention-ten-rules-best-practice
    - http://www.mnhs.org/preserve/records/electronicrecords/erfnaming.php
    - http://www.recordsmanagement.ed.ac.uk/InfoStaff/RMstaff/RMprojects/PP/FileNameRules/FileNameRules.htm
    - http://www.recordsmanagement.ed.ac.uk/InfoStaff/RMstaff/RMprojects/PP/FileNameRules/Rules.htm
- Filename extension conventions <http://en.wikipedia.org/wiki/List_of_file_formats>

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