Week 8 and 9 Literate programming

(Communicating Results)

Pengfei Liu

1 Default setting of the Quarto Manuscript

1.1 Create the folder

(1) Create an empty folder for Quarto Manuscript and give it a proper name.

(2) Click File-New File-Quarto project-Manuscript project.

(3) Choose the folder we created in step 1.

1.2 Check the main YAML

(1) title:

(2) authors:

(3) bibliography: article citation

1.3 Check the structure of working folder

(1) _quarto.yml: format YAML. This is related to metadata and front matter of the

manuscript. Different formats of output are customized in this file.

(2) index.qmd: we write in this main document.

(3) references.bib: your references (which can be downloaded through Google Scholar or

through Zotero).

(4) Rename index.qmd as 0_main_file.qmd.

11.4 Generate two additional markdown files

Those additional markdown files conduct analysis that complement this main file.

1_generate_number: remember to put your affiliation here.

2_generate_figure: remember to put your affiliation here.

2 Edit YAML section and YAML file

2.1 Change the main file name in YAML

Please go to _quarto.yml to change the default file name to manuscript: article:

0_main_file.qmd.

2.2 Python engine

jupyter: python3

2.3 Affiliation

title: Assignment 3

affiliation: University of Auckland

email: xxxx

2.4 Date

date: last-modified

2.5 Abstract

abstract: Please put your absract of assignment 3 here. Example: This course will teach

you data science workflow. The course will focus on Python for Finance and reproducible

analytical pipeline.

22.6 keywords

Please put your keywords here

keywords: - Quarto - Manuscript

2.7 Add PDF as one of the output

Go to _quarto.yml

add pdf: default at the next level paramater of format:

comment out jats: default

3 Render the manuscript

3.1 First try

Click the preview button in Vscode.

Additional folders generated: .quarto, _manuscript, _freeze

_freeze: code is not re-evaluated unless their source changes. A corresponding _freeze folder

will be created.

3.2 Click on Word and PDF icon form your folder

Please go to the folder you created at step 1 of Section 1.1

This probably does not work.

Solution 1:  代 写Week 8 and 9 Literate programmingClick on Word and PDF icon within Vscode.

Solution 2: manually edit the format parameter within YAML.

3.3 Add number for each section

number-sections: true

34 Python code cells

4.1 Article Notebook: wrong way

If you only run the following code, The article notebook will not appear..

Mylist = [1,2,3,4]

4.2 Article Notebook: correct way

We have to print something or return an object to make Article Notebook show up.

[1, 2, 3, 4]

4.3 Echo code or not

In the code, we can add the following parameter to control whether code will be echoed in the

main text (not Article Notebook):

#| echo: true

More about code cells on the following page: https://quarto.org/docs/reference/cells/cells

jupyter.html

4.4 Output results or not

#| output: false

Mylist = [1,2,3,4]

Mylist

4.5 Other useful code cells parametrs

#| code-fold: true (Collapse code into an HTML tag)

#| code-line-numbers: true (Include line numbers in code block output)

45 Numbers, figures, and tables

5.1 Inline code for numbers

The average gap of eruption is 2.5.

5.2 External embeds: a figure

Let us import a figure created in another QMD file.

Figure 1: Timeline of recent earthquakes on La Palma

Embed: please refer to https://quarto.org/docs/authoring/notebook-embed.html for details

of how to use embeds in Quarto.

5.3 External embeds: specific folded line of code

Use the following code to import pandas:

import pandas as pd

import numpy as np

5.4 Display tables

An example adapted from Quarto documentation. Table 1 shows information related to dif

ferent car models.

Table 1: Example

mpg cylinders displacement horsepower weight

18

8

307

130 3504

15

8

350

165 3693

5Table 1: Example

mpg cylinders displacement horsepower weight

18

8

318

150 3436

16

8

304

150 3433

17

8

302

140 3449

15

8

429

198 4341

14

8

454

220 4354

14

8

440

215 4312

14

8

455

225 4425

15

8

390

190 3850

5.5 Add existing figures from a folder

Figure 2: A logo for BUSFIN 711

5.6 Cross References

We can cross-reference figures, tables, equations, sections, etc.

5.7 External embeds: several line of code

This is mainly for the purpose of demonstration:

6 1_generate_number

A (University of Auckland)

import pandas as pd

import numpy as np

67 Reference

Indirect citation: This is a simple placeholder for the manuscript’s main document (Knuth

1984).

Direct citation: Knuth (1984) is am important paper.

Add more references to references.bib file.

Acknowledgement: some of materials are adapted from Quarto official documentation.

Knuth, Donald E. 1984. “Literate Programming.” Comput. J. 27 (2): 97–111. https://doi.or

g/10.1093/comjnl/27.2.97.

7