-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathindex.qmd
176 lines (106 loc) · 7.92 KB
/
index.qmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
# Course description
In order to **ensure robustness** of outputs and **maximise the benefits** of ACCE research to future researchers and society more generally, it is **important to share the underlying code and data**. But for sharing to have any impact, such materials need to be created **FAIR** (*findable, accessible, interoperable, reusable*), i.e. they must be adequately described, archived, and made discoverable to an appropriate standard.
Additionally, if analyses are to be deemed robust, they **must be at the very least reproducible**, but ideally well documented and reviewable.
R and Rstudio tools and conventions offer a powerful framework for making modern, open, reproducible and collaborative computational workflows more accessible to researchers.
This course focuses on **data and project management through R and Rstudio**, will introduce students to best practice and equip them with modern tools and techniques for managing data and computational workflows to their full potential. The course is designed to be relevant to students with a wide range of backgrounds, working with anything from relatively small sets of data collected from field or experimental observations, to those taking a more computational approach and bigger datasets.
<br>
## Learning Outcomes
By the end of the workshop, participants will be able to:
- Understand the basics of good research data management and be able to produce clean datasets with appropriate metadata.
- Manage computational projects for reproducibility, reuse and collaboration.
- Use version control to track the evolution of research projects.
- Use R tools and conventions to document code and analyses and produce reproducible reports.
- Be able to publish, share materials and collaborate through the web.
- Understand why this all matters!
------------------------------------------------------------------------
## Course Outline
:::: grid
::: {.g-col-8 .g-col-md-4 .email-sched-card}
#### {{< fa calendar >}} Day 1
##### {{< fa clock >}} 10:00 - 16:30
##### OPTIONAL
### Welcome
**Basics**
- Intro to R & Rstudio
- R basics
- Data types, structures & classes
- Indexing and Subsetting
- The tidyverse way
:::
::::
:::::: grid
::: {.g-col-8 .g-col-md-4 .email-sched-card}
#### {{< fa calendar >}} Day 2
##### {{< fa clock >}} 09:00 - 17:00
**Project Management**
- Data management basics
- Projects in Rstudio
- Good File Naming
- Paths and projects structure
**Data Munging**
- Iteration
- Merging data
- Functions
:::
::: {.g-col-8 .g-col-md-4 .email-sched-card}
#### {{< fa calendar >}} Day 3
##### {{< fa clock >}} 09:00 - 17:00
**Metadata**
- Intro to metadata
- Creating metadata with dataspice
**Analysing & Presenting data**
- Plotting with `ggplot2`
:::
::: {.g-col-8 .g-col-md-4 .email-sched-card}
#### {{< fa calendar >}} Day 4
##### {{< fa clock >}} 09:00 - 17:00
**Analysing & Presenting data**
- Scientific Reporting with Quarto
**Version Control**
- Version control with Git
- Collaboration through GitHub
**Packaging Code**
- Managing Dependencies
:::
::: {.g-col-8 .g-col-md-4 .email-sched-card}
#### {{< fa calendar >}} Day 5
##### {{< fa clock >}} 09:00 - 15:30
##### OPTIONAL
**Packaging Code**
- Writing & documenting functions
- Capturing metadata incl. dependencies
- Checking & Testing functions
**Putting it all together: Research Compendia**
- Creating a research compendium
:::
::::::
------------------------------------------------------------------------
<a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img src="https://i.creativecommons.org/l/by/4.0/88x31.png" alt="Creative Commons License" style="border-width:0"/></a><br />This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.
------------------------------------------------------------------------
#### Sources of Materials
The first few chapters of the **Basics** section were heavily sourced and adapted from [**"Software Carpentry: R for Reproducible Scientific Analysis."**](http://swcarpentry.github.io/r-novice-gapminder/) ***Thomas Wright and Naupaka Zimmerman (eds): Version 2016.06, June 2016*** https://github.com/swcarpentry/r-novice-gapminder, [](https://doi.org/10.5281/zenodo.57520).
- Licensed under [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) 2018–2020 by [The Carpentries](https://carpentries.org/).
<br>
The **Good File Naming** chapter was heavily sourced from [**"File organization for reproducible research."**](https://datacarpentry.org/rr-organization1/) ***Data Carpentry Reproducible Research Committee. 2016***.
- Licensed under [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) 2018–2020 by [The Carpentries](https://carpentries.org/). [ ](https://datacarpentry.org/rr-organization1/)
<br>
Small sections in the **Data Munging** section where inspired by text in the online version of [**"R 4 Data Science"**](https://r4ds.had.co.nz/), ***Garrett Grolemund & Hadley Wickham***.
- Licensed under the [Creative Commons Attribution-NonCommercial-NoDerivs 3.0](http://creativecommons.org/licenses/by-nc-nd/3.0/us/) License.
<br>
**Images** contained throughout the materials and watermarked with ***Scriberia*** were sourced from **"Illustrations from the Turing Way book dashes"**, [](https://doi.org/10.5281/zenodo.3332808). Images were created by [**Scriberia**](https://www.scriberia.co.uk/) for The [**Turing Way**](https://the-turing-way.netlify.app/introduction/introduction) community.
- Licensed under [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) by [The Turing Way](https://the-turing-way.netlify.app/introduction/introduction).
<br>
**Data** for the the main practical parts of the course were sourced from the [**NEON Data Portal**](https://data.neonscience.org/data-products/explore), provided by the **National Ecological Observatory Network**. 2019 Provisional data downloaded from http://data.neonscience.org on 2019-08-06. Battelle, Boulder, CO, USA.
- **Data Products:** NEON.DOM.SITE.DP1.10098.001
- **Name:** Woody plant vegetation structure
- **Description:** Structure measurements, including height, canopy diameter, and stem diameter, as well as mapped position of individual woody plants
- **Query information:**
- **Start Date-Time for Queried Data:** 2018-08-15 16:00 (UTC)
- **End Date-Time for Queried Data:** 2018-08-29 16:00 (UTC)
- **Domains:** D01:D9
- [**LICENSE**](https://www.neonscience.org/data/about-data/data-policies)
- **Disclaimer**
> THE NEON DATA PRODUCTS ARE PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE NEON DATA PRODUCTS BE LIABLE FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE NEON DATA PRODUCTS.
<br>
**Materials** for the **Research Compendium** section were sourced from ***Carl Boettiger. (2018, April 17).*** **cboettig/noise-phenomena: Supplement to: "From noise to knowledge: how randomness generates novel phenomena and reveals information"** [](https://doi.org/10.5281/zenodo.1219780), accompanying the publication: Carl Boettiger [](https://orcid.org/0000-0002-1642-628X). *From noise to knowledge: how randomness generates novel phenomena and reveals information*. Published in *Ecology Letters*, 22 May 2018 <https://doi.org/10.1111/ele.13085>.
<a href="https://www.netlify.com"> <img src="https://www.netlify.com/v3/img/components/netlify-color-accent.svg" alt="Deploys by Netlify"/> </a>