/
materials.Rmd
103 lines (85 loc) · 4.2 KB
/
materials.Rmd
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
---
title: "Class Materials"
output:
html_document:
toc: true
toc_depth: 3
toc_float: true
theme: cosmo
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
### Day 1
[Setup](https://rachelss.github.io/BigDataSetup/)
[Reading 1](https://www.practicereproducibleresearch.org/core-chapters/1-intro.html)
[Reading 2](https://www.practicereproducibleresearch.org/core-chapters/0-preface.html)
### Day 2
[Setup](http://swcarpentry.github.io/shell-novice/setup.html)
[Tutorial in writing (1-3)](http://swcarpentry.github.io/shell-novice/)
[Datacamp interactive shell lesson ch. 1 (for more practice)](https://www.datacamp.com/courses/introduction-to-shell-for-data-science)
Read: Janssens ch. 1.0-1.5, 2.3.1-2.3.2
### Days 3-6
[Tutorial in writing (3-7)](http://swcarpentry.github.io/shell-novice/)
[Datacamp interactive shell lesson ch. 2-5 (for more practice)](https://www.datacamp.com/courses/introduction-to-shell-for-data-science)
Read: Buffalo ch. 3, 7, 12
Read: Janssens ch. 4.0-4.2
### Day 7
[Using the cluster: in class instructions](cluster_instructions.html)
[HPC Slides](hpcslides.pdf)
[URI HPC website](https://web.uri.edu/hpc-research-computing/)
[Software carpentry HPC tutorial](https://hpc-carpentry.github.io/hpc-intro/)
[Slurm cheatsheet](https://isugenomics.github.io/bioinformatics-workbook/Appendix/HPC/SLURM/slurm-cheatsheat.html)
### Day 8 2/21
[Cloud computing](cloud_instructions.html)
Read: Buffalo ch. 4
### Day 9-10 2/26-2/28
[Version control with Git](http://swcarpentry.github.io/git-novice/)
Read: Buffalo ch. 5
### Day 11 3/5
[Intro R](https://datacarpentry.org/R-ecology-lesson/00-before-we-start.html)
[Intro to data in R](02-starting-with-data.html)
Read: Modern Dive ch. 2
### Day 12 3/7
[R Data Viz](https://datacarpentry.org/R-ecology-lesson/04-visualization-ggplot2.html)
Read: Modern Dive ch. 3
539: Read: R 4 Data Science ch. 3
### Day 13 3/19
[Data Wrangling in R](https://datacarpentry.org/R-ecology-lesson/03-dplyr.html)
Read: Modern Dive ch. 4
539: Read: R 4 Data Science ch. 5
### Day 14 3/21
[Tidy data](https://datacarpentry.org/spreadsheet-ecology-lesson/)
[Data to tidy](https://ndownloader.figshare.com/files/2252083)
[Spread and gather](http://swcarpentry.github.io/r-novice-gapminder/14-tidyr/index.html)
Read: Modern Dive ch. 5; R 4 Data Science ch. 12
### Day 15 3/26
Read: [Data organization in spreadsheets](https://www.tandfonline.com/doi/pdf/10.1080/00031305.2017.1375989)
Read: [Google Sheets best practices](https://matthewlincoln.net/2018/03/26/best-practices-for-using-google-sheets-in-your-data-project.html)
### Day 16 3/28
[RMarkdown reports (see links therein)](http://swcarpentry.github.io/r-novice-gapminder/15-knitr-markdown/index.html)
Read: R 4 Data Science ch. 13, 27
539: Read: R 4 Data Science ch. 29
### Day 17 4/2
[Functions in R Tutorial](http://swcarpentry.github.io/r-novice-gapminder/10-functions/index.html)
[Memory issues in R](https://privefl.github.io/advr38book/performance.html#rs-memory-management)
Read: R 4 Data Science ch. 21, 19
### Day 18-19 4/4-4/9
[Data](https://d37djvu3ytnwxt.cloudfront.net/assets/courseware/v1/1d1e264f416e27b22a0b8c970d52f3e3/asset-v1:HarvardX+PH526x+3T2016+type@asset+block/Books_EngFr.zip)
[Notes](text_analysis.html)
[Rabbit exercise online](https://mybinder.org/v2/gh/rachelss/BigDataAnalysis19/master?filepath=rabbit_exercise.ipynb)
[Rabbit exercise to download](rabbit_exercise.ipynb)
Read: A Whirlwind Tour of Python through Control Flow
### Day 20 4/11
Read: A Whirlwind Tour of Python (finish); Python Data Science Handbook ch. 1
### Day 21 4/16
[Complete rabbit exercise](rabbits_inclass.html)
[Count words notebook](text_inclass.html)
[Count words script](count_words_in_books_class.py)
[Pandas lesson](https://datacarpentry.org/python-ecology-lesson/03-index-slice-subset/index.html)
[Pandas lesson 2](https://datacarpentry.org/python-ecology-lesson/05-merging-data/index.html)
Read: Python Data Science Handbook ch. 3
FYI how to install Plotnine: conda install -c conda-forge plotnine
### Day 22 4/18
[Python testing tutorial](http://katyhuff.github.io/python-testing/)
Read: Effective computation in physics ch. 18