In selinaZitrone/YoMos2020: Example of Good Scientific Programming Practice
options(htmltools.dir.version = FALSE)
knitr::opts_chunk$set(
fig.width=9, fig.height=3.5, fig.retina=3,
out.width = "100%",
cache = FALSE,
echo = FALSE,
message = FALSE,
warning = FALSE,
fig.show = TRUE,
hiline = TRUE
)
library(xaringanthemer)
style_mono_accent(
base_color = "#2369bd",
header_font_google = google_font("Playfair"),
text_font_google = google_font("Roboto", "300", "300i"),
code_font_google = google_font("Fira Mono"),
text_font_size = "13pt",
header_h1_font_size = "30pt",
header_h2_font_size = "24pt",
header_background_content_padding_top = "0rem",
)
Workshop overview
.pull-left[
.left[.small[This image was created by Scriberia for The Turing Way community and is used under a CC-BY licence (DOI 10.5281/zenodo.3332807).]]]
--
.pull-right[
Two main topics
-
Research compendia
-
R packages
Resources
-
Code on github https://github.com/selinaZitrone/YoMos2020
-
Slides on https://selinazitrone.github.io/YoMos2020/index.html
-
How-To on https://selinazitrone.github.io/YoMos2020/how_to.html
]
Motivations for a better project organization and workflow
--
- Reproduciblity 🔃 (for you and others)
--
- Reliablity 🏋 (will it work again?)
--
- Re-usablity ⚙ (don't re-invent the wheel)
--
- Visiblity 🔍 (let others see and use your work)
How? Use a research compendium!
.pull-left[
.left[.small[This image was created by Scriberia for The Turing Way community and is used under a CC-BY licence (DOI 10.5281/zenodo.3332807).]]
]
.pull-right[
This is a collection of all digital parts of a research project including data,
code, texts (protocols, reports, questionnaires, metadata). The collection is created
in such a way that reproducing all results is straight forward.
(Definition from The Turing Way)1
.footnote[
[1] Excursion to the TTW website
]
]
What is a research compendium?
.pull-left[
Principles
-
stick with the conventions in your field
-
Keep data, methods and output separate
-
specify the computational environment
]
--
.pull-right[
Key components
-
License
-
VCS
-
Metadata
-
Archive
]
.footnote[
from Karthik Ram's talk at RStudio::conf 2019
]
It's an 📦 R Package!
.pull-left[
.center[
]]
--
.pull-right[
- packages generating similar project directory structures:
rrtoolsProjectTemplateprodigenrworkflowr
]
Advantages of using R Packages
--
- benefit from quality control mechanisms built around R packages (
R CMD check)
--
- easy documentation
--
- additional packages available to make your life easier
usethis: workflow package to automate tasks like project setup etc.pkgdown: build a quick and easy website for your packagegoodpractice: gives you advice about good
practices when building R packagestestthat: add unit testing to your package- ... and many more
class: inverse
Hands-on I
Create a research compendium with the R package structure
Version control
.center[
]
Git as a distributed version control system (VCS)
- complete and long-term history of every file in your project
- go back to specific versions of your project
- collaborate in teams
- branching and merging
- tracability: each change is commented and can be traced back to a developer
- host your repository on remote server (GitHub, Bitbucket, GitLab, ...)
- open-source collaborative development
- visibility: get new collaborators, feedback, bug reports
class: inverse
Hands-on II
Add version control to the research compendium
Automated testing
--
What?
- unit tests: functions that run a small amount of code: "units"
- input: defined and fixed
- compares output with an expected output
- returns true/false
--
Why?
- fewer bugs
- better code (needs to be testable)
- confidence and trust
--
How?
- write tests either before or after implementing your code
- when you found a bug: before fixing, write a test that would have detected it
- use a test framework, e.g. in R:
testthat package (Hadley Wickham)
class: inverse
Hands-on III
Unit tests
Continous integration (CI)
--
.pull-left[
"If it hurts, do it more often"
.right[(Martin Fowler)]
]
--
.pull-right[
Ideas
-
shared code repository (e.g. on github)
-
push code frequently (every day)
-
automated builds and tests after each commit
-
immediate feedback if something doesn't work anymore
-
however, can be time consuming and might be overkill for small or solo projects
]
background-image: url('images/github-actions-with-text.jpg')
background-position: 100% 50%
background-size: 40%
Github Actions for CI (and other automation tasks)
--
- supports mac-OS, windows, linux, docker containers
--
- integration with github, so no separate setup and authentication
--
- free for open source, academic or educational repos
--
- 20 concurrent jobs (40 with pro), 6 h per job, 72 h per workflow
--
- self host to remove the per job limit
--
- very easy to setup with R using the
usethis package
.right[.footer[.small[This image was created by Scriberiafor The Turing Way community
and is used under a CC-BY licence (DOI 10.5281/zenodo.3332807).]]]
class: inverse
Hands-on IV
Github Actions for R CMD check
Reproducibility and Accessability
Excursion to Karthik Ram's talk at RStudio::conf 2019
class: inverse
Hands-on V
Publish your repository on Binder with a live RStudio server instance
selinaZitrone/YoMos2020 documentation built on June 29, 2021, 2:08 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
options(htmltools.dir.version = FALSE) knitr::opts_chunk$set( fig.width=9, fig.height=3.5, fig.retina=3, out.width = "100%", cache = FALSE, echo = FALSE, message = FALSE, warning = FALSE, fig.show = TRUE, hiline = TRUE )
library(xaringanthemer) style_mono_accent( base_color = "#2369bd", header_font_google = google_font("Playfair"), text_font_google = google_font("Roboto", "300", "300i"), code_font_google = google_font("Fira Mono"), text_font_size = "13pt", header_h1_font_size = "30pt", header_h2_font_size = "24pt", header_background_content_padding_top = "0rem", )
Workshop overview
.pull-left[
.left[.small[This image was created by Scriberia for The Turing Way community and is used under a CC-BY licence (DOI 10.5281/zenodo.3332807).]]]
--
.pull-right[
Two main topics
-
Research compendia
-
R packages
Resources
-
Code on github https://github.com/selinaZitrone/YoMos2020
-
Slides on https://selinazitrone.github.io/YoMos2020/index.html
-
How-To on https://selinazitrone.github.io/YoMos2020/how_to.html
]
Motivations for a better project organization and workflow
--
- Reproduciblity 🔃 (for you and others)
--
- Reliablity 🏋 (will it work again?)
--
- Re-usablity ⚙ (don't re-invent the wheel)
--
- Visiblity 🔍 (let others see and use your work)
How? Use a research compendium!
.pull-left[
.left[.small[This image was created by Scriberia for The Turing Way community and is used under a CC-BY licence (DOI 10.5281/zenodo.3332807).]]
]
.pull-right[
This is a collection of all digital parts of a research project including data, code, texts (protocols, reports, questionnaires, metadata). The collection is created in such a way that reproducing all results is straight forward.
(Definition from The Turing Way)1
.footnote[ [1] Excursion to the TTW website
] ]
What is a research compendium?
.pull-left[
Principles
-
stick with the conventions in your field
-
Keep data, methods and output separate
-
specify the computational environment
]
--
.pull-right[
Key components
-
License
-
VCS
-
Metadata
-
Archive
]
.footnote[ from Karthik Ram's talk at RStudio::conf 2019 ]
It's an 📦 R Package!
.pull-left[
.center[
]]
--
.pull-right[
- packages generating similar project directory structures:
rrtoolsProjectTemplateprodigenrworkflowr
]
Advantages of using R Packages
--
- benefit from quality control mechanisms built around R packages (
R CMD check)
--
- easy documentation
--
- additional packages available to make your life easier
usethis: workflow package to automate tasks like project setup etc.pkgdown: build a quick and easy website for your packagegoodpractice: gives you advice about good practices when building R packagestestthat: add unit testing to your package- ... and many more
class: inverse
Hands-on I
Create a research compendium with the R package structure
Version control
.center[]
Git as a distributed version control system (VCS)
- complete and long-term history of every file in your project
- go back to specific versions of your project
- collaborate in teams
- branching and merging
- tracability: each change is commented and can be traced back to a developer
- host your repository on remote server (GitHub, Bitbucket, GitLab, ...)
- open-source collaborative development
- visibility: get new collaborators, feedback, bug reports
class: inverse
Hands-on II
Add version control to the research compendium
Automated testing
--
What?
- unit tests: functions that run a small amount of code: "units"
- input: defined and fixed
- compares output with an expected output
- returns true/false
--
Why?
- fewer bugs
- better code (needs to be testable)
- confidence and trust
--
How?
- write tests either before or after implementing your code
- when you found a bug: before fixing, write a test that would have detected it
- use a test framework, e.g. in R:
testthatpackage (Hadley Wickham)
class: inverse
Hands-on III
Unit tests
Continous integration (CI)
--
.pull-left[
"If it hurts, do it more often" .right[(Martin Fowler)]
]
--
.pull-right[
Ideas
-
shared code repository (e.g. on github)
-
push code frequently (every day)
-
automated builds and tests after each commit
-
immediate feedback if something doesn't work anymore
-
however, can be time consuming and might be overkill for small or solo projects ]
background-image: url('images/github-actions-with-text.jpg') background-position: 100% 50% background-size: 40%
Github Actions for CI (and other automation tasks)
--
- supports mac-OS, windows, linux, docker containers
--
- integration with github, so no separate setup and authentication
--
- free for open source, academic or educational repos
--
- 20 concurrent jobs (40 with pro), 6 h per job, 72 h per workflow
--
- self host to remove the per job limit
--
- very easy to setup with R using the
usethispackage
.right[.footer[.small[This image was created by Scriberiafor The Turing Way community
and is used under a CC-BY licence (DOI 10.5281/zenodo.3332807).]]]
class: inverse
Hands-on IV
Github Actions for R CMD check
Reproducibility and Accessability
Excursion to Karthik Ram's talk at RStudio::conf 2019
class: inverse
Hands-on V
Publish your repository on Binder with a live RStudio server instance
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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