Inspiring you to try out rOpenSci packages.
Motivating you to get involved with rOpenSci.
Inspiring you to try out rOpenSci packages.
Motivating you to get involved with rOpenSci.
Sharing a few tips from my experience.
Inspiring you to try out rOpenSci packages.
Motivating you to get involved with rOpenSci.
Sharing a few tips from my experience.
Slidedeck up at https://tiny.cc/animove
BSc in Biology, MSc in (Theoretical) Ecology
Master of Public Health
PhD in Statistics
Nowadays, more of a research software engineer.
Part-time software engineer at rOpenSci & at Locke Data.
BSc in Biology, MSc in (Theoretical) Ecology
Master of Public Health
PhD in Statistics
Nowadays, more of a research software engineer.
Part-time software engineer at rOpenSci & at Locke Data.
Not an actual birder. π
BSc in Biology, MSc in (Theoretical) Ecology
Master of Public Health
PhD in Statistics
Nowadays, more of a research software engineer.
Part-time software engineer at rOpenSci & at Locke Data.
Not an actual birder. π
All pics by my dad. π·
R-Ladies Global social master
R Weekly team member (and blogger myself!)
Volunteer editor for rOpenSci onboarding
Community of researchers and software developers
R packages for open and reproducible science
Community and staff contributions
How to ensure quality in the whole suite?
How to ensure quality in the whole suite?
Open software reviews.
How to ensure quality in the whole suite?
Open software reviews.
How to ensure quality in the whole suite?
Open software reviews.
drive adoption of best practices and standards
build a community of practice
How to ensure quality in the whole suite?
Open software reviews.
drive adoption of best practices and standards
build a community of practice
partnerships with the Journal of Open Source Software and Methods in Ecology and Evolution
magick::image_read("https://raw.github.com/jtleek/rpackages/master/documentation.png")
Open-source initiative (OSI) compatible license
Complete docs
High test coverage
Readable code
Usability
Open-source initiative (OSI) compatible license
Complete docs
High test coverage
Readable code
Usability
Bye bye source("myfunctions.R")
, hello library("mypkg")
!
Bye bye source("myfunctions.R")
, hello library("mypkg")
!
At least for future you!
Automatic tools make it easier
List of resources: https://masalmon.eu/2017/12/11/goodrpackages/
Open & non-adversarial
No rejections
Open & non-adversarial
No rejections
Makes the process constructive for everyone involved
Open & non-adversarial
No rejections
Makes the process constructive for everyone involved
Technically, using GitHub infrastructure
No rejections... but out-of-scope packages not onboarded.
https://ropensci.github.io/dev_guide/policies.html#aims-and-scope
No rejections... but out-of-scope packages not onboarded.
https://ropensci.github.io/dev_guide/policies.html#aims-and-scope
No rejections... but out-of-scope packages not onboarded.
https://ropensci.github.io/dev_guide/policies.html#aims-and-scope
fit in our categories: data retrieval, data extraction, database access, data munging, data deposition, reproducibility, geospatial data, text analysis.
application in science
No rejections... but out-of-scope packages not onboarded.
https://ropensci.github.io/dev_guide/policies.html#aims-and-scope
fit in our categories: data retrieval, data extraction, database access, data munging, data deposition, reproducibility, geospatial data, text analysis.
application in science
better than similar packages
No rejections... but out-of-scope packages not onboarded.
https://ropensci.github.io/dev_guide/policies.html#aims-and-scope
fit in our categories: data retrieval, data extraction, database access, data munging, data deposition, reproducibility, geospatial data, text analysis.
application in science
better than similar packages
When in doubt, pre-submission enquiry!
Ongoing discussion until acceptance and transfer
Ongoing discussion until acceptance and transfer
Often a blog post https://ropensci.org/tags/review/
5 use cases. Not all detailed in the talk! π
5 use cases. Not all detailed in the talk! π
All details in blog posts https://ropensci.org/tags/birder/
Leveraging rOpenSci packages and also:
the magrittr
pipe %>%
to pass output from one function to the following function
tidyverse
(ggplot2
, dplyr
, purrr
)
sf
R Markdown
Open geographical data (π OpenStreetMap)
opencage
osmdata
osmplotr
https://ropensci.org/blog/2018/08/14/where-to-bird/ (co-written with Mark Padgham)
What birds are observed in the county?
eBird occurrence data
rebird
, API, latest 30 days
auk
, access request needed, whole dataset
Occurrence data
rebird
and auk
more data sources via spocc
mapr
, scrubr
, CoordinateCleaner
https://ropensci.org/blog/2018/08/21/birds-radolfzell/
Taxonomy and traits data of these birds
Taxonomy and traits data of these birds
ids <- taxize::get_uid(unique(ebd$scientific_name))classif <- taxize::classification(ids)tree <- taxize::class2tree(classif)
library("ggplot2")ggtree::ggtree(tree$phylo) + ggtree::geom_tiplab(aes(), size = 2, vjust=0.25) + xlim(0, 150)
rphylopic
+ phylobase
+ ugly code
Taxonomy: taxize
Traits: traits
https://ropensci.org/blog/2018/09/04/birds-taxo-traits/
https://ropensci.org/blog/2018/09/11/birds-science/
Literature: fulltext
& more!
https://ropensci.org/blog/2018/09/11/birds-science/
Literature: fulltext
& more!
Open scientific data: dataone
(not rOpenSci), rfigshare
https://ropensci.org/blog/2018/08/28/birds-ocr/
magick
for image manipulationhttps://ropensci.org/blog/2018/08/28/birds-ocr/
magick
for image manipulation
tesseract
for optical character recognition (OCR)
https://ropensci.org/blog/2018/08/28/birds-ocr/
magick
for image manipulation
tesseract
for optical character recognition (OCR)
cld2
and cld3
for language recognition
https://ropensci.org/blog/2018/08/28/birds-ocr/
magick
for image manipulation
tesseract
for optical character recognition (OCR)
cld2
and cld3
for language recognition
taxize::gnr_resolve
for taxonomic name resolution
Missing from this overview: workflow packages such as drake
, gistr
, git2r
.
https://ropensci.org/packages/
https://ropensci.org/tags/birder/
Twitter #rstats hashtag
Conference programs & videos
Fine not to know everything!
Learn asking for help and advice
when you need
where you should https://masalmon.eu/2018/07/22/wheretogethelp/
Make R friends
By doing!
Try out stuff for yourself
Blog! blogdown
Danielle Navarro's 100 days of code https://djnavarro.net/#posts
My own blog https://masalmon.eu/2018/07/16/soapbox/
https://github.com/ropensci/onboarding
https://ropensci.org/community/
ma_salmon, maelle , masalmon.eu
rOpenSci, ropensci , ropensci.org
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