Scott Chamberlain
@recology_
Sharing data increases citations
Sort of a moral obligation as a scientist, right?
And to avoid this ->
Reinhart-Rogoff |
Chronic fatigue syndrome-XMRV |
Our workflow now
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What it could be |
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Cost = $$$$$$$ Open? = Nope Reproducible? = Nope |
Cost = 0 Open? = Yes! Reproducible? = Yep |
API: Application Programming Interface - APIs are the highways connecting providers to users.
knitr
and Markdown/LaTeX
- make an open science workflow
R
, including knitr
and Markdown/LaTeX
- make an open science workflow
Data |
Literature
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Hybrid
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library(rplos)
plot_throughtime(list("reproducible science"), 500)
library(rgbif)
key <- name_backbone(name='Danaus plexippus', kingdom='animals')$speciesKey
out <- occ_search(taxonKey=key, limit=300, return='data')
gbifmap(out)
library(rWBclimate)
country_dat <- get_historical_temp(c("USA", "MEX", "CAN", "BLZ"), "year")
ggplot(country_dat, aes(x = year, y = data, group = locator)) +
theme_bw(base_size=18) +
geom_point() +
geom_path() +
labs(y="Average annual temperature of Canada", x="Year") +
stat_smooth(se = F, colour = "black") +
facet_wrap(~locator, scale = "free")
library(spocc); library(rCharts)
spnames <- c('Accipiter striatus', 'Setophaga caerulescens',
'Spinus tristis')
out <- occ(query=spnames, from=c('gbif','bison'),
gbifopts=list(georeferenced=TRUE))
head(out$gbif$data)
## name key longitude latitude prov
## 1 Accipiter striatus Vieillot, 1808 773408845 -97.28 32.876 gbif
## 2 Accipiter striatus Vieillot, 1808 768992325 -76.10 4.724 gbif
## 3 Accipiter striatus Vieillot, 1808 773414146 -122.27 37.771 gbif
## 4 Accipiter striatus Vieillot, 1808 773440541 -98.00 32.800 gbif
## 5 Accipiter striatus Vieillot, 1808 773423188 -76.54 38.688 gbif
## 6 Accipiter striatus Vieillot, 1808 773432602 -122.78 38.613 gbif
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Xie Y (2012). knitr: A general-purpose package for dynamic report generation in R.
Piwowar paper on GitHub at https://github.com/hpiwowar/citation11k
knitr
and Markdown/LaTeX
- make an open science workflow