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karthik.github.io/BOSC

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Fostering
 open science with R

Karthik Ram

@_inundata




An article about [computational] science in a scientific publication is not the scholarship itself, it is merely advertising of the scholarship. The actual scholarship is the complete set of instructions [and data] which generated the figures.

- David Donoho (Stanford University)

The way we do science is also changing

The four pillars of scientific practice

Experimentation, theory, computing, data-intensive


How and where these data were obtained is often a black box



Data and computer code should be made available at an early stage
Article

Open data + code

Source: Wolkovich et al. Global Change Biology, 2012.





Enable access to scientific data repositories, full-text of articles, and science metrics and also facilitate a culture shift in the scientific community.



More info @ ropensci.org/packages

       
 Data
Treebase 
Fishbase
GBIF
Dryad

        
  Journals
PLOS
Springer
Mendeley
textmine
pensoft
        
 Data Viz
rMaps
plot.ly

        
  Data Publication figshare
git2r
rdat
DataONE 
rAltmetric
EML

50+ years of fisheries data

library(rfisheries)
library(dplyr)
who <- c("TUX", "COD", "VET", "NPA")
# Four well known commercial fisheries
species_data <- function(x) of_landings(species = x)
who %>% lapply(., species_data) %>% rbind_all

World Bank climate portal rWBclimate

library(rWBclimate)
eu_basin <- create_map_df(Eur_basin)
eu_basin_dat <- get_ensemble_temp(Eur_basin, "annualanom", 2080, 2100)

Data Viz

Interactively visualize and analyze data



Taxon specific databases - AntWeb

library(AntWeb); library(dplyr)
aw_data(genus = "acanthognathus") %>% aw_map

Document and upload your data

Easily deposit data alongside analysis



Sharing data - (rfigshare)

Using figshare's API it is possible to share figures, data and any other objects generated in R and obtain a data citation.


library(rfigshare)
id <- fs_create("Fisheries dataset", "A dataset containing catch for 4 important commercial fish species","dataset")
fs_upload(id, "dat.csv")

 


The scientific workflow


The scientific workflow

Made possible by generous support from

ropensci.org


karthik.github.io/BOSC

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