Name: rfigshare
Owner: rOpenSci
Description: Programmatic interface for Figshare
Created: 2012-06-13 15:34:22.0
Updated: 2017-08-25 05:20:28.0
Pushed: 2017-12-13 20:31:11.0
Homepage: null
Size: 1180
Language: R
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title: rfigshare tutorial
An R interface to FigShare
ire(devtools)
all_github("rfigshare", "ropensci")
ire(rfigshare)
The first time you use an rfigshare function, it will ask you to authenticate online. Just log in and click okay to authenticate rfigshare. R will allow you to cache your login credentials so that you won't be asked to authenticate again (even between R sessions), as long as you are using the same working directory in future.
Try a search for an author:
uthor_search("Boettiger")
ist()
Try creating your own content:
- fs_create("Test title", "description of test")
our article has been created! Your id number is 1126334
This creates an article with the essential metadata information. We can now upload the dataset to this newly created figshare object using fs_upload. For the purposes of this example, we'll just upload one of R's built-in datasets:
(mtcars)
e.csv(mtcars, "mtcars.csv")
pload(id, "mtcars.csv")
Not that we must pass the id number of our the newly created figshare object as the first argument. Similar functions let us add additional authors, tags, categories, and links, e.g.
dd_tags(id, "demo")
Minimal metadata includes title, description, type, and at least one tag and one category. We can add categories using either the category id or the name of the category, but it must be one of the preset categories available. We can ask the API for a list of all the categories:
ategory_list()
id name
[1,] 1 Biophysics
[2,] 4 Biochemistry
[3,] 7 Medicine
[4,] 8 Microbiology
[5,] 10 Anatomy
[6,] 11 Behavioral Neuroscience
[7,] 12 Cell Biology
[8,] 13 Genetics
[9,] 14 Molecular Biology
[10,] 15 Neuroscience
[11,] 16 Physiology
[12,] 17 Geography
[13,] 19 Pharmacology
[14,] 20 Computer Engineering
[15,] 21 Biotechnology
[16,] 23 Software Engineering
[17,] 24 Evolutionary Biology
[18,] 25 Anthropology
[19,] 27 Economics
[20,] 28 Paleontology
[21,] 29 Geology
[22,] 31 Environmental Chemistry
[23,] 32 Geochemistry
[24,] 34 Environmental Science
[25,] 35 Limnology
[26,] 36 Oceanography
[27,] 37 Organic Chemistry
[28,] 39 Ecology
[29,] 42 Biological Engineering
[30,] 44 Toxicology
[31,] 45 Sociology
[32,] 46 Immunology
[33,] 47 Stereochemistry
[34,] 54 Planetary Geology
[35,] 55 Stellar Astronomy
[36,] 56 Galactic Astronomy
[37,] 57 Cosmology
[38,] 58 Astrophysics
[39,] 59 Planetary Science
[40,] 61 Developmental Biology
[41,] 62 Marine Biology
[42,] 63 Parasitology
[43,] 64 Cancer
[44,] 65 Botany
[45,] 66 Crystallography
[46,] 69 Inorganic Chemistry
[47,] 70 Molecular Physics
[48,] 71 Nuclear Chemistry
[49,] 73 Radiochemistry
[50,] 75 Supramolecular Chemistry
[51,] 76 Theoretical Computer Science
[52,] 77 Applied Computer Science
[53,] 78 Atmospheric Sciences
[54,] 79 Geophysics
[55,] 80 Hydrology
[56,] 82 Mineralogy
[57,] 84 Paleoclimatology
[58,] 85 Palynology
[59,] 86 Physical Geography
[60,] 87 Soil Science
[61,] 88 Agricultural Engineering
[62,] 89 Aerospace Engineering
[63,] 90 Genetic Engineering
[64,] 91 Mechanical Engineering
[65,] 92 Nuclear Engineering
[66,] 94 Art
[67,] 95 Design
[68,] 97 Law
[69,] 98 Literature
[70,] 99 Performing Arts
[71,] 100 Philosophy
[72,] 102 Algebra
[73,] 103 Geometry
[74,] 104 Probability
[75,] 105 Statistics
[76,] 106 Science Policy
[77,] 107 Applied Physics
[78,] 108 Atomic Physics
[79,] 109 Computational Physics
[80,] 110 Condensed Matter Physics
[81,] 111 Mechanics
[82,] 112 Particle Physics
[83,] 113 Plasma Physics
[84,] 114 Quantum Mechanics
[85,] 115 Solid Mechanics
[86,] 116 Thermodynamics
[87,] 117 Entropy
[88,] 118 General Relativity
[89,] 119 M-Theory
[90,] 120 Special Relativity
[91,] 122 Mental Health
[92,] 125 Bioinformatics
[93,] 126 History
[94,] 127 Archaeology
[95,] 128 Hematology
[96,] 129 Education
[97,] 130 Survey Results
[98,] 131 Anesthesiology
[99,] 132 Infectious Diseases
100,] 133 Plant Biology
101,] 134 Virology
102,] 135 Computational Biology
103,] 136 NMR Spectroscopy
104,] 137 Cheminformatics
105,] 138 Numerical Analysis
106,] 139 Pathology
107,] 140 Cardiology
108,] 141 Computational Chemistry
109,] 143 Solid Earth Sciences
110,] 144 Climate Science
111,] 145 Solar System, Solar Physics, Planets and Exoplanets
112,] 146 Space Science
113,] 147 Stars, Variable Stars
114,] 148 Instrumentation, Techniques, and Astronomical Observations
115,] 149 Interstellar and Intergalactic Matter
116,] 150 Extragalactic Astronomy
117,] 151 Biomarkers
118,] 152 Pathogenesis
119,] 153 Health Care
120,] 154 Diseases
121,] 155 Stem Cells
122,] 156 Systems Biology
123,] 157 Structural Biology
124,] 158 Biological Techniques
125,] 159 Zoology
126,] 160 Digital Humanities
127,] 161 Disability Studies
128,] 162 Drama
129,] 163 Entertainment
130,] 164 Environmental Humanities
131,] 165 Ethnic Studies
132,] 166 Gender studies
133,] 167 Language
134,] 168 Linguistics
135,] 169 Media Studies
136,] 170 Museology
137,] 171 Religious Studies
138,] 172 Rhetoric
139,] 173 Applied Psychology
140,] 174 Clinical Psychology
141,] 175 Developmental and Educational Psychology
142,] 176 Neuroscience and Physiological Psychology
143,] 177 Organizational Behavioral Psychology
144,] 178 Personality, Social and Criminal Psychology
145,] 179 Artificial Intelligence and Image Processing
146,] 180 Computation Theory and Mathematics
147,] 181 Computer Software
148,] 182 Data Format
149,] 183 Distributed Computing
150,] 184 Information Systems
151,] 185 Library and Information Studies
And we can add the category or categories we like,
dd_categories(id, c("Education", "Software Engineering"))
The file we have created remains saved as a draft until we publish it, either publicly or privately. Note that once a file is declared public, it cannot be made private or deleted. Let's release this dataset privately:
ake_private(id)
esponse [http://api.figshare.com/v1/my_data/articles/1126334/action/make_private]
Status: 200
Content-type: application/json; charset=UTF-8
Size: 48 B
"success": "Article status changed to Private"}
We can now share the dataset with collaborators by way of the private url.
The rfigshare package will let you create a new figshare article with additional authors, tags, categories, etc in a single command usnig the fs_new_article function. The essential metadata title, description and type are required, but any other information we omit at this stage can be added later. If we set visibility to private or public, the article is published on figshare immediately.
(mtcars)
e.csv(mtcars,"mtcars.csv")
- fs_new_article(title="A Test of rfigshare",
description="This is a test",
type="dataset",
authors=c("Karthik Ram", "Scott Chamberlain"),
tags=c("ecology", "openscience"),
categories="Ecology",
links="http://ropensci.org",
files="mtcars.csv",
visibility="private")
our article has been created! Your id number is 1126335
nk("mtcars.csv") # clean up
We can view all available metadata of a figshare object.
etails(id)
rticle_id: 1.1263e+06
itle: A Test of rfigshare
aster_publisher_id: 0.0e+00
efined_type: dataset
tatus: Private
ersion: 1.0
ublished_date: 06:25, Aug 03, 2014
escription: This is a test
escription_nohtml: This is a test
otal_size: 1.70 KB
uthors:
first_name: Ropensci
last_name: Testaccount
id: 4.3142e+05
full_name: Ropensci TestAccount
first_name: Karthik
last_name: Ram
id: 9.7306e+04
full_name: Karthik Ram
first_name: Scott
last_name: Chamberlain
id: 9.6554e+04
full_name: Scott Chamberlain
ags:
id: 1.9539e+05
name: Published using rfigshare
id: 4.7864e+04
name: openscience
id: 1.1917e+04
name: ecology
ategories:
id: 39.0
name: Ecology
iles:
size: 2 KB
thumb: ~
id: 1.6204e+06
mime_type: text/plain
name: mtcars.csv
inks:
link: http://ropensci.org
id: 673.0
You can see all of the files you have (Currently only up to 10):
<- fs_browse()
[1:2]
[1]]
rticle_id: 1.1263e+06
itle: A Test of rfigshare
aster_publisher_id: 0.0e+00
efined_type: dataset
tatus: Private
ersion: 1.0
ublished_date: 06:25, Aug 03, 2014
escription: This is a test
escription_nohtml: This is a test
otal_size: 1.70 KB
uthors:
first_name: Ropensci
last_name: Testaccount
id: 4.3142e+05
full_name: Ropensci TestAccount
first_name: Karthik
last_name: Ram
id: 9.7306e+04
full_name: Karthik Ram
first_name: Scott
last_name: Chamberlain
id: 9.6554e+04
full_name: Scott Chamberlain
ags:
id: 1.9539e+05
name: Published using rfigshare
id: 4.7864e+04
name: openscience
id: 1.1917e+04
name: ecology
ategories:
id: 39.0
name: Ecology
iles:
size: 2 KB
thumb: ~
id: 1.6204e+06
mime_type: text/plain
name: mtcars.csv
inks:
link: http://ropensci.org
id: 673.0
[2]]
rticle_id: 1.1263e+06
itle: Test title
aster_publisher_id: 0.0e+00
efined_type: dataset
tatus: Private
ersion: 1.0
ublished_date: 06:25, Aug 03, 2014
escription: description of test
escription_nohtml: description of test
otal_size: 1.70 KB
uthors:
first_name: Ropensci
last_name: Testaccount
id: 4.3142e+05
full_name: Ropensci TestAccount
ags:
id: 1.5681e+04
name: demo
id: 1.9539e+05
name: Published using rfigshare
ategories:
id: 23.0
name: Software Engineering
id: 129.0
name: Education
iles:
size: 2 KB
thumb: ~
id: 1.6204e+06
mime_type: text/plain
name: mtcars.csv
inks: []
Note that we can easily grab the ids with the wrapper function fs_ids:
ds(mine)
[1] 1126335 1126334 1126332 1126329 1126328 1126324 1126322 1126321
[9] 1126318 1126317
We can delete unwanted files that are not public with fs_delete:
elete(id)
To cite package rfigshare in publications use:
tion("rfigshare")
o cite package 'rfigshare' in publications use:
Carl Boettiger, Scott Chamberlain, Karthik Ram and Edmund Hart
(2014). rfigshare: an R interface to figshare.com.. R package
version 0.3-1. http://CRAN.R-project.org/package=rfigshare
BibTeX entry for LaTeX users is
@Manual{,
title = {rfigshare: an R interface to figshare.com.},
author = {Carl Boettiger and Scott Chamberlain and Karthik Ram and Edmund Hart},
year = {2014},
note = {R package version 0.3-1},
url = {http://CRAN.R-project.org/package=rfigshare},
}
