BdDwC User Guide Bd Dw C
User Manual:
Open the PDF directly: View PDF 
.
Page Count: 25
| Download | |
| Open PDF In Browser | View PDF |
bdDwC User Guide
Authors: Tomer Gueta and Povilas Gibas
built on2018-11-28 - for bdDwC v0.1.21
2
Contents
Introduction
5
1 Installing bdDwC
1.1 Stable version from CRAN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.2 Development version from GitHub . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.3 Possible problems & solutions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
7
7
7
7
2 The
2.1
2.2
2.3
2.4
2.5
2.6
2.7
2.8
2.9
shiny app
Launching the app . . . . . . . .
App overview . . . . . . . . . . .
Data upload . . . . . . . . . . . .
Dictionaries . . . . . . . . . . . .
Darwinizing your dataset . . . .
Darwinizer results . . . . . . . .
Download your Darwinized data
Closing the app . . . . . . . . . .
References . . . . . . . . . . . . .
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
9
9
9
9
12
12
12
14
14
14
3 Command line operations
15
3.1 Load package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
3.2 Darwinizing a dataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
3.3 Updating the Darwin Cloud dictionary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
4 Examples
17
5 Getting your feedback
19
5.1 Report a bug . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
5.2 Contribute . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
6 bdDwC citation
21
7 Learn more about Darwin Core
23
3
4
CONTENTS
Introduction
bdDwC is a R package that supplies an interactive Shiny app and a set of functions for standardizing field
names in compliance to the Darwin Core (DwC) format. bdDwC is a key element in the bdverse– a collection
of tools, that form a general framework for facilitating biodiversity science in R.
What is the Darwin Core standard?
Darwin Core (DwC) is a global standard for publishing biodiversity data, whose goal is to facilitate the
sharing of biodiversity information, by providing identifiers, labels, and definitions (Wieczorek et al., 2012).
DwC was established as an evolving community-developed standard, by the Biodiversity Information Standards Working Group (www.tdwg.org). DwC is a library of definitions of common biodiversity data terms,
each of which represents a field within the database. There are around 200 such fields (not including DwC
extensions); a full set of the DwC terms with their descriptions is available in the Quick Reference Guide
(http://rs.tdwg.org/dwc/terms). For more information see section 6.
Why it’s important to “Darwinize” a dataset
Running the Darwinizer enables you to standardize many field names in your dataset – and that allows
the bdverse to handle data from various biodiversity portals seamlessly, and lets you enjoy all of bdvers
features, regardless of publishers variation in field names.
Fundings
• See the GSoC project idea page
5
6
CONTENTS
Figure 1: bdDwC in the bdverse
Figure 2:
Chapter 1
Installing bdDwC
1.1
Stable version from CRAN
install.packages("bdDwC")
1.2
Development version from GitHub
Windows users install Rtools first.
install.packages("devtools")
devtools::install_github("bd-R/bdDwC")
1.3
Possible problems & solutions
[ TBA ]
1.3.1
???
TBA
1.3.2
????
TBA
7
8
CHAPTER 1. INSTALLING BDDWC
Chapter 2
The shiny app
2.1
Launching the app
library(bdDwC) # Laod package library
runDwC() # Launch the app
2.2
App overview
In the first screen, you’ll need to load your biodiversity data; choose dictionary and run the Darwinizer.
There are two options, form a file on your computer, of fetch from a web based data provider.
2.3
Data upload
2.3.1
From a local file
A CSV file or a Darwin Core Archive (DwC-A) zip file can be uploaded.
2.3.2
From an online database
Also, data can be retrieved directly from various online biodiversity databases. You need only to:
•
•
•
•
•
Select the database
Specify the desired scientific name.
Specify the number of records (upper limit of 50,000).
Check the box if records must have coordinates.
Wait for data to be downloaded.
9
10
CHAPTER 2. THE SHINY APP
Figure 2.1: bdDwC App Overview
Figure 2.2: Data upload from a local file
2.3. DATA UPLOAD
11
Figure 2.3: Data upload from online biodiversity databases
12
CHAPTER 2. THE SHINY APP
Figure 2.4: Updating the Darwin Cloud dictionary
2.4
Dictionaries
A dictionary is a key component when Darwinizing a dataset. It’s basically a lookup table that lists a
possible variation of field name and it corresponding DwC name.
2.4.1
The Darwin Cloud dictionary
The Darwin Cloud dictionary (Wieczorek et al., 2017), is a lookup table that accumulates different variations in DwC field names from different publishers. This valuable and critical dictionary was created and
is maintained by the Kurator project (http://kurator.acis.ufl.edu/kurator-web/), which provides workflow
tools for data quality improvement of biodiversity data, via a user-friendly web interface. The development
of bdDwC was inspired by Kurator’s own Darwinizer.
Updating the Darwin Cloud dictionary
It’s recommended to update the Darwin Cloud dictionary file. This can be done easily by clicking the
Update DC button.
2.4.2
Custom dictionary
It’s also possible to add your own dictionary by creating a CSV file with two columns, one for the Field
Names and one for the Standard Names. After uploading the custom disctionary, we need to specify which
field denotes the ‘User fierld names’ and which is the ‘Standard (DwC) field names’.
2.5
Darwinizing your dataset
Once a dataset is uploaded, the ‘Submit to Darwinizer’ button is activated, Clicking it will begin the
interactive ‘Darwinize the dataset’ process.
2.6
2.6.1
Darwinizer results
Results page overwiew
Manually renaming field names can be done very easily, just choose the two corresponding fields and click
the Rename button.
Hovering over a DwC standard name will display its description.
2.6. DARWINIZER RESULTS
13
Figure 2.5: Uploading your own dictionary
Figure 2.6: Submit to Darwinizer button
Figure 2.7: Darwinizer results
14
CHAPTER 2. THE SHINY APP
Figure 2.8: Manually renaming fields
2.7
Download your Darwinized data
2.8
Closing the app
Just close the app browser tab, and the R session will be terminated. To reopen it run in the R Console
runDwC().
2.9
References
Chapter 3
Command line operations
3.1
Load package
Load the bdDwC package
library(bdDwC)
3.2
Darwinizing a dataset
bdDwC contains Indian Reptile dataset bdDwC:::dataReptiles.
The function to Darwinize a dataset isdarwinizeNames (replace bdDwC:::dataReptiles with wanted
dataset):
result <- darwinizeNames(dataUser = bdDwC:::dataReptiles,
dataDWC
= bdDwC:::dataDarwinCloud$data)
You can replace bdDwC:::dataReptiles with your dataset
Rename your dataset field names to Darwinized names using renameUserData:
renameUserData(bdDwC:::dataReptiles, result)
3.3
Updating the Darwin Cloud dictionary
To get newest version of Darwin Cloud Data run:
downloadCloudData()
which will download data from the remote repository and extract field and standard names.
15
16
CHAPTER 3. COMMAND LINE OPERATIONS
Chapter 4
Examples
[ TBA ]
17
18
CHAPTER 4. EXAMPLES
Chapter 5
Getting your feedback
Loading…
5.1
Report a bug
Submit an issue at https://github.com/bd-R/bdDwC/issues
5.2
Contribute
Contribute: https://github.com/bd-R/bdDwC
Join: https://bd-r-group.slack.com
19
20
CHAPTER 5. GETTING YOUR FEEDBACK
Chapter 6
bdDwC citation
citation("bdDwC")
##
## To cite package 'bdDwC' in publications use:
##
##
Povilas Gibas, Tomer Gueta, Vijay Barve, Thiloshon Nagarajah and
##
Yohay Carmel (2018). bdDwC: field names conversion to Darwin
##
Core (DwC) format. R package version 0.1.21.
##
https://github.com/bd-R/bdDwC
##
## A BibTeX entry for LaTeX users is
##
##
@Manual{,
##
title = {bdDwC: field names conversion to Darwin Core (DwC) format},
##
author = {Povilas Gibas and Tomer Gueta and Vijay Barve and Thiloshon Nagarajah and Yohay Carmel}
##
year = {2018},
##
note = {R package version 0.1.21},
##
url = {https://github.com/bd-R/bdDwC},
##
}
21
22
CHAPTER 6. BDDWC CITATION
Chapter 7
Learn more about Darwin Core
• The Darwin Core Questions & Answers Site
• Darwin Core Hour webinar series
• The Darwin Core Questions & Answers wiki
• GBIF: What is Darwin Core, and why does it matter?
• Darwin Core: An Evolving Community-Developed Biodiversity Data Standard (Wieczorek et al., 2012)
References
23
24
CHAPTER 7. LEARN MORE ABOUT DARWIN CORE
Bibliography
Wieczorek, J., Bloom, D., Guralnick, R., Blum, S., Döring, M., Giovanni, R., Robertson, T., and Vieglais, D.
(2012). Darwin Core: an evolving community-developed biodiversity data standard. PloS one, 7(1):e29715.
Wieczorek, J., Morris, P. J., Hanken, J., B. Lowery, D., Ludäscher, B., Macklin, J., McPhillips, T., A. Morris,
R., and Zhang, Q. (2017). Darwin cloud: Mapping real-world data to darwin core. Biodiversity Information
Science and Standards, 1:e20486.
25
Source Exif Data:
File Type : PDF File Type Extension : pdf MIME Type : application/pdf PDF Version : 1.5 Linearized : No Page Mode : UseOutlines Page Count : 25 Creator : LaTeX with hyperref package Title : bdDwC User Guide Author : Authors: Tomer Gueta and Povilas Gibas Producer : XeTeX 0.99999 Create Date : 2018:11:28 17:38:42+02:00EXIF Metadata provided by EXIF.tools