| Version: | 0.1.15 |
| Date: | 2018-08-28 |
| Title: | Darwinizer: Darwin Core (DwC) Field Names Standardization |
| Description: | The 'shiny' application 'bdDwC' makes biodiversity data field names Darwin Core compatible. |
| Maintainer: | Povilas Gibas <povilasgibas@gmail.com> |
| Depends: | R (≥ 2.10) |
| Imports: | shiny, shinyBS, shinydashboard, shinyjs, shinyFiles |
| LazyData: | true |
| RoxygenNote: | 6.1.0 |
| License: | GPL-3 |
| Encoding: | UTF-8 |
| Suggests: | testthat, covr |
| NeedsCompilation: | no |
| Packaged: | 2018-08-28 17:45:53 UTC; pogibas |
| Author: | Povilas Gibas 
[aut, cre],
Tomer Gueta [aut],
Vijay Barve [aut],
Thiloshon Nagarajah [aut],
Yohay Carmel [aut] |
| Repository: | CRAN |
| Date/Publication: | 2018-08-31 19:40:03 UTC |
Combine old/new name for checkboxes
Description
'combineOldNew()' is a function that combines ('paste') fieldname and standard names with unicode characters to present in checkboxes.
Usage
combineOldNew(data, symbolArrow = "->", symbolSpace = " ")
Arguments
data |
data.frame of matched names ('darwinizeNames()' output) |
symbolArrow |
character string for symbol that is used in 'paste0' to connect old and new name |
symbolSpace |
character string for symbol used instead of white space |
Value
data.frame of darwinized user names.
Darwinize names
Description
'darwinizeNames()' is a function to darwinize given names using reference (ie, Darwin Cloud) dataset. It returns $Old$ and $New$ ($fieldname$ and $standard$) name (ie, name from given user dataset that had a match in reference dataset).
Usage
darwinizeNames(dataUser, dataDWC)
Arguments
dataUser |
data.frame with user data |
dataDWC |
data.frame with Darwin Cloud data |
Value
data.frame of darwinized user names.
Examples
darwinizeNames(dataUser = bdDwC:::dataReptiles,
dataDWC = bdDwC:::dataDarwinCloud$data)
Darwin Cloud Data
Description
Darwin Cloud data used to Darwinize. Darwin Cloud data was retrieved using 'bdDwC::downloadCloudData()' function. This dataset contains Darwin Cloud data and download date.
Usage
dataDarwinCloud
Format
A list of length two. First entry contains a data frame with 422 rows and 2 columns. Second entry contains a 'Date' class object.
Indian Reptiles
Description
Dataset that contains subsample of Indian reptile observations from the iNaturalist platform.
Usage
dataReptiles
Format
A data frame with 50 rows and 41 columns.
Download Darwin Cloud Data
Description
'downloadCloudData()' is a function used to download Darwin Cloud data. First it downloads data, then it subsets informative columns and renames them so they could be used in 'shiny' app.
Usage
downloadCloudData(pathRemote = "https://raw.githubusercontent.com/kurator-org",
pathGithub = "/kurator-validation/master/packages/kurator_dwca/data/vocabularies/",
pathFile = "darwin_cloud.txt", columnField = "fieldname",
columnStand = "standard")
Arguments
pathRemote |
Path to remote repository (Kurator in Github). |
pathGithub |
Path within given repository. |
pathFile |
Name of a file. |
columnField |
Name of the column that contains field information. |
columnStand |
Name of the column that contains standard information. |
Value
data.frame of Darwin Cloud data.
Examples
downloadCloudData()
Retrieve Information about Darwin Core Terms
Description
'getDarwinCoreInfo()' is a function (not exported) to download Darwin Core Terms. This information is displayed when using manually renaming.
Usage
getDarwinCoreInfo(pathDarwinCloud = "http://tdwg.github.io/dwc/terms/")
Arguments
pathDarwinCloud |
Path to Darwin Cloud data. |
Value
data.frame that contains name and definition for each available Darwin Cloud term.
Rename Dataset According Darwinized Names
Description
'renameUserData()' is a function used to rename given dataset (usually given user data) according previously Darwinized Names.
Usage
renameUserData(dataUser, dataRenamed)
Arguments
dataUser |
data.frame of be renamed. |
dataRenamed |
data.frame that was created using 'bdDwC:::darwinizeNames()' function using same 'dataUser'. |
Value
data.frame of submitted user data, but renamed according given renames data.frame.
Examples
result <- darwinizeNames(dataUser = bdDwC:::dataReptiles,
dataDWC = bdDwC:::dataDarwinCloud$data)
renameUserData(bdDwC:::dataReptiles, result)
Launch bdDwC Shiny Application
Description
'bdDwC' is a function that starts bdverse Darwin Cloud cleaning 'shiny' app.
Usage
runDwC()
Value
'shiny::runApp()' result within browser.