Title: | Darwinizer: Darwin Core (DwC) Field Names Standardization |
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Description: | The 'shiny' application 'bdDwC' makes biodiversity data field names Darwin Core compatible. |
Authors: | Povilas Gibas [aut, cre]
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Maintainer: | Povilas Gibas <[email protected]> |
License: | GPL-3 |
Version: | 0.1.15 |
Built: | 2024-09-01 03:31:53 UTC |
Source: | https://github.com/cran/bdDwC |
'combineOldNew()' is a function that combines ('paste') fieldname and standard names with unicode characters to present in checkboxes.
combineOldNew(data, symbolArrow = "->", symbolSpace = " ")
combineOldNew(data, symbolArrow = "->", symbolSpace = " ")
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 |
data.frame of darwinized user names.
'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).
darwinizeNames(dataUser, dataDWC)
darwinizeNames(dataUser, dataDWC)
dataUser |
data.frame with user data |
dataDWC |
data.frame with Darwin Cloud data |
data.frame of darwinized user names.
darwinizeNames(dataUser = bdDwC:::dataReptiles, dataDWC = bdDwC:::dataDarwinCloud$data)
darwinizeNames(dataUser = bdDwC:::dataReptiles, dataDWC = bdDwC:::dataDarwinCloud$data)
Darwin Cloud data used to Darwinize. Darwin Cloud data was retrieved using 'bdDwC::downloadCloudData()' function. This dataset contains Darwin Cloud data and download date.
dataDarwinCloud
dataDarwinCloud
A list of length two. First entry contains a data frame with 422 rows and 2 columns. Second entry contains a 'Date' class object.
Dataset that contains subsample of Indian reptile observations from the iNaturalist platform.
dataReptiles
dataReptiles
A data frame with 50 rows and 41 columns.
'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.
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")
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")
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. |
data.frame of Darwin Cloud data.
downloadCloudData()
downloadCloudData()
'getDarwinCoreInfo()' is a function (not exported) to download Darwin Core Terms. This information is displayed when using manually renaming.
getDarwinCoreInfo(pathDarwinCloud = "http://tdwg.github.io/dwc/terms/")
getDarwinCoreInfo(pathDarwinCloud = "http://tdwg.github.io/dwc/terms/")
pathDarwinCloud |
Path to Darwin Cloud data. |
data.frame that contains name and definition for each available Darwin Cloud term.
'renameUserData()' is a function used to rename given dataset (usually given user data) according previously Darwinized Names.
renameUserData(dataUser, dataRenamed)
renameUserData(dataUser, dataRenamed)
dataUser |
data.frame of be renamed. |
dataRenamed |
data.frame that was created using 'bdDwC:::darwinizeNames()' function using same 'dataUser'. |
data.frame of submitted user data, but renamed according given renames data.frame.
result <- darwinizeNames(dataUser = bdDwC:::dataReptiles, dataDWC = bdDwC:::dataDarwinCloud$data) renameUserData(bdDwC:::dataReptiles, result)
result <- darwinizeNames(dataUser = bdDwC:::dataReptiles, dataDWC = bdDwC:::dataDarwinCloud$data) renameUserData(bdDwC:::dataReptiles, result)
'bdDwC' is a function that starts bdverse Darwin Cloud cleaning 'shiny' app.
runDwC()
runDwC()
'shiny::runApp()' result within browser.