bdchecks v0.1.7
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Biodiversity Data Checks
Supplies a Shiny app and a set of functions to perform and managing data checks for biodiversity data.
Readme
bdchecks
Managing all data checks
Install bdchecks with:
devtools::install_github("bd-R/bdchecks")
Load with:
library(bdchecks)
Run shiny app with:
runbdchecks()
Performing data checks
Perform data checks (not exported yet):
resultDC <- bdchecks::performDataCheck(dataBats)
Check what data checks were performed (default show method):
resultDC
Export data after data checks (file or R object) (not exported yet):
bdchecks::exportDataCheck(resultDC)
Quick glance at data check result (% of records that passed) (not exported yet):
# Nice summary
summary_DC(resultDC)
Dealing with data checks
Load data checks (DC) into R using getDC() function. Needs local yaml file:
DC <- getDC(pathToYAML)
Export DCs from a given yaml file to rda and roxygen2 comments:
bdchecks:::exportDC(pathToYAML)
Functions in bdchecks
| Name | Description | |
| DC_countryNameUnknown | Data check countryNameUnknown Check if the name of the country or major administrative unit in which the location occurs is within given vocabulary | |
| DC_basisOfRecordBadlyFormed | Data check basisOfRecordBadlyFormed Check if the specific nature of the data record is within controlled vocabulary | |
| DC_namePublishedYearInFuture | Data check namePublishedYearInFuture Check if year in which scientific name was published is not in the future | |
| DC_dateNull | Data check dateNull Check if eventDate, year, verbatimEventDate are not NULL | |
| DC_eventDateInFuture | Data check eventDateInFuture Check if event date is not in the future | |
| DC_dayInvalid | Data check dayInvalid Check if event day is valid (1 <= integer <= 31) | |
| dataCheckFlag_SINGLE-class | Single Data Check Flag Class | |
| DC_classUnknown | Data check classUnknown The full scientific name of the class in which the taxon is classified is within given vocabulary | |
| DC_uncertaintyRangeMismatch | Data check uncertaintyRangeMismatch Check if geopoint uncertainty range mismatch is a positive integer (meters). | |
| DC_individualcountInvalid | Data check individualcountInvalid Check if the number of individuals represented present at the time of the occurrence is and intiger | |
| DC_modifiedInFuture | Data check modifiedInFuture Check if date on which the resource was changed is not in the future | |
| DCtest | Data checks in YAML format | |
| DC_yearMissing | Data check yearMissing Check if year information is not missing | |
| DC_coordinatesZero | Data check coordinatesZero Check if decimal values given in decimalLatitude and decimalLongitude are not zero | |
| createDCclassMain | Create a data check object | |
| DC_countryMismatch | Data check countryMismatch Check if given country match given country code. | |
| filterDataCheck | Filter Data Checks | |
| DC_occurrenceIdNotGuid | Data check occurrenceIdNotGuid Check if an identifier for the occurrence is a globally uniquely identifier (currently we use regex pattern solution is implemented) | |
| DC_identifiedDateImprobable | Data check identifiedDateImprobable Check if identification date is between Linnaeus and current date | |
| generateDCfilts | Filter Data Checks | |
| runbdchecks | Launch bdchecks Shiny Application | |
| exportDC | Export data checks as R objects | |
| dataBats | Australian bats biodiversity data | |
| DC_precisionRangeMismatch | Data check precisionRangeMismatch Check if precision range mismatch is between 0 and 1 | |
| exportDataCheck | Export Data Checks | |
| performDC | Perform Data Checks | |
| createDCclassMeta | Create a data check metadata object | |
| dataCheckMeta-class | Data Check Meta-Data Class | |
| DC_dataGeneralised | Data check dataGeneralised Chech if dataGeneralizations is a NULL column (ie, latitude and longitude were not generalized) | |
| summary_DC | Summarise Data Checks | |
| dataCheck-class | Create Data Check Class | |
| DC_dateIdentifiedInFuture | Data check dateIdentifiedInFuture Check if record identification date is not in the future | |
| generateRoxygenComment | Generate roxygen2 documentation from data check object | |
| getDC | Load Data Checks | |
| DC_depthOutOfRange | Data check depthOutOfRange Check if depthOutOfRange is not out of range. | |
| DC_elevationOutOfRange | Data check elevationOutOfRange Check if elevationOutOfRange is not out of range. | |
| performDataCheck | Perform Data Checks | |
| dataCheckFlag-class | Combined Data Checks Class | |
| DC_monthInvalid | Data check monthInvalid Check if event month is valid (1 <= integer <= 12) | |
| DC_coordinatePrecisionMismatch | Data check coordinatePrecisionMismatch Check if decimal values given in decimalLatitude and decimalLongitude does agree witha a decimal representation of the precision of the coordinates (coordinatePrecision) | |
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Details
| Date | 2019-02-07 |
| License | GPL-3 | file LICENSE |
| URL | https://github.com/bd-R/bdchecks |
| BugReports | https://github.com/bd-R/bdchecks/issues |
| LazyData | true |
| RoxygenNote | 6.1.1 |
| Encoding | UTF-8 |
| NeedsCompilation | no |
| Packaged | 2019-02-09 09:38:55 UTC; pogibas |
| Repository | CRAN |
| Date/Publication | 2019-02-18 15:00:07 UTC |
| imports | bdDwC , data.table , DT , finch , knitr , methods , rgbif , shiny , shinyBS , shinydashboard , shinyjs , spocc , yaml |
| suggests | covr , testthat |
| depends | R (>= 2.10) |
| Contributors | Vijay Barve, Tomer Gueta, Thiloshon Nagarajah, Yohay Carmel |
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