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.

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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

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