Standardize pedigree column names — fixColumnNames • nprcgenekeepr

Standardizing converts the names to lower case, removes spaces, periods and underscores, and then renames by substring: egoid and ego become id, sireid becomes sire, damid becomes dam, birthdate becomes birth and deathdate becomes death. recordstatus, fromcenter and geographicorigin are restored to their camel case forms; a header already spelled recordStatus, fromCenter or geographicOrigin is not recorded as a change. The headers first_name and second_name keep their underscore. The matching is unanchored, so any name that contains one of these strings is changed (for example, category becomes catidry). A header that is NA is read as a blank one, so a nameless column is reported the way a column with a blank header is.

Usage

fixColumnNames(orgCols, errorLst)

Arguments

orgCols: character vector with ordered list of column names found in a pedigree file. A name that is NA counts as blank.
errorLst: list object with places to store the various column name changes, as returned by getEmptyErrorLst.

Value

A list object with newColNames and errorLst with a record of all changes made.

Examples

library(nprcgenekeepr)
fixColumnNames(c("Sire_ID", "EGO", "DAM", "Id", "birth_date"),
  errorLst = getEmptyErrorLst()
)
#> $newColNames
#> [1] "sire"  "id"    "dam"   "id"    "birth"
#> 
#> $errorLst
#> $failedDatabaseConnection
#> character(0)
#> 
#> $missingColumns
#> character(0)
#> 
#> $invalidDateRows
#> character(0)
#> 
#> $suspiciousParents
#> data frame with 0 columns and 0 rows
#> 
#> $femaleSires
#> character(0)
#> 
#> $maleDams
#> character(0)
#> 
#> $sireAndDam
#> character(0)
#> 
#> $duplicateIds
#> character(0)
#> 
#> $invalidIdChars
#> character(0)
#> 
#> $invalidPlaceholderRows
#> character(0)
#> 
#> $changedCols
#> $changedCols$caseChange
#> [1] "Sire_ID, EGO, DAM, and Id to sire_id, ego, dam, and id"
#> 
#> $changedCols$spaceRemoved
#> character(0)
#> 
#> $changedCols$periodRemoved
#> character(0)
#> 
#> $changedCols$underScoreRemoved
#> [1] "sire_id and birth_date to sireid and birthdate"
#> 
#> $changedCols$egoToId
#> [1] "ego to id"
#> 
#> $changedCols$egoidToId
#> character(0)
#> 
#> $changedCols$sireIdToSire
#> [1] "sireid to sire"
#> 
#> $changedCols$damIdToDam
#> character(0)
#> 
#> $changedCols$birthdateToBirth
#> [1] "birthdate to birth"
#> 
#> $changedCols$deathdateToDeath
#> character(0)
#> 
#> $changedCols$recordstatusToRecordStatus
#> character(0)
#> 
#> $changedCols$fromcenterToFromCenter
#> character(0)
#> 
#> $changedCols$geographicoriginToGeographicOrigin
#> character(0)
#> 
#> 
#> attr(,"class")
#> [1] "list"             "nprcgenekeeprErr"
#>