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. 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).

Usage

fixColumnNames(orgCols, errorLst)

Arguments

orgCols: character vector with ordered list of column names found in a pedigree file.
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"
#>