Main pedigree curation function that performs basic quality control on pedigree information
qcStudbook(sb, minParentAge = 2, reportChanges = FALSE, reportErrors = FALSE)A dataframe containing a table of pedigree and demographic information.
The function recognizes the following columns (optional columns will be used if present, but are not required):
id --- Character vector with Unique identifier for all individuals
sire --- Character vector with unique identifier for the father of the current id
dam --- Character vector with unique identifier for the mother of the current id
sex --- Factor levels: "M", "F", "U" Sex specifier for an individual
birth --- Date or NA (optional) with the individual's birth
date
departure --- Date or NA (optional) an individual was sold
or shipped from the colony
death --- date or NA (optional)
Date of death, if applicable
status --- Factor levels: ALIVE, DEAD, SHIPPED (optional) Status of an individual
origin --- Character or NA (optional)
Facility an individual originated from, if other than ONPRC
ancestry --- Character or NA (optional)
Geographic population to which the individual belongs
spf --- Character or NA (optional)
Specific pathogen-free status of an individual
vasxOvx --- Character or NA (optional)
Indicator of the vasectomy/ovariectomy status of an animal; NA if
animal is intact, assume all other values indicate surgical alteration
condition --- Character or NA (optional)
Indicator of the restricted status of an animal. "Nonrestricted" animals
are generally assumed to be naive.
numeric values to set the minimum age in years for an animal to have an offspring. Defaults to 2 years. The check is not performed for animals with missing birth dates.
logical value that if TRUE, the errorLst
contains the list of changes made to the column names. Default is
FALSE.
logical value if TRUE will scan the entire file
and report back changes made to input and errors in a
list of list where each sublist is a type of change or error found.
Changes will include column names, case of categorical values (male,
female, unknown), etc.
Errors will include missing columns, invalid date rows, male dams,
female sires, and records with one or more parents below minimum age
of parents.
The following changes are made to the cols.
Column cols are converted to all lower case
Periods (".") within column cols are collapsed to no space ""
egoid is converted to id
sireid is convert to sire
damid is converted to dam
If the dataframe (sb does not contain the five required columns
(id, sire, dam, sex), and
birth the function throws an error by calling stop().
If the id field has the string UNKNOWN (any case) or both
the fields sire or dam have NA or UNKNOWN
(any case), the record is removed.
If either of the fields sire or dam have the
string UNKNOWN (any case), they are replaced with a unique identifier
with the form Unnnn, where nnnn represents one of a series
of sequential integers representing the number of missing sires and
dams right justified in a pattern of 0000. See addUIds
function.
The function addParents is used to add records for parents missing
their own record in the pedigree.
The function convertSexCodes is used with ignoreHerm == TRUE
to convert sex codes according to the following factors of standardized
codes:
F -- replacing "FEMALE" or "2"
M -- replacing "MALE" or "1"
H -- replacing "HERMAPHRODITE" or "4", if ignore.herm == FALSE
U -- replacing "HERMAPHRODITE" or "4", if ignore.herm == TRUE
U -- replacing "UNKNOWN" or "3"
The function correctParentSex is used to ensure no parent is both
a sire and a dam. If this error is detected, the function throws an error
and halts the program.
The function convertStatusCodes converts status indicators to the
following factors of standardized codes. Case of the original status value
is ignored.
"ALIVE" --- replacing "alive", "A" and "1"
"DECEASED" --- replacing "deceased", "DEAD", "D", "2"
"SHIPPED" --- replacing "shipped", "sold", "sale", "s", "3"
"UNKNOWN" --- replacing is.na(status)
"UNKNOWN" --- replacing "unknown", "U", "4"
The function convertAncestry coverts ancestry indicators using
regular expressions such that the following conversions are made from
character strings that match selected substrings to the following factors.
"INDIAN" --- replacing "ind" and not "chin"
"CHINESE" --- replacing "chin" and not "ind"
"HYBRID" --- replacing "hyb" or "chin" and "ind"
"JAPANESE" --- replacing "jap"
"UNKNOWN" --- replacing NA
"OTHER" --- replacing not matching any of the above
The function convertDate converts character representations of
dates in the columns birth, death, departure, and
exit to dates using the as.Date function.
The function setExit uses heuristics and the columns death
and departure to set exit if it is not already defined.
The function calcAge uses the birth and the exit
columns to define the age column. The numerical values is rounded
to the nearest 0.1 of a year. If exit is not defined, the
current system date (Sys.Date()) is used.
The function findGeneration is used to define the generation number
for each animal in the pedigree.
The function removeDuplicates checks for any duplicated records and
removes the duplicates. I also throws an error and stops the program if an
ID appears in more
than one record where one or more of the other columns have a difference.
Columns that cannot be used subsequently are removed and the rows are ordered by generation number and then ID.
Finally the columns id sire, and dam are coerce to
character.
A data.frame with standardized and quality controlled pedigree information.
# NOT RUN {
examplePedigree <- nprcgenekeepr::examplePedigree
ped <- qcStudbook(examplePedigree, minParentAge = 2, reportChanges = FALSE,
reportErrors = FALSE)
names(ped)
# }
# NOT RUN {
# }
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