Takes pedigree data from get_colony() or get_ped() function and groups animals into families.
It also expands the pedigree data by adding information about the family that each individual was born in and the
family in which the individual is the reproductive animal.
Arguments
- ped
Data frame.
FamAggoutput ofget_colony()orget_ped()function. Withrm_obsolete_parentsparameter set toTRUE.- sampledata
Data frame. Metadata for all genetic samples that belong to the individuals included in pedigree reconstruction analysis. This data frame should adhere to the formatting and naming conventions outlined in the
check_sampledata()documentation.- output
Character string. Determines the format of the output. Options are: "ped": returns an extended pedigree data frame. "fams": returns a table of all families present in the pedigree. "both": returns a list with two data frames: "ped" and "fams". (Default)
Value
Depending on the output parameter, the function returns either a data frame
(ped or fams) or a list containing both data frames (ped and fams).
peddata frame. An extended version of the pedigree data fromget_colony()/get_ped(). In addition to common pedigree information (individual, mother, father, sex, family),pedincludes columns for:parents: Identifier codes of both parents separated with_.FamID: Numeric identifier for the family to which the individual belongs (seefamsbelow).FirstSeen: Date of first sample of individual.LastSeen: Date of last sample of individual.IsDead: Logical value (TRUE/FALSE) that identifies if the individual is dead.DadHSgroup: Identifier of paternal half-sib group (see Details).MomHSgroup: Identifier of maternal half-sib group (see Details).hsGroup: Numeric value indicating if the individual is part of a half-sib group (see Details).
famsdata frame includes information on families that individuals in the pedigree belong to. The families are described by:parents: Identifier codes of both parents separated with_.father: Identifier code of the father.mother: Identifier code of the mother.FamID: Numeric identifier for the family.famStart: Date when the first sample of one of the offspring from this family was collected (see Details).famEnd: Date when the last sample of mother or father of this family was collected (see Details).FamDead: Logical value (TRUE/FALSE) indicating if the family no longer exists.DadHSgroup: Identifier connecting families that share the same father.MomHSgroup: Identifier connecting families that share the same mother.hsGroup: Numeric value connecting families that share one of the parents.
Details
The result of org_fams() function introduces us to two important concepts
within the context of this package: family and half-sib group. A family in the
output of this function is defined as a group of animals where at least one
parent and at least one offspring is known. A half-sib group refers to a
group of half-siblings, either maternally or paternally related. In the
function output the DadHSgroup groups paternal half-siblings and MomHSgroup
maternal half-siblings.
The fams output dataframe contains famStart and famEnd columns, which estimate
a time window for the family based solely on sample collection dates provided in sampledata.
famStart marks the date of the earliest sample collected from any offspring
belonging to that family. famEnd indicates the date of the latest sample collected
from either the mother or the father of that family. It is important to recognize that this
method relies on observation (sampling) times. Consequently, famEnd (last parental sample date)
can precede famStart (first offspring sample date), creating a biologically impossible sequence
and a negative calculated family timespan. Users should interpret the interval
between famStart and famEnd with this understanding.
Examples
# Prepare the data for usage with org_fams() function.
# Get animal timespan data using the anim_timespan() function.
animal_ts <- anim_timespan(
wolf_samples$AnimalRef,
wolf_samples$Date,
wolf_samples$SType,
dead = c("Tissue")
)
# Add animal timespan to the sampledata
sampledata <- merge(wolf_samples, animal_ts, by.x = "AnimalRef", by.y = "ID", all.x = TRUE)
# Define the path to the pedigree data file.
path <- paste0(system.file("extdata", package = "wpeR"), "/wpeR_samplePed")
# Retrieve the pedigree data from the get_colony function.
ped_colony <- get_colony(path, sampledata, rm_obsolete_parents = TRUE, out = "FamAgg")
# Run the function
# Organize families and expand pedigree data using the org_fams function.
org_fams(
ped = ped_colony,
sampledata = sampledata
)
#> $ped
#> ClusterIndex id father mother sex parents FamID FirstSeen
#> 1 1 M2AM8 <NA> <NA> 1 <NA> 0 2017-04-07
#> 2 1 M273P <NA> <NA> 2 <NA> 0 2018-01-02
#> 3 1 M20AM <NA> <NA> 1 <NA> 0 2016-08-29
#> 4 1 M28TU <NA> <NA> 2 <NA> 0 2017-12-18
#> 5 1 M228J <NA> <NA> 1 <NA> 0 2016-09-30
#> 6 1 M200F <NA> <NA> 2 <NA> 0 2015-07-27
#> 7 1 M10XC M228J M200F 1 M228J_M200F 1 2017-11-16
#> 8 1 M1YP0 M228J M200F 2 M228J_M200F 1 2017-01-25
#> 9 1 M220J M228J M200F 1 M228J_M200F 1 2017-11-10
#> 10 1 M22AM M228J M200F 1 M228J_M200F 1 2017-01-26
#> 11 1 M2772 M228J M200F 1 M228J_M200F 1 2017-11-12
#> 12 1 M28LU M228J M200F 2 M228J_M200F 1 2017-09-18
#> 13 1 M2AXE M228J M200F 2 M228J_M200F 1 2017-12-16
#> 14 1 M2C1T M228J M200F 2 M228J_M200F 1 2017-10-31
#> 15 1 MSV10T MSV00E M28LU 2 MSV00E_M28LU 2 2020-08-16
#> 16 1 MSV1C0 MSV00E M28LU 1 MSV00E_M28LU 2 2021-02-16
#> 17 1 MSV1EX MSV00E M28LU 1 MSV00E_M28LU 2 2021-01-18
#> 18 1 MSV1F5 MSV00E M28LU 1 MSV00E_M28LU 2 2021-01-23
#> 19 1 MSV1F8 MSV00E M28LU 2 MSV00E_M28LU 2 2021-02-04
#> 20 1 MSV1FJ MSV00E M28LU 1 MSV00E_M28LU 2 2021-02-16
#> 21 1 MSV1FL MSV00E M28LU 1 MSV00E_M28LU 2 2021-02-17
#> 22 1 MSV1FT MSV00E M28LU 1 MSV00E_M28LU 2 2021-01-18
#> 23 1 MSV1TM MSV00E M28LU 2 MSV00E_M28LU 2 2020-11-15
#> 24 1 MSV01X M2772 M28TU 1 M2772_M28TU 3 2019-08-28
#> 25 1 MSV055 M2772 M28TU 2 M2772_M28TU 3 2019-12-11
#> 26 1 MSV0AL M2772 M28TU 1 M2772_M28TU 3 2019-12-11
#> 27 1 MSV0TA M2772 M28TU 1 M2772_M28TU 3 2020-01-12
#> 28 1 MSV0XT M2772 M28TU 1 M2772_M28TU 3 2020-10-08
#> 29 1 MSV17U M2772 M28TU 1 M2772_M28TU 3 2020-09-29
#> 30 1 MSV180 M2772 M28TU 2 M2772_M28TU 3 2020-09-29
#> 31 1 MSV18C M2772 M28TU 2 M2772_M28TU 3 2020-11-06
#> 32 1 MSV1KT M2772 M28TU 2 M2772_M28TU 3 2020-10-06
#> 33 1 M1J47 M2AM8 M200F 1 M2AM8_M200F 4 2019-08-20
#> 34 1 M221C M2AM8 M200F 2 M2AM8_M200F 4 2018-10-29
#> 35 1 M2C8Y M2AM8 M200F 2 M2AM8_M200F 4 2018-10-30
#> 36 1 M2F1L M2AM8 M200F 2 M2AM8_M200F 4 2019-04-07
#> 37 1 MSV02F M2AM8 M200F 1 M2AM8_M200F 4 2019-10-07
#> 38 1 MSV02L M2AM8 M200F 1 M2AM8_M200F 4 2019-09-15
#> 39 1 MSV0CK M2AM8 M200F 2 M2AM8_M200F 4 2019-08-05
#> 40 1 MSV0FK M2AM8 M200F 1 M2AM8_M200F 4 2020-01-18
#> 41 1 MSV0H5 M2AM8 M200F 2 M2AM8_M200F 4 2020-04-10
#> 42 1 MSV0P7 M2AM8 M200F 1 M2AM8_M200F 4 2019-11-23
#> 43 1 MSV0UP M2AM8 M200F 2 M2AM8_M200F 4 2020-06-10
#> 44 1 MSV0UT M2AM8 M200F 1 M2AM8_M200F 4 2020-06-10
#> 45 1 MSV0UU M2AM8 M200F 2 M2AM8_M200F 4 2020-06-10
#> 46 1 MSV16T M2AM8 M200F 2 M2AM8_M200F 4 2021-02-02
#> 47 1 MSV16U M2AM8 M200F 1 M2AM8_M200F 4 2021-02-02
#> 48 1 MSV170 M2AM8 M200F 1 M2AM8_M200F 4 2021-02-02
#> 49 1 MSV177 M2AM8 M200F 2 M2AM8_M200F 4 2020-04-22
#> 50 1 MSV1FE M2AM8 M200F 1 M2AM8_M200F 4 2021-02-10
#> 51 1 M2757 M20AM M273P 2 M20AM_M273P 5 2018-01-05
#> 52 1 M2ALK M20AM M273P 2 M20AM_M273P 5 2019-01-03
#> 53 1 M2ETE M20AM M273P 2 M20AM_M273P 5 2019-03-20
#> 54 1 M2EUJ M20AM M273P 2 M20AM_M273P 5 2019-04-23
#> 55 1 MSV00E M20AM M273P 1 M20AM_M273P 5 2019-08-12
#> 56 1 MSV018 M20AM M273P 1 M20AM_M273P 5 2019-09-12
#> 57 1 MSV05L M20AM M273P 1 M20AM_M273P 5 2020-01-27
#> 58 1 MSV0M6 M20AM M273P 1 M20AM_M273P 5 2020-02-24
#> 59 1 MSV0T4 M20AM M273P 1 M20AM_M273P 5 2020-02-07
#> 60 1 MSV0T7 M20AM M273P 1 M20AM_M273P 5 2019-08-11
#> 61 1 MSV0TJ M20AM M273P 2 M20AM_M273P 5 2019-12-28
#> 62 1 MSV0UL M20AM M273P 1 M20AM_M273P 5 2020-07-15
#> 63 1 MSV0X4 M20AM M273P 1 M20AM_M273P 5 2019-09-03
#> 64 1 MSV17F M20AM M273P 2 M20AM_M273P 5 2020-11-08
#> 65 1 MSV1MH M20AM M273P 2 M20AM_M273P 5 2021-02-25
#> LastSeen IsDead DadHSgroup MomHSgroup hsGroup
#> 1 2021-03-23 FALSE <NA> <NA> 0
#> 2 2020-07-22 FALSE <NA> <NA> 0
#> 3 2020-08-02 FALSE <NA> <NA> 0
#> 4 2021-04-23 FALSE <NA> <NA> 0
#> 5 2018-02-09 TRUE <NA> <NA> 0
#> 6 2018-08-22 FALSE <NA> <NA> 0
#> 7 2017-12-22 FALSE <NA> MomP_1 1
#> 8 2017-01-25 TRUE <NA> MomP_1 1
#> 9 2018-02-17 FALSE <NA> MomP_1 1
#> 10 2017-08-07 FALSE <NA> MomP_1 1
#> 11 2020-09-29 FALSE <NA> MomP_1 1
#> 12 2021-01-19 FALSE <NA> MomP_1 1
#> 13 2019-11-06 FALSE <NA> MomP_1 1
#> 14 2018-01-26 FALSE <NA> MomP_1 1
#> 15 2020-08-16 FALSE <NA> <NA> 2
#> 16 2021-03-30 FALSE <NA> <NA> 2
#> 17 2021-01-18 FALSE <NA> <NA> 2
#> 18 2021-01-23 FALSE <NA> <NA> 2
#> 19 2021-02-04 FALSE <NA> <NA> 2
#> 20 2021-03-07 FALSE <NA> <NA> 2
#> 21 2021-02-17 FALSE <NA> <NA> 2
#> 22 2021-02-26 FALSE <NA> <NA> 2
#> 23 2020-11-15 TRUE <NA> <NA> 2
#> 24 2019-08-29 FALSE <NA> <NA> 3
#> 25 2020-03-24 FALSE <NA> <NA> 3
#> 26 2021-04-29 FALSE <NA> <NA> 3
#> 27 2020-01-12 TRUE <NA> <NA> 3
#> 28 2021-04-29 FALSE <NA> <NA> 3
#> 29 2021-04-29 FALSE <NA> <NA> 3
#> 30 2020-09-29 FALSE <NA> <NA> 3
#> 31 2020-11-06 FALSE <NA> <NA> 3
#> 32 2021-02-16 FALSE <NA> <NA> 3
#> 33 2021-01-07 FALSE <NA> MomP_1 1
#> 34 2020-05-22 FALSE <NA> MomP_1 1
#> 35 2018-10-30 TRUE <NA> MomP_1 1
#> 36 2021-03-13 FALSE <NA> MomP_1 1
#> 37 2019-10-07 TRUE <NA> MomP_1 1
#> 38 2019-09-15 TRUE <NA> MomP_1 1
#> 39 2019-12-09 FALSE <NA> MomP_1 1
#> 40 2021-04-15 FALSE <NA> MomP_1 1
#> 41 2021-03-17 FALSE <NA> MomP_1 1
#> 42 2020-07-17 FALSE <NA> MomP_1 1
#> 43 2021-03-17 FALSE <NA> MomP_1 1
#> 44 2020-06-10 FALSE <NA> MomP_1 1
#> 45 2020-06-10 FALSE <NA> MomP_1 1
#> 46 2021-02-02 FALSE <NA> MomP_1 1
#> 47 2021-02-02 FALSE <NA> MomP_1 1
#> 48 2021-02-02 FALSE <NA> MomP_1 1
#> 49 2020-07-11 FALSE <NA> MomP_1 1
#> 50 2021-02-10 FALSE <NA> MomP_1 1
#> 51 2018-02-09 FALSE <NA> <NA> 4
#> 52 2020-07-08 FALSE <NA> <NA> 4
#> 53 2019-08-13 FALSE <NA> <NA> 4
#> 54 2019-08-11 FALSE <NA> <NA> 4
#> 55 2021-03-05 FALSE <NA> <NA> 4
#> 56 2019-09-12 FALSE <NA> <NA> 4
#> 57 2020-02-15 FALSE <NA> <NA> 4
#> 58 2021-04-08 FALSE <NA> <NA> 4
#> 59 2020-02-07 TRUE <NA> <NA> 4
#> 60 2020-02-09 TRUE <NA> <NA> 4
#> 61 2019-12-28 TRUE <NA> <NA> 4
#> 62 2020-07-15 FALSE <NA> <NA> 4
#> 63 2019-10-23 TRUE <NA> <NA> 4
#> 64 2020-12-04 FALSE <NA> <NA> 4
#> 65 2021-07-15 FALSE <NA> <NA> 4
#>
#> $fams
#> parents father mother FamID FamStart FamEnd FamDead
#> 7 M228J_M200F M228J M200F 1 2017-01-25 2018-08-22 TRUE
#> 15 MSV00E_M28LU MSV00E M28LU 2 2020-08-16 2021-03-05 FALSE
#> 24 M2772_M28TU M2772 M28TU 3 2019-08-28 2021-04-23 FALSE
#> 33 M2AM8_M200F M2AM8 M200F 4 2018-10-29 2021-03-23 FALSE
#> 51 M20AM_M273P M20AM M273P 5 2018-01-05 2020-08-02 FALSE
#> NA Unknown *Unknown #Unknown 0 2015-07-27 2021-04-23 FALSE
#> DadHSgroup MomHSgroup hsGroup
#> 7 <NA> MomP_1 1
#> 15 <NA> <NA> 2
#> 24 <NA> <NA> 3
#> 33 <NA> MomP_1 1
#> 51 <NA> <NA> 4
#> NA <NA> <NA> 0
#>