R/documentData.R

In R-Computing-Lab/BGMisc: An R Package for Extended Behavior Genetics Analysis

##' Artificial pedigree data on eight families with inbreeding
##'
##' A dataset created purely from imagination that includes several types of inbreeding.
##' Different kinds of inbreeding occur in each extended family.
##'
##' The types of inbreeding are as follows:
##'
#' \itemize{
#'     \item Extended Family 1: Sister wives - Children with the same father and different mothers who are sisters.
#'     \item Extended Family 2: Full siblings have children.
#'     \item Extended Family 3: Half siblings have children.
#'     \item Extended Family 4: First cousins have children.
#'     \item Extended Family 5: Father has child with his daughter.
#'     \item Extended Family 6: Half sister wives - Children with the same father and different mothers who are half sisters.
#'     \item Extended Family 7: Uncle-niece and Aunt-nephew have children.
#'     \item Extended Family 8: A father-son pairs has children with a corresponding mother-daughter pair.
#' }
##'
##' Although not all of the above structures are technically inbreeding, they aim to test pedigree diagramming and path tracing algorithms.
##'
##' The variables are as follows:
##'
##' \itemize{
##'   \item \code{ID}:  Person identification variable
##'   \item \code{sex}:  Sex of the ID: 1 is female; 0 is male
##'   \item \code{dadID}:  ID of the father
##'   \item \code{momID}:  ID of the mother
##'   \item \code{FamID}:  ID of the extended family
##'   \item \code{Gen}:  Generation of the person
##'   \item \code{proband}:  Always FALSE
##' }
##'
##' @docType data
##' @keywords datasets
##' @name inbreeding
##' @usage data(inbreeding)
##' @format A data frame (and ped object) with 134 rows and 7 variables
NULL

##' Simulated pedigree with two extended families and an age-related hazard
##'
##' A dataset simulated to have an age-related hazard.
##' There are two extended families that are sampled from the same population.
##'
##' The variables are as follows:
##'
##' \itemize{
##'   \item \code{FamID}:  ID of the extended family
##'   \item \code{ID}:  Person identification variable
##'   \item \code{sex}:  Sex of the ID: 1 is female; 0 is male
##'   \item \code{dadID}:  ID of the father
##'   \item \code{momID}:  ID of the mother
##'   \item \code{affected}:  logical.  Whether the person is affected or not
##'   \item \code{DA1}:  Binary variable signifying the meaninglessness of life
##'   \item \code{DA2}:  Binary variable signifying the fundamental unknowability of existence
##'   \item \code{birthYr}:  Birth year for person
##'   \item \code{onsetYr}:  Year of onset for person
##'   \item \code{deathYr}:  Death year for person
##'   \item \code{available}:  logical.  Whether
##'   \item \code{Gen}:  Generation of the person
##'   \item \code{proband}:  logical.  Whether the person is a proband or not
##' }
##'
##' @docType data
##' @keywords datasets
##' @name hazard
##' @usage data(hazard)
##' @format A data frame with 43 rows and 14 variables
NULL

##' Fictional pedigree data on a wizarding family
##'
##' A dataset created purely from imagination that includes a subset of the Potter extended family.
##'
##' The variables are as follows:
##'
##' \itemize{
##'   \item \code{personID}:  Person identification variable
##'   \item \code{famID}: Family identification variable
##'   \item \code{name}:  Name of the person
##'   \item \code{gen}: Generation of the person
##'   \item \code{momID}:  ID of the mother
##'   \item \code{dadID}:  ID of the father
##'   \item \code{spouseID}: ID of the spouse
##'   \item \code{sex}:  Sex of the ID: 1 is male; 0 is female
##'
##' }
##'
##' IDs in the 100s \code{momID}s and \code{dadID}s are for people not in the dataset.
##'
##' @docType data
##' @keywords datasets
##' @name potter
##' @usage data(potter)
##' @format A data frame (and ped object) with 36 rows and 8 variables
NULL


##' Royal pedigree data from 1992
##'
##' A dataset created by Denis Reid from the Royal Families of Europe.
##'
##' The variables are as follows:
##' id,momID,dadID,name,sex,birth_date,death_date,attribute_title
##' \itemize{
##'   \item \code{id}:  Person identification variable
##'   \item \code{momID}:  ID of the mother
##'   \item \code{dadID}:  ID of the father
##'   \item \code{name}:  Name of the person
##'   \item \code{sex}: Biological sex
##'   \item \code{birth_date}:  Date of birth
##'   \item \code{death_date}:  Date of death
##'   \item \code{attribute_title}:  Title of the person
##'
##' }
##'
##'
##' @docType data
##' @keywords datasets
##' @name royal92
##' @usage data(royal92)
##' @format A data frame with 3110 observations
NULL

##' A song of ice and fire pedigree data
##'
##' A dataset created from the Song of Ice and Fire series by George R. R. Martin. Core data is from the [Westeros.org forum](https://asoiaf.westeros.org/index.php?/topic/88863-all-the-family-trees/).
##'
##'
##'
##' The variables are as follows:
##' \itemize{
##'   \item \code{id}:  Person identification variable
##'   \item \code{momID}:  ID of the mother
##'   \item \code{dadID}:  ID of the father
##'   \item \code{name}:  Name of the person
##'   \item \code{sex}: Biological sex
##'   }
##'
##' @docType data
##' @keywords datasets
##' @name ASOIAF
##' @usage data(ASOIAF)
##' @format A data frame with 501 observations
NULL