devtools::install_github("GR3602/wpeR")

####DATA PREPARATION####
# 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")


# 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)

# Organize families and expand pedigree data using the org_fams function.
## families data frame
fams <- org_fams(ped_colony, sampledata, output = "fams")
## extended pedigree data frame
ped <- org_fams(ped_colony,sampledata, output = "ped")


# The example show just one family 
## Prepare data for plotting.
pt <- plot_table(plot_fams = 1,
                 org_tables$fams,
                 org_tables$ped,
                 sampledata,
                 deadSample = c("Tissue"))
                 

####VISUALIZATION####                 
## Get a temporal pedigree plot.
ped_satplot(plottable = pt)

# optional pedigre plot pedigree plot from kinship2
### extract parent codes
parents1 = strsplit(fams[fams$FamID == 1,]$parents, "_")[[1]]
### filter the family from pedigre
Fam1 = ped[(ped$FamID == 1 | ped$id %in% parents1),]
### plot using kinship2 
plot(kinship2::pedigree(Fam1$id, Fam1$father, Fam1$mother, Fam1$sex))

## Create spatial files
<!-- ps <- ped_spatial(pt) -->
summary(ps)