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Restore the tidyped class to a manipulated pedigree

Source: R/utils-s3.R
as_tidyped.Rd

Rapidly restores the tidyped class to a data.table or data.frame that was previously processed by tidyped() but lost its class attributes due to data manipulation.

Usage

as_tidyped(x)

Arguments

x

A data.table or data.frame that was previously a tidyped object. It must still contain the core columns: Ind, Sire, Dam, Sex, Gen, IndNum, SireNum, DamNum.

Value

A tidyped object.

Details

This is a lightweight operation that only checks for the required columns and re-attaches the class—it does not re-run the full pedigree sorting, generation inference, or loop detection.

This helper is intended for objects that still contain the core pedigree columns and numeric indices, but no longer inherit from tidyped. A common reproducible case is rbind() on two tidyped fragments, which typically returns a plain data.table. Converting a tidyped object to a plain data.frame and then subsetting it also drops the class.

Some operations, such as merge() or certain dplyr workflows, may or may not preserve the tidyped class depending on the versions of data.table, dplyr, and the exact method dispatch path used in the current R session. Therefore, as_tidyped() should be viewed as a safe recovery helper rather than something only needed after one specific verb.

Typical class-loss scenarios include:

  • rbind(tped1, tped2) — often returns plain data.table

  • as.data.frame(tped)[rows, ] — returns plain data.frame

  • manual class removal or serialization / import workflows

After such operations, downstream analysis functions (e.g., pedstats, pedne) will either error or automatically restore the class. You can also call as_tidyped() explicitly to restore the class yourself.

See also

tidyped, new_tidyped

Examples

library(visPedigree)
tp <- tidyped(simple_ped)
class(tp)
#> [1] "tidyped"    "data.table" "data.frame"
# [1] "tidyped"    "data.table" "data.frame"

# Simulate class loss via rbind()
tp2 <- rbind(tp[1:5], tp[6:10])
class(tp2)
#> [1] "data.table" "data.frame"
# [1] "data.table" "data.frame"

# Restore the class
tp3 <- as_tidyped(tp2)
class(tp3)
#> [1] "tidyped"    "data.table" "data.frame"
# [1] "tidyped"    "data.table" "data.frame"

# It can also restore from a plain data.frame if core columns are intact
tp_df <- as.data.frame(tp)
tp4 <- tp_df[tp_df$Gen > 1, ]
class(tp4)
#> [1] "data.frame"
# [1] "data.frame"

tp5 <- as_tidyped(tp4)
#> Warning: Subsetting removed parent records. Result is a plain data.table, not a tidyped.
#> Use tidyped(tp, cand = ids, trace = "up") to extract a valid sub-pedigree.
class(tp5)
#> [1] "tidyped"    "data.table" "data.frame"
# [1] "tidyped"    "data.table" "data.frame"