diff --git a/R/simulatePedigree.R b/R/simulatePedigree.R index 9539719c..eb4489f6 100644 --- a/R/simulatePedigree.R +++ b/R/simulatePedigree.R @@ -22,7 +22,7 @@ #' as well as assigning unique couple IDs. It does not return a value explicitly. #' -buildBetweenGenerations <- function(df_Fam, Ngen, sizeGens, verbose = FALSE, marR, sexR, kpc, +buildBtwnGenerations <- function(df_Fam, Ngen, sizeGens, verbose = FALSE, marR, sexR, kpc, rd_kpc, personID = "ID", momID = "momID", dadID = "dadID", @@ -41,7 +41,7 @@ buildBetweenGenerations <- function(df_Fam, Ngen, sizeGens, verbose = FALSE, mar } if (use_optimized) { - df_Fam <- buildBetweenGenerations_optimized( + df_Fam <- buildBtwnGenerations_opt( df_Fam = df_Fam, Ngen = Ngen, sizeGens = sizeGens, @@ -58,7 +58,7 @@ buildBetweenGenerations <- function(df_Fam, Ngen, sizeGens, verbose = FALSE, mar beta = TRUE ) } else { - df_Fam <- buildBetweenGenerations_base( + df_Fam <- buildBtwnGenerations_base( df_Fam = df_Fam, Ngen = Ngen, sizeGens = sizeGens, @@ -75,11 +75,11 @@ buildBetweenGenerations <- function(df_Fam, Ngen, sizeGens, verbose = FALSE, mar beta = FALSE ) } - return(df_Fam) + df_Fam } -buildBetweenGenerations_base <- function(df_Fam, +buildBtwnGenerations_base <- function(df_Fam, Ngen, sizeGens, verbose = FALSE, @@ -360,15 +360,10 @@ buildBetweenGenerations_base <- function(df_Fam, # Align lengths between couples and random_numbers. # If random_numbers is longer than couples, truncate random_numbers. - # If random_numbers is shorter than couples, drop extra couples. nCouples <- length(parent_rows) if (length(random_numbers) > nCouples) { random_numbers <- random_numbers[seq_len(nCouples)] - } else if (length(random_numbers) < nCouples) { - keep <- seq_len(length(random_numbers)) - ma_ids <- ma_ids[keep] - pa_ids <- pa_ids[keep] } # Expand from "one mother/father per couple" to "one mother/father per child". @@ -455,10 +450,10 @@ buildBetweenGenerations_base <- function(df_Fam, } } } - return(df_Fam) + df_Fam } -buildBetweenGenerations_optimized <- function(df_Fam, +buildBtwnGenerations_opt <- function(df_Fam, Ngen, sizeGens, verbose = FALSE, @@ -743,15 +738,10 @@ buildBetweenGenerations_optimized <- function(df_Fam, # Align lengths between couples and random_numbers. # If random_numbers is longer than couples, truncate random_numbers. - # If random_numbers is shorter than couples, drop extra couples. nCouples <- length(parent_rows) if (length(random_numbers) > nCouples) { random_numbers <- random_numbers[seq_len(nCouples)] - } else if (length(random_numbers) < nCouples) { - keep <- seq_len(length(random_numbers)) - ma_ids <- ma_ids[keep] - pa_ids <- pa_ids[keep] } # Expand from "one mother/father per couple" to "one mother/father per child". @@ -838,7 +828,7 @@ buildBetweenGenerations_optimized <- function(df_Fam, } } } - return(df_Fam) + df_Fam } #' Simulate Pedigrees @@ -956,7 +946,7 @@ simulatePedigree <- function(kpc = 3, ) } - df_Fam <- buildBetweenGenerations( + df_Fam <- buildBtwnGenerations( df_Fam = df_Fam, Ngen = Ngen, sizeGens = sizeGens, @@ -981,7 +971,7 @@ simulatePedigree <- function(kpc = 3, # connect the detached members df_Fam[is.na(df_Fam[[momID]]) & is.na(df_Fam[[dadID]]) & df_Fam$gen > 1, ] - return(df_Fam) + df_Fam } #' @rdname simulatePedigree diff --git a/man/buildBetweenGenerations.Rd b/man/buildBtwnGenerations.Rd similarity index 98% rename from man/buildBetweenGenerations.Rd rename to man/buildBtwnGenerations.Rd index f28622b2..42a955d3 100644 --- a/man/buildBetweenGenerations.Rd +++ b/man/buildBtwnGenerations.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/simulatePedigree.R -\name{buildBetweenGenerations} -\alias{buildBetweenGenerations} +\name{buildBtwnGenerations} +\alias{buildBtwnGenerations} \title{Process Generation Connections} \usage{ -buildBetweenGenerations( +buildBtwnGenerations( df_Fam, Ngen, sizeGens, diff --git a/vignettes/v5_ASOIAF_files/figure-html/unnamed-chunk-5-1.png b/vignettes/v5_ASOIAF_files/figure-html/unnamed-chunk-5-1.png deleted file mode 100644 index 2a2ff6f8..00000000 Binary files a/vignettes/v5_ASOIAF_files/figure-html/unnamed-chunk-5-1.png and /dev/null differ diff --git a/vignettes/v5_ASOIAF_files/figure-html/unnamed-chunk-5-2.png b/vignettes/v5_ASOIAF_files/figure-html/unnamed-chunk-5-2.png deleted file mode 100644 index 7e39189f..00000000 Binary files a/vignettes/v5_ASOIAF_files/figure-html/unnamed-chunk-5-2.png and /dev/null differ diff --git a/vignettes/v5_ASOIAF_files/figure-html/unnamed-chunk-5-3.png b/vignettes/v5_ASOIAF_files/figure-html/unnamed-chunk-5-3.png deleted file mode 100644 index c2558546..00000000 Binary files a/vignettes/v5_ASOIAF_files/figure-html/unnamed-chunk-5-3.png and /dev/null differ