Changelog

Source: NEWS.md

pedtricks 0.5

0.5.0

• ped_stats
  • Added more relationships; cousins and aunts/uncles, returned in cousinNums and auNums slots in ped_stats object
  • Removed relatedness categories (cumulativeRelatedness and relatednessCategories from output
  • Instead now directly outputs mean and variances of relatedness, and proportion >= 0.125, 0.25 and 0.5, which are returned in relatednessDistribution slot in ped_stats object
• summary.ped_stats
  • New relationships in ped_stats function not output from summary.ped_stats by default. Use extended=TRUE for them to be included in the output
• plot.ped_stats
  • plotting relatedness distribution now slightly different, due to removing relatednessCategories from ped_stats object. Will plot if A matrix is present on ped_stats object
• h2_samp_var
  • Added new function to calculate expected sampling variance for $h^2$ from Visscher and Goddard 2016

pedtricks 0.4

0.4.2

• more fix for CRAN submission

0.4.1

-ped_stats: more optimisation to run even faster. Now running in 0.7s on the gryphons pedigree instead of 160s so 210x faster. Loops are slow

0.4.0

• ped_stats: optimized to run much faster (I think it can even be improved). Now running in 1.6s on the gryphons pedigree instead of 160s so 100x faster. Now using sparse matrix format for A and removing some sluggish loops in estimations.

pedtricks 0.3

0.3.2

• ggpedigree()
  • adding functionality to highlight phenotyped individuals with pheno argument

0.3.1

• ggpedigree()
  • draw pedigree using ggplot2
  • compatible with dplyr/tidyverse use
  • return a ggplot object that can be modified with ggplot functions
  • optimized graph layout with igrah
• draw_pedA()
  • returns a trellis plot object for visualizing relatedness among pedigreed individuals

0.3.0

• ggpedigree()
  • draw pedigree using ggplot2
  • compatible with dplyr/tidyverse use
  • return a ggplot object that can be modified with ggplot functions

pedtricks 0.1

• Initial transfer and update of CRAN archived pedantics package under the new name pedtricks.

DEPRECATED from pedantics

• rpederr()and fpederr() are not implemented
• pedigreeStats() and pedStatSummary() have been replaced by ped_stats() with a summary() and plot() methods to simplify the workflow and allow to get the plots without running the statistics each time
• makePedigreeFactor() and makePedigreeNumeric() have been combined in convert_ped() which convert a pedigree to numeric or factor

Small changes

• fixPedigree() is now fix_ped()
• genomesim(), microsim() and phensim() have been renamed as genome_sim(), micro_sim() and phen_sim()