In charlotte-ngs/lbgfs2020: Livestock Breeding and Genomics (Fall 2020)

knitr::opts_chunk$set(echo = FALSE)
knitr::knit_hooks$set(hook_convert_odg = rmdhelp::hook_convert_odg)

s_png_start <- 3014
nr_slide <- as.integer(system("ls -1tr /Users/pvr/Data/Projects/Github/charlotte-ngs/lbgfs2020_ghroot/master/lbgfs2020/misc/20201022_ohp_lecture04/odg/*.png | wc -l", intern = TRUE))
sthisfile <- ifelse(rstudioapi::isAvailable(),
    rstudioapi::getActiveDocumentContext()$path, rprojroot::thisfile())
for (idx in 1:nr_slide){
  cat("\n##\n\n", file = sthisfile, append = TRUE)
  cat("```r\n", sep = '', file = sthisfile, append = TRUE)
  cat("rmdhelp::use_odg_graphic(ps_path = 'odg/odg_pic-", idx, ".odg')\n", sep = '', file = sthisfile, append = TRUE)
  # cat("knitr::include_graphics(path = 'odg/IMG_", s_png_start+idx, ".png')\n", sep = '', file = sthisfile, append = TRUE)
  cat("```\n\n", file = sthisfile, append = TRUE)
}

Import Data in R

#rmdhelp::use_odg_graphic(ps_path = 'odg/odg_pic-1.odg')
knitr::include_graphics(path = "odg/odg_pic-1.png")

Recap Genetic Model

#rmdhelp::use_odg_graphic(ps_path = 'odg/odg_pic-2.odg')
knitr::include_graphics(path = "odg/odg_pic-2.png")

Fixed Linear Effects Model

#rmdhelp::use_odg_graphic(ps_path = 'odg/odg_pic-3.odg')
knitr::include_graphics(path = "odg/odg_pic-3.png")

Mixed Linear Effects Model

#rmdhelp::use_odg_graphic(ps_path = 'odg/odg_pic-4.odg')
knitr::include_graphics(path = "odg/odg_pic-4.png")

Model Specification

#rmdhelp::use_odg_graphic(ps_path = 'odg/odg_pic-5.odg')
knitr::include_graphics(path = "odg/odg_pic-5.png")

Model Components

#rmdhelp::use_odg_graphic(ps_path = 'odg/odg_pic-6.odg')
knitr::include_graphics(path = "odg/odg_pic-6.png")

Fixed and Random Effects

#rmdhelp::use_odg_graphic(ps_path = 'odg/odg_pic-7.odg')
knitr::include_graphics(path = "odg/odg_pic-7.png")

Combining Components

#rmdhelp::use_odg_graphic(ps_path = 'odg/odg_pic-8.odg')
knitr::include_graphics(path = "odg/odg_pic-8.png")

Numerical Example

#rmdhelp::use_odg_graphic(ps_path = 'odg/odg_pic-9.odg')
knitr::include_graphics(path = "odg/odg_pic-9.png")

Solutions

#rmdhelp::use_odg_graphic(ps_path = 'odg/odg_pic-10.odg')
knitr::include_graphics(path = "odg/odg_pic-10.png")

Variance Structure

#rmdhelp::use_odg_graphic(ps_path = 'odg/odg_pic-11.odg')
knitr::include_graphics(path = "odg/odg_pic-11.png")

Genetic Variance

#rmdhelp::use_odg_graphic(ps_path = 'odg/odg_pic-12.odg')
knitr::include_graphics(path = "odg/odg_pic-12.png")

Numerator Relationship Matrix

#rmdhelp::use_odg_graphic(ps_path = 'odg/odg_pic-13.odg')
knitr::include_graphics(path = "odg/odg_pic-13.png")

NRM II

#rmdhelp::use_odg_graphic(ps_path = 'odg/odg_pic-14.odg')
knitr::include_graphics(path = "odg/odg_pic-14.png")

charlotte-ngs/lbgfs2020 documentation built on Dec. 20, 2020, 5:39 p.m.