kbroman

# elsa-fy for minecraft
# using the miner R package, https://github.com/ROpenSciLabs/iner
#
# when she walks on water, it turns to ice
elsafy <- function(player_id=NULL, water=c(8, 9), ice=174, delay=0.02)
{
    on.exit( { # clean up a bit
        for(i in 1:20) miner:::mc_receive()
        } )

kbroman

// [[Rcpp::depends(RcppEigen)]]

#include <RcppEigen.h>
using namespace Rcpp;
using namespace Eigen;

MatrixXd AtA(const MatrixXd A) {
    int n = A.cols();

    return MatrixXd(n,n).setZero().selfadjointView<Lower>()

kbroman

# calculating transition probabilities for 19-way Arabidopsis MAGIC
#
# full diallel both directions (F1)
# 3 generations random mating (F4) - 384 families
# selfed for 6 generations; could be "cousin" lines from an F4 family
# 1026 MAGIC lines; 527 in paper
#
# Kover et al (2009) PLOS Genet 5: e1000551
# https://doi.org/10.1371/journal.pgen.1000551
#

kbroman

# 2^n-way RIL by selfing
# binned two-locus probabilities, likelihood for rec frac, MLE

# 8-way RIL by selfing

probs8 <- function(r) c((1-r)^2, r*(1-r), r/2)/8/(1+2*r) * c(8, 8, 48)


llik8 <-
    function(r, counts)

kbroman

### Keybase proof

I hereby claim:

  * I am kbroman on github.
  * I am kbroman (https://keybase.io/kbroman) on keybase.
  * I have a public key ASDXTXYHggi4u82YcSipBqLzFN0_nIi2Fx_1To3szhvg7Ao

To claim this, I am signing this object:

kbroman

# Halloween 2016 counts figure
# Karl Broman
# http://kbroman.org

# the data: time and kid count
x <- read.csv("halloween2016.csv", comment.char="#")
colnames(x) <- c("time", "n.kids")

# cumulative numbers of kids
csum <- cumsum(x$n.kids)

kbroman

\documentclass{article}

\begin{document}

Here's a scatterplot:

<<scatterplot>>=
x <- rnorm(100)
y <- x + rnorm(100)
plot(x,y)

kbroman

# convert "5 min" "3 h" "4 d" etc to seconds

shit2sec <-
    function(shit)
{
    # remove leading space
    shit <- sub("^\\s+", "", shit)

    # remove ending space
    shit <- sub("\\s+$", "", shit)

kbroman

# simulating DOF1 data
# cross between DO individuals and some 9th strain

library(simcross)
library(qtl2geno)

# load some DO data, for the founder genotypes and map
file <- paste0("https://raw.githubusercontent.com/rqtl/",
               "qtl2data/master/DO_Recla/recla.zip")
do_recla <- read_cross2(file)

kbroman

# simulate RIL
#
# QTL on chr 6 at 19.9 cM
# a = -6.85, hsq = 0.1768

# load R/qtl
library(qtl)

# QTL effect and residual SD
a <- -6.85