kbroman

## simulate a cross, using genetic map from a CSV file

# read map.csv
maptab <- read.csv("map.csv")

# convert to map object
pos <- maptab[,3]
names(pos) <- maptab[,1]
chr <- maptab[,2]
map <- split(pos, chr)

kbroman

sapply(read.csv("test1.csv"), is.numeric) # 2nd column is factor
sapply(read.csv("test2.csv"), is.numeric) # both columns numeric

kbroman

# simulate some data and run anova with ranks + Kruskal-Wallis

k <- sample(1:3, 100, repl=TRUE)
eff <- (1:10)/10

pval <- matrix(nrow=length(eff), ncol=2)
dimnames(pval) <- list(as.character(eff), c("anova", "k-w"))
for(i in seq(along=eff)) {
    y <- k*eff[i] + rt(length(k), 3) # residuals ~ t(df=3)
    pval[i,1] <- anova(lm(rank(y) ~ factor(k)))[1,5]

kbroman

# these behave badly
read.csv("ragged.csv")
data.table::fread("ragged.csv")

(max_n_col <- max(sapply(strsplit( scan("ragged.csv", what=character()), ","), length)))

kbroman

 > test()
 Loading required package: testthat
 Testing aRxiv
 Loading aRxiv
 arxiv_errors : ...
 arxiv_search in batches : ..
 cleaning the records : ...................
 search range of dates : ....
 basic searches : .........
 sort_by and sort_order args work : ...1

kbroman

<?xml version="1.0" encoding="UTF-8"?>
<feed xmlns="http://www.w3.org/2005/Atom">
  <link
      href="http://arxiv.org/api/query?search_query%3Dti%3Adeconvolution%20AND%20submittedDate%3A%5B199001010000%20TO%20201409062400%5D%26id_list%3D%26start%3D0%26max_results%3D2"
      rel="self" type="application/atom+xml"/>
  <title type="html">ArXiv Query: search_query=ti:deconvolution AND
  submittedDate:[199001010000 TO
  201409062400]&amp;id_list=&amp;start=0&amp;max_results=2</title>
  <id>http://arxiv.org/api/PmrTD7mnJhK1VVvONMZIkrVVdAg</id>
  <updated>2014-09-09T00:00:00-04:00</updated>

kbroman

A regular code chunk:

```{r regular}
data(cars)
summary(cars)
```

A verbatim code chunk:

kbroman

options(show.signif.stars=FALSE, scipen=10, htmlhelp=TRUE)
options(width=115, repos="http://cran.rstudio.com",
        CRAN = "http://cran.rstudio.com",
        browserNLdisabled = TRUE,
        deparse.max.lines = 2)
if (interactive()) {
  suppressMessages(require(devtools))
}
options(error= function() cat("    \\\   \n     \\\

kbroman

# convert c("female", "Male") to c(0,1)

# magrittr is way nicer than nested function calls

convert_sexcodes <-
function(codes)
{
    require(magrittr)

    tolower(codes) %>%

kbroman

# if laundry contains n_pair pairs of socks and n_sing singletons,
# how many socks to draw to get first pair?

sim_socks <-
    function(n_pair=21, n_sing=3, n_sim=100000)
{
    socks <- c(rep(1:n_pair, 2), n_pair+(1:n_sing))
#    replicate(n_sim, min(which(duplicated(sample(socks)))))

    library(magrittr)