| parseMS <- function(file) { | |
| # simple MS parser | |
| lns <- readLines(file) | |
| header <- lns[1:3] | |
| body <- lns[-c(1:3)] | |
| brks <- body == "//" | |
| groups <- cumsum(brks) | |
| sims <- split(body, groups) |
| hpdi_stat <- function(x, prob=0.95) { | |
| # stat functions for ggplot that handle HPDI from samples | |
| # automatically. | |
| hpdi <- HPDinterval(as.mcmc(x)) | |
| c(y=mean(x), ymin=hpdi[1, 'lower'], ymax=hpdi[1, 'upper']) | |
| } |
devtools is a terrific package that makes creating, developing, and debugging R packages fast and easy. I'll step through a ten minute introduction here. This is a short talk for labmates demonstrating how easy it is to create packages (with the right tools); most of this is just pointing Hadley's terrific book on R packages.
First, I add the following line to my ~/.zshrc file:
| library(magrittr) | |
| write.table(iris, file="iris.txt", sep="\t", row.names=FALSE, quote=FALSE) | |
| plines <- function(cmd) readLines(pipe(cmd)) | |
| ptabs <- function(cmd) read.delim(pipe(cmd)) | |
| # just as a trivial example, process some shuffled lines using GNU shuf, sort, | |
| # etc. (we could do this in R, but this is to simulate command line operations) |
| # Sherman-Morrison formula for updating an inverted matrix | |
| # includes R and C++ implementations, as well as benchmarks | |
| library(microbenchmark) | |
| library(RcppEigen) | |
| library(Rcpp) | |
| sourceCpp("sherman.cpp") | |
| EPS <- 1e-8 |
| function range(from, to, by) { | |
| var by = typeof(by) === 'undefined' ? 1 : by; | |
| var out = []; | |
| for (var i = from; i <= to; i += by) out.push(i); | |
| return out; | |
| } | |
| function sampleArrayWithoutReplacement(x, n) { | |
| n = typeof x === 'undefined' ? 1 : n; |
| augroup Terminal | |
| au! | |
| au TermOpen * let g:last_terminal_job_id = b:terminal_job_id | |
| augroup END | |
| function! REPLSend(lines) | |
| call jobsend(g:last_terminal_job_id, add(a:lines, '')) | |
| endfunction | |
| command! REPLSendLine call REPLSend([getline('.')]) |
| var fs = require('fs'); | |
| var d3 = require('d3'); | |
| var jsdom = require('node-jsdom'); | |
| var xmlserializer = require('xmlserializer'); | |
| var margin = {top: 2, right: 4, bottom: 2, left: 4}; | |
| var width = 200 - margin.left - margin.right, | |
| height = 14 - margin.top - margin.bottom; |
| For every minute you are angry, you lose sixty seconds of happiness. ::: unknown | |
| Anger is a momentary madness, so control your passion or it will control you. ::: Horace Walpole | |
| When angry, count ten before you speak; if very angry, a hundred. ::: Jefferson | |
| Anger is a wind which blows out the lamp of the mind. ::: Robert G. Ingersoll | |
| Holding on to anger is like grasping a hot coal with the intent of throwing it at someone else; you are the one getting burned. ::: Buddha | |
| The best remedy for a short temper is a long walk. ::: Jacqueline Schiff |
| # Thanks https://github.com/EBI-predocs/latex-thesis/blob/master/Makefile for | |
| # some tips | |
| LATEXMK = latexmk -xelatex | |
| # CONFIG | |
| target = manuscript | |
| references = bib.bib | |
| # SETUP | |
| includes := $(shell ls *.tex) ${references} |